Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome
Identifieur interne : 001559 ( Pmc/Corpus ); précédent : 001558; suivant : 001560Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome
Auteurs : Susanna K. P. Lau ; Patrick C. Y. Woo ; Kenneth S. M. Li ; Yi Huang ; Ming Wang ; Carol S. F. Lam ; Huifang Xu ; Rongtong Guo ; Kwok-Hung Chan ; Bo-Jian Zheng ; Kwok-Yung YuenSource :
- Virology [ 0042-6822 ] ; 2007.
Abstract
Apart from bat-SARS-CoV, we have identified a novel group 1 coronavirus, bat-CoV HKU2, in
Url:
DOI: 10.1016/j.virol.2007.06.009
PubMed: 17617433
PubMed Central: 7103351
Links to Exploration step
PMC:7103351Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome</title><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Li, Kenneth S M" sort="Li, Kenneth S M" uniqKey="Li K" first="Kenneth S. M." last="Li">Kenneth S. M. Li</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Wang, Ming" sort="Wang, Ming" uniqKey="Wang M" first="Ming" last="Wang">Ming Wang</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Lam, Carol S F" sort="Lam, Carol S F" uniqKey="Lam C" first="Carol S. F." last="Lam">Carol S. F. Lam</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Xu, Huifang" sort="Xu, Huifang" uniqKey="Xu H" first="Huifang" last="Xu">Huifang Xu</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Guo, Rongtong" sort="Guo, Rongtong" uniqKey="Guo R" first="Rongtong" last="Guo">Rongtong Guo</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Chan, Kwok Hung" sort="Chan, Kwok Hung" uniqKey="Chan K" first="Kwok-Hung" last="Chan">Kwok-Hung Chan</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Zheng, Bo Jian" sort="Zheng, Bo Jian" uniqKey="Zheng B" first="Bo-Jian" last="Zheng">Bo-Jian Zheng</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17617433</idno><idno type="pmc">7103351</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103351</idno><idno type="RBID">PMC:7103351</idno><idno type="doi">10.1016/j.virol.2007.06.009</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">001559</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001559</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome</title><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Li, Kenneth S M" sort="Li, Kenneth S M" uniqKey="Li K" first="Kenneth S. M." last="Li">Kenneth S. M. Li</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Wang, Ming" sort="Wang, Ming" uniqKey="Wang M" first="Ming" last="Wang">Ming Wang</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Lam, Carol S F" sort="Lam, Carol S F" uniqKey="Lam C" first="Carol S. F." last="Lam">Carol S. F. Lam</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Xu, Huifang" sort="Xu, Huifang" uniqKey="Xu H" first="Huifang" last="Xu">Huifang Xu</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Guo, Rongtong" sort="Guo, Rongtong" uniqKey="Guo R" first="Rongtong" last="Guo">Rongtong Guo</name><affiliation><nlm:aff id="aff4">Guangzhou Center for Disease Control and Prevention, Guangzhou, China</nlm:aff></affiliation></author><author><name sortKey="Chan, Kwok Hung" sort="Chan, Kwok Hung" uniqKey="Chan K" first="Kwok-Hung" last="Chan">Kwok-Hung Chan</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Zheng, Bo Jian" sort="Zheng, Bo Jian" uniqKey="Zheng B" first="Bo-Jian" last="Zheng">Bo-Jian Zheng</name><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="aff1">State Key Laboratory of Emerging Infectious Diseases, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff2">Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Department of Microbiology, The University of Hong Kong, Hong Kong</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="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Apart from bat-SARS-CoV, we have identified a novel group 1 coronavirus, bat-CoV HKU2, in <italic>Rhinolophus sinicus</italic> (Chinese horseshoe bats). Since it has been suggested that the receptor-binding motif (RBM) of SARS-CoV may have been acquired from a group 1 coronavirus, we conducted a surveillance study and identified bat-SARS-CoV and bat-CoV HKU2 in 8.7% and 7.5% respectively of <italic>R. sinicus</italic> in Hong Kong and Guangdong. Complete genome sequencing of four strains of bat-CoV HKU2 revealed the smallest coronavirus genome (27164 nucleotides) and a unique spike protein evolutionarily distinct from the rest of the genome. This spike protein, sharing similar deletions with other group 2 coronaviruses in its C-terminus, also contained a 15-amino acid peptide homologous to a corresponding peptide within the RBM of spike protein of SARS-CoV, which was absent in other coronaviruses except bat-SARS-CoV. 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<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">17617433</article-id><article-id pub-id-type="pmc">7103351</article-id><article-id pub-id-type="publisher-id">S0042-6822(07)00409-6</article-id><article-id pub-id-type="doi">10.1016/j.virol.2007.06.009</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lau</surname><given-names>Susanna K.P.</given-names></name><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref><xref rid="aff3" ref-type="aff">c</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>Woo</surname><given-names>Patrick C.Y.</given-names></name><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref><xref rid="aff3" ref-type="aff">c</xref><xref rid="fn1" ref-type="fn">1</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Kenneth S.M.</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Yi</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Ming</given-names></name><xref rid="aff4" ref-type="aff">d</xref></contrib><contrib contrib-type="author"><name><surname>Lam</surname><given-names>Carol S.F.</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Huifang</given-names></name><xref rid="aff4" ref-type="aff">d</xref></contrib><contrib contrib-type="author"><name><surname>Guo</surname><given-names>Rongtong</given-names></name><xref rid="aff4" ref-type="aff">d</xref></contrib><contrib contrib-type="author"><name><surname>Chan</surname><given-names>Kwok-hung</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Zheng</surname><given-names>Bo-jian</given-names></name><xref rid="aff3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Yuen</surname><given-names>Kwok-yung</given-names></name><email>hkumicro@hkucc.hku.hk</email><xref rid="aff1" ref-type="aff">a</xref><xref rid="aff2" ref-type="aff">b</xref><xref rid="aff3" ref-type="aff">c</xref><xref rid="cor1" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff1"><label>a</label>State Key Laboratory of Emerging Infectious Diseases, Hong Kong</aff><aff id="aff2"><label>b</label>Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong</aff><aff id="aff3"><label>c</label>Department of Microbiology, The University of Hong Kong, Hong Kong</aff><aff id="aff4"><label>d</label>Guangzhou Center for Disease Control and Prevention, Guangzhou, China</aff><author-notes><corresp id="cor1"><label>⁎</label>Corresponding author. State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Hong Kong. Fax: +852 28551241. <email>hkumicro@hkucc.hku.hk</email></corresp><fn id="fn1"><label>1</label><p>SKP Lau and PCY Woo contributed equally to the manuscript.</p></fn></author-notes><pub-date pub-type="pmc-release"><day>6</day><month>7</month><year>2007</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"><day>25</day><month>10</month><year>2007</year></pub-date><pub-date pub-type="epub"><day>6</day><month>7</month><year>2007</year></pub-date><volume>367</volume><issue>2</issue><fpage>428</fpage><lpage>439</lpage><history><date date-type="received"><day>16</day><month>4</month><year>2007</year></date><date date-type="rev-recd"><day>16</day><month>5</month><year>2007</year></date><date date-type="accepted"><day>6</day><month>6</month><year>2007</year></date></history><permissions><copyright-statement>Copyright © 2007 Elsevier Inc. All rights reserved.</copyright-statement><copyright-year>2007</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><p>Apart from bat-SARS-CoV, we have identified a novel group 1 coronavirus, bat-CoV HKU2, in <italic>Rhinolophus sinicus</italic> (Chinese horseshoe bats). Since it has been suggested that the receptor-binding motif (RBM) of SARS-CoV may have been acquired from a group 1 coronavirus, we conducted a surveillance study and identified bat-SARS-CoV and bat-CoV HKU2 in 8.7% and 7.5% respectively of <italic>R. sinicus</italic> in Hong Kong and Guangdong. Complete genome sequencing of four strains of bat-CoV HKU2 revealed the smallest coronavirus genome (27164 nucleotides) and a unique spike protein evolutionarily distinct from the rest of the genome. This spike protein, sharing similar deletions with other group 2 coronaviruses in its C-terminus, also contained a 15-amino acid peptide homologous to a corresponding peptide within the RBM of spike protein of SARS-CoV, which was absent in other coronaviruses except bat-SARS-CoV. These suggest a common evolutionary origin in the spike protein of bat-CoV HKU2, bat-SARS-CoV, and SARS-CoV.