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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Extensive diversity of coronaviruses in bats from China</title><author><name sortKey="Lin, Xian Dan" sort="Lin, Xian Dan" uniqKey="Lin X" first="Xian-Dan" last="Lin">Xian-Dan Lin</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Wen" sort="Wang, Wen" uniqKey="Wang W" first="Wen" last="Wang">Wen Wang</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Hao, Zong Yu" sort="Hao, Zong Yu" uniqKey="Hao Z" first="Zong-Yu" last="Hao">Zong-Yu Hao</name><affiliation><nlm:aff id="aff0015">Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Zhao Xiao" sort="Wang, Zhao Xiao" uniqKey="Wang Z" first="Zhao-Xiao" last="Wang">Zhao-Xiao Wang</name><affiliation><nlm:aff id="aff0020">Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China</nlm:aff></affiliation></author><author><name sortKey="Guo, Wen Ping" sort="Guo, Wen Ping" uniqKey="Guo W" first="Wen-Ping" last="Guo">Wen-Ping Guo</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Guan, Xiao Qing" sort="Guan, Xiao Qing" uniqKey="Guan X" first="Xiao-Qing" last="Guan">Xiao-Qing Guan</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Miao Ruo" sort="Wang, Miao Ruo" uniqKey="Wang M" first="Miao-Ruo" last="Wang">Miao-Ruo Wang</name><affiliation><nlm:aff id="aff0025">Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Hong Wei" sort="Wang, Hong Wei" uniqKey="Wang H" first="Hong-Wei" last="Wang">Hong-Wei Wang</name><affiliation><nlm:aff id="aff0030">Neixiang Center for Disease Control and Prevention, Neixiang, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Zhou, Run Hong" sort="Zhou, Run Hong" uniqKey="Zhou R" first="Run-Hong" last="Zhou">Run-Hong Zhou</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Li, Ming Hui" sort="Li, Ming Hui" uniqKey="Li M" first="Ming-Hui" last="Li">Ming-Hui Li</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Tang, Guang Peng" sort="Tang, Guang Peng" uniqKey="Tang G" first="Guang-Peng" last="Tang">Guang-Peng Tang</name><affiliation><nlm:aff id="aff0020">Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China</nlm:aff></affiliation></author><author><name sortKey="Wu, Jun" sort="Wu, Jun" uniqKey="Wu J" first="Jun" last="Wu">Jun Wu</name><affiliation><nlm:aff id="aff0035">Jiyuan Center for Disease Control and Prevention, Jiyuan, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name><affiliation><nlm:aff id="aff0040">Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yong Zhen" sort="Zhang, Yong Zhen" uniqKey="Zhang Y" first="Yong-Zhen" last="Zhang">Yong-Zhen Zhang</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28384506</idno><idno type="pmc">7111643</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111643</idno><idno type="RBID">PMC:7111643</idno><idno type="doi">10.1016/j.virol.2017.03.019</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">001575</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001575</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Extensive diversity of coronaviruses in bats from China</title><author><name sortKey="Lin, Xian Dan" sort="Lin, Xian Dan" uniqKey="Lin X" first="Xian-Dan" last="Lin">Xian-Dan Lin</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Wen" sort="Wang, Wen" uniqKey="Wang W" first="Wen" last="Wang">Wen Wang</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Hao, Zong Yu" sort="Hao, Zong Yu" uniqKey="Hao Z" first="Zong-Yu" last="Hao">Zong-Yu Hao</name><affiliation><nlm:aff id="aff0015">Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Zhao Xiao" sort="Wang, Zhao Xiao" uniqKey="Wang Z" first="Zhao-Xiao" last="Wang">Zhao-Xiao Wang</name><affiliation><nlm:aff id="aff0020">Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China</nlm:aff></affiliation></author><author><name sortKey="Guo, Wen Ping" sort="Guo, Wen Ping" uniqKey="Guo W" first="Wen-Ping" last="Guo">Wen-Ping Guo</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Guan, Xiao Qing" sort="Guan, Xiao Qing" uniqKey="Guan X" first="Xiao-Qing" last="Guan">Xiao-Qing Guan</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Miao Ruo" sort="Wang, Miao Ruo" uniqKey="Wang M" first="Miao-Ruo" last="Wang">Miao-Ruo Wang</name><affiliation><nlm:aff id="aff0025">Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Hong Wei" sort="Wang, Hong Wei" uniqKey="Wang H" first="Hong-Wei" last="Wang">Hong-Wei Wang</name><affiliation><nlm:aff id="aff0030">Neixiang Center for Disease Control and Prevention, Neixiang, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Zhou, Run Hong" sort="Zhou, Run Hong" uniqKey="Zhou R" first="Run-Hong" last="Zhou">Run-Hong Zhou</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Li, Ming Hui" sort="Li, Ming Hui" uniqKey="Li M" first="Ming-Hui" last="Li">Ming-Hui Li</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author><author><name sortKey="Tang, Guang Peng" sort="Tang, Guang Peng" uniqKey="Tang G" first="Guang-Peng" last="Tang">Guang-Peng Tang</name><affiliation><nlm:aff id="aff0020">Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China</nlm:aff></affiliation></author><author><name sortKey="Wu, Jun" sort="Wu, Jun" uniqKey="Wu J" first="Jun" last="Wu">Jun Wu</name><affiliation><nlm:aff id="aff0035">Jiyuan Center for Disease Control and Prevention, Jiyuan, Henan Province, China</nlm:aff></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name><affiliation><nlm:aff id="aff0040">Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia</nlm:aff></affiliation></author><author><name sortKey="Zhang, Yong Zhen" sort="Zhang, Yong Zhen" uniqKey="Zhang Y" first="Yong-Zhen" last="Zhang">Yong-Zhen Zhang</name><affiliation><nlm:aff id="aff0005">State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</nlm:aff></affiliation></author></analytic><series><title level="j">Virology</title><idno type="ISSN">0042-6822</idno><idno type="eISSN">1096-0341</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>To help reveal the diversity and evolution of bat coronaviruses we collected 1067 bats from 21 species in China. A total of 73 coronaviruses (32 alphacoronaviruses and 41 betacoronaviruses) were identified in these bats, with an overall prevalence of 6.84%. All newly-identified betacoronaviruses were SARS-related Rhinolophus bat coronaviruses (SARSr-Rh-BatCoV). Importantly, with the exception of the S gene, the genome sequences of the SARSr-Rh-BatCoVs sampled in Guizhou province were closely related to SARS-related human coronavirus. Additionally, the newly-identified alphacoronaviruses exhibited high genetic diversity and some may represent novel species. Our phylogenetic analyses also provided insights into the transmission of these viruses among bat species, revealing a general clustering by geographic location rather than by bat species. Inter-species transmission among bats from the same genus was also commonplace in both the alphacoronaviruses and betacoronaviruses. Overall, these data suggest that high contact rates among specific bat species enable the acquisition and spread of coronaviruses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Annan, A" uniqKey="Annan A">A. Annan</name></author><author><name sortKey="Baldwin, H J" uniqKey="Baldwin H">H.J. Baldwin</name></author><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Klose, S M" uniqKey="Klose S">S.M. Klose</name></author><author><name sortKey="Owusu, M" uniqKey="Owusu M">M. Owusu</name></author><author><name sortKey="Nkrumah, E E" uniqKey="Nkrumah E">E.E. Nkrumah</name></author><author><name sortKey="Badu, E K" uniqKey="Badu E">E.K. Badu</name></author><author><name sortKey="Anti, P" uniqKey="Anti P">P. Anti</name></author><author><name sortKey="Agbenyega, O" uniqKey="Agbenyega O">O. Agbenyega</name></author><author><name sortKey="Meyer, B" uniqKey="Meyer B">B. Meyer</name></author><author><name sortKey="Oppong, S" uniqKey="Oppong S">S. Oppong</name></author><author><name sortKey="Sarkodie, Y A" uniqKey="Sarkodie Y">Y.A. Sarkodie</name></author><author><name sortKey="Kalko, E K" uniqKey="Kalko E">E.K. Kalko</name></author><author><name sortKey="Lina, P H" uniqKey="Lina P">P.H. Lina</name></author><author><name sortKey="Godlevska, E V" uniqKey="Godlevska E">E.V. Godlevska</name></author><author><name sortKey="Reusken, C" uniqKey="Reusken C">C. Reusken</name></author><author><name sortKey="Seebens, A" uniqKey="Seebens A">A. Seebens</name></author><author><name sortKey="Gloza Rausch, F" uniqKey="Gloza Rausch F">F. Gloza-Rausch</name></author><author><name sortKey="Vallo, P" uniqKey="Vallo P">P. Vallo</name></author><author><name sortKey="Tschapka, M" uniqKey="Tschapka M">M. Tschapka</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Balboni, A" uniqKey="Balboni A">A. Balboni</name></author><author><name sortKey="Battilani, M" uniqKey="Battilani M">M. Battilani</name></author><author><name sortKey="Prosperi, S" uniqKey="Prosperi S">S. Prosperi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bermingham, A" uniqKey="Bermingham A">A. Bermingham</name></author><author><name sortKey="Chand, M A" uniqKey="Chand M">M.A. Chand</name></author><author><name sortKey="Brown, C S" uniqKey="Brown C">C.S. Brown</name></author><author><name sortKey="Aarons, E" uniqKey="Aarons E">E. Aarons</name></author><author><name sortKey="Tong, C" uniqKey="Tong C">C. Tong</name></author><author><name sortKey="Langrish, C" uniqKey="Langrish C">C. Langrish</name></author><author><name sortKey="Hoschler, K" uniqKey="Hoschler K">K. Hoschler</name></author><author><name sortKey="Brown, K" uniqKey="Brown K">K. Brown</name></author><author><name sortKey="Galiano, M" uniqKey="Galiano M">M. Galiano</name></author><author><name sortKey="Myers, R" uniqKey="Myers R">R. Myers</name></author><author><name sortKey="Pebody, R G" uniqKey="Pebody R">R.G. Pebody</name></author><author><name sortKey="Green, H K" uniqKey="Green H">H.K. Green</name></author><author><name sortKey="Boddington, N L" uniqKey="Boddington N">N.L. Boddington</name></author><author><name sortKey="Gopal, R" uniqKey="Gopal R">R. Gopal</name></author><author><name sortKey="Price, N" uniqKey="Price N">N. Price</name></author><author><name sortKey="Newsholme, W" uniqKey="Newsholme W">W. Newsholme</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Fouchier, R A" uniqKey="Fouchier R">R.A. Fouchier</name></author><author><name sortKey="Zambon, M" uniqKey="Zambon M">M. Zambon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, D K" uniqKey="Chu D">D.K. Chu</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conow, C" uniqKey="Conow C">C. Conow</name></author><author><name sortKey="Fielder, D" uniqKey="Fielder D">D. Fielder</name></author><author><name sortKey="Ovadia, Y" uniqKey="Ovadia Y">Y. Ovadia</name></author><author><name sortKey="Libeskind Hadas, R" uniqKey="Libeskind Hadas R">R. Libeskind-Hadas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Ithete, N L" uniqKey="Ithete N">N.L. Ithete</name></author><author><name sortKey="Richards, L R" uniqKey="Richards L">L.R. Richards</name></author><author><name sortKey="Schoeman, M C" uniqKey="Schoeman M">M.C. Schoeman</name></author><author><name sortKey="Preiser, W" uniqKey="Preiser W">W. Preiser</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Baldwin, H J" uniqKey="Baldwin H">H.J. Baldwin</name></author><author><name sortKey="Tateno, A F" uniqKey="Tateno A">A.F. Tateno</name></author><author><name sortKey="Zerbinati, R M" uniqKey="Zerbinati R">R.M. Zerbinati</name></author><author><name sortKey="Annan, A" uniqKey="Annan A">A. Annan</name></author><author><name sortKey="Owusu, M" uniqKey="Owusu M">M. Owusu</name></author><author><name sortKey="Nkrumah, E E" uniqKey="Nkrumah E">E.E. Nkrumah</name></author><author><name sortKey="Maganga, G D" uniqKey="Maganga G">G.D. Maganga</name></author><author><name sortKey="Oppong, S" uniqKey="Oppong S">S. Oppong</name></author><author><name sortKey="Adu Sarkodie, Y" uniqKey="Adu Sarkodie Y">Y. Adu-Sarkodie</name></author><author><name sortKey="Vallo, P" uniqKey="Vallo P">P. Vallo</name></author><author><name sortKey="Da Silva Filho, L V" uniqKey="Da Silva Filho L">L.V. da Silva Filho</name></author><author><name sortKey="Leroy, E M" uniqKey="Leroy E">E.M. Leroy</name></author><author><name sortKey="Thiel, V" uniqKey="Thiel V">V. Thiel</name></author><author><name sortKey="Van Der Hoek, L" uniqKey="Van Der Hoek L">L. van der Hoek</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author><author><name sortKey="Tschapka, M" uniqKey="Tschapka M">M. Tschapka</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Rasche, A" uniqKey="Rasche A">A. Rasche</name></author><author><name sortKey="Diallo, T D" uniqKey="Diallo T">T.D. Diallo</name></author><author><name sortKey="Cottontail, V M" uniqKey="Cottontail V">V.M. Cottontail</name></author><author><name sortKey="Stocker, A" uniqKey="Stocker A">A. Stöcker</name></author><author><name sortKey="Souza, B F" uniqKey="Souza B">B.F. Souza</name></author><author><name sortKey="Correa, J I" uniqKey="Correa J">J.I. Corrêa</name></author><author><name sortKey="Carneiro, A J" uniqKey="Carneiro A">A.J. Carneiro</name></author><author><name sortKey="Franke, C R" uniqKey="Franke C">C.R. Franke</name></author><author><name sortKey="Nagy, M" uniqKey="Nagy M">M. Nagy</name></author><author><name sortKey="Metz, M" uniqKey="Metz M">M. Metz</name></author><author><name sortKey="Knornschild, M" uniqKey="Knornschild M">M. Knörnschild</name></author><author><name sortKey="Kalko, E K" uniqKey="Kalko E">E.K. Kalko</name></author><author><name sortKey="Ghanem, S J" uniqKey="Ghanem S">S.J. Ghanem</name></author><author><name sortKey="Morales, K D" uniqKey="Morales K">K.D. Morales</name></author><author><name sortKey="Salsamendi, E" uniqKey="Salsamendi E">E. Salsamendi</name></author><author><name sortKey="Spinola, M" uniqKey="Spinola M">M. Spínola</name></author><author><name sortKey="Herrler, G" uniqKey="Herrler G">G. Herrler</name></author><author><name sortKey="Voigt, C C" uniqKey="Voigt C">C.C. Voigt</name></author><author><name sortKey="Tschapka, M" uniqKey="Tschapka M">M. Tschapka</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cui, J" uniqKey="Cui J">J. Cui</name></author><author><name sortKey="Han, N" uniqKey="Han N">N. Han</name></author><author><name sortKey="Streicker, D" uniqKey="Streicker D">D. Streicker</name></author><author><name sortKey="Li, G" uniqKey="Li G">G. Li</name></author><author><name sortKey="Tang, X" uniqKey="Tang X">X. Tang</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z. Shi</name></author><author><name sortKey="Hu, Z" uniqKey="Hu Z">Z. Hu</name></author><author><name sortKey="Zhao, G" uniqKey="Zhao G">G. Zhao</name></author><author><name sortKey="Fontanet, A" uniqKey="Fontanet A">A. Fontanet</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name></author><author><name sortKey="Jones, G" uniqKey="Jones G">G. Jones</name></author><author><name sortKey="Field, H E" uniqKey="Field H">H.E. Field</name></author><author><name sortKey="Daszak, P" uniqKey="Daszak P">P. Daszak</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author><author><name sortKey="Gloza Rausch, F" uniqKey="Gloza Rausch F">F. Gloza-Rausch</name></author><author><name sortKey="Glende, J" uniqKey="Glende J">J. Glende</name></author><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Muth, D" uniqKey="Muth D">D. Muth</name></author><author><name sortKey="Goettsche, M" uniqKey="Goettsche M">M. Goettsche</name></author><author><name sortKey="Seebens, A" uniqKey="Seebens A">A. Seebens</name></author><author><name sortKey="Niedrig, M" uniqKey="Niedrig M">M. Niedrig</name></author><author><name sortKey="Pfefferle, S" uniqKey="Pfefferle S">S. Pfefferle</name></author><author><name sortKey="Yordanov, S" uniqKey="Yordanov S">S. Yordanov</name></author><author><name sortKey="Zhelyazkov, L" uniqKey="Zhelyazkov L">L. Zhelyazkov</name></author><author><name sortKey="Hermanns, U" uniqKey="Hermanns U">U. Hermanns</name></author><author><name sortKey="Vallo, P" uniqKey="Vallo P">P. Vallo</name></author><author><name sortKey="Lukashev, A" uniqKey="Lukashev A">A. Lukashev</name></author><author><name sortKey="Muller, M A" uniqKey="Muller M">M.A. Muller</name></author><author><name sortKey="Deng, H" uniqKey="Deng H">H. Deng</name></author><author><name sortKey="Herrler, G" uniqKey="Herrler G">G. Herrler</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</name></author><author><name sortKey="Li, J L" uniqKey="Li J">J.L. Li</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Chmura, A A" uniqKey="Chmura A">A.A. Chmura</name></author><author><name sortKey="Zhu, G" uniqKey="Zhu G">G. Zhu</name></author><author><name sortKey="Epstein, J H" uniqKey="Epstein J">J.H. Epstein</name></author><author><name sortKey="Mazet, J K" uniqKey="Mazet J">J.K. Mazet</name></author><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Peng, C" uniqKey="Peng C">C. Peng</name></author><author><name sortKey="Zhang, Y J" uniqKey="Zhang Y">Y.J. Zhang</name></author><author><name sortKey="Luo, C M" uniqKey="Luo C">C.M. Luo</name></author><author><name sortKey="Tan, B" uniqKey="Tan B">B. Tan</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N. Wang</name></author><author><name sortKey="Zhu, Y" uniqKey="Zhu Y">Y. Zhu</name></author><author><name sortKey="Crameri, G" uniqKey="Crameri G">G. Crameri</name></author><author><name sortKey="Zhang, S Y" uniqKey="Zhang S">S.Y. Zhang</name></author><author><name sortKey="Wang, L F" uniqKey="Wang L">L.F. Wang</name></author><author><name sortKey="Daszak, P" uniqKey="Daszak P">P. Daszak</name></author><author><name sortKey="Shi, Z L" uniqKey="Shi Z">Z.L. