Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats
Identifieur interne : 000480 ( Pmc/Checkpoint ); précédent : 000479; suivant : 000481Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats
Auteurs : Ning Wang [République populaire de Chine] ; Chuming Luo [République populaire de Chine] ; Haizhou Liu ; Xinglou Yang ; Ben Hu ; Wei Zhang ; Bei Li ; Yan Zhu ; Guangjian Zhu ; Xurui Shen [République populaire de Chine] ; Cheng Peng ; Zhengli ShiSource :
- Viruses [ 1999-4915 ] ; 2019.
Abstract
Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes,
Url:
DOI: 10.3390/v11040379
PubMed: 31022925
PubMed Central: 6521148
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats</title><author><name sortKey="Wang, Ning" sort="Wang, Ning" uniqKey="Wang N" first="Ning" last="Wang">Ning Wang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Luo, Chuming" sort="Luo, Chuming" uniqKey="Luo C" first="Chuming" last="Luo">Chuming Luo</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Haizhou" sort="Liu, Haizhou" uniqKey="Liu H" first="Haizhou" last="Liu">Haizhou Liu</name><affiliation><nlm:aff id="af3-viruses-11-00379">Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>liuhz@wh.iov.cn</email></nlm:aff></affiliation></author><author><name sortKey="Yang, Xinglou" sort="Yang, Xinglou" uniqKey="Yang X" first="Xinglou" last="Yang">Xinglou Yang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Hu, Ben" sort="Hu, Ben" uniqKey="Hu B" first="Ben" last="Hu">Ben Hu</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhang, Wei" sort="Zhang, Wei" uniqKey="Zhang W" first="Wei" last="Zhang">Wei Zhang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhu, Guangjian" sort="Zhu, Guangjian" uniqKey="Zhu G" first="Guangjian" last="Zhu">Guangjian Zhu</name><affiliation><nlm:aff id="af4-viruses-11-00379">EcoHealth Alliance, New York, NY 10001, USA;<email>zhugj609@126.com</email></nlm:aff></affiliation></author><author><name sortKey="Shen, Xurui" sort="Shen, Xurui" uniqKey="Shen X" first="Xurui" last="Shen">Xurui Shen</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Cheng" sort="Peng, Cheng" uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31022925</idno><idno type="pmc">6521148</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521148</idno><idno type="RBID">PMC:6521148</idno><idno type="doi">10.3390/v11040379</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">001616</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001616</idno><idno type="wicri:Area/Pmc/Curation">001616</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001616</idno><idno type="wicri:Area/Pmc/Checkpoint">000480</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000480</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats</title><author><name sortKey="Wang, Ning" sort="Wang, Ning" uniqKey="Wang N" first="Ning" last="Wang">Ning Wang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Luo, Chuming" sort="Luo, Chuming" uniqKey="Luo C" first="Chuming" last="Luo">Chuming Luo</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Haizhou" sort="Liu, Haizhou" uniqKey="Liu H" first="Haizhou" last="Liu">Haizhou Liu</name><affiliation><nlm:aff id="af3-viruses-11-00379">Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>liuhz@wh.iov.cn</email></nlm:aff></affiliation></author><author><name sortKey="Yang, Xinglou" sort="Yang, Xinglou" uniqKey="Yang X" first="Xinglou" last="Yang">Xinglou Yang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Hu, Ben" sort="Hu, Ben" uniqKey="Hu B" first="Ben" last="Hu">Ben Hu</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhang, Wei" sort="Zhang, Wei" uniqKey="Zhang W" first="Wei" last="Zhang">Wei Zhang</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Zhu, Guangjian" sort="Zhu, Guangjian" uniqKey="Zhu G" first="Guangjian" last="Zhu">Guangjian Zhu</name><affiliation><nlm:aff id="af4-viruses-11-00379">EcoHealth Alliance, New York, NY 10001, USA;<email>zhugj609@126.com</email></nlm:aff></affiliation></author><author><name sortKey="Shen, Xurui" sort="Shen, Xurui" uniqKey="Shen X" first="Xurui" last="Shen">Xurui Shen</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-viruses-11-00379">College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Cheng" sort="Peng, Cheng" uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author><author><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><affiliation><nlm:aff id="af1-viruses-11-00379">CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</nlm:aff></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, <italic>ORF4a</italic> and <italic>ORF4b</italic> were found between the spike gene and the envelope gene, while <italic>ORF8</italic> gene was found downstream of the nucleocapsid gene. All the putative genes were further confirmed by reverse-transcription analyses. One unique gene at the 3’ end of the BtCoV/Rh/YN2012 genome, <italic>ORF9</italic>, exhibits ~30% amino acid identity to <italic>ORF7a</italic> of the SARS-related coronavirus. Functional analysis showed ORF4a protein can activate IFN-β production, whereas ORF3a can regulate NF-κB production. We also screened the spike-mediated virus entry using the spike-pseudotyped retroviruses system, although failed to find any fully permissive cells. Our results expand the knowledge on the genetic diversity of bat coronaviruses. Continuous screening of bat viruses will help us further understand the important role played by bats in coronavirus evolution and transmission.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="David, M" uniqKey="David M">M. David</name></author><author><name sortKey="Knipe, P M H" uniqKey="Knipe P">P.M.H. Knipe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="King, A M Q" uniqKey="King A">A.M.Q. King</name></author><author><name sortKey="Lefkowitz, E J" uniqKey="Lefkowitz E">E.J. Lefkowitz</name></author><author><name sortKey="Mushegian, A R" uniqKey="Mushegian A">A.R. Mushegian</name></author><author><name sortKey="Adams, M J" uniqKey="Adams M">M.J. Adams</name></author><author><name sortKey="Dutilh, B E" uniqKey="Dutilh B">B.E. Dutilh</name></author><author><name sortKey="Gorbalenya, A E" uniqKey="Gorbalenya A">A.E. Gorbalenya</name></author><author><name sortKey="Harrach, B" uniqKey="Harrach B">B. Harrach</name></author><author><name sortKey="Harrison, R L" uniqKey="Harrison R">R.L. Harrison</name></author><author><name sortKey="Junglen, S" uniqKey="Junglen S">S. Junglen</name></author><author><name sortKey="Knowles, N J" uniqKey="Knowles N">N.J. Knowles</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C Y" uniqKey="Woo P">P.C.Y. Woo</name></author><author><name sortKey="Lau, S K P" uniqKey="Lau S">S.K.P. Lau</name></author><author><name sortKey="Lam, C S F" uniqKey="Lam C">C.S.F. Lam</name></author><author><name sortKey="Lau, C C Y" uniqKey="Lau C">C.C.Y. Lau</name></author><author><name sortKey="Tsang, A K L" uniqKey="Tsang A">A.K.L. Tsang</name></author><author><name sortKey="Lau, J H N" uniqKey="Lau J">J.H.N. Lau</name></author><author><name sortKey="Bai, R" uniqKey="Bai R">R. Bai</name></author><author><name sortKey="Teng, J L L" uniqKey="Teng J">J.L.L. Teng</name></author><author><name sortKey="Tsang, C C C" uniqKey="Tsang C">C.C.C. Tsang</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woo, P C Y" uniqKey="Woo P">P.C.Y. Woo</name></author><author><name sortKey="Lau, S K P" uniqKey="Lau S">S.K.P. Lau</name></author><author><name sortKey="Lam, C S F" uniqKey="Lam C">C.S.F. Lam</name></author><author><name sortKey="Tsang, A K L" uniqKey="Tsang A">A.K.L. Tsang</name></author><author><name sortKey="Hui, S W" uniqKey="Hui S">S.W. Hui</name></author><author><name sortKey="Fan, R Y Y" uniqKey="Fan R">R.Y.Y. Fan</name></author><author><name sortKey="Martelli, P" uniqKey="Martelli P">P. Martelli</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.Y. Yuen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</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="Jung, K" uniqKey="Jung K">K. Jung</name></author><author><name sortKey="Saif, L J" uniqKey="Saif L">L.J. Saif</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gong, L" uniqKey="Gong L">L. Gong</name></author><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Zhou, Q F" uniqKey="Zhou Q">Q.F. Zhou</name></author><author><name sortKey="Xu, Z C" uniqKey="Xu Z">Z.C. Xu</name></author><author><name sortKey="Chen, L" uniqKey="Chen L">L. Chen</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y. Zhang</name></author><author><name sortKey="Xue, C Y" uniqKey="Xue C">C.Y. Xue</name></author><author><name sortKey="Wen, Z F" uniqKey="Wen Z">Z.F. Wen</name></author><author><name sortKey="Cao, Y C" uniqKey="Cao Y">Y.C. Cao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pan, Y F" uniqKey="Pan Y">Y.F. Pan</name></author><author><name sortKey="Tian, X Y" uniqKey="Tian X">X.Y. Tian</name></author><author><name sortKey="Qin, P" uniqKey="Qin P">P. Qin</name></author><author><name sortKey="Wang, B" uniqKey="Wang B">B. Wang</name></author><author><name sortKey="Zhao, P W" uniqKey="Zhao P">P.W. Zhao</name></author><author><name sortKey="Yang, Y L" uniqKey="Yang Y">Y.L. Yang</name></author><author><name sortKey="Wang, L X" uniqKey="Wang L">L.X. Wang</name></author><author><name sortKey="Wang, D D" uniqKey="Wang D">D.D. Wang</name></author><author><name sortKey="Song, Y H" uniqKey="Song Y">Y.H. Song</name></author><author><name sortKey="Zhang, X B" uniqKey="Zhang X">X.B. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chae, C" uniqKey="Chae C">C. Chae</name></author><author><name sortKey="Kim, O" uniqKey="Kim O">O. Kim</name></author><author><name sortKey="Choi, C" uniqKey="Choi C">C. Choi</name></author><author><name sortKey="Min, K" uniqKey="Min K">K. Min</name></author><author><name sortKey="Cho, W S" uniqKey="Cho W">W.S. Cho</name></author><author><name sortKey="Kim, J" uniqKey="Kim J">J. Kim</name></author><author><name sortKey="Tai, J H" uniqKey="Tai J">J.H. Tai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Z Q" uniqKey="Wu Z">Z.Q. Wu</name></author><author><name sortKey="Yang, L" uniqKey="Yang L">L. Yang</name></author><author><name sortKey="Ren, X W" uniqKey="Ren X">X.W. Ren</name></author><author><name sortKey="He, G M" uniqKey="He G">G.M. He</name></author><author><name sortKey="Zhang, J P" uniqKey="Zhang J">J.P. Zhang</name></author><author><name sortKey="Yang, J" uniqKey="Yang J">J. Yang</name></author><author><name sortKey="Qian, Z H" uniqKey="Qian Z">Z.H. Qian</name></author><author><name sortKey="Dong, J" uniqKey="Dong J">J. Dong</name></author><author><name sortKey="Sun, L L" uniqKey="Sun L">L.L. Sun</name></author><author><name sortKey="Zhu, Y F" uniqKey="Zhu Y">Y.F. Zhu</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 J" uniqKey="Zhu G">G.J. 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></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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Menachery, V D" uniqKey="Menachery V">V.D. Menachery</name></author><author><name sortKey="Yount, B L" uniqKey="Yount B">B.L. Yount</name></author><author><name sortKey="Sims, A C" uniqKey="Sims A">A.C. Sims</name></author><author><name sortKey="Debbink, K" uniqKey="Debbink K">K. Debbink</name></author><author><name sortKey="Agnihothram, S S" uniqKey="Agnihothram S">S.S. Agnihothram</name></author><author><name sortKey="Gralinski, L E" uniqKey="Gralinski L">L.E. Gralinski</name></author><author><name sortKey="Graham, R L" uniqKey="Graham R">R.L. Graham</name></author><author><name sortKey="Scobey, T" uniqKey="Scobey T">T. Scobey</name></author><author><name sortKey="Plante, J A" uniqKey="Plante J">J.A. Plante</name></author><author><name sortKey="Royal, S R" uniqKey="Royal S">S.R. Royal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P. Zhou</name></author><author><name sortKey="Fan, H" uniqKey="Fan H">H. Fan</name></author><author><name sortKey="Lan, T" uniqKey="Lan T">T. Lan</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.