</p></abstract><kwd-group><title>Keywords</title><kwd>Chinese horseshoe bats</kwd><kwd>Coronavirus</kwd><kwd>HKU2</kwd><kwd>SARS</kwd><kwd>Novel</kwd><kwd>Receptor</kwd><kwd>Origin</kwd></kwd-group></article-meta></front><body><sec id="section0005"><title>Introduction</title><p id="para0005">Coronaviruses can infect a wide variety of animals in which they can cause respiratory, enteric, hepatic and neurological diseases of varying severity. Based on genotypic and serological characteristics, coronaviruses were classified into three distinct groups (<xref rid="bib4" ref-type="bibr">Brian and Baric, 2005</xref>, <xref rid="bib20" ref-type="bibr">Lai and Cavanagh, 1997</xref>, <xref rid="bib57" ref-type="bibr">Ziebuhr, 2004</xref>). As a result of the unique mechanism of viral replication, coronaviruses have a high frequency of recombination (<xref rid="bib20" ref-type="bibr">Lai and Cavanagh, 1997</xref>). Such a high recombination rate, coupled with the infidelity of the polymerases of RNA viruses, may allow them to adapt to new hosts and ecological niches (<xref rid="bib11" ref-type="bibr">Herrewegh et al., 1998</xref>, <xref rid="bib52" ref-type="bibr">Woo et al., 2006c</xref>).</p><p id="para0010">The severe acute respiratory syndrome (SARS) epidemic in 2003, caused by a novel coronavirus, SARS coronavirus (SARS-CoV), has aroused interests in the discovery of novel coronaviruses in both humans and animals (<xref rid="bib9" ref-type="bibr">Guan et al., 2003</xref>, <xref rid="bib30" ref-type="bibr">Marra et al., 2003</xref>, <xref rid="bib32" ref-type="bibr">Peiris et al., 2003</xref>, <xref rid="bib36" ref-type="bibr">Rota et al., 2003</xref>, <xref rid="bib46" ref-type="bibr">Woo et al., 2004</xref>). Before that, only 19 (two human, 13 mammalian and four avian) coronaviruses were known. After the epidemic, two novel human coronaviruses, human coronavirus NL63 (HCoV-NL63), a group 1 coronavirus, and coronavirus HKU1 (CoV-HKU1), a group 2 coronavirus, have been discovered (<xref rid="bib8" ref-type="bibr">Fouchier et al., 2004</xref>, <xref rid="bib22" ref-type="bibr">Lau et al., 2006</xref>, <xref rid="bib44" ref-type="bibr">van der Hoek et al., 2004</xref>, <xref rid="bib47" ref-type="bibr">Woo et al., 2005a</xref>, <xref rid="bib48" ref-type="bibr">Woo et al., 2005b</xref>). In the recent two years, at least 10 previously unrecognized coronaviruses from bats were also described in Hong Kong and mainland China (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib26" ref-type="bibr">Li et al., 2005b</xref>, <xref rid="bib33" ref-type="bibr">Poon et al., 2005</xref>, <xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>, <xref rid="bib50" ref-type="bibr">Woo et al., 2006a</xref>, <xref rid="bib53" ref-type="bibr">Woo et al., 2006d</xref>), suggesting that bats play an important role in the ecology and evolution of coronaviruses.</p><p id="para0015">Although the identification of SARS-CoV-like viruses in Himalayan palm civets and raccoon dogs in live-animal markets in southern China suggested that wild animals could be the origin of SARS (<xref rid="bib9" ref-type="bibr">Guan et al., 2003</xref>), the absence of related viruses in wild civets in extensive surveillance studies and the rapid evolution of SARS-CoV genomes in market civets suggested that these caged animals were likely only intermediate hosts and there is a yet unidentified natural reservoir for SARS-CoV (<xref rid="bib25" ref-type="bibr">Li et al., 2005a</xref>, <xref rid="bib38" ref-type="bibr">Song et al., 2005</xref>, <xref rid="bib42" ref-type="bibr">Tu et al., 2004</xref>, <xref rid="bib54" ref-type="bibr">Yang et al., 2005</xref>). Recently, we have described the discovery of a SARS-CoV-like virus, bat SARS coronavirus (bat-SARS-CoV), in Chinese horseshoe bats in Hong Kong (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>). Similar viruses have also been found in other species of horseshoe bats in mainland China (<xref rid="bib26" ref-type="bibr">Li et al., 2005b</xref>), suggesting that horseshoe bats are reservoir of SARS-CoV-like viruses. However, genome sequence comparison of SARS-CoV-like coronaviruses from horseshoe bats and human/civet SARS-CoV showed that they shared only 88–92% nucleotide identities. More importantly, the amino acid sequence identities between the spike (S) proteins of bat and human/civet viruses were only 78–80% (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib26" ref-type="bibr">Li et al., 2005b</xref>, <xref rid="bib35" ref-type="bibr">Ren et al., 2006</xref>). Therefore, events such as mutation and/or recombination would have occurred during the evolution of these SARS-CoV-like viruses before the possible emergence of direct progenitors of SARS-CoV capable of infecting palm civets and subsequently humans.</p><p id="para0020">In a recent report on angiotensin-converting enzyme 2 (ACE2)–S protein interactions of SARS-CoV, it was suggested that the receptor-binding motif (RBM) of SARS-CoV may have been acquired from a group 1 virus related to HCoV-NL63 (<xref rid="bib27" ref-type="bibr">Li et al., 2006</xref>). Interestingly, a novel group 1 coronavirus, bat coronavirus HKU2 (bat-CoV HKU2), was identified in Chinese horseshoe bats in addition to bat-SARS-CoV in our previous surveillance studies (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib53" ref-type="bibr">Woo et al., 2006d</xref>). To better understand the epidemiology and evolution of bat-CoV HKU2 and explore possible recombination events between this group 1 coronavirus and bat-SARS-CoV that could have led to the emergence of SARS-CoV, we conducted an extensive surveillance for coronaviruses in Chinese horseshoe bats in Hong Kong and Guangdong, the province in southern China where the SARS epidemic originated, over a 2-year period. Four complete genomes of bat-CoV HKU2, three from Hong Kong and one from Guangdong, were also sequenced and analyzed. Comparison of bat-CoV HKU2 genomes with other coronavirus genomes revealed a spike protein distinct from the spike proteins of other group 1 coronaviruses, with a peptide homologous to a segment of the RBM of the S protein of SARS-CoV.</p></sec><sec id="section0010"><title>Results</title><sec id="section0015"><title>Coronavirus surveillance in Chinese horseshoe bats</title><p id="para0025">A total of 770 respiratory and alimentary specimens from 348 and 64 Chinese horseshoe bats were obtained in Hong Kong and in the Guangdong province in Southern China, respectively. RT-PCR for a 440-bp fragment in the RdRp genes of coronaviruses was positive in alimentary specimens from 58 (16.7%) of the 348 bats from Hong Kong, and from 8 (12.5%) of the 64 bats from Guandong. None of the respiratory specimens was positive. Sequencing results suggested the presence of two different coronaviruses among the 64 positive bats. Of the 58 positive bats from Hong Kong, the sequences of 29 samples possessed ≥ 99% nucleotide identities to bat-CoV HKU2 (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="DQ249235">DQ249235</ext-link>), while those of the other 29 samples possessed ≥ 99% nucleotide identities to bat-SARS-CoV (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="DQ022305">DQ022305</ext-link>) (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib53" ref-type="bibr">Woo et al., 2006d</xref>). The bats positive for bat-CoV HKU2 and bat-SARS-CoV were from nine of the 18 sampling locations in Hong Kong, with bats from three locations harboring both viruses (<xref rid="fig1" ref-type="fig">Fig. 1</xref>). Of the eight positive bats from Guangdong, the sequences of six alimentary samples possessed 97–98% nucleotide identities to bat-CoV HKU2, while that of one possessed 98% nucleotide identities to bat-SARS-CoV. The remaining positive sample contained both bat-CoV HKU2 and bat-SARS-CoV with 98% nucleotide identities. Attempts to stably passage bat-CoV HKU2 in cell lines were unsuccessful.<fig id="fig1"><label>Fig. 1</label><caption><p>Map showing locations of sampling in Hong Kong. Dark circles represent locations positive for bat-CoV HKU2, squares represent locations positive for bat-SARS-CoV, and triangles represent locations positive for both bat-CoV HKU2 and bat-SARS-CoV. Blank circles represent locations negative for bat-SARS-CoV and bat-CoV HKU2. Location A was where bat-CoV HKU2/HK/33/2004 was found, location B was where bat-CoV HKU2/HK/298/2004 was found, and location C was where bat-CoV HKU2/HK/46/2006 was found.