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Groot, R J" uniqKey="De Groot R">R.J. de Groot</name></author><author><name sortKey="Baker, S C" uniqKey="Baker S">S.C. Baker</name></author><author><name sortKey="Baric, R" uniqKey="Baric R">R. Baric</name></author><author><name sortKey="Enjuanes, L" uniqKey="Enjuanes L">L. Enjuanes</name></author><author><name sortKey="Gorbalenya, A E" uniqKey="Gorbalenya A">A.E. Gorbalenya</name></author><author><name sortKey="Holmes, K V" uniqKey="Holmes K">K.V. Holmes</name></author><author><name sortKey="Perlman, S" uniqKey="Perlman S">S. Perlman</name></author><author><name sortKey="Poon, L" uniqKey="Poon L">L. Poon</name></author><author><name sortKey="Rottier, P J M" uniqKey="Rottier P">P.J.M. Rottier</name></author><author><name sortKey="Talbot, P J" uniqKey="Talbot P">P.J. Talbot</name></author><author><name sortKey="Woo, P C Y" uniqKey="Woo P">P.C.Y. Woo</name></author><author><name sortKey="Ziebuhr, J" uniqKey="Ziebuhr J">J. Ziebuhr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.J. Zheng</name></author><author><name sortKey="He, Y Q" uniqKey="He Y">Y.Q. He</name></author><author><name sortKey="Liu, X L" uniqKey="Liu X">X.L. Liu</name></author><author><name sortKey="Zhuang, Z X" uniqKey="Zhuang Z">Z.X. Zhuang</name></author><author><name sortKey="Cheung, C L" uniqKey="Cheung C">C.L. Cheung</name></author><author><name sortKey="Luo, S W" uniqKey="Luo S">S.W. Luo</name></author><author><name sortKey="Li, P H" uniqKey="Li P">P.H. Li</name></author><author><name sortKey="Zhang, L J" uniqKey="Zhang L">L.J. Zhang</name></author><author><name sortKey="Guan, Y J" uniqKey="Guan Y">Y.J. Guan</name></author><author><name sortKey="Butt, K M" uniqKey="Butt K">K.M. Butt</name></author><author><name sortKey="Wong, K L" uniqKey="Wong K">K.L. Wong</name></author><author><name sortKey="Chan, K W" uniqKey="Chan K">K.W. Chan</name></author><author><name sortKey="Lim, W" uniqKey="Lim W">W. Lim</name></author><author><name sortKey="Shortridge, K F" uniqKey="Shortridge K">K.F. Shortridge</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guindon, S" uniqKey="Guindon S">S. Guindon</name></author><author><name sortKey="Dufayard, J F" uniqKey="Dufayard J">J.F. Dufayard</name></author><author><name sortKey="Lefort, V" uniqKey="Lefort V">V. Lefort</name></author><author><name sortKey="Anisimova, M" uniqKey="Anisimova M">M. Anisimova</name></author><author><name sortKey="Hordijk, W" uniqKey="Hordijk W">W. Hordijk</name></author><author><name sortKey="Gascuel, O" uniqKey="Gascuel O">O. Gascuel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guo, W P" uniqKey="Guo W">W.P. Guo</name></author><author><name sortKey="Lin, X D" uniqKey="Lin X">X.D. Lin</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W. Wang</name></author><author><name sortKey="Tian, J H" uniqKey="Tian J">J.H. Tian</name></author><author><name sortKey="Cong, M L" uniqKey="Cong M">M.L. Cong</name></author><author><name sortKey="Zhang, H L" uniqKey="Zhang H">H.L. Zhang</name></author><author><name sortKey="Wang, M R" uniqKey="Wang M">M.R. Wang</name></author><author><name sortKey="Zhou, R H" uniqKey="Zhou R">R.H. Zhou</name></author><author><name sortKey="Wang, J B" uniqKey="Wang J">J.B. Wang</name></author><author><name sortKey="Li, M H" uniqKey="Li M">M.H. Li</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J. Xu</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="He, B" uniqKey="He B">B. He</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y. Zhang</name></author><author><name sortKey="Xu, L" uniqKey="Xu L">L. Xu</name></author><author><name sortKey="Yang, W" uniqKey="Yang W">W. Yang</name></author><author><name sortKey="Yang, F" uniqKey="Yang F">F. Yang</name></author><author><name sortKey="Feng, Y" uniqKey="Feng Y">Y. Feng</name></author><author><name sortKey="Xia, L" uniqKey="Xia L">L. Xia</name></author><author><name sortKey="Zhou, J" uniqKey="Zhou J">J. Zhou</name></author><author><name sortKey="Zhen, W" uniqKey="Zhen W">W. Zhen</name></author><author><name sortKey="Feng, Y" uniqKey="Feng Y">Y. Feng</name></author><author><name sortKey="Guo, H" uniqKey="Guo H">H. Guo</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H. Zhang</name></author><author><name sortKey="Tu, C" uniqKey="Tu C">C. Tu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Der Hoek, L" uniqKey="Van Der Hoek L">L. van der Hoek</name></author><author><name sortKey="Pyrc, K" uniqKey="Pyrc K">K. Pyrc</name></author><author><name sortKey="Jebbink, M F" uniqKey="Jebbink M">M.F. Jebbink</name></author><author><name sortKey="Vermeulen Oost, W" uniqKey="Vermeulen Oost W">W. Vermeulen-Oost</name></author><author><name sortKey="Berkhout, R J" uniqKey="Berkhout R">R.J. Berkhout</name></author><author><name sortKey="Wolthers, K C" uniqKey="Wolthers K">K.C. Wolthers</name></author><author><name sortKey="Wertheim Van" uniqKey="Wertheim Van">Wertheim-van</name></author><author><name sortKey="Dillen, P M" uniqKey="Dillen P">P.,M. Dillen</name></author><author><name sortKey="Kaandorp, J" uniqKey="Kaandorp J">J. Kaandorp</name></author><author><name sortKey="Spaargaren, J" uniqKey="Spaargaren J">J. Spaargaren</name></author><author><name sortKey="Berkhout, B" uniqKey="Berkhout B">B. Berkhout</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Ge, X" uniqKey="Ge X">X. Ge</name></author><author><name sortKey="Wang, L F" uniqKey="Wang L">L.F. Wang</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, C" uniqKey="Huang C">C. Huang</name></author><author><name sortKey="Liu, W J" uniqKey="Liu W">W.J. Liu</name></author><author><name sortKey="Xu, W" uniqKey="Xu W">W. Xu</name></author><author><name sortKey="Jin, T" uniqKey="Jin T">T. Jin</name></author><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y. Zhao</name></author><author><name sortKey="Song, J" uniqKey="Song J">J. Song</name></author><author><name sortKey="Shi, Y" uniqKey="Shi Y">Y. Shi</name></author><author><name sortKey="Ji, W" uniqKey="Ji W">W. Ji</name></author><author><name sortKey="Jia, H" uniqKey="Jia H">H. Jia</name></author><author><name sortKey="Zhou, Y" uniqKey="Zhou Y">Y. Zhou</name></author><author><name sortKey="Wen, H" uniqKey="Wen H">H. Wen</name></author><author><name sortKey="Zhao, H" uniqKey="Zhao H">H. Zhao</name></author><author><name sortKey="Liu, H" uniqKey="Liu H">H. Liu</name></author><author><name sortKey="Li, H" uniqKey="Li H">H. Li</name></author><author><name sortKey="Wang, Q" uniqKey="Wang Q">Q. Wang</name></author><author><name sortKey="Wu, Y" uniqKey="Wu Y">Y. Wu</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name></author><author><name sortKey="Liu, D" uniqKey="Liu D">D. Liu</name></author><author><name sortKey="Liu, G" uniqKey="Liu G">G. Liu</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H. Yu</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Lu, L" uniqKey="Lu L">L. Lu</name></author><author><name sortKey="Gao, G F" uniqKey="Gao G">G.F. Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, Y W" uniqKey="Huang Y">Y.W. Huang</name></author><author><name sortKey="Dickerman, A W" uniqKey="Dickerman A">A.W. Dickerman</name></author><author><name sortKey="Pi Eyro, P" uniqKey="Pi Eyro P">P. Piñeyro</name></author><author><name sortKey="Li, L" uniqKey="Li L">L. Li</name></author><author><name sortKey="Fang, L" uniqKey="Fang L">L. Fang</name></author><author><name sortKey="Kiehne, R" uniqKey="Kiehne R">R. Kiehne</name></author><author><name sortKey="Opriessnig, T" uniqKey="Opriessnig T">T. Opriessnig</name></author><author><name sortKey="Meng, X J" uniqKey="Meng X">X.J. Meng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huynh, J" uniqKey="Huynh J">J. Huynh</name></author><author><name sortKey="Li, S" uniqKey="Li S">S. Li</name></author><author><name sortKey="Yount, B" uniqKey="Yount B">B. Yount</name></author><author><name sortKey="Smith, A" uniqKey="Smith A">A. Smith</name></author><author><name sortKey="Sturges, L" uniqKey="Sturges L">L. Sturges</name></author><author><name sortKey="Olsen, J C" uniqKey="Olsen J">J.C. Olsen</name></author><author><name sortKey="Nagel, J" uniqKey="Nagel J">J. Nagel</name></author><author><name sortKey="Johnson, J B" uniqKey="Johnson J">J.B. Johnson</name></author><author><name sortKey="Agnihothram, S" uniqKey="Agnihothram S">S. Agnihothram</name></author><author><name sortKey="Gates, J E" uniqKey="Gates J">J.E. Gates</name></author><author><name sortKey="Frieman, M B" uniqKey="Frieman M">M.B. Frieman</name></author><author><name sortKey="Baric, R S" uniqKey="Baric R">R.S. Baric</name></author><author><name sortKey="Donaldson, E F" uniqKey="Donaldson E">E.F. Donaldson</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ithete, N L" uniqKey="Ithete N">N.L. Ithete</name></author><author><name sortKey="Stoffberg, S" uniqKey="Stoffberg S">S. Stoffberg</name></author><author><name sortKey="Corman, V M" uniqKey="Corman V">V.M. Corman</name></author><author><name sortKey="Cottontail, V M" uniqKey="Cottontail V">V.M. Cottontail</name></author><author><name sortKey="Richards, L R" uniqKey="Richards L">L.R. Richards</name></author><author><name sortKey="Schoeman, M C" uniqKey="Schoeman M">M.C. Schoeman</name></author><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. Drosten</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author><author><name sortKey="Preiser, W" uniqKey="Preiser W">W. Preiser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katoh, K" uniqKey="Katoh K">K. Katoh</name></author><author><name sortKey="Standley, D M" uniqKey="Standley D">D.M. Standley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ksiazek, T G" uniqKey="Ksiazek T">T.G. Ksiazek</name></author><author><name sortKey="Erdman, D" uniqKey="Erdman D">D. Erdman</name></author><author><name sortKey="Goldsmith, C S" uniqKey="Goldsmith C">C.S. Goldsmith</name></author><author><name sortKey="Zaki, S R" uniqKey="Zaki S">S.R. Zaki</name></author><author><name sortKey="Peret, T" uniqKey="Peret T">T. Peret</name></author><author><name sortKey="Emery, S" uniqKey="Emery S">S. Emery</name></author><author><name sortKey="Tong, S" uniqKey="Tong S">S. Tong</name></author><author><name sortKey="Urbani, C" uniqKey="Urbani C">C. Urbani</name></author><author><name sortKey="Comer, J A" uniqKey="Comer J">J.A. Comer</name></author><author><name sortKey="Lim, W" uniqKey="Lim W">W. Lim</name></author><author><name sortKey="Rollin, P E" uniqKey="Rollin P">P.E. Rollin</name></author><author><name sortKey="Dowell, S F" uniqKey="Dowell S">S.F. Dowell</name></author><author><name sortKey="Ling, A E" uniqKey="Ling A">A.E. Ling</name></author><author><name sortKey="Humphrey, C D" uniqKey="Humphrey C">C.D. Humphrey</name></author><author><name sortKey="Shieh, W J" uniqKey="Shieh W">W.J. Shieh</name></author><author><name sortKey="Guarner, J" uniqKey="Guarner J">J. Guarner</name></author><author><name sortKey="Paddock, C D" uniqKey="Paddock C">C.D. Paddock</name></author><author><name sortKey="Rota, P" uniqKey="Rota P">P. Rota</name></author><author><name sortKey="Fields, B" uniqKey="Fields B">B. Fields</name></author><author><name sortKey="Derisi, J" uniqKey="Derisi J">J. DeRisi</name></author><author><name sortKey="Yang, J Y" uniqKey="Yang J">J.Y. Yang</name></author><author><name sortKey="Cox, N" uniqKey="Cox N">N. Cox</name></author><author><name sortKey="Hughes, J M" uniqKey="Hughes J">J.M. Hughes</name></author><author><name sortKey="Leduc, J W" uniqKey="Leduc J">J.W. LeDuc</name></author><author><name sortKey="Bellini, W J" uniqKey="Bellini W">W.J. Bellini</name></author><author><name sortKey="Anderson, L J" uniqKey="Anderson L">L.J. Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Tsang, A K" uniqKey="Tsang A">A.K. Tsang</name></author><author><name sortKey="Lam, C S" uniqKey="Lam C">C.S. Lam</name></author><author><name sortKey="Ahmed, S" uniqKey="Ahmed S">S. Ahmed</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Tsoi, H W" uniqKey="Tsoi H">H.W. Tsoi</name></author><author><name sortKey="Wong, B H" uniqKey="Wong B">B.H. Wong</name></author><author><name sortKey="Wong, S S" uniqKey="Wong S">S.S. Wong</name></author><author><name sortKey="Leung, S Y" uniqKey="Leung S">S.Y. Leung</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Poon, R W" uniqKey="Poon R">R.W. Poon</name></author><author><name sortKey="Wong, B H" uniqKey="Wong B">B.H. Wong</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Xu, H" uniqKey="Xu H">H. Xu</name></author><author><name sortKey="Guo, R" uniqKey="Guo R">R. Guo</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Gao, K" uniqKey="Gao K">K. Gao</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.J. Zheng</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Tsang, A K" uniqKey="Tsang A">A.K. Tsang</name></author><author><name sortKey="Shek, C T" uniqKey="Shek C">C.T. Shek</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Choi, G K" uniqKey="Choi G">G.K. Choi</name></author><author><name sortKey="Guo, R" uniqKey="Guo R">R. Guo</name></author><author><name sortKey="Wong, B H" uniqKey="Wong B">B.H. Wong</name></author><author><name sortKey="Poon, R W" uniqKey="Poon R">R.W. Poon</name></author><author><name sortKey="Lam, C S" uniqKey="Lam C">C.S. Lam</name></author><author><name sortKey="Wang, S Y" uniqKey="Wang S">S.Y. Wang</name></author><author><name sortKey="Fan, R Y" uniqKey="Fan R">R.Y. Fan</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.J. Zheng</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Feng, Y" uniqKey="Feng Y">Y. Feng</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Luk, H K" uniqKey="Luk H">H.K. Luk</name></author><author><name sortKey="Yang, W H" uniqKey="Yang W">W.H. Yang</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Song, Z Z" uniqKey="Song Z">Z.Z. Song</name></author><author><name sortKey="Chow, W N" uniqKey="Chow W">W.N. Chow</name></author><author><name sortKey="Fan, R Y" uniqKey="Fan R">R.Y. Fan</name></author><author><name sortKey="Ahmed, S S" uniqKey="Ahmed S">S.S. Ahmed</name></author><author><name sortKey="Yeung, H C" uniqKey="Yeung H">H.C. Yeung</name></author><author><name sortKey="Lam, C S" uniqKey="Lam C">C.S. Lam</name></author><author><name sortKey="Cai, J P" uniqKey="Cai J">J.P. Cai</name></author><author><name sortKey="Wong, S S" uniqKey="Wong S">S.S. Wong</name></author><author><name sortKey="Chan, J F" uniqKey="Chan J">J.F. Chan</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author><author><name sortKey="Zhang, H L" uniqKey="Zhang H">H.L. Zhang</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Shi, Z" uniqKey="Shi Z">Z. Shi</name></author><author><name sortKey="Yu, M" uniqKey="Yu M">M. Yu</name></author><author><name sortKey="Ren, W" uniqKey="Ren W">W. Ren</name></author><author><name sortKey="Smith, C" uniqKey="Smith C">C. Smith</name></author><author><name sortKey="Epstein, J H" uniqKey="Epstein J">J.H. Epstein</name></author><author><name sortKey="Wang, H" uniqKey="Wang H">H. Wang</name></author><author><name sortKey="Crameri, G" uniqKey="Crameri G">G. Crameri</name></author><author><name sortKey="Hu, Z" uniqKey="Hu Z">Z. Hu</name></author><author><name sortKey="Zhang, H" uniqKey="Zhang H">H. Zhang</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name></author><author><name sortKey="Mceachern, J" uniqKey="Mceachern J">J. McEachern</name></author><author><name sortKey="Field, H" uniqKey="Field H">H. Field</name></author><author><name sortKey="Daszak, P" uniqKey="Daszak P">P. Daszak</name></author><author><name sortKey="Eaton, B T" uniqKey="Eaton B">B.T. Eaton</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S. Zhang</name></author><author><name sortKey="Wang, L F" uniqKey="Wang L">L.F. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lole, K S" uniqKey="Lole K">K.S. Lole</name></author><author><name sortKey="Bollinger, R C" uniqKey="Bollinger R">R.C. Bollinger</name></author><author><name sortKey="Paranjape, R S" uniqKey="Paranjape R">R.S. Paranjape</name></author><author><name sortKey="Gadkari, D" uniqKey="Gadkari D">D. Gadkari</name></author><author><name sortKey="Kulkarni, S S" uniqKey="Kulkarni S">S.S. Kulkarni</name></author><author><name sortKey="Novak, N G" uniqKey="Novak N">N.G. Novak</name></author><author><name sortKey="Ingersoll, R" uniqKey="Ingersoll R">R. Ingersoll</name></author><author><name sortKey="Sheppard, H W" uniqKey="Sheppard H">H.W. Sheppard</name></author><author><name sortKey="Ray, S C" uniqKey="Ray S">S.C. Ray</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, D P" uniqKey="Martin D">D.P. Martin</name></author><author><name sortKey="Murrell, B" uniqKey="Murrell B">B. Murrell</name></author><author><name sortKey="Golden, M" uniqKey="Golden M">M. Golden</name></author><author><name sortKey="Khoosal, A" uniqKey="Khoosal A">A. Khoosal</name></author><author><name sortKey="Muhire, B" uniqKey="Muhire B">B. Muhire</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Masters, P S" uniqKey="Masters P">P.S. Masters</name></author><author><name sortKey="Perlman, S" uniqKey="Perlman S">S. Perlman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowak, R M" uniqKey="Nowak R">R.M. Nowak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Lai, S T" uniqKey="Lai S">S.T. Lai</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Yam, L Y" uniqKey="Yam L">L.Y. Yam</name></author><author><name sortKey="Lim, W" uniqKey="Lim W">W. Lim</name></author><author><name sortKey="Nicholls, J" uniqKey="Nicholls J">J. Nicholls</name></author><author><name sortKey="Yee, W K" uniqKey="Yee W">W.K. Yee</name></author><author><name sortKey="Yan, W W" uniqKey="Yan W">W.W. Yan</name></author><author><name sortKey="Cheung, M T" uniqKey="Cheung M">M.T. Cheung</name></author><author><name sortKey="Cheng, V C" uniqKey="Cheng V">V.C. Cheng</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Tsang, D N" uniqKey="Tsang D">D.N. Tsang</name></author><author><name sortKey="Yung, R W" uniqKey="Yung R">R.W. Yung</name></author><author><name sortKey="Ng, T K" uniqKey="Ng T">T.K. Ng</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author><author><name sortKey="Chu, D K" uniqKey="Chu D">D.K. Chu</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Wong, O K" uniqKey="Wong O">O.K. Wong</name></author><author><name sortKey="Ellis, T M" uniqKey="Ellis T">T.M. Ellis</name></author><author><name sortKey="Leung, Y H" uniqKey="Leung Y">Y.H. Leung</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Suen, K Y" uniqKey="Suen K">K.Y. Suen</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shi, M" uniqKey="Shi M">M. Shi</name></author><author><name sortKey="Lin, X D" uniqKey="Lin X">X.D. Lin</name></author><author><name sortKey="Tian, J H" uniqKey="Tian J">J.H. Tian</name></author><author><name sortKey="Chen, L J" uniqKey="Chen L">L.J. Chen</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Li, C X" uniqKey="Li C">C.X. Li</name></author><author><name sortKey="Qin, X C" uniqKey="Qin X">X.C. Qin</name></author><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Cao, J P" uniqKey="Cao J">J.P. Cao</name></author><author><name sortKey="Eden, J S" uniqKey="Eden J">J.S. Eden</name></author><author><name sortKey="Buchmann, J" uniqKey="Buchmann J">J. Buchmann</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W. Wang</name></author><author><name sortKey="Xu, J" uniqKey="Xu J">J. Xu</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, C S" uniqKey="Smith C">C.S. Smith</name></author><author><name sortKey="De Jong, C E" uniqKey="De Jong C">C.E. de Jong</name></author><author><name sortKey="Meers, J" uniqKey="Meers J">J. Meers</name></author><author><name sortKey="Henning, J" uniqKey="Henning J">J. Henning</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name></author><author><name sortKey="Field, H E" uniqKey="Field H">H.E. Field</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Talavera, G" uniqKey="Talavera G">G. Talavera</name></author><author><name sortKey="Castresana, J" uniqKey="Castresana J">J. Castresana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D. Peterson</name></author><author><name sortKey="Peterson, N" uniqKey="Peterson N">N. Peterson</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G. Stecher</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M. Nei</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, X C" uniqKey="Tang X">X.C. Tang</name></author><author><name sortKey="Zhang, J X" uniqKey="Zhang J">J.X. Zhang</name></author><author><name sortKey="Zhang, S Y" uniqKey="Zhang S">S.Y. Zhang</name></author><author><name sortKey="Wang, P" uniqKey="Wang P">P. Wang</name></author><author><name