Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.
Identifieur interne : 000D85 ( PubMed/Curation ); précédent : 000D84; suivant : 000D86Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.
Auteurs : Susanna K P. Lau [République populaire de Chine] ; Yun Feng [République populaire de Chine] ; Honglin Chen [République populaire de Chine] ; Hayes K H. Luk [République populaire de Chine] ; Wei-Hong Yang [République populaire de Chine] ; Kenneth S M. Li [République populaire de Chine] ; Yu-Zhen Zhang [République populaire de Chine] ; Yi Huang [République populaire de Chine] ; Zhi-Zhong Song [République populaire de Chine] ; Wang-Ngai Chow [République populaire de Chine] ; Rachel Y Y. Fan [République populaire de Chine] ; Syed Shakeel Ahmed [République populaire de Chine] ; Hazel C. Yeung [République populaire de Chine] ; Carol S F. Lam [République populaire de Chine] ; Jian-Piao Cai [République populaire de Chine] ; Samson S Y. Wong [République populaire de Chine] ; Jasper F W. Chan [République populaire de Chine] ; Kwok-Yung Yuen [République populaire de Chine] ; Hai-Lin Zhang [Hong Kong] ; Patrick C Y. Woo [Hong Kong]Source :
- Journal of virology [ 1098-5514 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN messager (génétique), ARN messager (métabolisme), ARN viral (génétique), ARN viral (métabolisme), Alignement de séquences, Animaux, Chine, Chiroptera (virologie), Données de séquences moléculaires, Expression des gènes, Génome viral, Humains, Infections à coronavirus (génétique), Infections à coronavirus (médecine vétérinaire), Infections à coronavirus (transmission), Infections à coronavirus (virologie), Phylogénie, Phylogéographie, Protéines de la matrice virale (génétique), Protéines de la matrice virale (métabolisme), Recombinaison génétique, Similitude de séquences d'acides nucléiques, Syndrome respiratoire aigu sévère (génétique), Syndrome respiratoire aigu sévère (métabolisme), Syndrome respiratoire aigu sévère (transmission), Syndrome respiratoire aigu sévère (virologie), Séquence d'acides aminés, Séquence nucléotidique, Virus du SRAS (), Virus du SRAS (génétique), Virus du SRAS (métabolisme), Viverridae (virologie), Évolution moléculaire.
- MESH :
- génétique : ARN messager, ARN viral, Infections à coronavirus, Protéines de la matrice virale, Syndrome respiratoire aigu sévère, Virus du SRAS.
- médecine vétérinaire : Infections à coronavirus.
- métabolisme : ARN messager, ARN viral, Protéines de la matrice virale, Syndrome respiratoire aigu sévère, Virus du SRAS.
- virologie : Chiroptera, Infections à coronavirus, Syndrome respiratoire aigu sévère, Viverridae.
- Alignement de séquences, Animaux, Chine, Données de séquences moléculaires, Expression des gènes, Génome viral, Humains, Infections à coronavirus, Phylogénie, Phylogéographie, Recombinaison génétique, Similitude de séquences d'acides nucléiques, Syndrome respiratoire aigu sévère, Séquence d'acides aminés, Séquence nucléotidique, Virus du SRAS, Évolution moléculaire.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- Amino Acid Sequence, Animals, Base Sequence, China, Chiroptera (virology), Coronavirus Infections (genetics), Coronavirus Infections (transmission), Coronavirus Infections (veterinary), Coronavirus Infections (virology), Evolution, Molecular, Gene Expression, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Phylogeography, RNA, Messenger (genetics), RNA, Messenger (metabolism), RNA, Viral (genetics), RNA, Viral (metabolism), Recombination, Genetic, SARS Virus (classification), SARS Virus (genetics), SARS Virus (metabolism), Sequence Alignment, Sequence Homology, Nucleic Acid, Severe Acute Respiratory Syndrome (genetics), Severe Acute Respiratory Syndrome (metabolism), Severe Acute Respiratory Syndrome (transmission), Severe Acute Respiratory Syndrome (virology), Viral Matrix Proteins (genetics), Viral Matrix Proteins (metabolism), Viverridae (virology).
- MESH :
- chemical , genetics : RNA, Messenger, RNA, Viral, Viral Matrix Proteins.
- chemical , metabolism : RNA, Messenger, RNA, Viral, Viral Matrix Proteins.
- geographic : China.
- classification : SARS Virus.
- genetics : Coronavirus Infections, SARS Virus, Severe Acute Respiratory Syndrome.
- metabolism : SARS Virus, Severe Acute Respiratory Syndrome.
- transmission : Coronavirus Infections, Severe Acute Respiratory Syndrome.
- veterinary : Coronavirus Infections.
- virology : Chiroptera, Coronavirus Infections, Severe Acute Respiratory Syndrome, Viverridae.