</p></caption><graphic xlink:href="gr1_lrg"></graphic></fig></p></sec><sec id="section0020"><title>Characterization of bat-CoV HKU2 genomes</title><p id="para0030">Complete genome sequence data of four strains of bat-CoV HKU2 were obtained by assembly of the sequences of the RT-PCR products obtained directly from four individual specimens collected at different time and places. Three strains were obtained from Hong Kong (bat-CoV HKU2/HK/33/2004, bat-CoV HKU2/HK/298/2004 and bat-CoV HKU2/HK/46/2006) (<xref rid="fig1" ref-type="fig">Fig. 1</xref>), while one was obtained from Guangdong (bat-CoV HKU2/GD/430/2006). Their genomes were 27,164-nucleotide, polyadenylated RNA, the smallest genome size among all coronaviruses with genome sequences available (<xref rid="tbl1" ref-type="table">Table 1</xref>and <xref rid="fig2" ref-type="fig">Fig. 2</xref>). The G + C content was 39% (<xref rid="tbl1" ref-type="table">Table 1</xref>). The four strains share the same genome structures and were highly similar in their nucleotide sequence. The three Hong Kong strains were more closely related to each other with 99.9% overall nucleotide identities, while that from Guangdong had 98.5% nucleotide identities with the three Hong Kong strains. Their genome organization was similar to other coronaviruses (<xref rid="tbl2" ref-type="table">Table 2</xref>and <xref rid="fig2" ref-type="fig">Fig. 2</xref>). Bat-CoV HKU2 possessed the putative transcription regulatory sequence (TRS) motif, 5′-AACUAAA-3′, at the 3′ end of the leader sequence and precedes each ORF (<xref rid="tbl2" ref-type="table">Table 2</xref>). This TRS has also been shown to be the TRS for HCoV-NL63 (<xref rid="bib34" ref-type="bibr">Pyrc et al., 2004</xref>), whereas a shorter sequence, 5″-CUAAAC-3′, was found to be the TRS for other group 1 coronaviruses such as TGEV and FIPV (<xref rid="bib6" ref-type="bibr">Dye and Siddell, 2005</xref>, <xref rid="bib12" ref-type="bibr">Hiscox et al., 1995</xref>).<table-wrap position="float" id="tbl1"><label>Table 1</label><caption><p>Comparison of genomic features of bat-CoV HKU2 and other coronaviruses and amino acid identities between the predicted 3CL<sup>pro</sup>, RdRp, Hel, S, E, M, and N proteins of bat-CoV HKU2 and the corresponding proteins of other coronaviruses</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" valign="top">Coronaviruses<xref rid="tblfn1" ref-type="table-fn">a</xref></th><th valign="top">Genome<hr></hr></th><th valign="top">Features<hr></hr></th><th colspan="7" valign="top">Pairwise amino acid identity (%)<hr></hr></th></tr><tr><th valign="top">Size (bases)</th><th valign="top">G + C content</th><th valign="top">3CL<sup>pro</sup></th><th valign="top">RdRp</th><th valign="top">Hel</th><th valign="top">S</th><th valign="top">E</th><th valign="top">M</th><th valign="top">N</th></tr></thead><tbody><tr><td valign="top">Group 1a</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> TGEV</td><td valign="top">28586</td><td valign="top">0.38</td><td valign="top">63.2</td><td valign="top">75.8</td><td valign="top">77.5</td><td valign="top">21.9</td><td valign="top">28.9</td><td valign="top">47.3</td><td valign="top">40.3</td></tr><tr><td valign="top"> FIPV</td><td valign="top">29355</td><td valign="top">0.38</td><td valign="top">61.3</td><td valign="top">75.9</td><td valign="top">77.6</td><td valign="top">22.3</td><td valign="top">28.9</td><td valign="top">45.5</td><td valign="top">41.6</td></tr><tr><td valign="top"> PRCV</td><td valign="top">27550</td><td valign="top">0.37</td><td valign="top">62.9</td><td valign="top">75.6</td><td valign="top">77.3</td><td valign="top">26.0</td><td valign="top">30.1</td><td valign="top">47.5</td><td valign="top">40.0</td></tr><tr><td valign="top">Group 1b</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> HCoV-229E</td><td valign="top">27317</td><td valign="top">0.38</td><td valign="top">64.2</td><td valign="top">81.2</td><td valign="top">81.1</td><td valign="top">27.0</td><td valign="top">51.3</td><td valign="top">56.5</td><td valign="top">44.5</td></tr><tr><td valign="top"> HCoV-NL63</td><td valign="top">27553</td><td valign="top">0.34</td><td valign="top">64.0</td><td valign="top">79.4</td><td valign="top">81.6</td><td valign="top">25.7</td><td valign="top">50.0</td><td valign="top">59.6</td><td valign="top">46.8</td></tr><tr><td valign="top"> PEDV</td><td valign="top">28033</td><td valign="top">0.42</td><td valign="top">65.2</td><td valign="top">78.5</td><td valign="top">78.4</td><td valign="top">24.0</td><td valign="top">46.2</td><td valign="top">64.8</td><td valign="top">39.6</td></tr><tr><td valign="top"> BtCoV/512/2005</td><td valign="top">28203</td><td valign="top">0.40</td><td valign="top">62.3</td><td valign="top">77.8</td><td valign="top">78.2</td><td valign="top">25.9</td><td valign="top">50.0</td><td valign="top">61.3</td><td valign="top">46.9</td></tr><tr><td valign="top"> Bat-CoV HKU6</td><td valign="top">NA<xref rid="tblfn2" ref-type="table-fn">b</xref></td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">77.9</td><td valign="top">78.2</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td></tr><tr><td valign="top"> Bat-CoV HKU7</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">82.7</td><td valign="top">80.6</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">46.3</td></tr><tr><td valign="top"> Bat-CoV HKU8</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">80.7</td><td valign="top">81.6</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">48.7</td></tr><tr><td valign="top"> Bat-CoV 1A (partial CDS)</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">80.0</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">50.5</td></tr><tr><td valign="top"> Bat-CoV 1B (partial CDS)</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">80.0</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">NA</td><td valign="top">50.2</td></tr><tr><td valign="top"> Bat-CoV HKU2</td><td valign="top">27164</td><td valign="top">0.39</td><td valign="top">–</td><td valign="top">–</td><td valign="top">–</td><td valign="top">–</td><td valign="top">–</td><td valign="top">–</td><td valign="top">–</td></tr><tr><td valign="top">Group 2a</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> CoV-HKU1</td><td valign="top">29926</td><td valign="top">0.32</td><td valign="top">45.5</td><td valign="top">56.6</td><td valign="top">53.6</td><td valign="top">24.5</td><td valign="top">30.4</td><td valign="top">34.3</td><td valign="top">27.8</td></tr><tr><td valign="top"> HCoV-OC43</td><td valign="top">30738</td><td valign="top">0.37</td><td valign="top">44.2</td><td valign="top">57.4</td><td valign="top">54.5</td><td valign="top">24.1</td><td valign="top">32.3</td><td valign="top">36.6</td><td valign="top">24.7</td></tr><tr><td valign="top"> MHV</td><td valign="top">31357</td><td valign="top">0.42</td><td valign="top">46.9</td><td valign="top">56.3</td><td valign="top">54.2</td><td valign="top">24.8</td><td valign="top">28.6</td><td valign="top">36.5</td><td valign="top">26.9</td></tr><tr><td valign="top"> BCoV</td><td valign="top">31028</td><td valign="top">0.37</td><td valign="top">44.2</td><td valign="top">57.3</td><td valign="top">54.6</td><td valign="top">23.4</td><td valign="top">32.3</td><td valign="top">36.3</td><td valign="top">23.9</td></tr><tr><td valign="top"> PHEV</td><td valign="top">30480</td><td valign="top">0.37</td><td valign="top">43.9</td><td valign="top">57.2</td><td valign="top">54.5</td><td valign="top">24.5</td><td valign="top">33.3</td><td valign="top">35.7</td><td valign="top">24.7</td></tr><tr><td valign="top">Group 2b</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> SARS-CoV</td><td valign="top">29751</td><td valign="top">0.41</td><td valign="top">43.5</td><td valign="top">59.9</td><td valign="top">61.3</td><td valign="top">25.6</td><td valign="top">27.3</td><td valign="top">30.7</td><td valign="top">22.4</td></tr><tr><td valign="top"> Bat-SARS-CoV HKU3</td><td valign="top">29728</td><td valign="top">0.41</td><td valign="top">43.8</td><td valign="top">59.8</td><td valign="top">60.8</td><td valign="top">25.9</td><td valign="top">27.3</td><td valign="top">31.2</td><td valign="top">22.4</td></tr><tr><td valign="top">Group 2c</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> Bat-CoV HKU4</td><td valign="top">30286</td><td valign="top">0.38</td><td valign="top">47.7</td><td valign="top">59.4</td><td valign="top">61.8</td><td valign="top">23.6</td><td valign="top">22.6</td><td valign="top">33.9</td><td valign="top">26.3</td></tr><tr><td valign="top"> Bat-CoV HKU5</td><td valign="top">30488</td><td valign="top">0.43</td><td valign="top">46.6</td><td valign="top">58.7</td><td valign="top">61.8</td><td