sortKey="Fan, X H" uniqKey="Fan X">X.H. Fan</name></author><author><name sortKey="Li, L F" uniqKey="Li L">L.F. Li</name></author><author><name sortKey="Li, G" uniqKey="Li G">G. Li</name></author><author><name sortKey="Dong, B Q" uniqKey="Dong B">B.Q. Dong</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W. Liu</name></author><author><name sortKey="Cheung, C L" uniqKey="Cheung C">C.L. Cheung</name></author><author><name sortKey="Xu, K M" uniqKey="Xu K">K.M. Xu</name></author><author><name sortKey="Song, W J" uniqKey="Song W">W.J. Song</name></author><author><name sortKey="Vijaykrishna, D" uniqKey="Vijaykrishna D">D. Vijaykrishna</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Smith, G J" uniqKey="Smith G">G.J. Smith</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tao, Y" uniqKey="Tao Y">Y. Tao</name></author><author><name sortKey="Shi, M" uniqKey="Shi M">M. Shi</name></author><author><name sortKey="Chommanard, C" uniqKey="Chommanard C">C. Chommanard</name></author><author><name sortKey="Queen, K" uniqKey="Queen K">K. Queen</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name></author><author><name sortKey="Markotter, W" uniqKey="Markotter W">W. Markotter</name></author><author><name sortKey="Kuzmin, I V" uniqKey="Kuzmin I">I.V. Kuzmin</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Tong, S" uniqKey="Tong S">S. Tong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vijaykrishna, D" uniqKey="Vijaykrishna D">D. Vijaykrishna</name></author><author><name sortKey="Smith, G J" uniqKey="Smith G">G.J. Smith</name></author><author><name sortKey="Zhang, J X" uniqKey="Zhang J">J.X. Zhang</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, W" uniqKey="Wang W">W. Wang</name></author><author><name sortKey="Lin, X D" uniqKey="Lin X">X.D. Lin</name></author><author><name sortKey="Guo, W P" uniqKey="Guo W">W.P. Guo</name></author><author><name sortKey="Zhou, R H" uniqKey="Zhou R">R.H. Zhou</name></author><author><name sortKey="Wang, M R" uniqKey="Wang M">M.R. Wang</name></author><author><name sortKey="Wang, C Q" uniqKey="Wang C">C.Q. Wang</name></author><author><name sortKey="Ge, S" uniqKey="Ge S">S. Ge</name></author><author><name sortKey="Mei, S H" uniqKey="Mei S">S.H. Mei</name></author><author><name sortKey="Li, M H" uniqKey="Li M">M.H. Li</name></author><author><name sortKey="Shi, M" uniqKey="Shi M">M. Shi</name></author><author><name sortKey="Holmes, E C" uniqKey="Holmes E">E.C. Holmes</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wertheim, J O" uniqKey="Wertheim J">J.O. Wertheim</name></author><author><name sortKey="Chu, D K" uniqKey="Chu D">D.K. Chu</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Kosakovsky Pond, S L" uniqKey="Kosakovsky Pond S">S.L. Kosakovsky Pond</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Li, K S" uniqKey="Li K">K.S. Li</name></author><author><name sortKey="Poon, R W" uniqKey="Poon R">R.W. Poon</name></author><author><name sortKey="Wong, B H" uniqKey="Wong B">B.H. Wong</name></author><author><name sortKey="Tsoi, H W" uniqKey="Tsoi H">H.W. Tsoi</name></author><author><name sortKey="Yip, B C" uniqKey="Yip B">B.C. Yip</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Lam, C S" uniqKey="Lam C">C.S. Lam</name></author><author><name sortKey="Lau, C C" uniqKey="Lau C">C.C. Lau</name></author><author><name sortKey="Tsang, A K" uniqKey="Tsang A">A.K. Tsang</name></author><author><name sortKey="Lau, J H" uniqKey="Lau J">J.H. Lau</name></author><author><name sortKey="Bai, R" uniqKey="Bai R">R. Bai</name></author><author><name sortKey="Teng, J L" uniqKey="Teng J">J.L. Teng</name></author><author><name sortKey="Tsang, C C" uniqKey="Tsang C">C.C. Tsang</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Zheng, B J" uniqKey="Zheng B">B.J. Zheng</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="Chu, C M" uniqKey="Chu C">C.M. Chu</name></author><author><name sortKey="Chan, K H" uniqKey="Chan K">K.H. Chan</name></author><author><name sortKey="Tsoi, H W" uniqKey="Tsoi H">H.W. Tsoi</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Wong, B H" uniqKey="Wong B">B.H. Wong</name></author><author><name sortKey="Poon, R W" uniqKey="Poon R">R.W. Poon</name></author><author><name sortKey="Cai, J J" uniqKey="Cai J">J.J. Cai</name></author><author><name sortKey="Luk, W K" uniqKey="Luk W">W.K. Luk</name></author><author><name sortKey="Poon, L L" uniqKey="Poon L">L.L. Poon</name></author><author><name sortKey="Wong, S S" uniqKey="Wong S">S.S. Wong</name></author><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y. Guan</name></author><author><name sortKey="Peiris, J S" uniqKey="Peiris J">J.S. Peiris</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Z" uniqKey="Wu Z">Z. Wu</name></author><author><name sortKey="Yang, L" uniqKey="Yang L">L. Yang</name></author><author><name sortKey="Ren, X" uniqKey="Ren X">X. Ren</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name></author><author><name sortKey="Yang, F" uniqKey="Yang F">F. Yang</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S. Zhang</name></author><author><name sortKey="Jin, Q" uniqKey="Jin Q">Q. Jin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, L" uniqKey="Yang L">L. Yang</name></author><author><name sortKey="Wu, Z" uniqKey="Wu Z">Z. Wu</name></author><author><name sortKey="Ren, X" uniqKey="Ren X">X. Ren</name></author><author><name sortKey="Yang, F" uniqKey="Yang F">F. Yang</name></author><author><name sortKey="He, G" uniqKey="He G">G. He</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J. Zhang</name></author><author><name sortKey="Dong, J" uniqKey="Dong J">J. Dong</name></author><author><name sortKey="Sun, L" uniqKey="Sun L">L. Sun</name></author><author><name sortKey="Zhu, Y" uniqKey="Zhu Y">Y. Zhu</name></author><author><name sortKey="Du, J" uniqKey="Du J">J. Du</name></author><author><name sortKey="Zhang, S" uniqKey="Zhang S">S. Zhang</name></author><author><name sortKey="Jin, Q" uniqKey="Jin Q">Q. Jin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Wang, B" uniqKey="Wang B">B. Wang</name></author><author><name sortKey="Wang, M N" uniqKey="Wang M">M.N. Wang</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q. Zhang</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Wu, L J" uniqKey="Wu L">L.J. Wu</name></author><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author><author><name sortKey="Daszak, P" uniqKey="Daszak P">P. Daszak</name></author><author><name sortKey="Wang, L F" uniqKey="Wang L">L.F. Wang</name></author><author><name sortKey="Shi, Z L" uniqKey="Shi Z">Z.L. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zaki, A M" uniqKey="Zaki A">A.M. Zaki</name></author><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S. van Boheemen</name></author><author><name sortKey="Bestebroer, T M" uniqKey="Bestebroer T">T.M. Bestebroer</name></author><author><name sortKey="Osterhaus, A D" uniqKey="Osterhaus A">A.D. Osterhaus</name></author><author><name sortKey="Fouchier, R A" uniqKey="Fouchier R">R.A. Fouchier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, R Z" uniqKey="Zhang R">R.Z. Zhang</name></author><author><name sortKey="Jing, S K" uniqKey="Jing S">S.K. Jing</name></author><author><name sortKey="Quan, G Q" uniqKey="Quan G">G.Q. Quan</name></author><author><name sortKey="Li, S H" uniqKey="Li S">S.H. Li</name></author><author><name sortKey="Ye, Z Y" uniqKey="Ye Z">Z.Y. Ye</name></author><author><name sortKey="Wang, F G" uniqKey="Wang F">F.G. Wang</name></author><author><name sortKey="Zhang, M L" uniqKey="Zhang M">M.L. Zhang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Virology</journal-id><journal-id journal-id-type="iso-abbrev">Virology</journal-id><journal-title-group><journal-title>Virology</journal-title></journal-title-group><issn pub-type="ppub">0042-6822</issn><issn pub-type="epub">1096-0341</issn><publisher><publisher-name>Elsevier Inc.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28384506</article-id><article-id pub-id-type="pmc">7111643</article-id><article-id pub-id-type="publisher-id">S0042-6822(17)30100-9</article-id><article-id pub-id-type="doi">10.1016/j.virol.2017.03.019</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Extensive diversity of coronaviruses in bats from China</article-title></title-group><contrib-group><contrib contrib-type="author" id="au0005"><name><surname>Lin</surname><given-names>Xian-Dan</given-names></name><xref rid="aff0005" ref-type="aff">a</xref><xref rid="aff0010" ref-type="aff">b</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author" id="au0010"><name><surname>Wang</surname><given-names>Wen</given-names></name><xref rid="aff0005" ref-type="aff">a</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author" id="au0015"><name><surname>Hao</surname><given-names>Zong-Yu</given-names></name><xref rid="aff0015" ref-type="aff">c</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author" id="au0020"><name><surname>Wang</surname><given-names>Zhao-Xiao</given-names></name><xref rid="aff0020" ref-type="aff">d</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author" id="au0025"><name><surname>Guo</surname><given-names>Wen-Ping</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0030"><name><surname>Guan</surname><given-names>Xiao-Qing</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0035"><name><surname>Wang</surname><given-names>Miao-Ruo</given-names></name><xref rid="aff0025" ref-type="aff">e</xref></contrib><contrib contrib-type="author" id="au0040"><name><surname>Wang</surname><given-names>Hong-Wei</given-names></name><xref rid="aff0030" ref-type="aff">f</xref></contrib><contrib contrib-type="author" id="au0045"><name><surname>Zhou</surname><given-names>Run-Hong</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0050"><name><surname>Li</surname><given-names>Ming-Hui</given-names></name><xref rid="aff0005" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0055"><name><surname>Tang</surname><given-names>Guang-Peng</given-names></name><xref rid="aff0020" ref-type="aff">d</xref></contrib><contrib contrib-type="author" id="au0060"><name><surname>Wu</surname><given-names>Jun</given-names></name><xref rid="aff0035" ref-type="aff">g</xref></contrib><contrib contrib-type="author" id="au0065"><name><surname>Holmes</surname><given-names>Edward C.</given-names></name><xref rid="aff0040" ref-type="aff">h</xref></contrib><contrib contrib-type="author" id="au0070"><name><surname>Zhang</surname><given-names>Yong-Zhen</given-names></name><email>zhangyongzhen@icdc.cn</email><xref rid="aff0005" ref-type="aff">a</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff0005"><label>a</label>State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China</aff><aff id="aff0010"><label>b</label>Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China</aff><aff id="aff0015"><label>c</label>Henan Center for Disease Control and Prevention, Zhengzhou, Henan Province, China</aff><aff id="aff0020"><label>d</label>Guizhou Center for Disease Control and Prevention, Guiyang, Guizhou Province, China</aff><aff id="aff0025"><label>e</label>Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China</aff><aff id="aff0030"><label>f</label>Neixiang Center for Disease Control and Prevention, Neixiang, Henan Province, China</aff><aff id="aff0035"><label>g</label>Jiyuan Center for Disease Control and Prevention, Jiyuan, Henan Province, China</aff><aff id="aff0040"><label>h</label>Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia</aff><author-notes><corresp id="cor1"><label>⁎</label>Correspondence to: State Key Laboratory for Infectious Disease Prevention and Control, National Institute of Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, Beijing 102206, China. <email>zhangyongzhen@icdc.cn</email></corresp><fn id="fn1"><label>1</label><p id="ntp0005">Contributed to this work equally.</p></fn></author-notes><pub-date pub-type="pmc-release"><day>3</day><month>4</month><year>2017</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>7</month><year>2017</year></pub-date><pub-date pub-type="epub"><day>3</day><month>4</month><year>2017</year></pub-date><volume>507</volume><fpage>1</fpage><lpage>10</lpage><history><date date-type="received"><day>12</day><month>2</month><year>2017</year></date><date date-type="rev-recd"><day>27</day><month>3</month><year>2017</year></date><date date-type="accepted"><day>28</day><month>3</month><year>2017</year></date></history><permissions><copyright-statement>© 2017 Elsevier Inc.</copyright-statement><copyright-year>2017</copyright-year><copyright-holder>Elsevier Inc.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract id="ab0010"><p>To help reveal the diversity and evolution of bat coronaviruses we collected 1067 bats from 21 species in China. A total of 73 coronaviruses (32 alphacoronaviruses and 41 betacoronaviruses) were identified in these bats, with an overall prevalence of 6.84%. All newly-identified betacoronaviruses were SARS-related Rhinolophus bat coronaviruses (SARSr-Rh-BatCoV). Importantly, with the exception of the S gene, the genome sequences of the SARSr-Rh-BatCoVs sampled in Guizhou province were closely related to SARS-related human coronavirus. Additionally, the newly-identified alphacoronaviruses exhibited high genetic diversity and some may represent novel species. Our phylogenetic analyses also provided insights into the transmission of these viruses among bat species, revealing a general clustering by geographic location rather than by bat species. Inter-species transmission among bats from the same genus was also commonplace in both the alphacoronaviruses and betacoronaviruses. Overall, these data suggest that high contact rates among specific bat species enable the acquisition and spread of coronaviruses.</p></abstract><abstract abstract-type="author-highlights" id="ab0015"><title>Highlights</title><p><list list-type="simple" id="li0005"><list-item id="u0005"><label>•</label><p id="p0005">32 alpha-CoVs and 41 beta-CoVs were identified in bats sampled from China.</p></list-item><list-item id="u0010"><label>•</label><p id="p0010">SARSr-Rh-BatCoVs from Guizhou province were closely related to SARS-CoV.</p></list-item><list-item id="u0015"><label>•</label><p id="p0015">Some of the newly identified CoVs may be novel species in the genus <italic>Alphacoronavirus</italic>.</p></list-item><list-item id="u0020"><label>•</label><p id="p0020">High contact rates among some bat species enable the acquisition and spread of CoVs.</p></list-item></list></p></abstract><kwd-group id="keys0005"><title>Keywords</title><kwd>Bats</kwd><kwd>Coronavirus</kwd><kwd>Evolution</kwd><kwd>Phylogeny</kwd><kwd>Transmission</kwd><kwd>SARS</kwd></kwd-group></article-meta></front><body><sec id="s0005"><label>1</label><title>Introduction</title><p id="p0025">Coronaviruses (CoVs; family <italic>Coronaviridae</italic>) are enveloped positive-sense, single-stranded RNA viruses with the largest genomes (25–31 kb) among known RNA viruses (<xref rid="bib13" ref-type="bibr">de Groot et al., 2011</xref>). Based on genome-scale phylogenies the known CoVs are classified into 30 species within four genera: <italic>Alphacoronavirus</italic>, <italic>Betacoronavirus</italic>, <italic>Gammacoronavirus</italic>, and <italic>Deltacoronavirus</italic> (<xref rid="bib23" ref-type="bibr">ICTV, 2017</xref>). Coronaviruses can infect humans, other mammals, and birds, causing respiratory, enteric, hepatic, and neurological diseases of varying severity (<xref rid="bib35" ref-type="bibr">Masters and Perlman, 2013</xref>). Coronaviruses are well known globally due to the emergence of severe acute respiratory syndrome (SARS) during 2002–2003 caused by a previously unknown CoV (<xref rid="bib26" ref-type="bibr">Ksiazek et al., 2003</xref>, <xref rid="bib37" ref-type="bibr">Peiris et al., 2003</xref>). Subsequently, other two human CoVs (NL63 and HKU1) causing respiratory disease were identified (<xref rid="bib18" ref-type="bibr">van der Hoek et al., 2004</xref>, <xref rid="bib51" ref-type="bibr">Woo et al., 2005</xref>). Strikingly, the Middle East respiratory syndrome (MERS) that emerged in 2012 and characterized by a higher mortality than SARS was also caused by a previously unknown CoV (<xref rid="bib3" ref-type="bibr">Bermingham et al., 2012</xref>, <xref rid="bib55" ref-type="bibr">Zaki et al., 2012</xref>). The ongoing emergence of these CoVs in humans means that CoVs will likely remain a key public health threat for the foreseeable future.</p><p id="p0030">Since the discovery of SARS-CoV in Himalayan palm civets (<xref rid="bib14" ref-type="bibr">Guan et al., 2003</xref>), intense effort has been directed toward identifying and characterizing coronaviruses from animals globally. Consequently, a number of CoVs have been identified in a diverse range of vertebrates including domestic and wild mammals, and birds (<xref rid="bib38" ref-type="bibr">Poon et al., 2005</xref>, <xref rid="bib46" ref-type="bibr">Wang et al., 2015</xref>, <xref rid="bib50" ref-type="bibr">Woo et al., 2012</xref>). Bats (order Chiroptera), with more than 1240 species, have remarkable species diversity, and comprise more than 20% of living mammalian species (<xref rid="bib36" ref-type="bibr">Nowak, 1994</xref>). The discovery of SARS-related CoV in Rhinolophus horseshoe bats in China in 2005 (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib32" ref-type="bibr">Li et al., 2005</xref>) attracted the global attention to these mammals, such that diverse Alpha- and Beta-CoVs have now been identified in a variety of bats globally over the past decade (<xref rid="bib8" ref-type="bibr">Corman et al., 2013</xref>, <xref rid="bib6" ref-type="bibr">Corman et al., 2014</xref>, <xref rid="bib7" ref-type="bibr">Corman et al., 2015</xref>, <xref rid="bib10" ref-type="bibr">Drexler et al., 2014</xref>, <xref rid="bib17" ref-type="bibr">He et al., 2014</xref>, <xref rid="bib20" ref-type="bibr">Huang et al., 2016</xref>, <xref rid="bib40" ref-type="bibr">Smith et al., 2016</xref>, <xref rid="bib50" ref-type="bibr">Woo et al., 2012</xref>). More importantly, due to the close relationship between CoVs in bats and those causing human infections, it is believed that bats are the original source of human CoVs including SARS-CoV and MERS-CoV (<xref rid="bib7" ref-type="bibr">Corman et al., 2015</xref>, <xref rid="bib12" ref-type="bibr">Ge et al., 2013</xref>, <xref rid="bib22" ref-type="bibr">Huynh et al., 2012</xref>, <xref rid="bib24" ref-type="bibr">Ithete et al., 2013</xref>, <xref rid="bib44" ref-type="bibr">Tao et al., 2017</xref>). Due to their high diversity and biological and ecological characteristics that potentially facilitate virus maintenance and transmission, bats likely harbor a large number of viruses, some of which may then jump to other species (<xref rid="bib2" ref-type="bibr">Balboni et al., 2012</xref>). Hence, more effort is needed to identify and characterize the currently unrecognized CoVs that circulate in bats.</p><p id="p0035">At least 120 bat species are found in China, mainly distributed in the eastern, central, and southern regions of that country (<xref rid="bib56" ref-type="bibr">Zhang et al., 1997</xref>). Herein we report novel and diverse CoVs and SARS-related CoVs identified in <italic>Rhinolophus</italic>, <italic>Miniopterus</italic>, <italic>Murina</italic> and <italic>Myotis spp</italic>. bats sampled from several geographic regions of China. In addition, we inferred their genomic characteristics and evolutionary relationships with known viruses and their hosts.</p></sec><sec id="s0010"><label>2</label><title>Results</title><sec id="s0015"><label>2.1</label><title>Bats collected and prevalence of CoVs</title><p id="p0040">During 2012–2015 a total of 1067 bats were collected from five caves in five counties from Guizhou, Henan, and Zhejiang provinces (