-L. Yang</name></author><author><name sortKey="Shi, W F" uniqKey="Shi W">W.-F. Shi</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Zhu, Y" uniqKey="Zhu Y">Y. Zhu</name></author><author><name sortKey="Zhang, Y W" uniqKey="Zhang Y">Y.-W. Zhang</name></author><author><name sortKey="Xie, Q M" uniqKey="Xie Q">Q.-M. Xie</name></author><author><name sortKey="Mani, S" uniqKey="Mani S">S. Mani</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, W D" uniqKey="Li W">W.D. Li</name></author><author><name sortKey="Shi, Z L" uniqKey="Shi Z">Z.L. Shi</name></author><author><name sortKey="Yu, M" uniqKey="Yu M">M. Yu</name></author><author><name sortKey="Ren, W Z" uniqKey="Ren W">W.Z. 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 Z" uniqKey="Wang H">H.Z. Wang</name></author><author><name sortKey="Crameri, G" uniqKey="Crameri G">G. Crameri</name></author><author><name sortKey="Hu, Z H" uniqKey="Hu Z">Z.H. Hu</name></author><author><name sortKey="Zhang, H J" uniqKey="Zhang H">H.J. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luna, L K D" uniqKey="Luna L">L.K.D. Luna</name></author><author><name sortKey="Heiser, V" uniqKey="Heiser V">V. Heiser</name></author><author><name sortKey="Regamey, N" uniqKey="Regamey N">N. Regamey</name></author><author><name sortKey="Panning, M" uniqKey="Panning M">M. Panning</name></author><author><name sortKey="Drexler, J F" uniqKey="Drexler J">J.F. Drexler</name></author><author><name sortKey="Mulangu, S" uniqKey="Mulangu S">S. Mulangu</name></author><author><name sortKey="Poon, L" uniqKey="Poon L">L. Poon</name></author><author><name sortKey="Baumgarte, S" uniqKey="Baumgarte S">S. Baumgarte</name></author><author><name sortKey="Haijema, B J" uniqKey="Haijema B">B.J. Haijema</name></author><author><name sortKey="Kaiser, L" uniqKey="Kaiser L">L. Kaiser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Zeng, L P" uniqKey="Zeng L">L.P. Zeng</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Li, B" uniqKey="Li B">B. Li</name></author><author><name sortKey="Xie, J Z" uniqKey="Xie J">J.Z. Xie</name></author><author><name sortKey="Shen, X R" uniqKey="Shen X">X.R. Shen</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Irwin, D M" uniqKey="Irwin D">D.M. Irwin</name></author><author><name sortKey="Kocher, T D" uniqKey="Kocher T">T.D. Kocher</name></author><author><name sortKey="Wilson, A C" uniqKey="Wilson A">A.C. Wilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mayer, F" uniqKey="Mayer F">F. Mayer</name></author><author><name sortKey="Von Helversen, O" uniqKey="Von Helversen O">O. von Helversen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kearse, M" uniqKey="Kearse M">M. Kearse</name></author><author><name sortKey="Moir, R" uniqKey="Moir R">R. Moir</name></author><author><name sortKey="Wilson, A" uniqKey="Wilson A">A. Wilson</name></author><author><name sortKey="Stones Havas, S" uniqKey="Stones Havas S">S. Stones-Havas</name></author><author><name sortKey="Cheung, M" uniqKey="Cheung M">M. Cheung</name></author><author><name sortKey="Sturrock, S" uniqKey="Sturrock S">S. Sturrock</name></author><author><name sortKey="Buxton, S" uniqKey="Buxton S">S. Buxton</name></author><author><name sortKey="Cooper, A" uniqKey="Cooper A">A. Cooper</name></author><author><name sortKey="Markowitz, S" uniqKey="Markowitz S">S. Markowitz</name></author><author><name sortKey="Duran, C" uniqKey="Duran C">C. Duran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, D" uniqKey="Yang D">D. Yang</name></author><author><name sortKey="Leibowitz, J L" uniqKey="Leibowitz J">J.L. Leibowitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K. Tamura</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G. Stecher</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D. Peterson</name></author><author><name sortKey="Filipski, A" uniqKey="Filipski A">A. Filipski</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hall, B G" uniqKey="Hall B">B.G. Hall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Martin, D P" uniqKey="Martin D">D.P. Martin</name></author><author><name sortKey="Lemey, P" uniqKey="Lemey P">P. Lemey</name></author><author><name sortKey="Lott, M" uniqKey="Lott M">M. Lott</name></author><author><name sortKey="Moulton, V" uniqKey="Moulton V">V. Moulton</name></author><author><name sortKey="Posada, D" uniqKey="Posada D">D. Posada</name></author><author><name sortKey="Lefeuvre, P" uniqKey="Lefeuvre P">P. Lefeuvre</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="Siltberg, J" uniqKey="Siltberg J">J. Siltberg</name></author><author><name sortKey="Liberles, D A" uniqKey="Liberles D">D.A. Liberles</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zimmermann, L" uniqKey="Zimmermann L">L. Zimmermann</name></author><author><name sortKey="Stephens, A" uniqKey="Stephens A">A. Stephens</name></author><author><name sortKey="Nam, S Z" uniqKey="Nam S">S.Z. Nam</name></author><author><name sortKey="Rau, D" uniqKey="Rau D">D. Rau</name></author><author><name sortKey="Kubler, J" uniqKey="Kubler J">J. Kubler</name></author><author><name sortKey="Lozajic, M" uniqKey="Lozajic M">M. Lozajic</name></author><author><name sortKey="Gabler, F" uniqKey="Gabler F">F. Gabler</name></author><author><name sortKey="Soding, J" uniqKey="Soding J">J. Soding</name></author><author><name sortKey="Lupas, A N" uniqKey="Lupas A">A.N. Lupas</name></author><author><name sortKey="Alva, V" uniqKey="Alva V">V. Alva</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zeng, L P" uniqKey="Zeng L">L.P. Zeng</name></author><author><name sortKey="Gao, Y T" uniqKey="Gao Y">Y.T. Gao</name></author><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</name></author><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q. Zhang</name></author><author><name sortKey="Peng, C" uniqKey="Peng C">C. Peng</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Tan, B" uniqKey="Tan B">B. Tan</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name></author><author><name sortKey="Chmura, A A" uniqKey="Chmura A">A.A. Chmura</name></author><author><name sortKey="Daszak, P" uniqKey="Daszak P">P. Daszak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P. Zhou</name></author><author><name sortKey="Li, H X" uniqKey="Li H">H.X. Li</name></author><author><name sortKey="Wang, H Z" uniqKey="Wang H">H.Z. Wang</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="Wang, X Y" uniqKey="Wang X">X.Y. Wang</name></author><author><name sortKey="Li, M" uniqKey="Li M">M. Li</name></author><author><name sortKey="Zheng, H Y" uniqKey="Zheng H">H.Y. Zheng</name></author><author><name sortKey="Muster, T" uniqKey="Muster T">T. Muster</name></author><author><name sortKey="Palese, P" uniqKey="Palese P">P. Palese</name></author><author><name sortKey="Beg, A A" uniqKey="Beg A">A.A. Beg</name></author><author><name sortKey="Garcia Sastre, A" uniqKey="Garcia Sastre A">A. Garcia-Sastre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanzawa, N" uniqKey="Kanzawa N">N. Kanzawa</name></author><author><name sortKey="Nishigaki, K" uniqKey="Nishigaki K">K. Nishigaki</name></author><author><name sortKey="Hayashi, T" uniqKey="Hayashi T">T. Hayashi</name></author><author><name sortKey="Ishii, Y" uniqKey="Ishii Y">Y. Ishii</name></author><author><name sortKey="Furukawa, S" uniqKey="Furukawa S">S. Furukawa</name></author><author><name sortKey="Niiro, A" uniqKey="Niiro A">A. Niiro</name></author><author><name sortKey="Yasui, F" uniqKey="Yasui F">F. Yasui</name></author><author><name sortKey="Kohara, M" uniqKey="Kohara M">M. Kohara</name></author><author><name sortKey="Morita, K" uniqKey="Morita K">K. Morita</name></author><author><name sortKey="Matsushima, K" uniqKey="Matsushima K">K. Matsushima</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, H L" uniqKey="Luo H">H.L. Luo</name></author><author><name sortKey="Zhang, Z F" uniqKey="Zhang Z">Z.F. Zhang</name></author><author><name sortKey="Zheng, Z H" uniqKey="Zheng Z">Z.H. Zheng</name></author><author><name sortKey="Ke, X L" uniqKey="Ke X">X.L. Ke</name></author><author><name sortKey="Zhang, X W" uniqKey="Zhang X">X.W. Zhang</name></author><author><name sortKey="Li, Q" uniqKey="Li Q">Q. Li</name></author><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. Liu</name></author><author><name sortKey="Bai, B K" uniqKey="Bai B">B.K. Bai</name></author><author><name sortKey="Mao, P Y" uniqKey="Mao P">P.Y. Mao</name></author><author><name sortKey="Hu, Q X" uniqKey="Hu Q">Q.X. Hu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luo, C M" uniqKey="Luo C">C.-M. Luo</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N. Wang</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.-L. Yang</name></author><author><name sortKey="Liu, H Z" uniqKey="Liu H">H.-Z. Liu</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Li, B" uniqKey="Li B">B. Li</name></author><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Peng, C" uniqKey="Peng C">C. Peng</name></author><author><name sortKey="Geng, Q B" uniqKey="Geng Q">Q.-B. Geng</name></author><author><name sortKey="Zhu, G J" uniqKey="Zhu G">G.-J. Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Y" uniqKey="Yang Y">Y. Yang</name></author><author><name sortKey="Du, L Y" uniqKey="Du L">L.Y. Du</name></author><author><name sortKey="Liu, C" uniqKey="Liu C">C. Liu</name></author><author><name sortKey="Wang, L L" uniqKey="Wang L">L.L. Wang</name></author><author><name sortKey="Ma, C Q" uniqKey="Ma C">C.Q. Ma</name></author><author><name sortKey="Tang, J" uniqKey="Tang J">J. Tang</name></author><author><name sortKey="Baric, R S" uniqKey="Baric R">R.S. Baric</name></author><author><name sortKey="Jiang, S" uniqKey="Jiang S">S. Jiang</name></author><author><name sortKey="Li, F" uniqKey="Li F">F. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, D K W" uniqKey="Chu D">D.K.W. Chu</name></author><author><name sortKey="Peiris, J S M" uniqKey="Peiris J">J.S.M. 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 M" uniqKey="Poon L">L.L.M. Poon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marra, M A" uniqKey="Marra M">M.A. Marra</name></author><author><name sortKey="Jones, S J M" uniqKey="Jones S">S.J.M. Jones</name></author><author><name sortKey="Astell, C R" uniqKey="Astell C">C.R. Astell</name></author><author><name sortKey="Holt, R A" uniqKey="Holt R">R.A. Holt</name></author><author><name sortKey="Brooks Wilson, A" uniqKey="Brooks Wilson A">A. Brooks-Wilson</name></author><author><name sortKey="Butterfield, Y S N" uniqKey="Butterfield Y">Y.S.N. Butterfield</name></author><author><name sortKey="Khattra, J" uniqKey="Khattra J">J. Khattra</name></author><author><name sortKey="Asano, J K" uniqKey="Asano J">J.K. Asano</name></author><author><name sortKey="Barber, S A" uniqKey="Barber S">S.A. Barber</name></author><author><name sortKey="Chan, S Y" uniqKey="Chan S">S.Y. Chan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, S K P" uniqKey="Lau S">S.K.P. Lau</name></author><author><name sortKey="Woo, P C Y" uniqKey="Woo P">P.C.Y. Woo</name></author><author><name sortKey="Li, K S M" uniqKey="Li K">K.S.M. Li</name></author><author><name sortKey="Huang, Y" uniqKey="Huang Y">Y. Huang</name></author><author><name sortKey="Wang, M" uniqKey="Wang M">M. Wang</name></author><author><name sortKey="Lam, C S F" uniqKey="Lam C">C.S.F. Lam</name></author><author><name sortKey="Xu, H F" uniqKey="Xu H">H.F. Xu</name></author><author><name sortKey="Guo, R T" uniqKey="Guo R">R.T. Guo</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ge, X Y" uniqKey="Ge X">X.Y. Ge</name></author><author><name sortKey="Wang, N" uniqKey="Wang N">N. Wang</name></author><author><name sortKey="Zhang, W" uniqKey="Zhang W">W. Zhang</name></author><author><name