valign="top">23.5</td><td valign="top">25.3</td><td valign="top">30.6</td><td valign="top">26.4</td></tr><tr><td valign="top">Group 2d</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> Bat-CoV HKU9</td><td valign="top">29114</td><td valign="top">0.41</td><td valign="top">45.6</td><td valign="top">58.0</td><td valign="top">61.8</td><td valign="top">25.5</td><td valign="top">23.8</td><td valign="top">34.2</td><td valign="top">19.3</td></tr><tr><td valign="top">Group 3</td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td><td valign="top"></td></tr><tr><td valign="top"> IBV</td><td valign="top">27608</td><td valign="top">0.38</td><td valign="top">40.1</td><td valign="top">58.5</td><td valign="top">56.1</td><td valign="top">24.2</td><td valign="top">18.9</td><td valign="top">22.7</td><td valign="top">22.1</td></tr></tbody></table><table-wrap-foot><fn id="tblfn1"><label>a</label><p>TGEV, porcine transmissible gastroenteritis virus; FIPV, feline infectious peritonitis virus; PRCV, porcine respiratory coronavirus; HCoV-229E, human coronavirus 229E; HCoV-NL63, human coronavirus NL63; PEDV, porcine epidemic diarrhea virus; CoV-HKU1, coronavirus HKU1; HCoV-OC43, human coronavirus OC43; MHV, murine hepatitis virus; BCoV, bovine coronavirus; PHEV, porcine hemagglutinating encephalomyelitis virus; SARS-CoV, SARS coronavirus; bat-SARS-CoV HKU3, bat SARS coronavirus HKU3; IBV, infectious bronchitis virus.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tblfn2"><label>b</label><p>NA, data not available for analysis.</p></fn></table-wrap-foot></table-wrap><fig id="fig2"><label>Fig. 2</label><caption><p>Genome organizations of bat-CoV HKU2 compared to representative coronaviruses from each group. The conserved functional domains ORF 1ab and the structural proteins are represented by gray boxes. The genome sizes (bp) are shown on the right.</p></caption><graphic xlink:href="gr2_lrg"></graphic></fig><table-wrap position="float" id="tbl2"><label>Table 2</label><caption><p>Coding potential and putative transcription regulatory sequences of bat-CoV HKU2</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" valign="top">Coronaviruses</th><th rowspan="2" valign="top">ORFs</th><th rowspan="2" valign="top">Start-end (nucleotide position)</th><th rowspan="2" valign="top">No. of nucleotides</th><th rowspan="2" valign="top">No. of amino acids</th><th rowspan="2" valign="top">Frame</th><th colspan="2" valign="top">Putative TRS<hr></hr></th></tr><tr><th valign="top">Nucleotide position in genome</th><th valign="top">TRS sequence</th></tr></thead><tbody><tr><td valign="top">Bat-CoV HKU2</td><td valign="top">1ab</td><td valign="top">297–20,479 (shift at 12,446)</td><td align="char" valign="top">20,183</td><td align="char" valign="top">6727</td><td valign="top">+3/+2</td><td align="char" valign="top">122</td><td valign="top"><underline>AACUAAA</underline>C(167)AUG</td></tr><tr><td valign="top"></td><td valign="top">S</td><td valign="top">20,476–23,862</td><td align="char" valign="top">3387</td><td align="char" valign="top">1128</td><td valign="top">+1</td><td align="char" valign="top">20,470</td><td valign="top"><underline>AACUAAA</underline>UG</td></tr><tr><td valign="top"></td><td valign="top">NS3</td><td valign="top">23,862–24,551</td><td align="char" valign="top">690</td><td align="char" valign="top">229</td><td valign="top">+3</td><td align="char" valign="top">23,817</td><td valign="top"><underline>AACUAAA</underline>C(37)AUG</td></tr><tr><td valign="top"></td><td valign="top">E</td><td valign="top">24,532–24,759</td><td align="char" valign="top">228</td><td align="char" valign="top">75</td><td valign="top">+1</td><td align="char" valign="top">24,523</td><td valign="top"><underline>AACUAAA</underline>C(1)AUG</td></tr><tr><td valign="top"></td><td valign="top">M</td><td valign="top">24,768–25,457</td><td align="char" valign="top">690</td><td align="char" valign="top">229</td><td valign="top">+3</td><td align="char" valign="top">24,754</td><td valign="top"><underline>AACUAAA</underline>C(6)AUG</td></tr><tr><td valign="top"></td><td valign="top">N</td><td valign="top">25,469–26,596</td><td align="char" valign="top">1128</td><td align="char" valign="top">375</td><td valign="top">+2</td><td align="char" valign="top">25,452</td><td valign="top"><underline>AACUAAA</underline>C(9)AUG</td></tr><tr><td valign="top"></td><td valign="top">NS7a</td><td valign="top">26,608–26,907</td><td align="char" valign="top">300</td><td align="char" valign="top">99</td><td valign="top">+1</td><td align="char" valign="top">26,600</td><td valign="top"><underline>AACUAAA</underline>CAUG</td></tr></tbody></table></table-wrap></p><p id="para0035">Similar to other coronaviruses, the replicase ORF1ab encodes a number of putative proteins, including nsp3 [which contains the putative papain-like protease (PL<sup>pro</sup>)], nsp5 [putative chymotrypsin-like protease (3CL<sup>pro</sup>)], nsp12 (putative RdRp), nsp13 [putative helicase (Hel)], which are produced by proteolytic cleavage by PL<sup>pro</sup> and 3CL<sup>pro</sup> at specific sites (<xref rid="bib49" ref-type="bibr">Woo et al., 2005c</xref>). Similar to other group 1 coronaviruses, the genome of bat-CoV HKU2 has two putative PL<sup>pro</sup>, which are homologous to PL1<sup>pro</sup> and PL2<sup>pro</sup> of other group 1 coronaviruses (<xref rid="fig2" ref-type="fig">Fig. 2</xref>).</p><p id="para0040">One ORF, which encodes a putative 229-amino acid nonstructural protein, NS3, was observed between the S and E genes. This NS3 possessed 42% amino acid identities to the NS3 of HCoV-NL63, 37% identities to that of BtCoV/512/05, 36% identities to that of PEDV, and 29% identities to the NS3b of TGEV. No functional domains were identified by PFAM and InterProScan. TMHMM analysis showed three putative transmembrane domains in NS3 of bat-CoV HKU2 (residues 38–60, 81–103, and 118–140).</p><p id="para0045">The most striking feature of bat-CoV HKU2 genome was observed in its S protein which possessed the shortest amino acid sequence (1128 amino acid residues) among the S proteins of all coronaviruses, as a result of deletions in the N-terminal region (<xref rid="app1" ref-type="sec">Supplementary Fig. 1</xref>). It had ≤ 27% amino acid identities to the S proteins of all known coronaviruses, as opposed to other genes which showed higher amino acid identities to the corresponding genes in other group 1 coronaviruses (especially group 1b) than to group 2 and group 3 coronaviruses (<xref rid="tbl1" ref-type="table">Table 1</xref>). When the S protein of bat-CoV HKU2 is aligned with the S protein of other group 1 coronaviruses, many of the amino acid residues conserved among and specific to group 1b coronaviruses were not found; whereas residues conserved among all coronaviruses, especially those in the C-terminal region, were identified (<xref rid="app1" ref-type="sec">Supplementary Fig. 1</xref>). In fact, the N-terminal region of the S protein of bat-CoV HKU2 possessed very low amino acid identities to the corresponding regions in any group of coronaviruses, which was due to both amino acid substitutions and deletions. Despite this, a short peptide consisting of 15 amino acids (residues 314 to 328) was found to be homologous to a corresponding peptide within the RBM in the S1 domain of SARS-CoV (residues 437 to 451) (<xref rid="fig3" ref-type="fig">Fig. 3</xref>). A similar peptide was also observed in bat-SARS-CoV, but not in any other known coronaviruses, suggesting that it is specific to SARS-CoV, bat-SARS-CoV and bat-CoV HKU2, with a common origin. Of the 15 amino acids within this homologous peptide, six (tyrosine 438, leucine 442, glycine 445, lysine 446, proline 449, and phenylalanine 450) were conserved between SARS-CoV and bat-CoV HKU2, with four using identical codons. Of these six amino acid residues, only four (tyrosine 438, lysine 446, proline 449, and phenylalaine) were found in bat-SARS-CoV, with two using identical codons. On the other hand, four additional amino acid residues (tyrosine 439, arginine 440, arginine 443, and leucine 447), not found in bat-CoV HKU2, were conserved between SARS-CoV and bat-SARS-CoV, though with different codon usage. In contrast to a previous study which suggested that the extended receptor-binding domain of HCoV-NL63 includes a stretch of residues with weak homology to the RBM of SARS-CoV (unpublished observations, <xref rid="bib27" ref-type="bibr">Li et al., 2006</xref>), we and another group of researchers did not identify any significant homology between the spike protein of the two coronaviruses (<xref rid="bib14" ref-type="bibr">Hofmann et al., 2006</xref>). When compared to the S proteins of other group 1 coronaviruses and SARS-CoV, large deletions