<xref rid="f0005" ref-type="fig">Fig. 1</xref>,
<xref rid="t0005" ref-type="table">Table 1</xref> and <xref rid="s0090" ref-type="sec">S1</xref>). After morphological examination and sequence analysis of the mitochondrial cytochrome <italic>b</italic> (mt-<italic>cyt b</italic>) gene, these bats were assigned to 21 species. The species and their abundance varied among regions, with <italic>Miniopterus schreibersii</italic> (47%) in Guizhou, <italic>Rhinolophus ferrumequinum</italic> (45%) and <italic>R. pusillus</italic> (32%) in Henan, and <italic>R. monoceros</italic> (41%) and <italic>R. sinicus</italic> (50%) in Zhejiang as the predominant species. Notably, only <italic>R. pusillus</italic> bats were found in all five regions.<fig id="f0005"><label>Fig. 1</label><caption><p>A map of China illustrating the location of trap sites in which bats (red circles) were captured.</p></caption><alt-text id="at0005">Fig. 1.</alt-text><graphic xlink:href="gr1_lrg"></graphic></fig><table-wrap position="float" id="t0005"><label>Table 1</label><caption><p>Prevalence of coronaviruses in the bats collected during 2012–2015 in Guizhou, Henan and Zhejiang provinces, China.</p></caption><alt-text id="at0035">Table 1.</alt-text><table frame="hsides" rules="groups"><thead><tr><th rowspan="2">Species</th><th>Guizhou</th><th colspan="3">Henan<hr></hr></th><th>Zhejiang</th><th rowspan="2">Total</th></tr><tr><th>Anlong</th><th>Neixiang</th><th>Lushi</th><th>Jiyuan</th><th>Longquan</th></tr></thead><tbody><tr><td><italic>Aselliscus stoliczkanus</italic></td><td>0/2</td><td>–</td><td>–</td><td>–</td><td>–</td><td>0/2</td></tr><tr><td><italic>Barbastella beijingensis</italic></td><td>–</td><td>–</td><td>–</td><td>0/2</td><td>–</td><td>0/2</td></tr><tr><td><italic>Hipposideros armiger</italic></td><td>1/35</td><td>–</td><td>–</td><td>–</td><td>–</td><td>1/35</td></tr><tr><td><italic>Hypsugo savii</italic></td><td>–</td><td>–</td><td>–</td><td>0/1</td><td>–</td><td>0/1</td></tr><tr><td><italic>Miniopterus ricketti</italic></td><td>–</td><td>–</td><td>0/1</td><td>–</td><td>–</td><td>0/1</td></tr><tr><td><italic>Miniopterus schreibersii</italic></td><td>14/179</td><td>2/19</td><td>–</td><td>–</td><td>–</td><td>16/198</td></tr><tr><td><italic>Murina leucogaster</italic></td><td>–</td><td>3/21</td><td>2/19</td><td>0/2</td><td>–</td><td>5/42</td></tr><tr><td><italic>Murina</italic> sp.</td><td>–</td><td>–</td><td>–</td><td>0/3</td><td>–</td><td>0/3</td></tr><tr><td><italic>Myotis davidii</italic></td><td>3/5</td><td>2/4</td><td>0/1</td><td>0/1</td><td>–</td><td>5/11</td></tr><tr><td><italic>Myotis siligorensis</italic></td><td>1/4</td><td>–</td><td>–</td><td>–</td><td>–</td><td>1/4</td></tr><tr><td><italic>Plecotus auritus</italic></td><td>–</td><td>–</td><td>–</td><td>0/4</td><td>–</td><td>0/4</td></tr><tr><td><italic>Rhinolophus affinis</italic></td><td>–</td><td>0/3</td><td>–</td><td>–</td><td>–</td><td>0/3</td></tr><tr><td><italic>Rhinolophus ferrumequinum</italic></td><td>–</td><td>0/8</td><td>0/18</td><td>2/157</td><td>–</td><td>2/183</td></tr><tr><td><italic>Rhinolophus luctus</italic></td><td>–</td><td>–</td><td>0/2</td><td>–</td><td>0/1</td><td>0/3</td></tr><tr><td><italic>Rhinolophus macrotis</italic></td><td>1/1</td><td>–</td><td>–</td><td>–</td><td>–</td><td>1/1</td></tr><tr><td><italic>Rhinolophus pearsonii</italic></td><td>2/30</td><td>0/7</td><td>–</td><td>–</td><td>1/21</td><td>3/58</td></tr><tr><td><italic>Rhinolophus pusillus</italic></td><td>1/22</td><td>0/45</td><td>0/57</td><td>0/29</td><td>0/1</td><td>1/154</td></tr><tr><td><italic>Rhinolophus rex</italic></td><td>1/23</td><td>–</td><td>–</td><td>–</td><td>–</td><td>1/23</td></tr><tr><td><italic>Rhinolophus sinicus</italic></td><td>5/83</td><td>–</td><td>–</td><td>–</td><td>3/136</td><td>8/219</td></tr><tr><td><italic>Rhinolophus thomasi</italic></td><td>–</td><td>–</td><td>–</td><td>–</td><td>1/1</td><td>1/1</td></tr><tr><td><italic>Rhinolophus monoceros</italic></td><td>0/1</td><td>0/4</td><td>0/2</td><td>–</td><td>28/112</td><td>28/119</td></tr><tr><td>Total</td><td>29/385</td><td>7/111</td><td>2/100</td><td>2/199</td><td>33/272</td><td>73/1067</td></tr></tbody></table><table-wrap-foot><fn><p>Note: ‘‘-’’ no animals were captured.</p></fn></table-wrap-foot></table-wrap></p><p id="p0045">Using RT-PCR targeting a conserved fragment of the RdRp (RNA-dependent RNA polymerase) gene of CoV as described previously (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib46" ref-type="bibr">Wang et al., 2015</xref>), viral RNA was identified in a total of 73 bat fecal samples, with an overall detection rate of 6.84% (<xref rid="t0005" ref-type="table">Table 1</xref>). Phylogenetic analysis revealed that all these viral sequences were clearly closely related to coronaviruses. Among the predominant bat species, CoV prevalence was high in <italic>R. monoceros</italic> (28/119, 23.53%) and <italic>M. schreibersii</italic> (16/198, 8.08%), but was lower in <italic>R. sinicus</italic> (8/219, 3.65%), <italic>R. ferrumequinum</italic> (2/183, 1.09%) and <italic>R. pusillus</italic> (1/154, 0.64%).</p><p id="p0050">Of the 73 newly-identified CoVs, 32 belong to alphacoronaviruses and 41 to betacoronaviruses. To better characterize these newly-identified bat CoVs, the complete viral RdRp gene sequence was obtained from 65 (89%) of the viral RNA positive bat samples. In addition, 5 complete and 4 near-complete viral genome sequences were successfully obtained from CoV positive samples.</p></sec><sec id="s0020"><label>2.2</label><title>Newly-identified SARS-related Rhinolophus bat coronaviruses in bats</title><p id="p0055">Genetic analysis of the conserved domains in the replicase polyprotein pp1ab – ADP-ribose 1-phosphatase (ADRP), nsp5 (3CLpro), nsp12 (RdRp), nsp13 (Hel), nsp14 (ExoN), nsp15 (NendoU) and nsp16 (O-MT) – revealed that newly-identified bat betacoronaviruses shared more than 90% amino acid sequence identity with <italic>Severe acute respiratory syndrome-related coronavirus</italic> (SARSr-CoV) (<xref rid="s0090" ref-type="sec">Table S2</xref>) and clustered together in a phylogenetic analysis (
<xref rid="f0010" ref-type="fig">Fig. 2</xref>). Hence, these data suggest that these bat viruses belong to the species SARSr-CoV according to the criteria for species demarcation in the subfamily <italic>Coronavirinae</italic> defined by the International Committeeon Taxomony of Viruses (ICTV) (<xref rid="bib13" ref-type="bibr">de Groot et al., 2011</xref>). As these viruses were from <italic>Rhinolophus</italic> bats we therefore designed them as SARS-related Rhinolophus bat coronaviruses (SARSr-Rh-BatCoV). Among these, 33 SARSr-Rh-BatCoVs were identified in 28 <italic>R. monoceros</italic>, 1 <italic>R. pearsonii</italic>, 3 <italic>R. sinicus</italic> and 1 <italic>R. thomasi</italic> sampled from the city of Longquan, Zhejiang province. Similarly, 2 SARS-related CoVs were identified in <italic>R. ferrumequinum</italic> sampled from the city of Jiyuan, Henan province, while the remaining 6 viruses were identified in 5 <italic>R. sinicus</italic>, and 1 <italic>R. rex</italic> sampled from the county of Anlong, Guizhou province.<fig id="f0010"><label>Fig. 2</label><caption><p>Phylogenetic analysis of the nucleotide sequences of the RdRp and S genes including those CoVs obtained here. Bootstrap values (>70%) are shown at relevant nodes. The trees were mid-point rooted for clarity only. The scale bar depicts the number of nucleotide substitutions per site.</p></caption><alt-text id="at0010">Fig. 2.</alt-text><graphic xlink:href="gr2_lrg"></graphic></fig></p><p id="p0060">On the RdRp phylogeny (<xref rid="f0010" ref-type="fig">Fig. 2</xref>) all known SARSr-Rh-BatCoVs from China could be divided into four clusters, within which the newly-identified viruses fell into three clusters that reflect their geographic origins. Specifically: (i) the viruses identified in <italic>Rhinolophus</italic> bats sampled in Zhejiang province (denoted <italic>Rhinolophus</italic> bat Longquan-) were closely related to each other and clustered with <italic>Rhinolophus</italic> bat CoV HKU3 sampled from <italic>R. sinicus</italic> in Hong Kong (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>); (ii) The viruses identified in <italic>R. ferrumequinum</italic> from Jiyuan in Henan province (Jiyuan-84 and Jiyuan-331) formed a cluster with those viruses identified in <italic>R. ferrumequinum</italic> from other regions of China. The viruses within the cluster were from central China (Henan, Hubei and Shaanxi provinces), with the exception of the lineage comprising JMC15 and BtRf-BetaCoV/JL2012 identified in <italic>R. ferrumequinum</italic> sampled in northeastern China (Jilin province); (iii) The viruses identified in <italic>R. sinicus</italic> sampled from Anlong in Guizhou province clustered with those identified in <italic>Rhinolophus</italic> bats from southwestern China including Guangxi, Guizhou and Yunnan provinces (<xref rid="bib12" ref-type="bibr">Ge et al., 2013</xref>, <xref rid="bib32" ref-type="bibr">Li et al., 2005</xref>). Strikingly, only the bat SARSr-Rh-BatCoVs from southwestern China exhibited a close evolutionary relationship with SARS-related human coronavirus (SARS-CoV) and SARS-related palm civet coronavirus (SARSr-CiCoV) (Tor2 and SZ3), suggesting that SARS-CoV may have originated in this region. Finally, within each of these three clusters the SARS-related coronaviruses clustered according to their geographic origins.</p><p id="p0065">Unlike the RdRp gene tree, all SARSr-Rh-BatCoVs and SARS-CoVs from China fell into two distant clades on the S gene phylogeny (<xref rid="f0010" ref-type="fig">Fig. 2</xref>). The first included the SARS-CoVs and two bat SARSr-Rh-BatCoVs (Rs3367 and RsSHC014), while the second comprised all the remaining bat SARSr-Rh-BatCoVs including the newly-identified CoVs, which could be further sub-divided into three clusters according to their geographic and/or host origins. Finally, additional analysis revealed that the <xref rid="s0090" ref-type="sec">S1 and S2</xref> gene tree topologies differed from that of the S gene as a whole (<xref rid="s0090" ref-type="sec">Fig. S1</xref>), suggestive of potential recombination events (see below).</p></sec><sec id="s0025"><label>2.3</label><title>Characterization of the SARSr-Rh-BatCoV genome</title><p id="p0070">To better characterize these newly-identified SARSr-Rh-BatCoVs we recovered the complete genome sequences from each of the lineages described. Their genome sizes varied from 29,665 to 29,693 nucleotides, and shared similar genome organizations with known SARS-related CoV viruses (
<xref rid="f0015" ref-type="fig">Fig. 3</xref>), including the putative transcription regulatory sequence (TRS) motif, 5′-ACGAAC-3′, at the 3′ end of the 5′ leader sequence and preceding each ORF except ORF7b. Additionally, a single long ORF8 was observed in all newly-identified SARSr-Rh-BatCoVs.<fig id="f0015"><label>Fig. 3</label><caption><p>Genome organization of coronaviruses. The four CoVs discovered in this study are shown in bold.</p></caption><alt-text id="at0015">Fig. 3.</alt-text><graphic xlink:href="gr3_lrg"></graphic></fig></p><p id="p0075">The SARSr-Rh-BatCoVs from Longquan (Zhejiang) were closely related to the HKU3 strain with nucleotide identities ranging from 94.7% to 97.0% and amino acid identities of 98.2–99.1% in the RdRp. Notably, however, in the nsp2 gene they differed at up to 23% at the amino acid level. Additionally, the Longquan-140 virus was markedly different from SARSr-CiCoV at the amino acid level in the nsp2 (25.3%), S (20.3%), ORF3 (17.5%), and ORF8 (62.9%) gene sequences. The SARS-related viruses from Jiyuan (Henan) were closely related to BtRf-BetaCoV/HeB2013 and BtRf-BetaCoV/SX2013, with 99.0–99.2% nucleotide identities. Strikingly, the SARSr-Rh-BatCoVs sampled from Anlong (Guizhou) were closely related to SARS- and SARSr-CiCoVs, with >94% nucleotide identities.</p></sec><sec id="s0030"><label>2.4</label><title>Recombination of SARSr-Rh-BatCoVs</title><p id="p0080">We next conducted an analysis of possible recombination events using available genome sequence of SARSr-Rh-BatCoVs and other betacoronaviruses, including those discovered in this study and SARS- and SARSr-CiCoVs (Tor2 and SZ3). As noted in <xref rid="s0090" ref-type="sec">Table S2</xref>, the Longquan-140 virus was markedly different from HKU3 in the nsp2 gene, suggestive of possible recombination. When the Longquan-140 sequence was used as the query for a sliding widow analysis with HKU3 as a potential parent, two recombination breakpoints, located at the nsp2 (nucleotide 1727) and nsp3 (nucleotide 3055) genes, were detected in Longquan-140 with strong p-values (<10<sup>–25</sup>), and supported by a similarity plot (
<xref rid="f0020" ref-type="fig">Fig. 4</xref>). Indeed, there was an abrupt change in the topological position of Longquan-140 and HKU3 downstream of the first breakpoint (position 1727) and upstream of the second breakpoint (position 3055). Accordingly, the Longquan-140 genome can be divided into three regions with different evolutionary histories: regions A (nucleotides 1–1726), B 1727–3055) and C (3056 to the end of the genome sequence). In regions A and C, Longquan-140 was most closely related to HKU3 with 96.0% nucleotide similarities, while in region B it occupied basal position, suggesting the recombination event originated from a currently un-sampled parental virus. No other putative recombination events received significant statistical support.<fig id="f0020"><label>Fig. 4</label><caption><p>Recombination within the genome of the Longquan-140 virus. A sequence similarity plot (A) reveals two recombination breakpoints shown by black arrows with their locations. The plot shows genome-scale similarity comparisons of the Longquan-140 (query) against HKU3 and other selected SARS-related CoVs. Phylogenies of regions A, B and C are shown below the similarity plot. Numbers (>70%) above or below branches indicate percentage bootstrap values.</p></caption><alt-text id="at0020">Fig. 4.</alt-text><graphic xlink:href="gr4_lrg"></graphic></fig></p></sec><sec id="s0035"><label>2.5</label><title>Newly-identified alphacoronaviruses in bats</title><p id="p0085">All remaining bat viruses discovered here belong to genus <italic>Alphacoronavirus</italic>, and had genome organizations similar to those of known alphacoronaviruses (<xref rid="f0015" ref-type="fig">Fig. 3</xref>). In the RdRp phylogeny these viruses fell into seven distinct lineages within three clusters (
<xref rid="f0025" ref-type="fig">Fig. 5</xref>). The first cluster included the two newly-identified lineages, comprising the virus (Neixiang-31) identified in one <italic>Myotis davidii</italic> bat from Neixiang (Henan) and those identified in <italic>Hipposideros armiger</italic>, <italic>M. davidii</italic>, <italic>M. siligorensis</italic>, <italic>R. macrotis</italic>, <italic>R. pearsonii</italic>, <italic>R. pusillus</italic> bats from Anlong (Guizhou). Further comparison of the CoV replicase domains (ADRP, 3CLpro, RdRp, Hel, ExoN, NendoU and O-MT) revealed that these newly-identified bat viruses, as well as the bat virus BtMr-AlphaCoV/SAX2011 (<ext-link ext-link-type="uri" xlink:href="ncbi-n:NC_028811.1" id="ir0005">NC_028811.1</ext-link>), exhibited more than 10% amino acid difference in all seven replicase domains (<xref rid="s0090" ref-type="sec">Table S3</xref>). These viruses also formed a distinct cluster in all gene trees, and exhibited a clear cluster according to their geographic origins (<xref rid="f0025" ref-type="fig">Fig. 5</xref> and <xref rid="s0090" ref-type="sec">S2</xref>). Together, these data suggest that these viruses satisfy the species demarcation criterion defined by ICTV and should therefore be considered as a novel member of the genus <italic>Alphacoronavirus</italic>, which we denote as Neixiang Md bat coronavirus (NMBV).<fig id="f0025"><label>Fig. 5</label><caption><p>Phylogenetic analyses of the amino acid sequences of the RdRp including those CoVs obtained here. Numbers (>70%) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site.</p></caption><alt-text id="at0025">Fig. 5.</alt-text><graphic xlink:href="gr5_lrg"></graphic></fig></p><p id="p0090">Within the second cluster, the viruses discovered in bats from both Anlong (Guizhou province) and Neixiang (Henan province) formed a distinct lineage that was closely related to <italic>Scotophilus bat coronavirus 512</italic> (Sc-BatCoV 512) (<xref rid="bib43" ref-type="bibr">Tang et al., 2006</xref>). As these viruses exhibited 10% amino acid difference from members of the genus <italic>Alphacoronavirus</italic> in the conserved replicase domains (with the exception of O-MT to Sc-BatCoV 512 (9.3%; <xref rid="s0090" ref-type="sec">Table S2</xref>)) it is possible that Anlong-190 and Neixiang-32 represent a novel CoV species which we denote as Anlong Ms bat coronavirus. However, further studies are clearly needed to determine whether this virus indeed represents a novel coronavirus. The remaining viruses, which were discovered in bats sampled from Lushi and Neixiang and designated as Lushi Ml bat coronaviruses, formed another distinct lineage that showed a close evolutionary relationship with the bat virus JTAC2 (KU182966). Remarkably, these viruses were most closely related to <italic>porcine epidemic diarrhea virus</italic> (PEDV) in all five gene trees (<xref rid="f0025" ref-type="fig">Fig. 5</xref> and <xref rid="s0090" ref-type="sec">S2</xref>) and exhibited >10% difference in six conserved replicase domains from known members of the genus <italic>Alphacoronavirus</italic> in other genes (<xref rid="s0090" ref-type="sec">Table S3</xref>). However, the O-MT gene of Lushi Ml bat coronaviruses was most closely related to that of PEDV with 7.3% amino acid difference, indicating that it is a novel variant of PEDV (designed as Lushi Ml bat coronavirus). Clearly, these data support the evolutionary origin of PEDV from bats (<xref rid="bib21" ref-type="bibr">Huang et al., 2013</xref>).</p><p id="p0095">Within the third cluster, the newly-identified bat viruses fell into three lineages. The newly-identified virus (Neixiang-64) in <italic>Miniopterus schreibersii</italic> from Neixiang formed a lineage with viruses in <italic>M. fuliginosus</italic> (KJ473799.1), and showed a close relationship with the HKU8 virus (<xref rid="bib4" ref-type="bibr">Chu et al., 2008</xref>). Notably, the viruses from Anlong were grouped into two lineages, one of which contained <italic>Miniopterus</italic> bat coronavirus 1 A AFCD62 (<xref rid="bib4" ref-type="bibr">Chu et al., 2008</xref>). In sum, our data reveal a high genetic diversity of alphacoronaviruses from bats in China.</p></sec><sec id="s0040"><label>2.6</label><title>Phylogenetic relationships between newly-identified viruses and their bat hosts</title><p id="p0100">Comparison of the tree topologies of SARSr-Rh-BatCoVs and their bat hosts revealed strong incongruence between the SARSr-Rh-BatCoVs and their <italic>Rhinolophus</italic> bats hosts at the species level, with only two likely co-divergence events (