sortKey="Hu, B" uniqKey="Hu B">B. Hu</name></author><author><name sortKey="Li, B" uniqKey="Li B">B. Li</name></author><author><name sortKey="Zhang, Y Z" uniqKey="Zhang Y">Y.Z. Zhang</name></author><author><name sortKey="Zhou, J H" uniqKey="Zhou J">J.H. Zhou</name></author><author><name sortKey="Luo, C M" uniqKey="Luo C">C.M. Luo</name></author><author><name sortKey="Yang, X L" uniqKey="Yang X">X.L. Yang</name></author><author><name sortKey="Wu, L J" uniqKey="Wu L">L.J. Wu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yuan, J F" uniqKey="Yuan J">J.F. Yuan</name></author><author><name sortKey="Hon, C C" uniqKey="Hon C">C.C. Hon</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y. Li</name></author><author><name sortKey="Wang, D M" uniqKey="Wang D">D.M. Wang</name></author><author><name sortKey="Xu, G L" uniqKey="Xu G">G.L. Xu</name></author><author><name sortKey="Zhang, H J" uniqKey="Zhang H">H.J. Zhang</name></author><author><name sortKey="Zhou, P" uniqKey="Zhou P">P. Zhou</name></author><author><name sortKey="Poon, L L M" uniqKey="Poon L">L.L.M. Poon</name></author><author><name sortKey="Lam, T T Y" uniqKey="Lam T">T.T.Y. Lam</name></author><author><name sortKey="Leung, F C C" uniqKey="Leung F">F.C.C. Leung</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></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, D X" uniqKey="Liu D">D.X. Liu</name></author><author><name sortKey="Fung, T S" uniqKey="Fung T">T.S. Fung</name></author><author><name sortKey="Chong, K K L" uniqKey="Chong K">K.K.L. Chong</name></author><author><name sortKey="Shukla, A" uniqKey="Shukla A">A. Shukla</name></author><author><name sortKey="Hilgenfeld, R" uniqKey="Hilgenfeld R">R. Hilgenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, H W" uniqKey="Chang H">H.W. Chang</name></author><author><name sortKey="De Groot, R J" uniqKey="De Groot R">R.J. de Groot</name></author><author><name sortKey="Egberink, H F" uniqKey="Egberink H">H.F. Egberink</name></author><author><name sortKey="Rottier, P J M" uniqKey="Rottier P">P.J.M. Rottier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, H W" uniqKey="Chang H">H.W. Chang</name></author><author><name sortKey="Egberink, H F" uniqKey="Egberink H">H.F. Egberink</name></author><author><name sortKey="Rottier, P J M" uniqKey="Rottier P">P.J.M. Rottier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedersen, N C" uniqKey="Pedersen N">N.C. Pedersen</name></author><author><name sortKey="Liu, H W" uniqKey="Liu H">H.W. Liu</name></author><author><name sortKey="Scarlett, J" uniqKey="Scarlett J">J. Scarlett</name></author><author><name sortKey="Leutenegger, C M" uniqKey="Leutenegger C">C.M. Leutenegger</name></author><author><name sortKey="Golovko, L" uniqKey="Golovko L">L. Golovko</name></author><author><name sortKey="Kennedy, H" uniqKey="Kennedy H">H. Kennedy</name></author><author><name sortKey="Kamal, F M" uniqKey="Kamal F">F.M. Kamal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Haan, C A M" uniqKey="De Haan C">C.A.M. De Haan</name></author><author><name sortKey="Masters, P S" uniqKey="Masters P">P.S. Masters</name></author><author><name sortKey="Shen, X L" uniqKey="Shen X">X.L. Shen</name></author><author><name sortKey="Weiss, S" uniqKey="Weiss S">S. Weiss</name></author><author><name sortKey="Rottier, P J M" uniqKey="Rottier P">P.J.M. Rottier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karjee, S" uniqKey="Karjee S">S. Karjee</name></author><author><name sortKey="Minhas, A" uniqKey="Minhas A">A. Minhas</name></author><author><name sortKey="Sood, V" uniqKey="Sood V">V. Sood</name></author><author><name sortKey="Ponia, S S" uniqKey="Ponia S">S.S. Ponia</name></author><author><name sortKey="Banerjea, A C" uniqKey="Banerjea A">A.C. Banerjea</name></author><author><name sortKey="Chow, V T K" uniqKey="Chow V">V.T.K. Chow</name></author><author><name sortKey="Mukherjee, S K" uniqKey="Mukherjee S">S.K. Mukherjee</name></author><author><name sortKey="Lal, S K" uniqKey="Lal S">S.K. Lal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kopecky Bromberg, S A" uniqKey="Kopecky Bromberg S">S.A. Kopecky-Bromberg</name></author><author><name sortKey="Martinez Sobrido, L" uniqKey="Martinez Sobrido L">L. Martinez-Sobrido</name></author><author><name sortKey="Palese, P" uniqKey="Palese P">P. Palese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yuan, X L" uniqKey="Yuan X">X.L. Yuan</name></author><author><name sortKey="Wu, J" uniqKey="Wu J">J. Wu</name></author><author><name sortKey="Shan, Y J" uniqKey="Shan Y">Y.J. Shan</name></author><author><name sortKey="Yao, Z Y" uniqKey="Yao Z">Z.Y. Yao</name></author><author><name sortKey="Dong, B" uniqKey="Dong B">B. Dong</name></author><author><name sortKey="Chen, B" uniqKey="Chen B">B. Chen</name></author><author><name sortKey="Zhao, Z H" uniqKey="Zhao Z">Z.H. Zhao</name></author><author><name sortKey="Wang, S Q" uniqKey="Wang S">S.Q. Wang</name></author><author><name sortKey="Chen, J P" uniqKey="Chen J">J.P. Chen</name></author><author><name sortKey="Cong, Y W" uniqKey="Cong Y">Y.W. Cong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tan, Y J" uniqKey="Tan Y">Y.J. Tan</name></author><author><name sortKey="Fielding, B C" uniqKey="Fielding B">B.C. Fielding</name></author><author><name sortKey="Goh, P Y" uniqKey="Goh P">P.Y. Goh</name></author><author><name sortKey="Shen, S" uniqKey="Shen S">S. Shen</name></author><author><name sortKey="Tan, T H P" uniqKey="Tan T">T.H.P. Tan</name></author><author><name sortKey="Lim, S G" uniqKey="Lim S">S.G. Lim</name></author><author><name sortKey="Hong, W J" uniqKey="Hong W">W.J. Hong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tan, Y X" uniqKey="Tan Y">Y.X. Tan</name></author><author><name sortKey="Tan, T H P" uniqKey="Tan T">T.H.P. Tan</name></author><author><name sortKey="Lee, M J R" uniqKey="Lee M">M.J.R. Lee</name></author><author><name sortKey="Tham, P Y" uniqKey="Tham P">P.Y. Tham</name></author><author><name sortKey="Gunalan, V" uniqKey="Gunalan V">V. Gunalan</name></author><author><name sortKey="Druce, J" uniqKey="Druce J">J. Druce</name></author><author><name sortKey="Birch, C" uniqKey="Birch C">C. Birch</name></author><author><name sortKey="Catton, M" uniqKey="Catton M">M. Catton</name></author><author><name sortKey="Fu, N Y" uniqKey="Fu N">N.Y. Fu</name></author><author><name sortKey="Yu, V C" uniqKey="Yu V">V.C. Yu</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">Viruses</journal-id><journal-id journal-id-type="iso-abbrev">Viruses</journal-id><journal-id journal-id-type="publisher-id">viruses</journal-id><journal-title-group><journal-title>Viruses</journal-title></journal-title-group><issn pub-type="epub">1999-4915</issn><publisher><publisher-name>MDPI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">31022925</article-id><article-id pub-id-type="pmc">6521148</article-id><article-id pub-id-type="doi">10.3390/v11040379</article-id><article-id pub-id-type="publisher-id">viruses-11-00379</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Ning</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref><xref ref-type="aff" rid="af2-viruses-11-00379">2</xref><xref ref-type="author-notes" rid="fn1-viruses-11-00379">†</xref></contrib><contrib contrib-type="author"><name><surname>Luo</surname><given-names>Chuming</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref><xref ref-type="aff" rid="af2-viruses-11-00379">2</xref><xref ref-type="author-notes" rid="fn1-viruses-11-00379">†</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Haizhou</given-names></name><xref ref-type="aff" rid="af3-viruses-11-00379">3</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Xinglou</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Ben</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Bei</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Guangjian</given-names></name><xref ref-type="aff" rid="af4-viruses-11-00379">4</xref></contrib><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Xurui</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref><xref ref-type="aff" rid="af2-viruses-11-00379">2</xref></contrib><contrib contrib-type="author"><name><surname>Peng</surname><given-names>Cheng</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="true">https://orcid.org/0000-0001-8089-163X</contrib-id><name><surname>Shi</surname><given-names>Zhengli</given-names></name><xref ref-type="aff" rid="af1-viruses-11-00379">1</xref><xref rid="c1-viruses-11-00379" ref-type="corresp">*</xref></contrib></contrib-group><aff id="af1-viruses-11-00379"><label>1</label>CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>wuzhongxiaoliu@163.com</email> (N.W.);<email>chine.lcm@163.com</email> (C.L.);<email>yangxl@wh.iov.cn</email> (X.Y.);<email>ouihaagendazs@hotmail.com</email> (B.H.);<email>happyzhang_2007@163.com</email> (W.Z.);<email>shenqi0622@126.com</email> (B.L.);<email>zhuyan@wh.iov.cn</email> (Y.Z.);<email>pukulovesu@163.com</email> (X.S.);<email>pengcheng@wh.iov.cn</email> (C.P.)</aff><aff id="af2-viruses-11-00379"><label>2</label>College of Life Science, University of Chinese Academy of Sciences, Beijing 100864, China</aff><aff id="af3-viruses-11-00379"><label>3</label>Center for Emerging Infectious Disease, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;<email>liuhz@wh.iov.cn</email></aff><aff id="af4-viruses-11-00379"><label>4</label>EcoHealth Alliance, New York, NY 10001, USA;<email>zhugj609@126.com</email></aff><author-notes><corresp id="c1-viruses-11-00379"><label>*</label>Correspondence: <email>zlshi@wh.iov.cn</email>; Tel.: +86-27-8719-7240</corresp><fn id="fn1-viruses-11-00379"><label>†</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub"><day>24</day><month>4</month><year>2019</year></pub-date><pub-date pub-type="collection"><month>4</month><year>2019</year></pub-date><volume>11</volume><issue>4</issue><elocation-id>379</elocation-id><history><date date-type="received"><day>13</day><month>3</month><year>2019</year></date><date date-type="accepted"><day>22</day><month>4</month><year>2019</year></date></history><permissions><copyright-statement>© 2019 by the authors.</copyright-statement><copyright-year>2019</copyright-year><license license-type="open-access"><license-p>Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>).</license-p></license></permissions><abstract><p>Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, <italic>ORF4a</italic> and <italic>ORF4b</italic> were found between the spike gene and the envelope gene, while <italic>ORF8</italic> gene was found downstream of the nucleocapsid gene. All the putative genes were further confirmed by reverse-transcription analyses. One unique gene at the 3’ end of the BtCoV/Rh/YN2012 genome, <italic>ORF9</italic>, exhibits ~30% amino acid identity to <italic>ORF7a</italic> of the SARS-related coronavirus. Functional analysis showed ORF4a protein can activate IFN-β production, whereas ORF3a can regulate NF-κB production. We also screened the spike-mediated virus entry using the spike-pseudotyped retroviruses system, although failed to find any fully permissive cells. Our results expand the knowledge on the genetic diversity of bat coronaviruses. Continuous screening of bat viruses will help us further understand the important role played by bats in coronavirus evolution and transmission.</p></abstract><kwd-group><kwd>coronavirus</kwd><kwd>alphacoronavirus</kwd><kwd><italic>Rhinolophus</italic> bat</kwd><kwd>unique genes</kwd></kwd-group></article-meta></front><floats-group><fig id="viruses-11-00379-f001" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Sampling map (<bold>A</bold>) and phylogenetic analysis of CoVs detected in Rhinolophus bats (<bold>B</bold>). A total of 19 provinces (indicated in gray) in China were involved. 