were observed in the S protein of bat-CoV HKU2 in the region corresponding to the RBM of SARS-CoV. Since the amino acid sequence of the S protein of bat-SARS-CoV also differed significantly from that of SARS-CoV in this region, it is likely that this is a site of frequent mutation and/or recombination among coronaviruses in Chinese horseshoe bats. This highly variable region within the S protein of bat-CoV HKU2 and bat-SARS-CoV may have been important for host receptor adaptation. Although the overall amino acid identities of the S protein of bat-CoV HKU2 were equally low when compared to the S proteins of all three groups of coronaviruses, the S protein of bat-CoV HKU2 shares the two conserved regions of deletions both of 14 amino acids among group 2 coronaviruses in its C-terminus (<xref rid="app1" ref-type="sec">Supplementary Fig. 1</xref>). This suggests that this segment of the S protein of bat-CoV HKU2 may have co-evolved with the corresponding regions in group 2 coronaviruses. Nevertheless, the receptor for bat-CoV HKU2 remains to be determined. Aminopeptidase N (CD13) has been shown to be the receptor for many group 1 coronaviruses including HCoV-229E, canine coronavirus, FIPV, PEDV, and TGEV (<xref rid="bib5" ref-type="bibr">Delmas et al., 1992</xref>, <xref rid="bib55" ref-type="bibr">Yeager et al., 1992</xref>). As for group 2 coronaviruses, carcinoembryonic antigen-cell adhesion molecule 1 (CEACAM1) was identified as the receptor for murine hepatitis virus (MHV), while sialic acids were found to be the receptor for bovine coronavirus (BCoV) and human coronavirus OC43 (HCoV-OC43) (<xref rid="bib17" ref-type="bibr">Krempl et al., 1995</xref>, <xref rid="bib45" ref-type="bibr">Williams et al., 1991</xref>). However, human ACE2 (hACE2) have been shown to be the receptor for both SARS-CoV, a group 2 coronavirus, and HCoV-NL63, a group 1 coronavirus, although the two viruses utilize different binding sites for receptor recognition (<xref rid="bib13" ref-type="bibr">Hofmann et al., 2005</xref>, <xref rid="bib24" ref-type="bibr">Li et al., 2003</xref>). The S protein of bat-CoV HKU2 does not exhibit significant homology to the known receptor binding domains of HCoV-229E, HCoV-NL63, or MHV (<xref rid="bib3" ref-type="bibr">Bonavia et al., 2003</xref>, <xref rid="bib14" ref-type="bibr">Hofmann et al., 2006</xref>, <xref rid="bib18" ref-type="bibr">Kubo et al., 1994</xref>). Further experiments are required to delineate the receptor for bat-CoV HKU2.<fig id="fig3"><label>Fig. 3</label><caption><p>A short stretch of peptide within the RBM of S protein of SARS-CoV with homology to the corresponding region in the S of bat-CoV HKU2 and bat-SARS-CoV. The conserved amino acids are in bold and boxed.</p></caption><graphic xlink:href="gr3_lrg"></graphic></fig></p><p id="para0050">At the 3′ end of the genome after the N gene, there is one ORF that encodes a 99-amino acid nonstructural protein, NS7a. BLAST search revealed no amino acid similarities between this putative nonstructural protein and other known proteins and no functional domain was identified by PFAM and InterProScan. TMHMM analysis showed two putative transmembrane domains in NS7a (residues 4–26 and 59–81). Previously, FIPV and TGEV, both group 1a coronavirus, were the only coronaviruses known to possess genes downstream of N (<xref rid="fig1" ref-type="fig">Fig. 1</xref>). It has been suggested that the two genes downstream of N in FIPV may be important for virulence (<xref rid="bib10" ref-type="bibr">Haijema et al., 2004</xref>, <xref rid="bib31" ref-type="bibr">Olsen, 1993</xref>). In TGEV, the gene downstream of N has been suggested to play a role in membrane association of replication complexes or assembly of the virus (<xref rid="bib43" ref-type="bibr">Tung et al., 1992</xref>). In our recent report on the discovery of bat coronavirus HKU9, a novel bat coronavirus belonging to group 2d coronaviruses, two ORFs downstream to N were also found (<xref rid="bib50" ref-type="bibr">Woo et al., 2006a</xref>). In another group 1b coronavirus recently identified from bats in China, BtCoV/512/05, an ORF downstream to N was also identified (<xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>). These suggest that ORFs downstream to N can be present in coronaviruses other than group 1a and may be more prevalent among bat coronaviruses. Further experiments will delineate the function of such ORFs in bat coronaviruses.</p></sec><sec id="section0025"><title>Phylogenetic analyses</title><p id="para0055">The phylogenetic trees constructed using the amino acid sequences of the 3CL<sup>pro</sup>, RdRp, Hel, S, M, and N of bat-CoV HKU2 and other coronaviruses are shown in <xref rid="fig4" ref-type="fig">Fig. 4</xref>and the corresponding pairwise amino acid identities are shown in <xref rid="tbl1" ref-type="table">Table 1</xref>. As shown in all six trees, the four strains of bat-CoV HKU2 were clustered together, reflecting their high sequence similarities. For all the genes except S, bat-CoV HKU2 formed a distinct branch that clustered with other group 1 coronaviruses. This is supported by the higher amino acid identities to the corresponding genes in other group 1 coronaviruses (especially group 1b) than to those of group 2 and group 3 coronaviruses (<xref rid="tbl1" ref-type="table">Table 1</xref>). However, for the S gene, bat-CoV HKU2 formed a branch distinct from the three groups of known coronaviruses. The same tree topology was obtained when using the maximum likelihood method and Bayesian approach (data not shown). This finding is in line with results obtained from pairwise amino acid comparisons, which showed that the S of bat-CoV HKU2 possessed equally low amino acid identities (≤ 27%) to the S of all three groups of coronaviruses (<xref rid="tbl1" ref-type="table">Table 1</xref>).<fig id="fig4"><label>Fig. 4</label><caption><p>Phylogenetic analysis of 3CL<sup>pro</sup>, RdRp, Hel, S, M, and N of bat-CoV HKU2. The trees were constructed by neighbor joining method using Kimura's two-parameter correction and bootstrap values calculated from 1000 trees. 306, 949, 609, 1758, 270, and 586 amino acid positions in 3CL<sup>pro</sup>, RdRp, Hel, S, M, and N, respectively, were included in the analysis. The scale bar indicates the estimated number of substitutions per 10 amino acids. HCoV-229E, human coronavirus 229E; PEDV, porcine epidemic diarrhea virus; TGEV, porcine transmissible gastroenteritis virus; FIPV, feline infectious peritonitis virus; HCoV-NL63, human coronavirus NL63; CoV-HKU1, coronavirus HKU1; HCoV-OC43, human coronavirus OC43; MHV, murine hepatitis virus; BCoV, bovine coronavirus; PHEV, porcine hemagglutinating encephalomyelitis virus; IBV, infectious bronchitis virus; SARS-CoV, SARS coronavirus; bat-SARS-CoV HKU3, bat-SARS-like coronavirus HKU3; bat-CoV HKU4, bat coronavirus HKU4; bat-CoV HKU5, bat coronavirus HKU5; bat-CoV HKU9, bat coronavirus HKU9.</p></caption><graphic xlink:href="gr4_lrg"></graphic></fig></p></sec><sec id="section0030"><title>Recombination analysis</title><p id="para0060">To evaluate if segments of the SARS-CoV genome have arisen as a result of recombination between bat-SARS-CoV and bat-CoV HKU2, a sliding window analysis was conducted. No statistical support for recombination was obtained, which may be due to the high sequence divergence between the bat-SARS-CoV and bat-CoV HKU2 genomes.</p></sec><sec id="section0035"><title>Estimation of synonymous and non-synonymous substitution rates</title><p id="para0065">The Ka/Ks ratios for the various coding regions in bat-CoV HKU2 are shown in <xref rid="tbl3" ref-type="table">Table 3</xref>. Higher Ka/Ks ratios were observed within ORF1ab, especially nsp3 (which encodes the putative PL<sup>pro</sup> domains), nsp5 (which encodes the putative 3CL<sup>pro</sup>), and nsp14 (which encodes the helicase), whereas the ratios appeared to be lower among the structural genes. Notably, the Ka/Ks ratio for the S of bat-CoV HKU2 is only 0.03, suggesting that this gene is unlikely undergoing rapid evolution under positive selection.