<xref rid="f0030" ref-type="fig">Fig. 6</xref>A). Similarly, our co-phylogenetic analysis of alphacoronaviruses and their bat hosts provided evidence for 6–7 co-divergence events, 11–12 host switching events, 0 lineage duplication, 1–2 losses and 0 failure to diverge events (<xref rid="f0030" ref-type="fig">Fig. 6</xref>B). Overall, our co-phylogenetic analysis did not identify significant congruence between the phylogenetic trees of viruses and their bat hosts (<italic>P</italic>=0.04).<fig id="f0030"><label>Fig. 6</label><caption><p>Co-phylogenetic analyses of bats hosts and their associated coronaviruses. (A) SARS-related coronaviruses from bats, (B) alphacoronaviruses from bats. The coronavirus tree is shown in blue while the host phylogeny is shown in black. The host tree was based on mitochondrial cytochrome b gene sequences, and the coronavirus trees were based on the RdRp gene. Filled circles at the nodes indicate co-divergence events, empty circles indicate lineage duplication events, arrows indicate host-switching events, while dotted lines indicate loss events.</p></caption><alt-text id="at0030">Fig. 6.</alt-text><graphic xlink:href="gr6_lrg"></graphic></fig></p><p id="p0105">Clearly, more SARSr-Rh-BatCoVs were identified in <italic>R. sinicus</italic> and <italic>R. ferrumequinum</italic> bats sampled from a variety of locations (<xref rid="f0010" ref-type="fig">Fig. 2</xref>), as well as in <italic>R. monoceros</italic> sampled from Zhejiang province. In addition, the same virus could be identified in several species from the same geographic locality. For example, SARSr-Rh-BatCoVs were identified in four species of <italic>Rhinolophus</italic> bats from Longquan (Zhejiang) and in two bat species from Anlong (Guizhou). Similarly, Neixiang Md bat coronavirus (alphacoronavirus) was identified in six bat species sampled in Anlong (Guizhou). Hence, it is possible that high contact rates among some animal species may enable the acquisition and spread of CoVs.</p></sec></sec><sec id="s0045"><label>3</label><title>Discussion</title><p id="p0110">Since the discovery of SARSr-Rh-BatCoVs in bats in 2005 (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib32" ref-type="bibr">Li et al., 2005</xref>), intense effort has focused on characterizing additional CoVs in bats, leading to the identification of diverse SARS-like viruses and other bat CoVs worldwide (<xref rid="bib10" ref-type="bibr">Drexler et al., 2014</xref>, <xref rid="bib19" ref-type="bibr">Hu et al., 2015</xref>, <xref rid="bib20" ref-type="bibr">Huang et al., 2016</xref>, <xref rid="bib49" ref-type="bibr">Woo et al., 2006</xref>). More importantly, recent studies provide more evidence that human CoVs including MERS and SARS viruses may have their ultimate ancestry in bats (<xref rid="bib1" ref-type="bibr">Annan et al., 2013</xref>, <xref rid="bib6" ref-type="bibr">Corman et al., 2014</xref>, <xref rid="bib7" ref-type="bibr">Corman et al., 2015</xref>, <xref rid="bib12" ref-type="bibr">Ge et al., 2013</xref>, <xref rid="bib22" ref-type="bibr">Huynh et al., 2012</xref>, <xref rid="bib19" ref-type="bibr">Hu et al., 2015</xref>, <xref rid="bib24" ref-type="bibr">Ithete et al., 2013</xref>, <xref rid="bib44" ref-type="bibr">Tao et al., 2017</xref>). These results highlight the potential significance of detecting and characterizing of CoVs in bats before their emergence in humans. Herein we describe diverse SARSr-Rh-BatCoVs and alphacoronaviruses (including novel species) in 13 species of bats sampled from three provinces in China, with an overall prevalence of 6.84%. As such, these data reveal both the high genetic diversity and the wide geographic distribution of CoVs in diverse bats in China.</p><p id="p0115">Among the known SARSr-Rh-BatCoVs, those discovered by <xref rid="bib54" ref-type="bibr">Yang et al. (2015)</xref> are most closely related to human SARS CoVs in the S gene (>90% amino acid similarities), but distant in the ORF8 gene (<43% amino acid similarities). Interestingly, other CoVs have been described that are closely related to SARS-CoVs in the ORF8 gene, but relatively distant in the S, nsp2, nsp11, and ORF3 genes (<xref rid="s0090" ref-type="sec">Table S2</xref>) (<xref rid="bib31" ref-type="bibr">Lau et al., 2015</xref>, <xref rid="bib52" ref-type="bibr">Wu et al., 2016</xref>). In this study, with the exception of the S and ORF3 genes, the viruses discovered in bats sampled in Guizhou province were most closely related to SARS-CoVs including the ORF8 gene. That all these SARSr-Rh-BatCoVs were sampled in southwestern China provides evidence for the origin of SARS-CoVs from bats in this region.</p><p id="p0120">To date, SARSr-Rh-BatCoVs have been detected in bats sampled from diverse geographic regions in China as well as in Europe (<xref rid="bib11" ref-type="bibr">Drexler et al., 2010</xref>). Notably, the majority of SARSr-Rh-BatCoVs have been discovered in Chinese <italic>Rhinolophus</italic> bats, while only one study reported the detection of SARS-related CoVs in <italic>Chaerephon plicata</italic> bats sampled from Yunnan province (<xref rid="bib53" ref-type="bibr">Yang et al., 2013</xref>). In our study a total of 1067 bats from 21 bat species were captured, with SARSr-Rh-BatCoVs identified in 5 species of <italic>Rhinolophus</italic> bats. Although previous studies indicated that <italic>R. sinicus</italic> and <italic>R. ferrumequinum</italic> bats exhibited a higher prevalence of SARS-related viruses (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib32" ref-type="bibr">Li et al., 2005</xref>, <xref rid="bib43" ref-type="bibr">Tang et al., 2006</xref>), more SARSr-Rh-BatCoVs were identified in <italic>R. monoceros</italic> bats (<xref rid="s0090" ref-type="sec">Table S1</xref>). In sum, these data suggest that SARSr-Rh-BatCoVs may be specifically associated with <italic>Rhinolophus</italic> bats.</p><p id="p0125">It is commonly stated that all the alphacoronaviruses originate from bat species (<xref rid="bib50" ref-type="bibr">Woo et al., 2012</xref>), as may also be the case for the human CoVs NL63 and 229E (<xref rid="bib7" ref-type="bibr">Corman et al., 2015</xref>, <xref rid="bib44" ref-type="bibr">Tao et al., 2017</xref>). In addition, it is believed that PEDV might have originated from bats, although direct evidence is lacking (<xref rid="bib21" ref-type="bibr">Huang et al., 2013</xref>). In this study, Lushi MI bat coronaviruses discovered in bats (<italic>M. leucogaster</italic>, <italic>M. schreibersii</italic>) from Lushi and Neixiang exhibited a close relationship to PEDV, especially in the O-MT domain (92.7% amino acid identity). In addition, all other viruses within the cluster were sampled from bats. Hence, these data provide more compelling evidence that PEDV may have originated from bats.</p><p id="p0130">The evolutionary history of RNA viruses is characterized by both host switching and co-divergence (Li et al., 2015; <xref rid="bib39" ref-type="bibr">Shi et al., 2016</xref>), which also appears to be true of coronaviruses (<xref rid="bib1" ref-type="bibr">Annan et al., 2013</xref>, <xref rid="bib9" ref-type="bibr">Cui et al., 2007</xref>; <xref rid="bib10" ref-type="bibr">Drexler et al., 2014</xref>; <xref rid="bib29" ref-type="bibr">Lau et al., 2010</xref>, <xref rid="bib30" ref-type="bibr">Lau et al., 2012</xref>, <xref rid="bib27" ref-type="bibr">Lau et al., 2013</xref>; <xref rid="bib43" ref-type="bibr">Tang et al., 2006</xref>; <xref rid="bib45" ref-type="bibr">Vijaykrishna et al., 2007</xref>; <xref rid="bib47" ref-type="bibr">Wertheim et al., 2013</xref>; <xref rid="bib48" ref-type="bibr">Woo et al., 2009</xref>, <xref rid="bib50" ref-type="bibr">Woo et al., 2012</xref>). Similarly to previous studies (<xref rid="bib11" ref-type="bibr">Drexler et al., 2010</xref>, <xref rid="bib12" ref-type="bibr">Ge et al., 2013</xref>, <xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib32" ref-type="bibr">Li et al., 2005</xref>, <xref rid="bib52" ref-type="bibr">Wu et al., 2016</xref>, <xref rid="bib53" ref-type="bibr">Yang et al., 2013</xref>), SARSr-Rh-BatCoVs were mainly identified in <italic>Rhinolophus</italic> bats, but not in other bats even when sampled in the same locality (e.g. in Guizhou and Henan). In contrast, alphacoronaviruses were mainly identified in non-<italic>Rhinolophus</italic> bats and no alphacoronaviruses were discovered in the colony that only comprised <italic>Rhinolophus</italic> bats. Finally, it was noteworthy that a SARSr-Rh-BatCoVs and Neixiang Md bat coronavirus (alphacoronavirus) were identified in several bat species (from up to three families) in the localities of Anlong and Longquan, indicative of local inter-species transmission. Hence, these data suggest that high contact rates among specific animal species enable the acquisition and spread of CoVs.</p></sec><sec id="s0050"><label>4</label><title>Material and methods</title><sec id="s0055"><label>4.1</label><title>Bat trapping and specimen collection</title><p id="p0135">Bats were captured alive with mist nets or harp traps in caves of natural roosts in Guizhou, Henan, and Zhejiang provinces during 2012–2015 (<xref rid="f0005" ref-type="fig">Fig. 1</xref>). Bat species were initially identified by morphological examination and further confirmed by sequence analysis of the mt-<italic>cyt b</italic> gene (<xref rid="bib16" ref-type="bibr">Guo et al., 2013</xref>). All bats were anesthetized before surgery with every effort made to minimize suffering. Tissue samples, including those from the rectum, were collected from bats for coronavirus detection.</p></sec><sec id="s0060"><label>4.2</label><title>DNA and RNA extraction, PCR and sequencing</title><p id="p0140">We extracted total DNA from bat tissue samples using the DNeasy Blood & Tissue kit (QIAGEN, Valencia, USA) according to protocols suggested by the manufacturer. Total RNA was extracted from fecal or tissue samples using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. Coronavirus RNA was detected by RT-PCR as described previously (<xref rid="bib28" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib46" ref-type="bibr">Wang et al., 2015</xref>). Other coronavirus gene sequences were amplified using the primers designed based on the conserved regions of known genome sequences.</p><p id="p0145">RT-PCR amplicons were purified using the QIAquick Gel Extraction kit (Qiagen, Valencia, USA) according to the manufacturer's recommendations. Purified DNA <700 bp was subjected to a direct sequencing protocol, while purified DNA >700 bp was cloned into pMD18-T vector (TaKaRa, Dalian, China), which was subsequently transformed into JM109-143 competent cells. DNA sequencing was performed with Applied Biosystems 377 gene sequencers.</p></sec><sec id="s0065"><label>4.3</label><title>Complete genome sequencing</title><p id="p0150">Four representatives of CoV in bats were selected for full-genome sequencing. The initial PCR primer sets for PCR were designed from each pan-CoV amplicon sequence and/or from a conserved region in the CoV RdRp. As required, walking primers were designed for further PCR and sequencing. All primer sets used in this study are available upon request.</p><p id="p0155">All sequences generated in this study have been deposited in GenBank and assigned accession numbers KF294268-KF294282, KF294373-KF294378, KF294381-KF294383, KF294420-KF294457, KY770850-KY770860.</p></sec><sec id="s0070"><label>4.4</label><title>Phylogenetic analysis of CoV sequences</title><p id="p0160">In addition to the sequences recovered here, reference sequences that cover the phylogenetic diversity of CoVs were compiled for evolutionary analyses. Accordingly, sequence alignments were performed using the MAFFT algorithm (<xref rid="bib25" ref-type="bibr">Katoh and Standley, 2013</xref>). After alignment, gaps and ambiguously aligned regions were removed using Gblocks (v0.91b) (<xref rid="bib41" ref-type="bibr">Talavera and Castresana, 2007</xref>). Phylogenetic trees were estimated using the maximum likelihood (ML) method implemented in PhyML v3.0 (<xref rid="bib15" ref-type="bibr">Guindon et al., 2010</xref>) with bootstrap support values calculated from 1000 replicate trees. The best-fit amino acid substitution models were determined using MEGA version 5 (<xref rid="bib42" ref-type="bibr">Tamura et al., 2011</xref>).</p></sec><sec id="s0075"><label>4.5</label><title>Recombination analysis</title><p id="p0165">Full-length genomic sequences of the SL-CoVs Longquan-140, Anlong-103 and Jiyuan-84 viruses were aligned with those of bat SARSr-Rh-BatCoVs and other betacoronaviruses using MEGA 5.0. The aligned sequences were preliminarily scanned for recombination events using the Recombination Detection Program 4.0 (RDP4), employing the RDP, GENECONV, and Bootscan methods (with default parameters) (<xref rid="bib34" ref-type="bibr">Martin et al., 2015</xref>). The potential recombination events suggested by RDP (i.e. those with strong <italic>P</italic> values) were investigated further by similarity plots implemented in Simplot 3.5.1 (<xref rid="bib33" ref-type="bibr">Lole et al., 1999</xref>). For each of the putative recombinant regions, phylogenies were estimated using the maximum likelihood method available in PhyML v3.0 (<xref rid="bib15" ref-type="bibr">Guindon et al., 2010</xref>).</p></sec><sec id="s0080"><label>4.6</label><title>Analysis of CoV and host co-phylogenies</title><p id="p0170">Co-phylogenetic analyses of bats hosts and their associated coronaviruses were conducted using the heuristic event-based method available in the Jane software package (<xref rid="bib5" ref-type="bibr">Conow et al., 2010</xref>). We reconstructed patterns co-divergence (and hence cross-species transmission) using a weight of 0 for co-divergence and a weight of 1 for duplication, host switching, lineage loss and failure to diverge. We used Jane with 100 generations and a population size of 100 as parameters for the genetic algorithm. To test the probability of observing the inferred co-divergence number by chance, we employed the random tip mapping method with the generation number =100, population size =100, and sample size =50.</p></sec></sec></body><back><ref-list id="bibliog0005"><title>References</title><ref id="bib1"><element-citation publication-type="journal" id="sbref1"><person-group person-group-type="author"><name><surname>Annan</surname><given-names>A.</given-names></name><name><surname>Baldwin</surname><given-names>H.J.</given-names></name><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Klose</surname><given-names>S.M.</given-names></name><name><surname>Owusu</surname><given-names>M.</given-names></name><name><surname>Nkrumah</surname><given-names>E.E.</given-names></name><name><surname>Badu</surname><given-names>E.K.</given-names></name><name><surname>Anti</surname><given-names>P.</given-names></name><name><surname>Agbenyega</surname><given-names>O.</given-names></name><name><surname>Meyer</surname><given-names>B.</given-names></name><name><surname>Oppong</surname><given-names>S.</given-names></name><name><surname>Sarkodie</surname><given-names>Y.A.</given-names></name><name><surname>Kalko</surname><given-names>E.K.</given-names></name><name><surname>Lina</surname><given-names>P.H.</given-names></name><name><surname>Godlevska</surname><given-names>E.V.</given-names></name><name><surname>Reusken</surname><given-names>C.</given-names></name><name><surname>Seebens</surname><given-names>A.</given-names></name><name><surname>Gloza-Rausch</surname><given-names>F.</given-names></name><name><surname>Vallo</surname><given-names>P.</given-names></name><name><surname>Tschapka</surname><given-names>M.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Drexler</surname><given-names>J.F.</given-names></name></person-group><article-title>Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe</article-title><source>Emerg. Infect. Dis.</source><volume>19</volume><year>2013</year><fpage>456</fpage><lpage>459</lpage><pub-id pub-id-type="pmid">23622767</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal" id="sbref2"><person-group person-group-type="author"><name><surname>Balboni</surname><given-names>A.</given-names></name><name><surname>Battilani</surname><given-names>M.</given-names></name><name><surname>Prosperi</surname><given-names>S.</given-names></name></person-group><article-title>The SARS-like coronaviruses: the role of bats and evolutionary relationships with SARS coronavirus</article-title><source>New Microbiol.</source><volume>35</volume><year>2012</year><fpage>1</fpage><lpage>16</lpage><pub-id pub-id-type="pmid">22378548</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal" id="sbref3"><person-group person-group-type="author"><name><surname>Bermingham</surname><given-names>A.</given-names></name><name><surname>Chand</surname><given-names>M.A.</given-names></name><name><surname>Brown</surname><given-names>C.S.</given-names></name><name><surname>Aarons</surname><given-names>E.</given-names></name><name><surname>Tong</surname><given-names>C.</given-names></name><name><surname>Langrish</surname><given-names>C.</given-names></name><name><surname>Hoschler</surname><given-names>K.</given-names></name><name><surname>Brown</surname><given-names>K.</given-names></name><name><surname>Galiano</surname><given-names>M.</given-names></name><name><surname>Myers</surname><given-names>R.</given-names></name><name><surname>Pebody</surname><given-names>R.G.</given-names></name><name><surname>Green</surname><given-names>H.K.</given-names></name><name><surname>Boddington</surname><given-names>N.L.</given-names></name><name><surname>Gopal</surname><given-names>R.</given-names></name><name><surname>Price</surname><given-names>N.</given-names></name><name><surname>Newsholme</surname><given-names>W.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Fouchier</surname><given-names>R.A.</given-names></name><name><surname>Zambon</surname><given-names>M.</given-names></name></person-group><article-title>Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012</article-title><source>Eur. Surveill.