1. Beijing (BJ); 2. Chongqing (CA); 3. Fujian (FJ); 4. Gansu (GS); 5. Guangdong (GD); 6. Guangxi (GX); 7. Guizhou (GZ); 8. Hainan (HaN); 9. Hebei (HeB); 10. Henan (HeN); 11. Hubei (HuB); 12. Hunan (HuN); 13.Jiangsu (JS); 14.Shandong (SD); 15.Shanxi (SX); 16. Sichuan (SC). 17. Tibet (T); 18. Yunnan (YN); and 19. Zhejiang (ZJ). The partial sequences of RdRp gene (327-bp) of CoVs detected in Rhinolophus bats were aligned with those of published representative CoV strains. The tree was constructed by the maximum-likelihood method with bootstrap values determined with 1000 replicates. The scale bar indicates the estimated number of substitutions per 10 nucleotides. Filled triangles indicate the CoVs published previously by our lab (KU343197, KP876536, KP876544, MF094687, KP876546, KY417143, FJ588686) [<xref rid="B15-viruses-11-00379" ref-type="bibr">15</xref>,<xref rid="B18-viruses-11-00379" ref-type="bibr">18</xref>,<xref rid="B40-viruses-11-00379" ref-type="bibr">40</xref>,<xref rid="B41-viruses-11-00379" ref-type="bibr">41</xref>], filled diamonds indicate CoVs detected in this study. Putative novel alphaCoVs are labeled in green. BtCoV/Rh/YN2012 detected in Guangdong and Yunnan province in this study are in bold. FIPV, Feline infectious peritonitis virus; PEDV, porcine epidemic diarrhea virus; MHV, mouse hepatitis virus. Other abbreviations are defined as those in the text. Numbers in parentheses indicate numbers of sequences sharing >97% identity.</p></caption><graphic xlink:href="viruses-11-00379-g001"></graphic></fig><fig id="viruses-11-00379-f002" orientation="portrait" position="float"><label>Figure 2</label><caption><p>Schematic diagram of genomic organization of BtCoV/Rh/YN2012. The genomic regions or ORFs of BtCoV/Rh/YN2012 were compared with BatCoV HKU10. Solid bars indicate conserved genes and grey letters indicate species or group-specific genes. Hollow arrowheads indicate distinct array of accessory genes (Grey hollow arrowheads: RaGD; black hollow arrowheads: RsYN1, RsYN2, and RsYN3). Upper letters indicate structural proteins and lower letters indicate nonstructural proteins (p1a and p1b) and accessory proteins. HKU10, Ro-BatCoV HKU10.</p></caption><graphic xlink:href="viruses-11-00379-g002"></graphic></fig><fig id="viruses-11-00379-f003" orientation="portrait" position="float"><label>Figure 3</label><caption><p>Subgenomic structure of 4 stains of BtCoV/Rh/YN2012. Agarose gel electrophoresis of the PCR products of subgenomic mRNA. The lowest band on each lane was the specific amplicon of each subgenomic mRNA. Other bands are amplicons of first-round PCR products or upper subgenomic mRNAs.</p></caption><graphic xlink:href="viruses-11-00379-g003"></graphic></fig><fig id="viruses-11-00379-f004" orientation="portrait" position="float"><label>Figure 4</label><caption><p>Phylogenetic trees generated based on aa sequences of RdRp and S. Trees were constructed by the maximum likelihood method using the Poisson model with bootstrap value determined with 1000 replicates. The scale bar indicates the estimated number of substitutions per 10 amino acids. Filled diamonds indicate viruses detected in this study.</p></caption><graphic xlink:href="viruses-11-00379-g004"></graphic></fig><fig id="viruses-11-00379-f005" orientation="portrait" position="float"><label>Figure 5</label><caption><p>Functional analysis of BtCoV/Rh/YN2012 accessory genes. (<bold>A</bold>) ORF4a proteins inhibit the production of Type Ι interferon. 293T cells seeded in 24-well plates were transfected with 100 ng pIFN-β-Luc, 5 ng pRL-TK, empty vector (625 ng), an influenza A NS1-expressing plasmid (625 ng), a HBoV VP2-espressing plasmid (625 ng), or ORF4a-expressing plasmids (625 ng). The cells were infected with Sendi virus (100 hemagglutinating units/mL) at 24 h posttransfection. Samples were collected at 6 h postinfection, followed by dual-luciferase assay. The results were expressed as the firefly luciferase value normalized to that of Renilla luciferase. (<bold>B</bold>) ORF3a protein activate NF-κB. 293T cells were transfected with 100 ng pNF-κB-Luc, 10 ng pRL-TK, empty vector (500 ng), an NS1-expressing plasmid (500 ng), a SARS-CoV ORF7a-expressing plasmid (500 ng), or ORF3a-expressing plasmids (500 ng). After 24 h, the cells were treated with TNF-α. Dual-luciferase activity was determined after 6 h. The results were expressed as the firefly luciferase activity normalized to that of Renilla luciferase. The experiments were performed three times independently. Data are representative of at least three independent experiments, with each determination performed in triplicate (mean ± SD of fold change). Asterisks indicate significant differences between groups (compared with Empty vector-NC, <italic>p</italic> < 0.05, as determined by student <italic>t</italic> test).</p></caption><graphic xlink:href="viruses-11-00379-g005"></graphic></fig><table-wrap id="viruses-11-00379-t001" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-00379-t001_Table 1</object-id><label>Table 1</label><caption><p>Detection of CoVs in <italic>Rhinolophus</italic> bats by RT-PCR.</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Bat Species</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Samples</th><th colspan="7" align="center" valign="middle" style="border-top:solid thin" rowspan="1">CoV Species Positive (Positive Rate %)</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Province<sup>1</sup></th></tr><tr><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HKU2</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HKU8</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HuB2013</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Mi-BtCoV 1</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">SARSr-CoV</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">BtCoV/Rh/YN2012</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Other AlphaCoVs</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.affinis</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">499</td><td align="center" valign="middle" rowspan="1" colspan="1">52(10.4)</td><td align="center" valign="middle" rowspan="1" colspan="1">2(0.4)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">2(0.4)</td><td align="center" valign="middle" rowspan="1" colspan="1">3(0.6)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">5, 7, 8, 10, 13, 18, 19</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.blythi</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">17</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">5,11,18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.ferrumequinum</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">238</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">1(0.4)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">12(5.0)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">1,3,4,7,9,10,14,15,18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.lepidus</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">21</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">3</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.luctus</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">8</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">5,8,19</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.macrotis</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">31</td><td align="center" valign="middle" rowspan="1" colspan="1">1(3.2)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">1(3.2)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">2,5,6,9,11,13,1,18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.monoceros</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">5</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.pearsoni</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">106</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">3,5,6,7,10,17,18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.pusillus</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">283</td><td align="center" valign="middle" rowspan="1" colspan="1">4(1.4)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">2(0.7)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">3,5,6,9,10,11,13,14</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.shamelli</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">55</td><td align="center" valign="middle" rowspan="1" colspan="1">25(45.5)</td><td align="center" valign="middle" rowspan="1" colspan="1">10(18.2)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">1(0.4)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">2(0.7)<sup>2</sup></td><td align="center" valign="middle" rowspan="1" colspan="1">18</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.sinicus</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">740</td><td align="center" valign="middle" rowspan="1" colspan="1">12(1.6)</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">3(0.4)</td><td align="center" valign="middle" rowspan="1" colspan="1">72(9.7)</td><td align="center" valign="middle" rowspan="1" colspan="1">6(0.8)</td><td align="center" valign="middle" rowspan="1" colspan="1">2(0.3)<sup>3</sup></td><td align="center" valign="middle" rowspan="1" colspan="1">3,5,6,7,8,11,12,13,16,18,19</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1"><italic>R.spp.</italic></td><td align="center" valign="middle" rowspan="1" colspan="1">58</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">2,6,7,18</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Total</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2061</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">94(4.6)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">12(0.6)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">1(0.05)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4(0.2)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">89(4.3)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">9(0.4)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4(0.2)</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><fn><p><sup>1</sup> Abbreviations for provinces: 1. Beijing; 2.Chongqing; 3. Fujian; 4. Gansu; 5. Guangdong; 6. Guangxi; 7. Guizhou; 8. Hainan; 9. Hebei; 10. Henan; 11: Hubei; 12. Hunan; 13.Jiangsu; 14.Shandong; 15.Shanxi; 16. Sichuan. 17: Tibet; 18.Yunnan; 19.Zhejiang. <sup>2</sup> Putatitive novel AlphaCoVs (RshBtCoV/4017-1), previously published.<sup>3</sup> Putative novel AlphaCoVs (RsBtCoV/13187), unpublished.</p></fn></table-wrap-foot></table-wrap><table-wrap id="viruses-11-00379-t002" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-00379-t002_Table 2</object-id><label>Table 2</label><caption><p>Comparison of coding regions, TRSs, and whole genome of BtCoV/Rh/YN2012 and with BtRf AlphaCoV/HuB2013 (HuB2013) and Ro-BatCoV HKU10 (HKU10).