<table-wrap position="float" id="tbl3"><label>Table 3</label><caption><p>Estimation of non-synonymous substitution and synonymous rates in the genomes of bat-CoV HKU2</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" valign="top">Coding regions</th><th valign="top">Ka/Ks<hr></hr></th></tr><tr><th valign="top">Bat-CoV HKU2</th></tr></thead><tbody><tr><td valign="top">nsp1</td><td valign="top">0.197</td></tr><tr><td valign="top">nsp2</td><td valign="top">0.105</td></tr><tr><td valign="top">nsp3</td><td valign="top">0.470</td></tr><tr><td valign="top">nsp4</td><td valign="top">0.059</td></tr><tr><td valign="top">nsp5</td><td valign="top">0.320</td></tr><tr><td valign="top">nsp6</td><td valign="top">0.133</td></tr><tr><td valign="top">nsp7</td><td valign="top">Ka = 0, Ks = 0.01925</td></tr><tr><td valign="top">nsp8</td><td valign="top">0.855</td></tr><tr><td valign="top">nsp9</td><td valign="top">Ka = 0, Ks = 0.00864</td></tr><tr><td valign="top">nsp10</td><td valign="top">Ka = 0, Ks = 0</td></tr><tr><td valign="top">nsp11</td><td valign="top">Ka = 0, Ks = 0</td></tr><tr><td valign="top">nsp12</td><td valign="top">0.037</td></tr><tr><td valign="top">nsp13</td><td valign="top">0.027</td></tr><tr><td valign="top">nsp14</td><td valign="top">0.338</td></tr><tr><td valign="top">nsp15</td><td valign="top">0.178</td></tr><tr><td valign="top">nsp16</td><td valign="top">Ka = 0.00071, Ks = 0</td></tr><tr><td valign="top">S</td><td valign="top">0.030</td></tr><tr><td valign="top">NS3</td><td valign="top">0.194</td></tr><tr><td valign="top">E</td><td valign="top">0.098</td></tr><tr><td valign="top">M</td><td valign="top">0.148</td></tr><tr><td valign="top">N</td><td valign="top">0.076</td></tr><tr><td valign="top">NS7a</td><td valign="top">Ka = 0, Ks = 0.01847</td></tr></tbody></table></table-wrap></p></sec></sec><sec id="section0040"><title>Discussion</title><p id="para0070">In this study, bat-CoV HKU2 was found among 29 (8.3%) of 348 Chinese horseshoe bats from Hong Kong and 7 (10.9%) of 64 bats from Guangdong. All bats infected with bat-CoV HKU2 appeared healthy. The finding that bat-CoV HKU2 can only be detected in alimentary specimens suggests that it possesses enteric tropism. The genomes of the four strains of bat-CoV HKU2 being sequenced were highly similar, with conserved nucleotide and amino acid sequences in most of their genes (<xref rid="fig4" ref-type="fig">Fig. 4</xref>). Traditionally, coronaviruses have been classified into groups 1, 2, and 3. Based on a comprehensive comparative analysis of the genomes of the various groups of coronaviruses, coronaviruses can be classified into group 1 (subgroups 1a and 1b), group 2 (subgroups 2a, 2b, 2c, and 2d) and group 3 (<xref rid="bib50" ref-type="bibr">Woo et al., 2006a</xref>), with SARS-CoV being classified as group 2b coronaviruses (<xref rid="bib7" ref-type="bibr">Eickmann et al., 2003</xref>, <xref rid="bib37" ref-type="bibr">Snijder et al., 2003</xref>). Comparative amino acid sequence analysis showed that the predicted proteins in bat-CoV HKU2, except the S protein, were most similar to subgroup 1b of group 1 coronaviruses than to other groups of coronaviruses (<xref rid="tbl1" ref-type="table">Table 1</xref>). Based on phylogenetic analysis of the 3CL<sup>pro</sup>, RdRp, Hel, M, and N genes, the four strains of bat-CoV HKU2 formed a distinct branch within subgroup 1b of group 1 coronaviruses. They also possessed genomic features most similar to other members within this subgroup (<xref rid="fig2" ref-type="fig">Fig. 2</xref>). The genomes of group 1a coronaviruses encode two to three nonstructural proteins between S and E, whereas most group 1b coronaviruses encode only one such protein, except HCoV-229E which encodes two (<xref rid="bib41" ref-type="bibr">Thiel et al., 2001</xref>). The genome organization of bat-CoV HKU2, most similar to Bt/CoV/512/05, a recently reported bat coronavirus from <italic>Scotophilus kuhlii</italic> in China, contains a small ORF downstream to the N gene, which is not observed in other group 1b coronaviruses. These results support that bat-CoV HKU2 represents a novel member within subgroup 1b of group 1 coronaviruses.</p><p id="para0075">The S protein of bat-CoV HKU2 possesses several unique features. First, it represents the shortest S protein among the S proteins of known coronaviruses, as a result of substantial deletions especially in the N-terminal region corresponding to the RBM of SARS-CoV. These deletions within the S protein were also largely responsible for the smallest coronavirus genome observed among all coronaviruses. Second, although comparative genome analysis strongly suggests that bat-CoV HKU2 belonged to group 1b coronaviruses, its S protein is not closely related to the S proteins of any known coronaviruses. The S proteins of coronaviruses, being responsible for receptor binding and host species adaptation, are known to be one of the most variable regions within coronavirus genomes. Nevertheless, S proteins of coronaviruses within the same group or subgroup are more closely related among themselves than to members from a different group or subgroup, as shown in the same cluster upon phylogenetic analysis (<xref rid="fig4" ref-type="fig">Fig. 4</xref>). As demonstrated in a previous study, the within-group amino acid similarities of the S proteins of coronaviruses ranged from 59 to 91% while between-group similarities were from 22 to 36% (<xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>). In particular, the within-group similarity of the S proteins of group 1 coronavirus was found to be 59%. In contrast, the S protein of bat-CoV HKU2 possessed ≤ 27% amino acid identities to the S proteins of any known coronaviruses and formed a distinct branch away from the three groups of coronaviruses on phylogenetic analysis, suggesting that this gene had a very different phylogenetic position and hence evolutionary history as compared to other regions within the genome of bat-CoV HKU2. This virus would have either acquired this unique S protein from a yet unidentified coronavirus through recombination, or undergone rapid evolution in its S protein because of strong selective pressure. Since the Ka/Ks ratio for the S gene of bat-CoV HKU2 was found to be low when using the four strains collected from different sites and dates (<xref rid="tbl3" ref-type="table">Table 3</xref>), the latter hypothesis would be less supported. Moreover, further analysis revealed a unique short peptide with significant homology to a corresponding peptide within the RBM of SARS-CoV, which was not seen in any other coronaviruses except bat-SARS-CoV. The C-terminus of the S protein of bat-CoV HKU2 also contained regions of deletions conserved among group 2 coronaviruses. Therefore, the S protein of bat-CoV HKU2 is likely to share a common origin with other group 2 coronaviruses, especially group 2b coronaviruses, although bat-CoV HKU2 belongs to group 1 coronaviruses. This suggests that the S of bat-CoV HKU2 could have been acquired from a group 2 or related coronavirus by recombination. Although recombination between different groups of coronaviruses has not been reported previously, targeted recombination between MHV and it has been proposed that recombination may have occurred between influenza C virus and coronavirus (<xref rid="bib29" ref-type="bibr">Luytjes et al., 1988</xref>). Since the hemagglutinin esterase (HE), a unique protein only found in group 2 but not in group 1 or 3 coronaviruses, shared 30% amino acid homology to the hemagglutinin protein of influenza C virus, it was suggested that the HE of group 2 coronaviruses could have been acquired from influenza C virus by their ancestor through recombination. The present data suggest that the S protein of bat-CoV HKU2, bat-SARS-CoV, and SARS-CoV could have originated from an unknown ancestor coronavirus and was thereafter separately evolved, with the 15-amino acid homologous region being left-in molecular signatures. Further studies are required to elucidate the possible common ancestor virus and its host species.</p><p id="para0080">Although it remains to be determined if bats are reservoir for the direct precursor of SARS-CoV, Chinese horseshoe bats are a potential mixing vessel for the generation of new coronavirus variants. Apart from bat-CoV HKU2, bat-SARS-CoV was also found among 29 (8.3%) Chinese horseshoe bats from Hong Kong and 2 (3.1%) bats from Guangdong in the present study. Coinfection by both bat-CoV HKU2 and bat-SARS-CoV was also found in one bat from China. In our previous study, bat-CoV HKU2 was also detected in a bat positive for antibodies against bat-SARS-CoV (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>). Recombination, a characteristic feature of coronaviruses, has been observed between both different strains of the same coronavirus species and different species of coronaviruses. Recombination between different strains of coronaviruses was first recognized in MHV, which has been utilized as a valuable molecular tool in the generation of mutants by targeted RNA recombination (<xref rid="bib15" ref-type="bibr">Keck et al., 1988</xref>). Similar phenomenon was subsequently demonstrated in other coronaviruses such as infectious bronchitis virus, a group 3 coronavirus and between MHV and BCoV, both being group 2 coronaviruses (<xref rid="bib16" ref-type="bibr">Kottier et al., 1995</xref>, <xref rid="bib23" ref-type="bibr">Lavi et al., 1998</xref>). Recently, by complete genome analysis of 22 strains of CoV-HKU1, we have also documented for the first time natural recombination events in a human coronavirus giving rise to at least three different genotypes (<xref rid="bib52" ref-type="bibr">Woo et al., 2006c</xref>). Recombination between two different species of coronavirus, feline coronavirus type I and canine coronavirus, has also been suggested to be responsible for generation of feline coronavirus type II (<xref rid="bib11" ref-type="bibr">Herrewegh et al., 1998</xref>). Although the existing data did not provide enough evidence for recombination between bat-CoV HKU2 and bat-SARS-CoV in the generation of SARS-CoV, their co-infection of the same bat species would allow ample opportunities for recombination and emergence of other SARS-CoV-like viruses capable of inter-species transmission.