</source><volume>17</volume><year>2012</year><fpage>20290</fpage></element-citation></ref><ref id="bib4"><element-citation publication-type="journal" id="sbref4"><person-group person-group-type="author"><name><surname>Chu</surname><given-names>D.K.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name></person-group><article-title>Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in <italic>Miniopterus</italic> bats</article-title><source>J. Gen. Virol.</source><volume>89</volume><year>2008</year><fpage>1282</fpage><lpage>1287</lpage><pub-id pub-id-type="pmid">18420807</pub-id></element-citation></ref><ref id="bib5"><element-citation publication-type="journal" id="sbref5"><person-group person-group-type="author"><name><surname>Conow</surname><given-names>C.</given-names></name><name><surname>Fielder</surname><given-names>D.</given-names></name><name><surname>Ovadia</surname><given-names>Y.</given-names></name><name><surname>Libeskind-Hadas</surname><given-names>R.</given-names></name></person-group><article-title>Jane: a new tool for the cophylogeny reconstruction problem</article-title><source>Algorithms Mol. Biol.</source><volume>5</volume><year>2010</year><fpage>16</fpage><pub-id pub-id-type="pmid">20181081</pub-id></element-citation></ref><ref id="bib6"><element-citation publication-type="journal" id="sbref6"><person-group person-group-type="author"><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Ithete</surname><given-names>N.L.</given-names></name><name><surname>Richards</surname><given-names>L.R.</given-names></name><name><surname>Schoeman</surname><given-names>M.C.</given-names></name><name><surname>Preiser</surname><given-names>W.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Drexler</surname><given-names>J.F.</given-names></name></person-group><article-title>Rooting the phylogenetic tree of Middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat</article-title><source>J. Virol.</source><volume>88</volume><year>2014</year><fpage>11297</fpage><lpage>11303</lpage><pub-id pub-id-type="pmid">25031349</pub-id></element-citation></ref><ref id="bib7"><element-citation publication-type="journal" id="sbref7"><person-group person-group-type="author"><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Baldwin</surname><given-names>H.J.</given-names></name><name><surname>Tateno</surname><given-names>A.F.</given-names></name><name><surname>Zerbinati</surname><given-names>R.M.</given-names></name><name><surname>Annan</surname><given-names>A.</given-names></name><name><surname>Owusu</surname><given-names>M.</given-names></name><name><surname>Nkrumah</surname><given-names>E.E.</given-names></name><name><surname>Maganga</surname><given-names>G.D.</given-names></name><name><surname>Oppong</surname><given-names>S.</given-names></name><name><surname>Adu-Sarkodie</surname><given-names>Y.</given-names></name><name><surname>Vallo</surname><given-names>P.</given-names></name><name><surname>da Silva Filho</surname><given-names>L.V.</given-names></name><name><surname>Leroy</surname><given-names>E.M.</given-names></name><name><surname>Thiel</surname><given-names>V.</given-names></name><name><surname>van der Hoek</surname><given-names>L.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name><name><surname>Tschapka</surname><given-names>M.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Drexler</surname><given-names>J.F.</given-names></name></person-group><article-title>Evidence for an ancestral association of human coronavirus 229E with bats</article-title><source>J. Virol.</source><volume>89</volume><year>2015</year><fpage>11858</fpage><lpage>11870</lpage><pub-id pub-id-type="pmid">26378164</pub-id></element-citation></ref><ref id="bib8"><element-citation publication-type="journal" id="sbref8"><person-group person-group-type="author"><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Rasche</surname><given-names>A.</given-names></name><name><surname>Diallo</surname><given-names>T.D.</given-names></name><name><surname>Cottontail</surname><given-names>V.M.</given-names></name><name><surname>Stöcker</surname><given-names>A.</given-names></name><name><surname>Souza</surname><given-names>B.F.</given-names></name><name><surname>Corrêa</surname><given-names>J.I.</given-names></name><name><surname>Carneiro</surname><given-names>A.J.</given-names></name><name><surname>Franke</surname><given-names>C.R.</given-names></name><name><surname>Nagy</surname><given-names>M.</given-names></name><name><surname>Metz</surname><given-names>M.</given-names></name><name><surname>Knörnschild</surname><given-names>M.</given-names></name><name><surname>Kalko</surname><given-names>E.K.</given-names></name><name><surname>Ghanem</surname><given-names>S.J.</given-names></name><name><surname>Morales</surname><given-names>K.D.</given-names></name><name><surname>Salsamendi</surname><given-names>E.</given-names></name><name><surname>Spínola</surname><given-names>M.</given-names></name><name><surname>Herrler</surname><given-names>G.</given-names></name><name><surname>Voigt</surname><given-names>C.C.</given-names></name><name><surname>Tschapka</surname><given-names>M.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Drexler</surname><given-names>J.F.</given-names></name></person-group><article-title>Highly diversified coronaviruses in neotropical bats</article-title><source>J. Gen. Virol.</source><volume>94</volume><year>2013</year><fpage>1984</fpage><lpage>1994</lpage><pub-id pub-id-type="pmid">23761408</pub-id></element-citation></ref><ref id="bib9"><element-citation publication-type="journal" id="sbref9"><person-group person-group-type="author"><name><surname>Cui</surname><given-names>J.</given-names></name><name><surname>Han</surname><given-names>N.</given-names></name><name><surname>Streicker</surname><given-names>D.</given-names></name><name><surname>Li</surname><given-names>G.</given-names></name><name><surname>Tang</surname><given-names>X.</given-names></name><name><surname>Shi</surname><given-names>Z.</given-names></name><name><surname>Hu</surname><given-names>Z.</given-names></name><name><surname>Zhao</surname><given-names>G.</given-names></name><name><surname>Fontanet</surname><given-names>A.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Wang</surname><given-names>L.</given-names></name><name><surname>Jones</surname><given-names>G.</given-names></name><name><surname>Field</surname><given-names>H.E.</given-names></name><name><surname>Daszak</surname><given-names>P.</given-names></name><name><surname>Zhang</surname><given-names>S.</given-names></name></person-group><article-title>Evolutionary relationships between bat coronaviruses and their hosts</article-title><source>Emerg. Infect. Dis.</source><volume>13</volume><year>2007</year><fpage>1526</fpage><lpage>1532</lpage><pub-id pub-id-type="pmid">18258002</pub-id></element-citation></ref><ref id="bib10"><element-citation publication-type="journal" id="sbref10"><person-group person-group-type="author"><name><surname>Drexler</surname><given-names>J.F.</given-names></name><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name></person-group><article-title>Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS</article-title><source>Antivir. Res.</source><volume>101</volume><year>2014</year><fpage>45</fpage><lpage>56</lpage><pub-id pub-id-type="pmid">24184128</pub-id></element-citation></ref><ref id="bib11"><element-citation publication-type="journal" id="sbref11"><person-group person-group-type="author"><name><surname>Drexler</surname><given-names>J.F.</given-names></name><name><surname>Gloza-Rausch</surname><given-names>F.</given-names></name><name><surname>Glende</surname><given-names>J.</given-names></name><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Muth</surname><given-names>D.</given-names></name><name><surname>Goettsche</surname><given-names>M.</given-names></name><name><surname>Seebens</surname><given-names>A.</given-names></name><name><surname>Niedrig</surname><given-names>M.</given-names></name><name><surname>Pfefferle</surname><given-names>S.</given-names></name><name><surname>Yordanov</surname><given-names>S.</given-names></name><name><surname>Zhelyazkov</surname><given-names>L.</given-names></name><name><surname>Hermanns</surname><given-names>U.</given-names></name><name><surname>Vallo</surname><given-names>P.</given-names></name><name><surname>Lukashev</surname><given-names>A.</given-names></name><name><surname>Muller</surname><given-names>M.A.</given-names></name><name><surname>Deng</surname><given-names>H.</given-names></name><name><surname>Herrler</surname><given-names>G.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name></person-group><article-title>Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences</article-title><source>J. Virol.</source><volume>84</volume><year>2010</year><fpage>11336</fpage><lpage>11349</lpage><pub-id pub-id-type="pmid">20686038</pub-id></element-citation></ref><ref id="bib12"><element-citation publication-type="journal" id="sbref12"><person-group person-group-type="author"><name><surname>Ge</surname><given-names>X.Y.</given-names></name><name><surname>Li</surname><given-names>J.L.</given-names></name><name><surname>Yang</surname><given-names>X.L.</given-names></name><name><surname>Chmura</surname><given-names>A.A.</given-names></name><name><surname>Zhu</surname><given-names>G.</given-names></name><name><surname>Epstein</surname><given-names>J.H.</given-names></name><name><surname>Mazet</surname><given-names>J.K.</given-names></name><name><surname>Hu</surname><given-names>B.</given-names></name><name><surname>Zhang</surname><given-names>W.</given-names></name><name><surname>Peng</surname><given-names>C.</given-names></name><name><surname>Zhang</surname><given-names>Y.J.</given-names></name><name><surname>Luo</surname><given-names>C.M.</given-names></name><name><surname>Tan</surname><given-names>B.</given-names></name><name><surname>Wang</surname><given-names>N.</given-names></name><name><surname>Zhu</surname><given-names>Y.</given-names></name><name><surname>Crameri</surname><given-names>G.</given-names></name><name><surname>Zhang</surname><given-names>S.Y.</given-names></name><name><surname>Wang</surname><given-names>L.F.</given-names></name><name><surname>Daszak</surname><given-names>P.</given-names></name><name><surname>Shi</surname><given-names>Z.L.</given-names></name></person-group><article-title>Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor</article-title><source>Nature</source><volume>503</volume><year>2013</year><fpage>535</fpage><lpage>538</lpage><pub-id pub-id-type="pmid">24172901</pub-id></element-citation></ref><ref id="bib13"><element-citation publication-type="book" id="sbref13"><person-group person-group-type="author"><name><surname>de Groot</surname><given-names>R.J.</given-names></name><name><surname>Baker</surname><given-names>S.C.</given-names></name><name><surname>Baric</surname><given-names>R.</given-names></name><name><surname>Enjuanes</surname><given-names>L.</given-names></name><name><surname>Gorbalenya</surname><given-names>A.E.</given-names></name><name><surname>Holmes</surname><given-names>K.V.</given-names></name><name><surname>Perlman</surname><given-names>S.</given-names></name><name><surname>Poon</surname><given-names>L.</given-names></name><name><surname>Rottier</surname><given-names>P.J.M.</given-names></name><name><surname>Talbot</surname><given-names>P.J.</given-names></name><name><surname>Woo</surname><given-names>P.C.Y.</given-names></name><name><surname>Ziebuhr</surname><given-names>J.</given-names></name></person-group><chapter-title>Family Coronaviridae</chapter-title><person-group person-group-type="editor"><name><surname>King</surname><given-names>A.M.Q.</given-names></name><name><surname>Lefkowitz</surname><given-names>E.</given-names></name><name><surname>Adams</surname><given-names>M.J.</given-names></name><name><surname>Carstens</surname><given-names>E.B.</given-names></name></person-group><source>VirusTaxonomy: 9th report of the International Committeeon Taxonomy of Viruses</source><year>2011</year><publisher-name>Elsevier</publisher-name><publisher-loc>CA, San Diego</publisher-loc><fpage>806</fpage><lpage>828</lpage></element-citation></ref><ref id="bib14"><element-citation publication-type="journal" id="sbref14"><person-group person-group-type="author"><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Zheng</surname><given-names>B.J.</given-names></name><name><surname>He</surname><given-names>Y.Q.</given-names></name><name><surname>Liu</surname><given-names>X.L.</given-names></name><name><surname>Zhuang</surname><given-names>Z.X.</given-names></name><name><surname>Cheung</surname><given-names>C.L.</given-names></name><name><surname>Luo</surname><given-names>S.W.</given-names></name><name><surname>Li</surname><given-names>P.H.</given-names></name><name><surname>Zhang</surname><given-names>L.J.</given-names></name><name><surname>Guan</surname><given-names>Y.J.</given-names></name><name><surname>Butt</surname><given-names>K.M.</given-names></name><name><surname>Wong</surname><given-names>K.L.</given-names></name><name><surname>Chan</surname><given-names>K.W.</given-names></name><name><surname>Lim</surname><given-names>W.</given-names></name><name><surname>Shortridge</surname><given-names>K.F.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name></person-group><article-title>Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China</article-title><source>Science</source><volume>302</volume><year>2003</year><fpage>276</fpage><lpage>278</lpage><pub-id pub-id-type="pmid">12958366</pub-id></element-citation></ref><ref id="bib15"><element-citation publication-type="journal" id="sbref15"><person-group person-group-type="author"><name><surname>Guindon</surname><given-names>S.</given-names></name><name><surname>Dufayard</surname><given-names>J.F.</given-names></name><name><surname>Lefort</surname><given-names>V.</given-names></name><name><surname>Anisimova</surname><given-names>M.</given-names></name><name><surname>Hordijk</surname><given-names>W.</given-names></name><name><surname>Gascuel</surname><given-names>O.</given-names></name></person-group><article-title>New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0</article-title><source>Syst. Biol.</source><volume>59</volume><year>2010</year><fpage>307</fpage><lpage>321</lpage><pub-id pub-id-type="pmid">20525638</pub-id></element-citation></ref><ref id="bib16"><element-citation publication-type="journal" id="sbref16"><person-group person-group-type="author"><name><surname>Guo</surname><given-names>W.P.</given-names></name><name><surname>Lin</surname><given-names>X.D.</given-names></name><name><surname>Wang</surname><given-names>W.</given-names></name><name><surname>Tian</surname><given-names>J.H.</given-names></name><name><surname>Cong</surname><given-names>M.L.</given-names></name><name><surname>Zhang</surname><given-names>H.L.</given-names></name><name><surname>Wang</surname><given-names>M.R.</given-names></name><name><surname>Zhou</surname><given-names>R.H.</given-names></name><name><surname>Wang</surname><given-names>J.B.</given-names></name><name><surname>Li</surname><given-names>M.H.</given-names></name><name><surname>Xu</surname><given-names>J.</given-names></name><name><surname>Holmes</surname><given-names>E.C.</given-names></name><name><surname>Zhang</surname><given-names>Y.Z.</given-names></name></person-group><article-title>Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents</article-title><source>PLoS Pathog.</source><volume>9</volume><year>2013</year><fpage>1003159</fpage></element-citation></ref><ref id="bib17"><element-citation publication-type="journal" id="sbref17"><person-group person-group-type="author"><name><surname>He</surname><given-names>B.</given-names></name><name><surname>Zhang</surname><given-names>Y.</given-names></name><name><surname>Xu</surname><given-names>L.</given-names></name><name><surname>Yang</surname><given-names>W.</given-names></name><name><surname>Yang</surname><given-names>F.</given-names></name><name><surname>Feng</surname><given-names>Y.</given-names></name><name><surname>Xia</surname><given-names>L.</given-names></name><name><surname>Zhou</surname><given-names>J.</given-names></name><name><surname>Zhen</surname><given-names>W.</given-names></name><name><surname>Feng</surname><given-names>Y.</given-names></name><name><surname>Guo</surname><given-names>H.</given-names></name><name><surname>Zhang</surname><given-names>H.</given-names></name><name><surname>Tu</surname><given-names>C.</given-names></name></person-group><article-title>Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China</article-title><source>J. Virol.</source><volume>88</volume><year>2014</year><fpage>7070</fpage><lpage>7082</lpage><pub-id pub-id-type="pmid">24719429</pub-id></element-citation></ref><ref id="bib18"><element-citation publication-type="journal" id="sbref18"><person-group person-group-type="author"><name><surname>van der Hoek</surname><given-names>L.</given-names></name><name><surname>Pyrc</surname><given-names>K.</given-names></name><name><surname>Jebbink</surname><given-names>M.F.</given-names></name><name><surname>Vermeulen-Oost</surname><given-names>W.</given-names></name><name><surname>Berkhout</surname><given-names>R.J.</given-names></name><name><surname>Wolthers</surname><given-names>K.C.</given-names></name><name><surname>Wertheim-van</surname></name><name><surname>Dillen</surname><given-names>P.,M.</given-names></name><name><surname>Kaandorp</surname><given-names>J.</given-names></name><name><surname>Spaargaren</surname><given-names>J.</given-names></name><name><surname>Berkhout</surname><given-names>B.</given-names></name></person-group><article-title>Identification of a new human coronavirus</article-title><source>Nat. Med.</source><volume>10</volume><year>2004</year><fpage>368</fpage><lpage>373</lpage><pub-id pub-id-type="pmid">15034574</pub-id></element-citation></ref><ref id="bib19"><element-citation publication-type="journal" id="sbref19"><person-group person-group-type="author"><name><surname>Hu</surname><given-names>B.</given-names></name><name><surname>Ge</surname><given-names>X.</given-names></name><name><surname>Wang</surname><given-names>L.F.</given-names></name><name><surname>Shi</surname><given-names>Z.</given-names></name></person-group><article-title>Bat origin of human coronaviruses</article-title><source>Virol. J.</source><volume>12</volume><year>2015</year><fpage>221</fpage><pub-id pub-id-type="pmid">26689940</pub-id></element-citation></ref><ref id="bib20"><element-citation publication-type="journal" id="sbref20"><person-group person-group-type="author"><name><surname>Huang</surname><given-names>C.</given-names></name><name><surname>Liu</surname><given-names>W.J.</given-names></name><name><surname>Xu</surname><given-names>W.</given-names></name><name><surname>Jin</surname><given-names>T.</given-names></name><name><surname>Zhao</surname><given-names>Y.</given-names></name><name><surname>Song</surname><given-names>J.</given-names></name><name><surname>Shi</surname><given-names>Y.</given-names></name><name><surname>Ji</surname><given-names>W.</given-names></name><name><surname>Jia</surname><given-names>H.