</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">CoV</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">ORFs</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Nucleotide Positions</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Predicted Size (AA) of Protein</th><th colspan="6" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">Pairwise AA Identity (%)</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">TRS Sequence</th></tr><tr><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">RsYN1</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">RsYN2</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">RsYN3</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">RaGD</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HuB2013</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">HKU10</th></tr></thead><tbody><tr><td rowspan="14" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">RsYN1</td><td align="center" valign="middle" rowspan="1" colspan="1">1ab</td><td align="center" valign="middle" rowspan="1" colspan="1">298–20465</td><td align="center" valign="middle" rowspan="1" colspan="1">6722</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">93.0</td><td align="center" valign="middle" rowspan="1" colspan="1">93.0</td><td align="center" valign="middle" rowspan="1" colspan="1">83.7</td><td align="center" valign="middle" rowspan="1" colspan="1">81.8</td><td align="center" valign="middle" rowspan="1" colspan="1">76.4</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(216)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S</td><td align="center" valign="middle" rowspan="1" colspan="1">20472–24533</td><td align="center" valign="middle" rowspan="1" colspan="1">1353</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">68.4</td><td align="center" valign="middle" rowspan="1" colspan="1">67.9</td><td align="center" valign="middle" rowspan="1" colspan="1">64.9</td><td align="center" valign="middle" rowspan="1" colspan="1">62.3</td><td align="center" valign="middle" rowspan="1" colspan="1">61.7</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAT(8)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S1</td><td align="center" valign="middle" rowspan="1" colspan="1">20541–22634</td><td align="center" valign="middle" rowspan="1" colspan="1">698</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">60.2</td><td align="center" valign="middle" rowspan="1" colspan="1">59.4</td><td align="center" valign="middle" rowspan="1" colspan="1">56.7</td><td align="center" valign="middle" rowspan="1" colspan="1">53.7</td><td align="center" valign="middle" rowspan="1" colspan="1">53.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S2</td><td align="center" valign="middle" rowspan="1" colspan="1">22659–24527</td><td align="center" valign="middle" rowspan="1" colspan="1">623</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">76.9</td><td align="center" valign="middle" rowspan="1" colspan="1">77.0</td><td align="center" valign="middle" rowspan="1" colspan="1">74.0</td><td align="center" valign="middle" rowspan="1" colspan="1">72.1</td><td align="center" valign="middle" rowspan="1" colspan="1">71.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS3a</td><td align="center" valign="middle" rowspan="1" colspan="1">24533–25201</td><td align="center" valign="middle" rowspan="1" colspan="1">222</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">65.0</td><td align="center" valign="middle" rowspan="1" colspan="1">65.0</td><td align="center" valign="middle" rowspan="1" colspan="1">54.3</td><td align="center" valign="middle" rowspan="1" colspan="1">52.4</td><td align="center" valign="middle" rowspan="1" colspan="1">53.5</td><td align="center" valign="middle" rowspan="1" colspan="1">CAATAC(26)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS3b</td><td align="center" valign="middle" rowspan="1" colspan="1">24978–25070</td><td align="center" valign="middle" rowspan="1" colspan="1">30</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CCTTAC(35)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4a</td><td align="center" valign="middle" rowspan="1" colspan="1">25222–25581</td><td align="center" valign="middle" rowspan="1" colspan="1">119</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">47.1</td><td align="center" valign="middle" rowspan="1" colspan="1">62.2</td><td align="center" valign="middle" rowspan="1" colspan="1">18.6</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTTTAC(50)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4b</td><td align="center" valign="middle" rowspan="1" colspan="1">25563–26009</td><td align="center" valign="middle" rowspan="1" colspan="1">148</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">57.8</td><td align="center" valign="middle" rowspan="1" colspan="1">52.9</td><td align="center" valign="middle" rowspan="1" colspan="1">11.4</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">E</td><td align="center" valign="middle" rowspan="1" colspan="1">25993–26217</td><td align="center" valign="middle" rowspan="1" colspan="1">74</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.1</td><td align="center" valign="middle" rowspan="1" colspan="1">68.7</td><td align="center" valign="middle" rowspan="1" colspan="1">75.9</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(66)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">M</td><td align="center" valign="middle" rowspan="1" colspan="1">26229–26912</td><td align="center" valign="middle" rowspan="1" colspan="1">227</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">88.8</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">78.1</td><td align="center" valign="middle" rowspan="1" colspan="1">86.6</td><td align="center" valign="middle" rowspan="1" colspan="1">85.5</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(1)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">N</td><td align="center" valign="middle" rowspan="1" colspan="1">26923–28134</td><td align="center" valign="middle" rowspan="1" colspan="1">403</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" rowspan="1" colspan="1">68.1</td><td align="center" valign="middle" rowspan="1" colspan="1">70.3</td><td align="center" valign="middle" rowspan="1" colspan="1">61.8</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS8</td><td align="center" valign="middle" rowspan="1" colspan="1">28290–28409</td><td align="center" valign="middle" rowspan="1" colspan="1">39</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">26.7</td><td align="center" valign="middle" rowspan="1" colspan="1">33.3</td><td align="center" valign="middle" rowspan="1" colspan="1">28.6</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(0)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS9</td><td align="center" valign="middle" rowspan="1" colspan="1">28454–28819</td><td align="center" valign="middle" rowspan="1" colspan="1">121</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">78.1</td><td align="center" valign="middle" rowspan="1" colspan="1">50.6</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">TTTCAC(3)ATG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concatenated domains<sup>1</sup></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">13,650</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4550</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">97.3</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">97.4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">84.2</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">86.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr><tr><td rowspan="13" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">RsYN2</td><td align="center" valign="middle" rowspan="1" colspan="1">1ab</td><td align="center" valign="middle" rowspan="1" colspan="1">298–20435</td><td align="center" valign="middle" rowspan="1" colspan="1">6712</td><td align="center" valign="middle" rowspan="1" colspan="1">93.0</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.4</td><td align="center" valign="middle" rowspan="1" colspan="1">84.4</td><td align="center" valign="middle" rowspan="1" colspan="1">82.5</td><td align="center" valign="middle" rowspan="1" colspan="1">76.9</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(216)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S</td><td align="center" valign="middle" rowspan="1" colspan="1">20437–24495</td><td align="center" valign="middle" rowspan="1" colspan="1">1352</td><td align="center" valign="middle" rowspan="1" colspan="1">68.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">93.6</td><td align="center" valign="middle" rowspan="1" colspan="1">66.9</td><td align="center" valign="middle" rowspan="1" colspan="1">65.7</td><td align="center" valign="middle" rowspan="1" colspan="1">62.4</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAT(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S1</td><td align="center" valign="middle" rowspan="1" colspan="1">20509–22599</td><td align="center" valign="middle" rowspan="1" colspan="1">697</td><td align="center" valign="middle" rowspan="1" colspan="1">60.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">88.2</td><td align="center" valign="middle" rowspan="1" colspan="1">58.7</td><td align="center" valign="middle" rowspan="1" colspan="1">58.8</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S2</td><td align="center" valign="middle" rowspan="1" colspan="1">22624–24489</td><td align="center" valign="middle" rowspan="1" colspan="1">623</td><td align="center" valign="middle" rowspan="1" colspan="1">76.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.9</td><td align="center" valign="middle" rowspan="1" colspan="1">76.3</td><td align="center" valign="middle" rowspan="1" colspan="1">72.8</td><td align="center" valign="middle" rowspan="1" colspan="1">70.0</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS3a</td><td align="center" valign="middle" rowspan="1" colspan="1">24495–25154</td><td align="center" valign="middle" rowspan="1" colspan="1">219</td><td align="center" valign="middle" rowspan="1" colspan="1">65.0</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">100.0</td><td align="center" valign="middle" rowspan="1" colspan="1">55.9</td><td align="center" valign="middle" rowspan="1" colspan="1">52.8</td><td align="center" valign="middle" rowspan="1" colspan="1">55.5</td><td align="center" valign="middle" rowspan="1" colspan="1">CGTTAC(26)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4a</td><td align="center" valign="middle" rowspan="1" colspan="1">25164–25488</td><td align="center" valign="middle" rowspan="1" colspan="1">104</td><td align="center" valign="middle" rowspan="1" colspan="1">47.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">64.4</td><td align="center" valign="middle" rowspan="1" colspan="1">17.5</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTTCAC(24)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4b</td><td align="center" valign="middle" rowspan="1" colspan="1">25507–25953</td><td align="center" valign="middle" rowspan="1" colspan="1">148</td><td align="center" valign="middle" rowspan="1" colspan="1">57.8</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">94.2</td><td align="center" valign="middle" rowspan="1" colspan="1">12.5</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">E</td><td align="center" valign="middle" rowspan="1" colspan="1">25934–26158</td><td align="center" valign="middle" rowspan="1" colspan="1">74</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">100.0</td><td align="center" valign="middle" rowspan="1" colspan="1">81.9</td><td align="center" valign="middle" rowspan="1" colspan="1">66.3</td><td align="center" valign="middle" rowspan="1" colspan="1">77.1</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(66)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">M</td><td align="center" valign="middle" rowspan="1" colspan="1">26170–26859</td><td align="center" valign="middle" rowspan="1" colspan="1">229</td><td align="center" valign="middle" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1">79.9</td><td align="center" valign="middle" rowspan="1" colspan="1">90.0</td><td align="center" valign="middle" rowspan="1" colspan="1">88.8</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(1)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">N</td><td align="center" valign="middle" rowspan="1" colspan="1">26870–28096</td><td align="center" valign="middle" rowspan="1" colspan="1">408</td><td align="center" valign="middle" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1">68.3</td><td align="center" valign="middle" rowspan="1" colspan="1">69.9</td><td align="center" valign="middle" rowspan="1" colspan="1">63.0</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS8</td><td align="center" valign="middle" rowspan="1" colspan="1">28107–28385</td><td align="center" valign="middle" rowspan="1" colspan="1">92</td><td align="center" valign="middle" rowspan="1" colspan="1">26.7</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">66.7</td><td align="center" valign="middle" rowspan="1" colspan="1">64.8</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(0)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS9</td><td align="center" valign="middle" rowspan="1" colspan="1">28425–28790</td><td align="center" valign="middle" rowspan="1" colspan="1">121</td><td align="center" valign="middle" rowspan="1" colspan="1">78.