</p><p id="para0085">The role of bats in the evolution and ecology of coronaviruses is yet to be explored. The existence of coronaviruses in bats was unknown until after the SARS epidemic when we first identified a novel group 1 coronavirus and bat-SARS-CoV from bats in Hong Kong (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib33" ref-type="bibr">Poon et al., 2005</xref>). An astonishing diversity of coronaviruses was subsequently found among the bat population in Hong Kong and other parts of China (<xref rid="bib26" ref-type="bibr">Li et al., 2005b</xref>, <xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>, <xref rid="bib50" ref-type="bibr">Woo et al., 2006a</xref>, <xref rid="bib53" ref-type="bibr">Woo et al., 2006d</xref>). Since bats are commonly found and served in wild animal markets and restaurants in Guangdong (<xref rid="bib51" ref-type="bibr">Woo et al., 2006b</xref>), and given their species diversity, roosting behavior, and migrating ability, these animals could well be the source for emergence of zoonotic epidemics like SARS. In a previous study, it has been suggested that there was species-specific host restriction of coronavirus in bats, with most coronaviruses from a single bat species clustered together (<xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>). However, there is evidence that one bat species can be infected by more than one coronavirus species, and more than one bat species can be infected by the same coronavirus. The consistent detection of bat-CoV-HKU2 and bat-SARS-CoV in Chinese horseshoe bats over the 2-year study period from both Hong Kong and Guangdong suggested that this bat species is an established reservoir for both viruses which belonged to two different groups. Chinese horseshoe bat, under the family Rhinolophidae, is a common insectivorous species found in Hong Kong and China. Apart from <italic>Rhinolophus sinicus</italic>, <italic>R. ferrumequinum</italic>, another horseshoe bat species found in China, has also been found to harbor both group 1 and group 2 coronaviruses (<xref rid="bib40" ref-type="bibr">Tang et al., 2006</xref>). Therefore, it is likely that bats, especially members of Rhinolophidae, can be infected by both group 1 and group 2 coronaviruses, a situation similar to humans who can be infected by group 1 (HCoV-229E and HCoV-NL63) and group 2 (SARS-CoV, HCoV-OC43, and CoV-HKU1) coronaviruses. As for the infection of more than one bat species by the same coronavirus, SARS-CoV-like viruses have been detected in at least three different species of Rhinolophidae in China (<xref rid="bib26" ref-type="bibr">Li et al., 2005b</xref>). More extensive surveillance for coronaviruses in different species of horseshoe bats would shed light on the role of this bat family in the ecology and evolution of coronaviruses.</p></sec><sec id="section0045"><title>Materials and methods</title><sec id="section0050"><title>Sample collection</title><p id="para0090">Chinese horseshoe bats (<italic>R. sinicus</italic>) were captured from various locations in Hong Kong and in the Guangdong province of Southern China over a 2-year period (April 2004 to April 2006). Their respiratory and alimentary specimens were collected using procedures described previously (<xref rid="bib21" ref-type="bibr">Lau et al., 2005</xref>, <xref rid="bib56" ref-type="bibr">Yob et al., 2001</xref>). All specimens were placed in viral transport medium before transportation to the laboratory for RNA extraction.</p></sec><sec id="section0055"><title>RNA extraction</title><p id="para0095">Viral RNA was extracted from the respiratory and alimentary specimens using QIAamp Viral RNA Mini Kit (QIAgen, Hilden, Germany). The RNA was eluted in 50 μl of AVE buffer and was used as the template for RT-PCR.</p></sec><sec id="section0060"><title>RT-PCR for coronaviruses and DNA sequencing</title><p id="para0100">Coronavirus screening was performed by amplifying a 440-bp fragment of the RNA-dependent RNA polymerase (RdRp) gene of coronaviruses using conserved primers (5′-GGTTGGGACTATCCTAAGTGTGA-3′ and 5′-CCATCATCAGATAGAATCATCATA-3′) designed by multiple alignments of the nucleotide sequences of available RdRp genes of known coronaviruses (<xref rid="bib47" ref-type="bibr">Woo et al., 2005a</xref>). Reverse transcription was performed using the SuperScript III kit (Invitrogen, San Diego, CA, USA). The PCR mixture (25 μl) contained cDNA, PCR buffer (10 mM Tris–HCl pH 8.3, 50 mM KCl, 3 mM MgCl<sub>2</sub>, and 0.01% gelatin), 200 μM of each dNTPs, and 1.0 U <italic>Taq</italic> polymerase (Applied Biosystem, Foster City, CA, USA). The mixtures were amplified in 60 cycles of 94 °C for 1 min, 48 °C for 1 min, and 72 °C for 1 min and a final extension at 72 °C for 10 min in an automated thermal cycler (Applied Biosystem, Foster City, CA, USA). Standard precautions were taken to avoid PCR contamination and no false-positive was observed in negative controls.</p><p id="para0105">The PCR products were gel-purified using the QIAquick gel extraction kit (QIAgen, Hilden, Germany). Both strands of the PCR products were sequenced twice with an ABI Prism 3700 DNA Analyzer (Applied Biosystems, Foster City, CA, USA), using the two PCR primers. The sequences of the PCR products were compared with known sequences of the RdRp genes of coronaviruses in the GenBank database.</p></sec><sec id="section0065"><title>Viral culture</title><p id="para0110">Three of the samples positive for bat-CoV HKU2 were cultured in LLC-Mk2 (rhesus monkey kidney), MRC-5 (human lung fibroblast), FRhK-4 (rhesus monkey kidney), Huh-7.5 (human hepatoma), Vero E6 (African green monkey kidney), HRT-18 (colorectal adenocarcinoma) cell lines and primary kidney epithelium and lung fibroblast cells derived from a Chinese horseshoe bat.</p></sec><sec id="section0070"><title>Complete genome sequencing of bat-CoV HKU2</title><p id="para0115">Four complete genomes of bat-CoV HKU2 detected in the present study were amplified and sequenced using the RNA extracted from the alimentary specimens as templates. The RNA was converted to cDNA by a combined random-priming and oligo(dT) priming strategy. As the initial results revealed that they were group 1 coronaviruses, the cDNA was amplified by degenerate primers designed by multiple alignment of the genomes of human coronavirus 229E (HCoV-229E) (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="NC_002645">NC_002645</ext-link>), porcine epidemic diarrhea virus (PEDV) (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="NC_003436">NC_003436</ext-link>), porcine transmissible gastroenteritis virus (TGEV) (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="NC_002306">NC_002306</ext-link>), feline infectious peritonitis virus (FIPV) (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="AY994055">AY994055</ext-link>), and HCoV-NL63 (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="NC_005831">NC_005831</ext-link>), and additional primers covering the original degenerate primer sites were designed from the results of the first and subsequent rounds of sequencing. These primer sequences are available on request. The 5′ ends of the viral genomes were confirmed by rapid amplification of cDNA ends using the 5′/3′ RACE kit (Roche, Germany). Sequences were assembled and manually edited to produce final sequences of the viral genomes.</p></sec><sec id="section0075"><title>Genome analysis</title><p id="para0120">The nucleotide sequences of the genomes and the deduced amino acid sequences of the open reading frames (ORFs) were compared to those of other coronaviruses. Phylogenetic tree construction was performed using neighbor joining method with ClustalX 1.83. Protein family analysis was performed using PFAM and InterProScan (<xref rid="bib1" ref-type="bibr">Apweiler et al., 2001</xref>, <xref rid="bib2" ref-type="bibr">Bateman et al., 2002</xref>). Prediction of transmembrane domains was performed using TMHMM (<xref rid="bib39" ref-type="bibr">Sonnhammer et al., 1998</xref>).