</given-names></name><name><surname>Zhou</surname><given-names>Y.</given-names></name><name><surname>Wen</surname><given-names>H.</given-names></name><name><surname>Zhao</surname><given-names>H.</given-names></name><name><surname>Liu</surname><given-names>H.</given-names></name><name><surname>Li</surname><given-names>H.</given-names></name><name><surname>Wang</surname><given-names>Q.</given-names></name><name><surname>Wu</surname><given-names>Y.</given-names></name><name><surname>Wang</surname><given-names>L.</given-names></name><name><surname>Liu</surname><given-names>D.</given-names></name><name><surname>Liu</surname><given-names>G.</given-names></name><name><surname>Yu</surname><given-names>H.</given-names></name><name><surname>Holmes</surname><given-names>E.C.</given-names></name><name><surname>Lu</surname><given-names>L.</given-names></name><name><surname>Gao</surname><given-names>G.F.</given-names></name></person-group><article-title>A bat-derived putative cross-family recombinant coronavirus with a EEO virus Gene</article-title><source>PLoS Pathog.</source><volume>12</volume><year>2016</year><fpage>e1005883</fpage><pub-id pub-id-type="pmid">27676249</pub-id></element-citation></ref><ref id="bib21"><element-citation publication-type="journal" id="sbref21"><person-group person-group-type="author"><name><surname>Huang</surname><given-names>Y.W.</given-names></name><name><surname>Dickerman</surname><given-names>A.W.</given-names></name><name><surname>Piñeyro</surname><given-names>P.</given-names></name><name><surname>Li</surname><given-names>L.</given-names></name><name><surname>Fang</surname><given-names>L.</given-names></name><name><surname>Kiehne</surname><given-names>R.</given-names></name><name><surname>Opriessnig</surname><given-names>T.</given-names></name><name><surname>Meng</surname><given-names>X.J.</given-names></name></person-group><article-title>Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States</article-title><source>MBio</source><volume>4</volume><year>2013</year><fpage>e00737-13</fpage><pub-id pub-id-type="pmid">24129257</pub-id></element-citation></ref><ref id="bib22"><element-citation publication-type="journal" id="sbref22"><person-group person-group-type="author"><name><surname>Huynh</surname><given-names>J.</given-names></name><name><surname>Li</surname><given-names>S.</given-names></name><name><surname>Yount</surname><given-names>B.</given-names></name><name><surname>Smith</surname><given-names>A.</given-names></name><name><surname>Sturges</surname><given-names>L.</given-names></name><name><surname>Olsen</surname><given-names>J.C.</given-names></name><name><surname>Nagel</surname><given-names>J.</given-names></name><name><surname>Johnson</surname><given-names>J.B.</given-names></name><name><surname>Agnihothram</surname><given-names>S.</given-names></name><name><surname>Gates</surname><given-names>J.E.</given-names></name><name><surname>Frieman</surname><given-names>M.B.</given-names></name><name><surname>Baric</surname><given-names>R.S.</given-names></name><name><surname>Donaldson</surname><given-names>E.F.</given-names></name></person-group><article-title>Evidence supporting a zoonotic origin of human coronavirus strain NL63</article-title><source>J. Virol.</source><volume>86</volume><year>2012</year><fpage>12816</fpage><lpage>12825</lpage><pub-id pub-id-type="pmid">22993147</pub-id></element-citation></ref><ref id="bib23"><mixed-citation publication-type="other" id="othref0005">International Committee on Taxonomy of Viruses (ICTV), 2017. Taxonomy. <ext-link ext-link-type="uri" xlink:href="https://talk.ictvonline.org/taxonomy" id="ir0015">〈https://talk.ictvonline.org/taxonomy〉</ext-link>.</mixed-citation></ref><ref id="bib24"><element-citation publication-type="journal" id="sbref23"><person-group person-group-type="author"><name><surname>Ithete</surname><given-names>N.L.</given-names></name><name><surname>Stoffberg</surname><given-names>S.</given-names></name><name><surname>Corman</surname><given-names>V.M.</given-names></name><name><surname>Cottontail</surname><given-names>V.M.</given-names></name><name><surname>Richards</surname><given-names>L.R.</given-names></name><name><surname>Schoeman</surname><given-names>M.C.</given-names></name><name><surname>Drosten</surname><given-names>C.</given-names></name><name><surname>Drexler</surname><given-names>J.F.</given-names></name><name><surname>Preiser</surname><given-names>W.</given-names></name></person-group><article-title>Close relative of human Middle East respiratory syndrome coronavirus in bat, South Africa</article-title><source>Emerg. Infect. Dis.</source><volume>19</volume><year>2013</year><fpage>1697</fpage><lpage>1699</lpage><pub-id pub-id-type="pmid">24050621</pub-id></element-citation></ref><ref id="bib25"><element-citation publication-type="journal" id="sbref24"><person-group person-group-type="author"><name><surname>Katoh</surname><given-names>K.</given-names></name><name><surname>Standley</surname><given-names>D.M.</given-names></name></person-group><article-title>MAFFT multiple sequence alignment software version 7: improvements in performance and usability</article-title><source>Mol. Biol. Evol.</source><volume>30</volume><year>2013</year><fpage>772</fpage><lpage>780</lpage><pub-id pub-id-type="pmid">23329690</pub-id></element-citation></ref><ref id="bib26"><element-citation publication-type="journal" id="sbref25"><person-group person-group-type="author"><name><surname>Ksiazek</surname><given-names>T.G.</given-names></name><name><surname>Erdman</surname><given-names>D.</given-names></name><name><surname>Goldsmith</surname><given-names>C.S.</given-names></name><name><surname>Zaki</surname><given-names>S.R.</given-names></name><name><surname>Peret</surname><given-names>T.</given-names></name><name><surname>Emery</surname><given-names>S.</given-names></name><name><surname>Tong</surname><given-names>S.</given-names></name><name><surname>Urbani</surname><given-names>C.</given-names></name><name><surname>Comer</surname><given-names>J.A.</given-names></name><name><surname>Lim</surname><given-names>W.</given-names></name><name><surname>Rollin</surname><given-names>P.E.</given-names></name><name><surname>Dowell</surname><given-names>S.F.</given-names></name><name><surname>Ling</surname><given-names>A.E.</given-names></name><name><surname>Humphrey</surname><given-names>C.D.</given-names></name><name><surname>Shieh</surname><given-names>W.J.</given-names></name><name><surname>Guarner</surname><given-names>J.</given-names></name><name><surname>Paddock</surname><given-names>C.D.</given-names></name><name><surname>Rota</surname><given-names>P.</given-names></name><name><surname>Fields</surname><given-names>B.</given-names></name><name><surname>DeRisi</surname><given-names>J.</given-names></name><name><surname>Yang</surname><given-names>J.Y.</given-names></name><name><surname>Cox</surname><given-names>N.</given-names></name><name><surname>Hughes</surname><given-names>J.M.</given-names></name><name><surname>LeDuc</surname><given-names>J.W.</given-names></name><name><surname>Bellini</surname><given-names>W.J.</given-names></name><name><surname>Anderson</surname><given-names>L.J.</given-names></name></person-group><article-title>SARS working group. A novel coronavirus associated with severeacute respiratory syndrome</article-title><source>N. Engl. J. Med.</source><volume>348</volume><year>2003</year><fpage>1953</fpage><lpage>1966</lpage><pub-id pub-id-type="pmid">12690092</pub-id></element-citation></ref><ref id="bib27"><element-citation publication-type="journal" id="sbref26"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Tsang</surname><given-names>A.K.</given-names></name><name><surname>Lam</surname><given-names>C.S.</given-names></name><name><surname>Ahmed</surname><given-names>S.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of <italic>Pipistrellus</italic> bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus</article-title><source>J. Virol.</source><volume>87</volume><year>2013</year><fpage>8638</fpage><lpage>8650</lpage><pub-id pub-id-type="pmid">23720729</pub-id></element-citation></ref><ref id="bib28"><element-citation publication-type="journal" id="sbref27"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Tsoi</surname><given-names>H.W.</given-names></name><name><surname>Wong</surname><given-names>B.H.</given-names></name><name><surname>Wong</surname><given-names>S.S.</given-names></name><name><surname>Leung</surname><given-names>S.Y.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats</article-title><source>Proc. Natl. Acad. Sci. USA.</source><volume>102</volume><year>2005</year><fpage>14040</fpage><lpage>14045</lpage><pub-id pub-id-type="pmid">16169905</pub-id></element-citation></ref><ref id="bib29"><element-citation publication-type="journal" id="sbref28"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Poon</surname><given-names>R.W.</given-names></name><name><surname>Wong</surname><given-names>B.H.</given-names></name><name><surname>Wang</surname><given-names>M.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Xu</surname><given-names>H.</given-names></name><name><surname>Guo</surname><given-names>R.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Gao</surname><given-names>K.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Zheng</surname><given-names>B.J.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Coexistence of different genotypes in the same bat and serological characterization of Rousettus bat coronavirus HKU9 belonging to a novel Betacoronavirus subgroup</article-title><source>J. Virol.</source><volume>84</volume><year>2010</year><fpage>11385</fpage><lpage>11394</lpage><pub-id pub-id-type="pmid">20702646</pub-id></element-citation></ref><ref id="bib30"><element-citation publication-type="journal" id="sbref29"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Tsang</surname><given-names>A.K.</given-names></name><name><surname>Shek</surname><given-names>C.T.</given-names></name><name><surname>Wang</surname><given-names>M.</given-names></name><name><surname>Choi</surname><given-names>G.K.</given-names></name><name><surname>Guo</surname><given-names>R.</given-names></name><name><surname>Wong</surname><given-names>B.H.</given-names></name><name><surname>Poon</surname><given-names>R.W.</given-names></name><name><surname>Lam</surname><given-names>C.S.</given-names></name><name><surname>Wang</surname><given-names>S.Y.</given-names></name><name><surname>Fan</surname><given-names>R.Y.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Zheng</surname><given-names>B.J.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Recent transmission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault's rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders</article-title><source>J. Virol.</source><volume>86</volume><year>2012</year><fpage>11906</fpage><lpage>11918</lpage><comment>(See comment in PubMed Commons below)</comment><pub-id pub-id-type="pmid">22933277</pub-id></element-citation></ref><ref id="bib31"><element-citation publication-type="journal" id="sbref30"><person-group person-group-type="author"><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Feng</surname><given-names>Y.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Luk</surname><given-names>H.K.</given-names></name><name><surname>Yang</surname><given-names>W.H.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Zhang</surname><given-names>Y.Z.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Song</surname><given-names>Z.Z.</given-names></name><name><surname>Chow</surname><given-names>W.N.</given-names></name><name><surname>Fan</surname><given-names>R.Y.</given-names></name><name><surname>Ahmed</surname><given-names>S.S.</given-names></name><name><surname>Yeung</surname><given-names>H.C.</given-names></name><name><surname>Lam</surname><given-names>C.S.</given-names></name><name><surname>Cai</surname><given-names>J.P.</given-names></name><name><surname>Wong</surname><given-names>S.S.</given-names></name><name><surname>Chan</surname><given-names>J.F.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name><name><surname>Zhang</surname><given-names>H.L.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name></person-group><article-title>Severe acute respiratory syndrome (SARS) coronavirus ORF8 protein is acquired from SARS-related coronavirus from greater horseshoe bats through recombination</article-title><source>J. Virol.</source><volume>89</volume><year>2015</year><fpage>10532</fpage><lpage>10547</lpage><pub-id pub-id-type="pmid">26269185</pub-id></element-citation></ref><ref id="bib32"><element-citation publication-type="journal" id="sbref31"><person-group person-group-type="author"><name><surname>Li</surname><given-names>W.</given-names></name><name><surname>Shi</surname><given-names>Z.</given-names></name><name><surname>Yu</surname><given-names>M.</given-names></name><name><surname>Ren</surname><given-names>W.</given-names></name><name><surname>Smith</surname><given-names>C.</given-names></name><name><surname>Epstein</surname><given-names>J.H.</given-names></name><name><surname>Wang</surname><given-names>H.</given-names></name><name><surname>Crameri</surname><given-names>G.</given-names></name><name><surname>Hu</surname><given-names>Z.</given-names></name><name><surname>Zhang</surname><given-names>H.</given-names></name><name><surname>Zhang</surname><given-names>J.</given-names></name><name><surname>McEachern</surname><given-names>J.</given-names></name><name><surname>Field</surname><given-names>H.</given-names></name><name><surname>Daszak</surname><given-names>P.</given-names></name><name><surname>Eaton</surname><given-names>B.T.</given-names></name><name><surname>Zhang</surname><given-names>S.</given-names></name><name><surname>Wang</surname><given-names>L.F.</given-names></name></person-group><article-title>Bats are natural reservoirs of SARS-like coronaviruses</article-title><source>Science</source><volume>310</volume><year>2005</year><fpage>676</fpage><lpage>679</lpage><pub-id pub-id-type="pmid">16195424</pub-id></element-citation></ref><ref id="bib33"><element-citation publication-type="journal" id="sbref32"><person-group person-group-type="author"><name><surname>Lole</surname><given-names>K.S.</given-names></name><name><surname>Bollinger</surname><given-names>R.C.</given-names></name><name><surname>Paranjape</surname><given-names>R.S.</given-names></name><name><surname>Gadkari</surname><given-names>D.</given-names></name><name><surname>Kulkarni</surname><given-names>S.S.</given-names></name><name><surname>Novak</surname><given-names>N.G.</given-names></name><name><surname>Ingersoll</surname><given-names>R.</given-names></name><name><surname>Sheppard</surname><given-names>H.W.</given-names></name><name><surname>Ray</surname><given-names>S.C.</given-names></name></person-group><article-title>Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination</article-title><source>J. Virol.</source><volume>73</volume><year>1999</year><fpage>52</fpage><lpage>160</lpage></element-citation></ref><ref id="bib34"><element-citation publication-type="journal" id="sbref33"><person-group person-group-type="author"><name><surname>Martin</surname><given-names>D.P.</given-names></name><name><surname>Murrell</surname><given-names>B.</given-names></name><name><surname>Golden</surname><given-names>M.</given-names></name><name><surname>Khoosal</surname><given-names>A.</given-names></name><name><surname>Muhire</surname><given-names>B.</given-names></name></person-group><article-title>RDP4: detection and analysis of recombination patterns in virus genomes</article-title><source>Virus Evol.</source><volume>1</volume><year>2015</year><comment>(vev003)</comment></element-citation></ref><ref id="bib35"><element-citation publication-type="book" id="sbref34"><person-group person-group-type="author"><name><surname>Masters</surname><given-names>P.S.</given-names></name><name><surname>Perlman</surname><given-names>S.</given-names></name></person-group><chapter-title>Coronaviridae</chapter-title><person-group person-group-type="editor"><name><surname>Knipe</surname><given-names>D.M.</given-names></name><name><surname>Howley</surname><given-names>P.M.</given-names></name></person-group><source>Fields Virology</source><year>2013</year><publisher-name>Lippincott Williams & Wilkines</publisher-name><publisher-loc>Wolters Kluwer</publisher-loc><fpage>825</fpage><lpage>858</lpage></element-citation></ref><ref id="bib36"><element-citation publication-type="book" id="sbref35"><person-group person-group-type="author"><name><surname>Nowak</surname><given-names>R.M.</given-names></name></person-group><chapter-title>Walker's Bats of the World</chapter-title><year>1994</year><publisher-name>The Johns Hopkins University Press</publisher-name></element-citation></ref><ref id="bib37"><element-citation publication-type="journal" id="sbref36"><person-group person-group-type="author"><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Lai</surname><given-names>S.T.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Yam</surname><given-names>L.Y.</given-names></name><name><surname>Lim</surname><given-names>W.</given-names></name><name><surname>Nicholls</surname><given-names>J.</given-names></name><name><surname>Yee</surname><given-names>W.K.</given-names></name><name><surname>Yan</surname><given-names>W.W.</given-names></name><name><surname>Cheung</surname><given-names>M.T.</given-names></name><name><surname>Cheng</surname><given-names>V.C.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Tsang</surname><given-names>D.N.</given-names></name><name><surname>Yung</surname><given-names>R.W.</given-names></name><name><surname>Ng</surname><given-names>T.K.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>SARS study group. Coronavirus as a possible cause of severe acute respiratory syndrome</article-title><source>Lancet</source><volume>361</volume><year>2003</year><fpage>1319</fpage><lpage>1325</lpage><pub-id pub-id-type="pmid">12711465</pub-id></element-citation></ref><ref id="bib38"><element-citation publication-type="journal" id="sbref37"><person-group person-group-type="author"><name><surname>Poon</surname><given-names>L.L.</given-names></name><name><surname>Chu</surname><given-names>D.K.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Wong</surname><given-names>O.K.</given-names></name><name><surname>Ellis</surname><given-names>T.M.</given-names></name><name><surname>Leung</surname><given-names>Y.H.</given-names></name><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Suen</surname><given-names>K.Y.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name></person-group><article-title>Identification of a novel coronavirus in bats</article-title><source>J. Virol.</source><volume>79</volume><year>2005</year><fpage>2001</fpage><lpage>2009</lpage><pub-id pub-id-type="pmid">15681402</pub-id></element-citation></ref><ref id="bib39"><element-citation publication-type="journal" id="sbref38"><person-group person-group-type="author"><name><surname>Shi</surname><given-names>M.