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">77.5</td><td align="center" valign="middle" rowspan="1" colspan="1">58.1</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">TTTCAC(3)ATG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concatenated domains</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">13641</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4547</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">97.3</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">87.1</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr><tr><td rowspan="13" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">RsYN3</td><td align="center" valign="middle" rowspan="1" colspan="1">1ab</td><td align="center" valign="middle" rowspan="1" colspan="1">298–20435</td><td align="center" valign="middle" rowspan="1" colspan="1">6712</td><td align="center" valign="middle" rowspan="1" colspan="1">93.0</td><td align="center" valign="middle" rowspan="1" colspan="1">99.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">84.4</td><td align="center" valign="middle" rowspan="1" colspan="1">82.5</td><td align="center" valign="middle" rowspan="1" colspan="1">76.9</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(216)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S</td><td align="center" valign="middle" rowspan="1" colspan="1">20437–24495</td><td align="center" valign="middle" rowspan="1" colspan="1">1352</td><td align="center" valign="middle" rowspan="1" colspan="1">67.9</td><td align="center" valign="middle" rowspan="1" colspan="1">93.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">66.6</td><td align="center" valign="middle" rowspan="1" colspan="1">65.8</td><td align="center" valign="middle" rowspan="1" colspan="1">62.4</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAT(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S1</td><td align="center" valign="middle" rowspan="1" colspan="1">20506–22599</td><td align="center" valign="middle" rowspan="1" colspan="1">698</td><td align="center" valign="middle" rowspan="1" colspan="1">59.4</td><td align="center" valign="middle" rowspan="1" colspan="1">88.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">57.9</td><td align="center" valign="middle" rowspan="1" colspan="1">59.2</td><td align="center" valign="middle" rowspan="1" colspan="1">54.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S2</td><td align="center" valign="middle" rowspan="1" colspan="1">22621–24489</td><td align="center" valign="middle" rowspan="1" colspan="1">623</td><td align="center" valign="middle" rowspan="1" colspan="1">77.0</td><td align="center" valign="middle" rowspan="1" colspan="1">99.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">76.4</td><td align="center" valign="middle" rowspan="1" colspan="1">72.9</td><td align="center" valign="middle" rowspan="1" colspan="1">70.1</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS3a</td><td align="center" valign="middle" rowspan="1" colspan="1">24495–25154</td><td align="center" valign="middle" rowspan="1" colspan="1">219</td><td align="center" valign="middle" rowspan="1" colspan="1">65.0</td><td align="center" valign="middle" rowspan="1" colspan="1">100.0</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">55.9</td><td align="center" valign="middle" rowspan="1" colspan="1">52.8</td><td align="center" valign="middle" rowspan="1" colspan="1">55.5</td><td align="center" valign="middle" rowspan="1" colspan="1">CGTTAC(26)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4a</td><td align="center" valign="middle" rowspan="1" colspan="1">25164–25526</td><td align="center" valign="middle" rowspan="1" colspan="1">120</td><td align="center" valign="middle" rowspan="1" colspan="1">62.2</td><td align="center" valign="middle" rowspan="1" colspan="1">64.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">17.6</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTTCAC(24)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4b</td><td align="center" valign="middle" rowspan="1" colspan="1">25508–25954</td><td align="center" valign="middle" rowspan="1" colspan="1">148</td><td align="center" valign="middle" rowspan="1" colspan="1">52.9</td><td align="center" valign="middle" rowspan="1" colspan="1">94.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">12.5</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">E</td><td align="center" valign="middle" rowspan="1" colspan="1">25935–26159</td><td align="center" valign="middle" rowspan="1" colspan="1">74</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">100.0</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">81.9</td><td align="center" valign="middle" rowspan="1" colspan="1">66.3</td><td align="center" valign="middle" rowspan="1" colspan="1">77.1</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(66)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">M</td><td align="center" valign="middle" rowspan="1" colspan="1">26171–26860</td><td align="center" valign="middle" rowspan="1" colspan="1">229</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">80.3</td><td align="center" valign="middle" rowspan="1" colspan="1">90.3</td><td align="center" valign="middle" rowspan="1" colspan="1">89.2</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(1)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">N</td><td align="center" valign="middle" rowspan="1" colspan="1">26871–28097</td><td align="center" valign="middle" rowspan="1" colspan="1">408</td><td align="center" valign="middle" rowspan="1" colspan="1">84.3</td><td align="center" valign="middle" rowspan="1" colspan="1">99.8</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">68.3</td><td align="center" valign="middle" rowspan="1" colspan="1">69.9</td><td align="center" valign="middle" rowspan="1" colspan="1">62.8</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS8</td><td align="center" valign="middle" rowspan="1" colspan="1">28108–28386</td><td align="center" valign="middle" rowspan="1" colspan="1">92</td><td align="center" valign="middle" rowspan="1" colspan="1">33.3</td><td align="center" valign="middle" rowspan="1" colspan="1">66.7</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">63.8</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(0)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS9</td><td align="center" valign="middle" rowspan="1" colspan="1">28434–28793</td><td align="center" valign="middle" rowspan="1" colspan="1">119</td><td align="center" valign="middle" rowspan="1" colspan="1">71.2</td><td align="center" valign="middle" rowspan="1" colspan="1">77.5</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">50.6</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">TTTCAC(3)ATG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concatenated domains</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">13641</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4547</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">97.4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">99.6</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">84.4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">87.2</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr><tr><td rowspan="13" align="center" valign="middle" style="border-bottom:solid thin" colspan="1">RaGD</td><td align="center" valign="middle" rowspan="1" colspan="1">1ab</td><td align="center" valign="middle" rowspan="1" colspan="1">296–20466</td><td align="center" valign="middle" rowspan="1" colspan="1">6723</td><td align="center" valign="middle" rowspan="1" colspan="1">83.7</td><td align="center" valign="middle" rowspan="1" colspan="1">84.4</td><td align="center" valign="middle" rowspan="1" colspan="1">84.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">80.0</td><td align="center" valign="middle" rowspan="1" colspan="1">76.4</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(215)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S</td><td align="center" valign="middle" rowspan="1" colspan="1">20463–24542</td><td align="center" valign="middle" rowspan="1" colspan="1">1359</td><td align="center" valign="middle" rowspan="1" colspan="1">64.9</td><td align="center" valign="middle" rowspan="1" colspan="1">66.9</td><td align="center" valign="middle" rowspan="1" colspan="1">66.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">61.9</td><td align="center" valign="middle" rowspan="1" colspan="1">62.4</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(4)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S1</td><td align="center" valign="middle" rowspan="1" colspan="1">20520–22652</td><td align="center" valign="middle" rowspan="1" colspan="1">711</td><td align="center" valign="middle" rowspan="1" colspan="1">56.7</td><td align="center" valign="middle" rowspan="1" colspan="1">58.7</td><td align="center" valign="middle" rowspan="1" colspan="1">57.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">53.6</td><td align="center" valign="middle" rowspan="1" colspan="1">54.5</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S2</td><td align="center" valign="middle" rowspan="1" colspan="1">22674–24535</td><td align="center" valign="middle" rowspan="1" colspan="1">621</td><td align="center" valign="middle" rowspan="1" colspan="1">74.0</td><td align="center" valign="middle" rowspan="1" colspan="1">76.3</td><td align="center" valign="middle" rowspan="1" colspan="1">76.4</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">71.4</td><td align="center" valign="middle" rowspan="1" colspan="1">72.2</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS3a</td><td align="center" valign="middle" rowspan="1" colspan="1">24542–25198</td><td align="center" valign="middle" rowspan="1" colspan="1">218</td><td align="center" valign="middle" rowspan="1" colspan="1">54.3</td><td align="center" valign="middle" rowspan="1" colspan="1">55.9</td><td align="center" valign="middle" rowspan="1" colspan="1">55.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">48.0</td><td align="center" valign="middle" rowspan="1" colspan="1">52.0</td><td align="center" valign="middle" rowspan="1" colspan="1">CGTTAC(26)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4a</td><td align="center" valign="middle" rowspan="1" colspan="1">25200–25663</td><td align="center" valign="middle" rowspan="1" colspan="1">157</td><td align="center" valign="middle" rowspan="1" colspan="1">18.6</td><td align="center" valign="middle" rowspan="1" colspan="1">17.5</td><td align="center" valign="middle" rowspan="1" colspan="1">17.