</p></sec><sec id="section0080"><title>Estimation of synonymous and non-synonymous substitution rates</title><p id="para0125">The number of synonymous substitutions per synonymous site, Ks, and the number of non-synonymous substitutions per non-synonymous site, Ka, for each coding region were calculated using the Nei-Gojobori method (Jukes-Cantor) in MEGA 3.1 (<xref rid="bib19" ref-type="bibr">Kumar et al., 2004</xref>). Six pairwise comparisons on the four strains of bat-CoV HKU2 were performed for each coding region.</p></sec><sec id="section0085"><title>Recombination analysis</title><p id="para0130">Sliding window analysis was used to detect possible recombination, using a nucleotide alignment of the genome sequences of the four strains of bat-CoV HKU2 and bat-SARS-CoV (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="DQ022305">DQ022305</ext-link>) generated by ClustalX version 1.83 and edited manually. Bootscan analysis was performed using Simplot version 3.5.1 (<xref rid="bib28" ref-type="bibr">Lole et al., 1999</xref>) (F84 model; window size, 1000 bp; step, 200 bp) with the genome sequence of SARS-CoV (GenBank accession no. <ext-link ext-link-type="gen" xlink:href="NC_004718">NC_004718</ext-link>) as a query.</p></sec><sec id="section0090"><title>Nucleotide sequence accession numbers</title><p id="para0135">The nucleotide sequences of the four genomes of bat-CoV HKU2 have been lodged within the GenBank sequence database under accession no. <ext-link ext-link-type="gen" xlink:href="EF203064">EF203064</ext-link> to <ext-link ext-link-type="gen" xlink:href="EF203067">EF203067</ext-link>.</p></sec></sec></body><back><ref-list id="bibliography0005"><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Apweiler</surname><given-names>R.</given-names></name><name><surname>Attwood</surname><given-names>T.K.</given-names></name><name><surname>Bairoch</surname><given-names>A.</given-names></name><name><surname>Bateman</surname><given-names>A.</given-names></name><name><surname>Birney</surname><given-names>E.</given-names></name><name><surname>Biswas</surname><given-names>M.</given-names></name><name><surname>Bucher</surname><given-names>P.</given-names></name><name><surname>Cerutti</surname><given-names>L.</given-names></name><name><surname>Corpet</surname><given-names>F.</given-names></name><name><surname>Croning</surname><given-names>M.D.</given-names></name><name><surname>Durbin</surname><given-names>R.</given-names></name><name><surname>Falquet</surname><given-names>L.</given-names></name><name><surname>Fleischmann</surname><given-names>W.</given-names></name><name><surname>Gouzy</surname><given-names>J.</given-names></name><name><surname>Hermjakob</surname><given-names>H.</given-names></name><name><surname>Hulo</surname><given-names>N.</given-names></name><name><surname>Jonassen</surname><given-names>I.</given-names></name><name><surname>Kahn</surname><given-names>D.</given-names></name><name><surname>Kanapin</surname><given-names>A.</given-names></name><name><surname>Karavidopoulou</surname><given-names>Y.</given-names></name><name><surname>Lopez</surname><given-names>R.</given-names></name><name><surname>Marx</surname><given-names>B.</given-names></name><name><surname>Mulder</surname><given-names>N.J.</given-names></name><name><surname>Oinn</surname><given-names>T.M.</given-names></name><name><surname>Pagni</surname><given-names>M.</given-names></name><name><surname>Servant</surname><given-names>F.</given-names></name><name><surname>Sigrist</surname><given-names>C.J.</given-names></name><name><surname>Zdobnov</surname><given-names>E.M.</given-names></name></person-group><article-title>The InterPro database, an integrated documentation resource for protein families, domains and functional sites</article-title><source>Nucleic Acids Res.</source><volume>29</volume><year>2001</year><fpage>37</fpage><lpage>40</lpage><pub-id pub-id-type="pmid">11125043</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bateman</surname><given-names>A.</given-names></name><name><surname>Birney</surname><given-names>E.</given-names></name><name><surname>Cerruti</surname><given-names>L.</given-names></name><name><surname>Durbin</surname><given-names>R.</given-names></name><name><surname>Etwiller</surname><given-names>L.</given-names></name><name><surname>Eddy</surname><given-names>S.R.</given-names></name><name><surname>Griffiths-Jones</surname><given-names>S.</given-names></name><name><surname>Howe</surname><given-names>K.L.</given-names></name><name><surname>Marshall</surname><given-names>M.</given-names></name><name><surname>Sonnhammer</surname><given-names>E.L.</given-names></name></person-group><article-title>The Pfam protein families database</article-title><source>Nucleic Acids Res.</source><volume>30</volume><year>2002</year><fpage>276</fpage><lpage>280</lpage><pub-id pub-id-type="pmid">11752314</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bonavia</surname><given-names>A.</given-names></name><name><surname>Zelus</surname><given-names>B.D.</given-names></name><name><surname>Wentworth</surname><given-names>D.E.</given-names></name><name><surname>Talbot</surname><given-names>P.J.</given-names></name><name><surname>Holmes</surname><given-names>K.V.</given-names></name></person-group><article-title>Identification of a receptor-binding domain of the spike glycoprotein of human coronavirus HCoV-229E</article-title><source>J. 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Infect. Dis.</source><volume>7</volume><year>2001</year><fpage>439</fpage><lpage>441</lpage><pub-id pub-id-type="pmid">11384522</pub-id></element-citation></ref><ref id="bib57"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ziebuhr</surname><given-names>J.</given-names></name></person-group><article-title>Molecular biology of severe acute respiratory syndrome coronavirus</article-title><source>Curr. Opin. Microbiol.</source><volume>7</volume><year>2004</year><fpage>412</fpage><lpage>419</lpage><pub-id pub-id-type="pmid">15358261</pub-id></element-citation></ref></ref-list><sec id="app1" sec-type="supplementary-material"><label>Appendix A</label><title>Supplementary data</title><p id="para0150"><supplementary-material content-type="local-data" id="e-component0005"><caption><title>Supplementary Fig. 1</title><p>Multiple alignments of S proteins of bat-CoV HKU2, other group 1 coronaviruses, human and civet SARS-CoV and bat-SARS-CoV. Amino acid residues fully conserved across all coronaviruses are marked with ‘⁎’; strongly conserved residues are marked with ‘:’; and weakly conserved residues are marked with ‘.’. RBM of SARS-CoV, and RBDs of HCoV-229E and HCoV-NL63 were shaded in grey. Residues within the S of SARS-CoV that directly contact hACE2 are in white letters. The cysteines that contribute to ACE2 binding in SARS-CoV are bolded. The short stretch of homologous peptide between bat-CoV HKU2 and SARS-CoV within the RBM of SARS-CoV is boxed. Large deletions within the S of bat-CoV HKU2 were shaded in dark grey. The two regions of deletions in the C-terminal conserved between bat-CoV HKU2 and group 2 coronaviruses are boxed and shaded.</p></caption><media xlink:href="mmc1.doc"></media></supplementary-material></p></sec><ack><title>Acknowledgments</title><p>We thank Director Stella Hung, Sin-Pang Lau, Chik-Chuen Lay, and Ping-Man So [HKSAR Department of Agriculture, Fisheries, and Conservation (AFCD)] and Hong Kong Police Force for facilitation and support; Chung-Tong Shek, Cynthia S. M. Chan, and Tak-yin Lau from AFCD for their excellent technical assistance; and Dr. King-Shun Lo (Laboratory Animal Unit) and Dr. Cassius Chan for collection of animal specimens.</p><p>We are grateful to the generous support of Mr. Hui Hoy and Mr. Hui Ming in the genomic sequencing platform. This work is partly supported by the Research Grant Council Grant; University Development Fund and Outstanding Young Researcher Award, The University of Hong Kong; The Tung Wah Group of Hospitals Fund for Research in Infectious Diseases; the HKSAR Research Fund for the Control of Infectious Diseases (04050232) of the Health, Welfare and Food Bureau; and the Providence Foundation Limited in memory of the late Dr. Lui Hac Minh.</p></ack><fn-group><fn id="section0095" fn-type="supplementary-material"><label>Appendix A</label><p id="para0155">Supplementary data associated with this article can be found, in the online version, at <ext-link ext-link-type="doi" xlink:href="10.1016/j.virol.2007.06.009">doi:10.1016/j.virol.2007.06.009</ext-link>.</p></fn></fn-group></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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