</given-names></name><name><surname>Lin</surname><given-names>X.D.</given-names></name><name><surname>Tian</surname><given-names>J.H.</given-names></name><name><surname>Chen</surname><given-names>L.J.</given-names></name><name><surname>Chen</surname><given-names>X.</given-names></name><name><surname>Li</surname><given-names>C.X.</given-names></name><name><surname>Qin</surname><given-names>X.C.</given-names></name><name><surname>Li</surname><given-names>J.</given-names></name><name><surname>Cao</surname><given-names>J.P.</given-names></name><name><surname>Eden</surname><given-names>J.S.</given-names></name><name><surname>Buchmann</surname><given-names>J.</given-names></name><name><surname>Wang</surname><given-names>W.</given-names></name><name><surname>Xu</surname><given-names>J.</given-names></name><name><surname>Holmes</surname><given-names>E.C.</given-names></name><name><surname>Zhang</surname><given-names>Y.Z.</given-names></name></person-group><article-title>Redefining the invertebrate RNA virosphere</article-title><source>Nature</source><volume>540</volume><year>2016</year><fpage>539</fpage><lpage>543</lpage><pub-id pub-id-type="pmid">27880757</pub-id></element-citation></ref><ref id="bib40"><element-citation publication-type="journal" id="sbref39"><person-group person-group-type="author"><name><surname>Smith</surname><given-names>C.S.</given-names></name><name><surname>de Jong</surname><given-names>C.E.</given-names></name><name><surname>Meers</surname><given-names>J.</given-names></name><name><surname>Henning</surname><given-names>J.</given-names></name><name><surname>Wang</surname><given-names>L.</given-names></name><name><surname>Field</surname><given-names>H.E.</given-names></name></person-group><article-title>Coronavirus infection and diversity in bats in the Australasian region</article-title><source>Ecohealth</source><volume>13</volume><year>2016</year><fpage>72</fpage><lpage>82</lpage><pub-id pub-id-type="pmid">27048154</pub-id></element-citation></ref><ref id="bib41"><element-citation publication-type="journal" id="sbref40"><person-group person-group-type="author"><name><surname>Talavera</surname><given-names>G.</given-names></name><name><surname>Castresana</surname><given-names>J.</given-names></name></person-group><article-title>Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments</article-title><source>Syst. Biol.</source><volume>56</volume><year>2007</year><fpage>564</fpage><lpage>577</lpage><pub-id pub-id-type="pmid">17654362</pub-id></element-citation></ref><ref id="bib42"><element-citation publication-type="journal" id="sbref41"><person-group person-group-type="author"><name><surname>Tamura</surname><given-names>K.</given-names></name><name><surname>Peterson</surname><given-names>D.</given-names></name><name><surname>Peterson</surname><given-names>N.</given-names></name><name><surname>Stecher</surname><given-names>G.</given-names></name><name><surname>Nei</surname><given-names>M.</given-names></name><name><surname>Kumar</surname><given-names>S.</given-names></name></person-group><article-title>MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods</article-title><source>Mol. Biol. Evol.</source><volume>28</volume><year>2011</year><fpage>2731</fpage><lpage>2739</lpage><pub-id pub-id-type="pmid">21546353</pub-id></element-citation></ref><ref id="bib43"><element-citation publication-type="journal" id="sbref42"><person-group person-group-type="author"><name><surname>Tang</surname><given-names>X.C.</given-names></name><name><surname>Zhang</surname><given-names>J.X.</given-names></name><name><surname>Zhang</surname><given-names>S.Y.</given-names></name><name><surname>Wang</surname><given-names>P.</given-names></name><name><surname>Fan</surname><given-names>X.H.</given-names></name><name><surname>Li</surname><given-names>L.F.</given-names></name><name><surname>Li</surname><given-names>G.</given-names></name><name><surname>Dong</surname><given-names>B.Q.</given-names></name><name><surname>Liu</surname><given-names>W.</given-names></name><name><surname>Cheung</surname><given-names>C.L.</given-names></name><name><surname>Xu</surname><given-names>K.M.</given-names></name><name><surname>Song</surname><given-names>W.J.</given-names></name><name><surname>Vijaykrishna</surname><given-names>D.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Smith</surname><given-names>G.J.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name></person-group><article-title>Prevalence and genetic diversity of coronaviruses in bats from China</article-title><source>J. Virol.</source><volume>80</volume><year>2006</year><fpage>7481</fpage><lpage>7490</lpage><pub-id pub-id-type="pmid">16840328</pub-id></element-citation></ref><ref id="bib44"><element-citation publication-type="journal" id="sbref43"><person-group person-group-type="author"><name><surname>Tao</surname><given-names>Y.</given-names></name><name><surname>Shi</surname><given-names>M.</given-names></name><name><surname>Chommanard</surname><given-names>C.</given-names></name><name><surname>Queen</surname><given-names>K.</given-names></name><name><surname>Zhang</surname><given-names>J.</given-names></name><name><surname>Markotter</surname><given-names>W.</given-names></name><name><surname>Kuzmin</surname><given-names>I.V.</given-names></name><name><surname>Holmes</surname><given-names>E.C.</given-names></name><name><surname>Tong</surname><given-names>S.</given-names></name></person-group><article-title>Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history</article-title><source>J. Virol.</source><year>2017</year><comment>(pii: JVI.01953-16)</comment></element-citation></ref><ref id="bib45"><element-citation publication-type="journal" id="sbref44"><person-group person-group-type="author"><name><surname>Vijaykrishna</surname><given-names>D.</given-names></name><name><surname>Smith</surname><given-names>G.J.</given-names></name><name><surname>Zhang</surname><given-names>J.X.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Chen</surname><given-names>H.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name></person-group><article-title>Evolutionary insights into the ecology of coronaviruses</article-title><source>J. Virol.</source><volume>81</volume><year>2007</year><fpage>4012</fpage><lpage>4020</lpage><pub-id pub-id-type="pmid">17267506</pub-id></element-citation></ref><ref id="bib46"><element-citation publication-type="journal" id="sbref45"><person-group person-group-type="author"><name><surname>Wang</surname><given-names>W.</given-names></name><name><surname>Lin</surname><given-names>X.D.</given-names></name><name><surname>Guo</surname><given-names>W.P.</given-names></name><name><surname>Zhou</surname><given-names>R.H.</given-names></name><name><surname>Wang</surname><given-names>M.R.</given-names></name><name><surname>Wang</surname><given-names>C.Q.</given-names></name><name><surname>Ge</surname><given-names>S.</given-names></name><name><surname>Mei</surname><given-names>S.H.</given-names></name><name><surname>Li</surname><given-names>M.H.</given-names></name><name><surname>Shi</surname><given-names>M.</given-names></name><name><surname>Holmes</surname><given-names>E.C.</given-names></name><name><surname>Zhang</surname><given-names>Y.Z.</given-names></name></person-group><article-title>Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China</article-title><source>Virology</source><volume>474</volume><year>2015</year><fpage>19</fpage><lpage>27</lpage><pub-id pub-id-type="pmid">25463600</pub-id></element-citation></ref><ref id="bib47"><element-citation publication-type="journal" id="sbref46"><person-group person-group-type="author"><name><surname>Wertheim</surname><given-names>J.O.</given-names></name><name><surname>Chu</surname><given-names>D.K.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Kosakovsky Pond</surname><given-names>S.L.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name></person-group><article-title>A case for the ancient origin of coronaviruses</article-title><source>J. Virol.</source><volume>87</volume><year>2013</year><fpage>7039</fpage><lpage>7045</lpage><pub-id pub-id-type="pmid">23596293</pub-id></element-citation></ref><ref id="bib48"><element-citation publication-type="journal" id="sbref47"><person-group person-group-type="author"><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Coronavirus diversity, phylogeny and interspecies jumping</article-title><source>Exp. Biol. Med. (Maywood).</source><volume>234</volume><year>2009</year><fpage>1117</fpage><lpage>1127</lpage><pub-id pub-id-type="pmid">19546349</pub-id></element-citation></ref><ref id="bib49"><element-citation publication-type="journal" id="sbref48"><person-group person-group-type="author"><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Li</surname><given-names>K.S.</given-names></name><name><surname>Poon</surname><given-names>R.W.</given-names></name><name><surname>Wong</surname><given-names>B.H.</given-names></name><name><surname>Tsoi</surname><given-names>H.W.</given-names></name><name><surname>Yip</surname><given-names>B.C.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Molecular diversity of coronaviruses in bats</article-title><source>Virology</source><volume>351</volume><year>2006</year><fpage>180</fpage><lpage>187</lpage><pub-id pub-id-type="pmid">16647731</pub-id></element-citation></ref><ref id="bib50"><element-citation publication-type="journal" id="sbref49"><person-group person-group-type="author"><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Lam</surname><given-names>C.S.</given-names></name><name><surname>Lau</surname><given-names>C.C.</given-names></name><name><surname>Tsang</surname><given-names>A.K.</given-names></name><name><surname>Lau</surname><given-names>J.H.</given-names></name><name><surname>Bai</surname><given-names>R.</given-names></name><name><surname>Teng</surname><given-names>J.L.</given-names></name><name><surname>Tsang</surname><given-names>C.C.</given-names></name><name><surname>Wang</surname><given-names>M.</given-names></name><name><surname>Zheng</surname><given-names>B.J.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus</article-title><source>J. Virol.</source><volume>86</volume><year>2012</year><fpage>3995</fpage><lpage>4008</lpage><pub-id pub-id-type="pmid">22278237</pub-id></element-citation></ref><ref id="bib51"><element-citation publication-type="journal" id="sbref50"><person-group person-group-type="author"><name><surname>Woo</surname><given-names>P.C.</given-names></name><name><surname>Lau</surname><given-names>S.K.</given-names></name><name><surname>Chu</surname><given-names>C.M.</given-names></name><name><surname>Chan</surname><given-names>K.H.</given-names></name><name><surname>Tsoi</surname><given-names>H.W.</given-names></name><name><surname>Huang</surname><given-names>Y.</given-names></name><name><surname>Wong</surname><given-names>B.H.</given-names></name><name><surname>Poon</surname><given-names>R.W.</given-names></name><name><surname>Cai</surname><given-names>J.J.</given-names></name><name><surname>Luk</surname><given-names>W.K.</given-names></name><name><surname>Poon</surname><given-names>L.L.</given-names></name><name><surname>Wong</surname><given-names>S.S.</given-names></name><name><surname>Guan</surname><given-names>Y.</given-names></name><name><surname>Peiris</surname><given-names>J.S.</given-names></name><name><surname>Yuen</surname><given-names>K.Y.</given-names></name></person-group><article-title>Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia</article-title><source>J. Virol.</source><volume>79</volume><year>2005</year><fpage>884</fpage><lpage>895</lpage><pub-id pub-id-type="pmid">15613317</pub-id></element-citation></ref><ref id="bib52"><element-citation publication-type="journal" id="sbref51"><person-group person-group-type="author"><name><surname>Wu</surname><given-names>Z.</given-names></name><name><surname>Yang</surname><given-names>L.</given-names></name><name><surname>Ren</surname><given-names>X.</given-names></name><name><surname>Zhang</surname><given-names>J.</given-names></name><name><surname>Yang</surname><given-names>F.</given-names></name><name><surname>Zhang</surname><given-names>S.</given-names></name><name><surname>Jin</surname><given-names>Q.</given-names></name></person-group><article-title>ORF8-related genetic evidence for Chinese horseshoe bats as the source of human severe acute respiratory syndrome coronavirus</article-title><source>J. Infect. Dis.</source><volume>213</volume><year>2016</year><fpage>579</fpage><lpage>583</lpage><pub-id pub-id-type="pmid">26433221</pub-id></element-citation></ref><ref id="bib53"><element-citation publication-type="journal" id="sbref52"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>L.</given-names></name><name><surname>Wu</surname><given-names>Z.</given-names></name><name><surname>Ren</surname><given-names>X.</given-names></name><name><surname>Yang</surname><given-names>F.</given-names></name><name><surname>He</surname><given-names>G.</given-names></name><name><surname>Zhang</surname><given-names>J.</given-names></name><name><surname>Dong</surname><given-names>J.</given-names></name><name><surname>Sun</surname><given-names>L.</given-names></name><name><surname>Zhu</surname><given-names>Y.</given-names></name><name><surname>Du</surname><given-names>J.</given-names></name><name><surname>Zhang</surname><given-names>S.</given-names></name><name><surname>Jin</surname><given-names>Q.</given-names></name></person-group><article-title>Novel SARS-like betacoronaviruses in bats, China, 2011</article-title><source>Emerg. Infect. Dis.</source><volume>19</volume><year>2013</year><fpage>989</fpage><lpage>991</lpage><pub-id pub-id-type="pmid">23739658</pub-id></element-citation></ref><ref id="bib54"><element-citation publication-type="journal" id="sbref53"><person-group person-group-type="author"><name><surname>Yang</surname><given-names>X.L.</given-names></name><name><surname>Hu</surname><given-names>B.</given-names></name><name><surname>Wang</surname><given-names>B.</given-names></name><name><surname>Wang</surname><given-names>M.N.</given-names></name><name><surname>Zhang</surname><given-names>Q.</given-names></name><name><surname>Zhang</surname><given-names>W.</given-names></name><name><surname>Wu</surname><given-names>L.J.</given-names></name><name><surname>Ge</surname><given-names>X.Y.</given-names></name><name><surname>Zhang</surname><given-names>Y.Z.</given-names></name><name><surname>Daszak</surname><given-names>P.</given-names></name><name><surname>Wang</surname><given-names>L.F.</given-names></name><name><surname>Shi</surname><given-names>Z.L.</given-names></name></person-group><article-title>Isolation and characterization of a novel bat Coronavirus closely related to the Direct progenitor of severe acute respiratory syndrome Coronavirus</article-title><source>J. Virol.</source><volume>90</volume><year>2015</year><fpage>3253</fpage><lpage>3256</lpage><pub-id pub-id-type="pmid">26719272</pub-id></element-citation></ref><ref id="bib55"><element-citation publication-type="journal" id="sbref54"><person-group person-group-type="author"><name><surname>Zaki</surname><given-names>A.M.</given-names></name><name><surname>van Boheemen</surname><given-names>S.</given-names></name><name><surname>Bestebroer</surname><given-names>T.M.</given-names></name><name><surname>Osterhaus</surname><given-names>A.D.</given-names></name><name><surname>Fouchier</surname><given-names>R.A.</given-names></name></person-group><article-title>Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia</article-title><source>N. Engl. J. Med.</source><volume>367</volume><year>2012</year><fpage>1814</fpage><lpage>1820</lpage><pub-id pub-id-type="pmid">23075143</pub-id></element-citation></ref><ref id="bib56"><element-citation publication-type="book" id="sbref55"><person-group person-group-type="author"><name><surname>Zhang</surname><given-names>R.Z.</given-names></name><name><surname>Jing</surname><given-names>S.K.</given-names></name><name><surname>Quan</surname><given-names>G.Q.</given-names></name><name><surname>Li</surname><given-names>S.H.</given-names></name><name><surname>Ye</surname><given-names>Z.Y.</given-names></name><name><surname>Wang</surname><given-names>F.G.</given-names></name><name><surname>Zhang</surname><given-names>M.L.</given-names></name></person-group><chapter-title>Distribution of Mammalian Species in China</chapter-title><year>1997</year><publisher-name>China Forestry Publishing House</publisher-name><publisher-loc>Beijing</publisher-loc><fpage>23</fpage><lpage>55</lpage></element-citation></ref></ref-list><sec id="s0090" sec-type="supplementary-material"><label>Appendix A</label><title>Supplementary material</title><p id="p0185"><supplementary-material content-type="local-data" id="ec0005"><caption><p><bold>Figure S1.</bold> Phylogenetic analysis of the nucleotide sequences of the coronavirus S1 and S2 genes including those CoVs here. Bootstrap values (>70%) are shown at appropriate nodes. The trees were mid-point rooted for clarity only. The scale bar represents the number of nucleotide substitutions per site.</p></caption><media xlink:href="mmc1.pdf"></media></supplementary-material>.</p><p id="p0190"><supplementary-material content-type="local-data" id="ec0010"><caption><p><bold>Figure S2.</bold> Phylogenetic analyses of the amino acid sequences of the 3CL, Hel, S and N genes including those CoVs obtained here. Numbers (>70%) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site.</p></caption><media xlink:href="mmc2.pdf"></media></supplementary-material>.</p><p id="p0195"><supplementary-material content-type="local-data" id="ec0015"><caption><p>Supplementary material</p></caption><media xlink:href="mmc3.docx"></media></supplementary-material>.</p><p id="p0200"><supplementary-material content-type="local-data" id="ec0020"><caption><p>Supplementary material</p></caption><media xlink:href="mmc4.docx"></media></supplementary-material>.</p><p id="p0205"><supplementary-material content-type="local-data" id="ec0025"><caption><p>Supplementary material</p></caption><media xlink:href="mmc5.docx"></media></supplementary-material>.</p></sec><ack id="ack0005"><title>Acknowledgments</title><p>This study was supported by the <funding-source id="gs1">12th Five-Year Major National Science and Technology Projects of China</funding-source> (2014ZX10004001-005), the <funding-source id="gs2">Special National Project on Research and Development of Key Biosafety Technologies</funding-source> (2016YFC1201900). <funding-source id="gs3">ECH is supported by an NHMRC Australia Fellowship</funding-source> (GNT1037231).</p></ack><fn-group><fn id="s0085" fn-type="supplementary-material"><label>Appendix A</label><p id="p0180">Supplementary data associated with this article can be found in the online version at <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1016/j.virol.2017.03.019" id="ir0010">doi:10.1016/j.virol.2017.03.019</ext-link>.</p></fn></fn-group></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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