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTTTGC(34)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS4b</td><td align="center" valign="middle" rowspan="1" colspan="1">25294–25611</td><td align="center" valign="middle" rowspan="1" colspan="1">105</td><td align="center" valign="middle" rowspan="1" colspan="1">11.4</td><td align="center" valign="middle" rowspan="1" colspan="1">12.5</td><td align="center" valign="middle" rowspan="1" colspan="1">12.5</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">E</td><td align="center" valign="middle" rowspan="1" colspan="1">25654–25878</td><td align="center" valign="middle" rowspan="1" colspan="1">74</td><td align="center" valign="middle" rowspan="1" colspan="1">77.1</td><td align="center" valign="middle" rowspan="1" colspan="1">81.9</td><td align="center" valign="middle" rowspan="1" colspan="1">81.9</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">63.9</td><td align="center" valign="middle" rowspan="1" colspan="1">81.9</td><td align="center" valign="middle" rowspan="1" colspan="1">CCAAAC(66)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">M</td><td align="center" valign="middle" rowspan="1" colspan="1">25884–26624</td><td align="center" valign="middle" rowspan="1" colspan="1">246</td><td align="center" valign="middle" rowspan="1" colspan="1">78.1</td><td align="center" valign="middle" rowspan="1" colspan="1">79.9</td><td align="center" valign="middle" rowspan="1" colspan="1">80.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">78.1</td><td align="center" valign="middle" rowspan="1" colspan="1">78.8</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">N</td><td align="center" valign="middle" rowspan="1" colspan="1">26635–27810</td><td align="center" valign="middle" rowspan="1" colspan="1">391</td><td align="center" valign="middle" rowspan="1" colspan="1">68.1</td><td align="center" valign="middle" rowspan="1" colspan="1">68.3</td><td align="center" valign="middle" rowspan="1" colspan="1">68.3</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">67.3</td><td align="center" valign="middle" rowspan="1" colspan="1">60.8</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(3)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS8</td><td align="center" valign="middle" rowspan="1" colspan="1">27821–28099</td><td align="center" valign="middle" rowspan="1" colspan="1">92</td><td align="center" valign="middle" rowspan="1" colspan="1">28.6</td><td align="center" valign="middle" rowspan="1" colspan="1">64.8</td><td align="center" valign="middle" rowspan="1" colspan="1">63.8</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTAAAC(0)ATG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NS9</td><td align="center" valign="middle" rowspan="1" colspan="1">28123–28485</td><td align="center" valign="middle" rowspan="1" colspan="1">120</td><td align="center" valign="middle" rowspan="1" colspan="1">55.6</td><td align="center" valign="middle" rowspan="1" colspan="1">58.1</td><td align="center" valign="middle" rowspan="1" colspan="1">50.6</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">NA</td><td align="center" valign="middle" rowspan="1" colspan="1">CTTTAC(3)ATG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Concatenated domains</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">13,674</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">4558</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">91.8</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">83.0</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">87.4</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr></tbody></table><table-wrap-foot><fn><p>Concatenated domains including following conserved domains in replicase polyprotein pp1ab: ADRP, nsp5 (3CL<sup>pro</sup>), nsp12 (RdRp), nsp13 (Hel), nsp14 (ExoN), nsp15 (NendoU), and nsp16 (O-MT).</p></fn></table-wrap-foot></table-wrap><table-wrap id="viruses-11-00379-t003" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-00379-t003_Table 3</object-id><label>Table 3</label><caption><p>Characteristics of predicted nonstructural proteins of ORF1ab in different stains of BtCoV/Rh/YN2012.</p></caption><table frame="hsides" rules="groups"><thead><tr><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">NSP</th><th rowspan="2" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" colspan="1">Putative Functional Domain(s)</th><th colspan="3" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">RsYN1</th><th colspan="3" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">RsYN2</th><th colspan="3" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">RsYN3</th><th colspan="3" align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1">RaGD</th></tr><tr><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Amino Acides Position in ORF1ab</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Predicted Size (aa of Protein)</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">C-end Predicted Cleavage Site</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Amino Acides Position in ORF1ab</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Predicted Size (aa of Protein)</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">C-End Predicted Cleavage Site</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Amino Acides Position in ORF1ab</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Predicted Size (aa of Protein)</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">C-end Predicted Cleavage Site</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Amino Acides Position in ORF1ab</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">Predicted Size (aa of Protein)</th><th align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">C-end Predicted Cleavage Site</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP1</td><td align="center" valign="middle" rowspan="1" colspan="1">Unknown</td><td align="center" valign="middle" rowspan="1" colspan="1">M1–A195</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">VA│AP</td><td align="center" valign="middle" rowspan="1" colspan="1">M1-A195</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">VA│SP</td><td align="center" valign="middle" rowspan="1" colspan="1">M1-A195</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">VA│SP</td><td align="center" valign="middle" rowspan="1" colspan="1">M1-A195</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">TA│PP</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP2</td><td align="center" valign="middle" rowspan="1" colspan="1">Unknown</td><td align="center" valign="middle" rowspan="1" colspan="1">A196–C896</td><td align="center" valign="middle" rowspan="1" colspan="1">701</td><td align="center" valign="middle" rowspan="1" colspan="1">RC│GG</td><td align="center" valign="middle" rowspan="1" colspan="1">S196-S889</td><td align="center" valign="middle" rowspan="1" colspan="1">694</td><td align="center" valign="middle" rowspan="1" colspan="1">RC│GG</td><td align="center" valign="middle" rowspan="1" colspan="1">S196-S889</td><td align="center" valign="middle" rowspan="1" colspan="1">694</td><td align="center" valign="middle" rowspan="1" colspan="1">RC│GG</td><td align="center" valign="middle" rowspan="1" colspan="1">P196-S889</td><td align="center" valign="middle" rowspan="1" colspan="1">694</td><td align="center" valign="middle" rowspan="1" colspan="1">RS│GG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP3</td><td align="center" valign="middle" rowspan="1" colspan="1">ADRP, PL2 pro</td><td align="center" valign="middle" rowspan="1" colspan="1">G897–G2463</td><td align="center" valign="middle" rowspan="1" colspan="1">1567</td><td align="center" valign="middle" rowspan="1" colspan="1">QG│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">G890-G2453</td><td align="center" valign="middle" rowspan="1" colspan="1">1564</td><td align="center" valign="middle" rowspan="1" colspan="1">AG│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">G890-G2453</td><td align="center" valign="middle" rowspan="1" colspan="1">1564</td><td align="center" valign="middle" rowspan="1" colspan="1">AG│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">G890-G2462</td><td align="center" valign="middle" rowspan="1" colspan="1">1573</td><td align="center" valign="middle" rowspan="1" colspan="1">NG│SG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP4</td><td align="center" valign="middle" rowspan="1" colspan="1">Hydrophobid domain</td><td align="center" valign="middle" rowspan="1" colspan="1">S2464–Q2941</td><td align="center" valign="middle" rowspan="1" colspan="1">478</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">S2454–Q2931</td><td align="center" valign="middle" rowspan="1" colspan="1">478</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">S2454-Q2931</td><td align="center" valign="middle" rowspan="1" colspan="1">478</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">S2463-Q2940</td><td align="center" valign="middle" rowspan="1" colspan="1">478</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP5</td><td align="center" valign="middle" rowspan="1" colspan="1">3CL pro</td><td align="center" valign="middle" rowspan="1" colspan="1">S2942–Q3243</td><td align="center" valign="middle" rowspan="1" colspan="1">302</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│ST</td><td align="center" valign="middle" rowspan="1" colspan="1">S2932–Q3233</td><td align="center" valign="middle" rowspan="1" colspan="1">302</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│ST</td><td align="center" valign="middle" rowspan="1" colspan="1">S2932-Q3233</td><td align="center" valign="middle" rowspan="1" colspan="1">302</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│ST</td><td align="center" valign="middle" rowspan="1" colspan="1">S2941-Q3242</td><td align="center" valign="middle" rowspan="1" colspan="1">302</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SN</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP6</td><td align="center" valign="middle" rowspan="1" colspan="1">Hydrophobid domain</td><td align="center" valign="middle" rowspan="1" colspan="1">S3244–Q3519</td><td align="center" valign="middle" rowspan="1" colspan="1">276</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SK</td><td align="center" valign="middle" rowspan="1" colspan="1">S3234–Q3509</td><td align="center" valign="middle" rowspan="1" colspan="1">276</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SK</td><td align="center" valign="middle" rowspan="1" colspan="1">S3234-Q3509</td><td align="center" valign="middle" rowspan="1" colspan="1">276</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SK</td><td align="center" valign="middle" rowspan="1" colspan="1">S3243-Q3518</td><td align="center" valign="middle" rowspan="1" colspan="1">276</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SK</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP7</td><td align="center" valign="middle" rowspan="1" colspan="1">Replicase</td><td align="center" valign="middle" rowspan="1" colspan="1">S3520–Q3602</td><td align="center" valign="middle" rowspan="1" colspan="1">83</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SV</td><td align="center" valign="middle" rowspan="1" colspan="1">S3510–Q3592</td><td align="center" valign="middle" rowspan="1" colspan="1">83</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SV</td><td align="center" valign="middle" rowspan="1" colspan="1">S3510-Q3592</td><td align="center" valign="middle" rowspan="1" colspan="1">83</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SV</td><td align="center" valign="middle" rowspan="1" colspan="1">S3519-Q3601</td><td align="center" valign="middle" rowspan="1" colspan="1">83</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SV</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP8</td><td align="center" valign="middle" rowspan="1" colspan="1">Replicase</td><td align="center" valign="middle" rowspan="1" colspan="1">S3603–Q3797</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│NN</td><td align="center" valign="middle" rowspan="1" colspan="1">S3593–Q3787</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│NN</td><td align="center" valign="middle" rowspan="1" colspan="1">S3593-Q3787</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│NN</td><td align="center" valign="middle" rowspan="1" colspan="1">S3602-Q3796</td><td align="center" valign="middle" rowspan="1" colspan="1">195</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│NN</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP9</td><td align="center" valign="middle" rowspan="1" colspan="1">Replicase</td><td align="center" valign="middle" rowspan="1" colspan="1">N3798–Q3905</td><td align="center" valign="middle" rowspan="1" colspan="1">108</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">N3788–Q3895</td><td align="center" valign="middle" rowspan="1" colspan="1">108</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">N3788-Q3895</td><td align="center" valign="middle" rowspan="1" colspan="1">108</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">N3797-Q3904</td><td align="center" valign="middle" rowspan="1" colspan="1">108</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP10</td><td align="center" valign="middle" rowspan="1" colspan="1">RNA synthesis protein</td><td align="center" valign="middle" rowspan="1" colspan="1">A3906–Q4041</td><td align="center" valign="middle" rowspan="1" colspan="1">136</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SL</td><td align="center" valign="middle" rowspan="1" colspan="1">A3896–Q4031</td><td align="center" valign="middle" rowspan="1" colspan="1">136</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│AL</td><td align="center" valign="middle" rowspan="1" colspan="1">A3896-Q4031</td><td align="center" valign="middle" rowspan="1" colspan="1">136</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│AL</td><td align="center" valign="middle" rowspan="1" colspan="1">A3905-Q4040</td><td align="center" valign="middle" rowspan="1" colspan="1">136</td><td align="center" valign="middle" rowspan="1" colspan="1">VQ│SL</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP11</td><td align="center" valign="middle" rowspan="1" colspan="1">Unknown (short peptide at the end of ORF1a)</td><td align="center" valign="middle" rowspan="1" colspan="1">S–D</td><td align="center" valign="middle" rowspan="1" colspan="1">17</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">A-D</td><td align="center" valign="middle" rowspan="1" colspan="1">17</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">A-D</td><td align="center" valign="middle" rowspan="1" colspan="1">17</td><td align="center" valign="middle" rowspan="1" colspan="1"></td><td align="center" valign="middle" rowspan="1" colspan="1">S-N</td><td align="center" valign="middle" rowspan="1" colspan="1">17</td><td align="center" valign="middle" rowspan="1" colspan="1"></td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP12</td><td align="center" valign="middle" rowspan="1" colspan="1">RdRp</td><td align="center" valign="middle" rowspan="1" colspan="1">S4042–Q4968</td><td align="center" valign="middle" rowspan="1" colspan="1">927</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AA</td><td align="center" valign="middle" rowspan="1" colspan="1">A4032-Q4958</td><td align="center" valign="middle" rowspan="1" colspan="1">927</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AA</td><td align="center" valign="middle" rowspan="1" colspan="1">A4032-Q4958</td><td align="center" valign="middle" rowspan="1" colspan="1">927</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AA</td><td align="center" valign="middle" rowspan="1" colspan="1">S4041-Q4967</td><td align="center" valign="middle" rowspan="1" colspan="1">927</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AA</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP13</td><td align="center" valign="middle" rowspan="1" colspan="1">Hel, NTPase</td><td align="center" valign="middle" rowspan="1" colspan="1">A4969–Q5565</td><td align="center" valign="middle" rowspan="1" colspan="1">597</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">A4959-Q5555</td><td align="center" valign="middle" rowspan="1" colspan="1">597</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">A4959-Q5555</td><td align="center" valign="middle" rowspan="1" colspan="1">597</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">A4968-Q5564</td><td align="center" valign="middle" rowspan="1" colspan="1">597</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP14</td><td align="center" valign="middle" rowspan="1" colspan="1">ExoN, NMT</td><td align="center" valign="middle" rowspan="1" colspan="1">A5566–Q6083</td><td align="center" valign="middle" rowspan="1" colspan="1">518</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│GL</td><td align="center" valign="middle" rowspan="1" colspan="1">A5556-Q6073</td><td align="center" valign="middle" rowspan="1" colspan="1">518</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│GL</td><td align="center" valign="middle" rowspan="1" colspan="1">A5556-Q6073</td><td align="center" valign="middle" rowspan="1" colspan="1">518</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│GL</td><td align="center" valign="middle" rowspan="1" colspan="1">A5565-Q6082</td><td align="center" valign="middle" rowspan="1" colspan="1">518</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│GL</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP15</td><td align="center" valign="middle" rowspan="1" colspan="1">NeudoU</td><td align="center" valign="middle" rowspan="1" colspan="1">G6084–Q6422</td><td align="center" valign="middle" rowspan="1" colspan="1">339</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│AG</td><td align="center" valign="middle" rowspan="1" colspan="1">G6074-Q6412</td><td align="center" valign="middle" rowspan="1" colspan="1">339</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">G6074-Q6412</td><td align="center" valign="middle" rowspan="1" colspan="1">339</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td><td align="center" valign="middle" rowspan="1" colspan="1">G6083-Q6421</td><td align="center" valign="middle" rowspan="1" colspan="1">339</td><td align="center" valign="middle" rowspan="1" colspan="1">LQ│SG</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">NSP16</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">2’-O-MT</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">A6423–K6722</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">300</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">S6413-K6712</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">300</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">S6413-K6712</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">300</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">S6422-K6723</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">302</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1"></td></tr></tbody></table></table-wrap><table-wrap id="viruses-11-00379-t004" orientation="portrait" position="float"><object-id pub-id-type="pii">viruses-11-00379-t004_Table 4</object-id><label>Table 4</label><caption><p>Estimation of nonsynonymous and synonymous substitution rates in the genomes of BtCoV/Rh/YN2012.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Gene</th><th align="center" valign="middle" style="border-top:solid thin;border-bottom:solid thin" rowspan="1" colspan="1">Ka/Ks Ratio</th></tr></thead><tbody><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP1</td><td align="center" valign="middle" rowspan="1" colspan="1">0.256</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP2</td><td align="center" valign="middle" rowspan="1" colspan="1">0.390</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP3</td><td align="center" valign="middle" rowspan="1" colspan="1">0.315</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP4</td><td align="center" valign="middle" rowspan="1" colspan="1">0.276</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP5</td><td align="center" valign="middle" rowspan="1" colspan="1">0.128</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP6</td><td align="center" valign="middle" rowspan="1" colspan="1">0.323</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP7</td><td align="center" valign="middle" rowspan="1" colspan="1">0.067</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP8</td><td align="center" valign="middle" rowspan="1" colspan="1">0.125</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP9</td><td align="center" valign="middle" rowspan="1" colspan="1">0.230</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP10</td><td align="center" valign="middle" rowspan="1" colspan="1">0.098</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP11</td><td align="center" valign="middle" rowspan="1" colspan="1">0.236</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP12</td><td align="center" valign="middle" rowspan="1" colspan="1">0.073</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP13</td><td align="center" valign="middle" rowspan="1" colspan="1">0.045</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP14</td><td align="center" valign="middle" rowspan="1" colspan="1">0.121</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP15</td><td align="center" valign="middle" rowspan="1" colspan="1">0.124</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">NSP16</td><td align="center" valign="middle" rowspan="1" colspan="1">0.083</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">S</td><td align="center" valign="middle" rowspan="1" colspan="1">0.258</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">ORF3a</td><td align="center" valign="middle" rowspan="1" colspan="1">0.357</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">ORF4a</td><td align="center" valign="middle" rowspan="1" colspan="1">0.727</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">ORF4b</td><td align="center" valign="middle" rowspan="1" colspan="1">0.623</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">E</td><td align="center" valign="middle" rowspan="1" colspan="1">0.062</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">M</td><td align="center" valign="middle" rowspan="1" colspan="1">0.0691</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">N</td><td align="center" valign="middle" rowspan="1" colspan="1">0.230</td></tr><tr><td align="center" valign="middle" rowspan="1" colspan="1">ORF8</td><td align="center" valign="middle" rowspan="1" colspan="1">0.276</td></tr><tr><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">ORF9</td><td align="center" valign="middle" style="border-bottom:solid thin" rowspan="1" colspan="1">0.843</td></tr></tbody></table></table-wrap></floats-group></pmc><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><noCountry><name sortKey="Hu, Ben" sort="Hu, Ben" uniqKey="Hu B" first="Ben" last="Hu">Ben Hu</name><name sortKey="Li, Bei" sort="Li, Bei" uniqKey="Li B" first="Bei" last="Li">Bei Li</name><name sortKey="Liu, Haizhou" sort="Liu, Haizhou" uniqKey="Liu H" first="Haizhou" last="Liu">Haizhou Liu</name><name sortKey="Peng, Cheng" sort="Peng, Cheng" uniqKey="Peng C" first="Cheng" last="Peng">Cheng Peng</name><name sortKey="Shi, Zhengli" sort="Shi, Zhengli" uniqKey="Shi Z" first="Zhengli" last="Shi">Zhengli Shi</name><name sortKey="Yang, Xinglou" sort="Yang, Xinglou" uniqKey="Yang X" first="Xinglou" last="Yang">Xinglou Yang</name><name sortKey="Zhang, Wei" sort="Zhang, Wei" uniqKey="Zhang W" first="Wei" last="Zhang">Wei Zhang</name><name sortKey="Zhu, Guangjian" sort="Zhu, Guangjian" uniqKey="Zhu G" first="Guangjian" last="Zhu">Guangjian Zhu</name><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Ning" sort="Wang, Ning" uniqKey="Wang N" first="Ning" last="Wang">Ning Wang</name></noRegion><name sortKey="Luo, Chuming" sort="Luo, Chuming" uniqKey="Luo C" first="Chuming" last="Luo">Chuming Luo</name><name sortKey="Shen, Xurui" sort="Shen, Xurui" uniqKey="Shen X" first="Xurui" last="Shen">Xurui Shen</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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