- Amino Acid Sequence, Animals, Base Sequence, Evolution, Molecular, Gene Expression, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Phylogeography, Recombination, Genetic, Sequence Alignment, Sequence Homology, Nucleic Acid.
Abstract
Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.
DOI: 10.1128/JVI.01048-15
PubMed: 26269185
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Yeung</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Lam, Carol S F" sort="Lam, Carol S F" uniqKey="Lam C" first="Carol S F" last="Lam">Carol S F. Lam</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Cai, Jian Piao" sort="Cai, Jian Piao" uniqKey="Cai J" first="Jian-Piao" last="Cai">Jian-Piao Cai</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Samson S Y" sort="Wong, Samson S Y" uniqKey="Wong S" first="Samson S Y" last="Wong">Samson S Y. Wong</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Chan, Jasper F W" sort="Chan, Jasper F W" uniqKey="Chan J" first="Jasper F W" last="Chan">Jasper F W. Chan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hai Lin" sort="Zhang, Hai Lin" uniqKey="Zhang H" first="Hai-Lin" last="Zhang">Hai-Lin Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China pcywoo@hku.hk zhangHL715@163.com.</nlm:affiliation><country wicri:rule="url">Hong Kong</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C Y" last="Woo">Patrick C Y. Woo</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China pcywoo@hku.hk zhangHL715@163.com.</nlm:affiliation><country wicri:rule="url">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26269185</idno><idno type="pmid">26269185</idno><idno type="doi">10.1128/JVI.01048-15</idno><idno type="wicri:Area/PubMed/Corpus">000D85</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D85</idno><idno type="wicri:Area/PubMed/Curation">000D85</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D85</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.</title><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K P" last="Lau">Susanna K P. Lau</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Feng, Yun" sort="Feng, Yun" uniqKey="Feng Y" first="Yun" last="Feng">Yun Feng</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Honglin" sort="Chen, Honglin" uniqKey="Chen H" first="Honglin" last="Chen">Honglin Chen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Luk, Hayes K H" sort="Luk, Hayes K H" uniqKey="Luk H" first="Hayes K H" last="Luk">Hayes K H. Luk</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Yang, Wei Hong" sort="Yang, Wei Hong" uniqKey="Yang W" first="Wei-Hong" last="Yang">Wei-Hong Yang</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Li, Kenneth S M" sort="Li, Kenneth S M" uniqKey="Li K" first="Kenneth S M" last="Li">Kenneth S M. Li</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Yu Zhen" sort="Zhang, Yu Zhen" uniqKey="Zhang Y" first="Yu-Zhen" last="Zhang">Yu-Zhen Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Song, Zhi Zhong" sort="Song, Zhi Zhong" uniqKey="Song Z" first="Zhi-Zhong" last="Song">Zhi-Zhong Song</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Chow, Wang Ngai" sort="Chow, Wang Ngai" uniqKey="Chow W" first="Wang-Ngai" last="Chow">Wang-Ngai Chow</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Fan, Rachel Y Y" sort="Fan, Rachel Y Y" uniqKey="Fan R" first="Rachel Y Y" last="Fan">Rachel Y Y. Fan</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Ahmed, Syed Shakeel" sort="Ahmed, Syed Shakeel" uniqKey="Ahmed S" first="Syed Shakeel" last="Ahmed">Syed Shakeel Ahmed</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Yeung, Hazel C" sort="Yeung, Hazel C" uniqKey="Yeung H" first="Hazel C" last="Yeung">Hazel C. Yeung</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Lam, Carol S F" sort="Lam, Carol S F" uniqKey="Lam C" first="Carol S F" last="Lam">Carol S F. Lam</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Cai, Jian Piao" sort="Cai, Jian Piao" uniqKey="Cai J" first="Jian-Piao" last="Cai">Jian-Piao Cai</name><affiliation wicri:level="1"><nlm:affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Samson S Y" sort="Wong, Samson S Y" uniqKey="Wong S" first="Samson S Y" last="Wong">Samson S Y. Wong</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Chan, Jasper F W" sort="Chan, Jasper F W" uniqKey="Chan J" first="Jasper F W" last="Chan">Jasper F W. Chan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Hai Lin" sort="Zhang, Hai Lin" uniqKey="Zhang H" first="Hai-Lin" last="Zhang">Hai-Lin Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China pcywoo@hku.hk zhangHL715@163.com.</nlm:affiliation><country wicri:rule="url">Hong Kong</country><wicri:regionArea>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan</wicri:regionArea></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C Y" last="Woo">Patrick C Y. Woo</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China pcywoo@hku.hk zhangHL715@163.com.</nlm:affiliation><country wicri:rule="url">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of virology</title><idno type="eISSN">1098-5514</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Base Sequence</term><term>China</term><term>Chiroptera (virology)</term><term>Coronavirus Infections (genetics)</term><term>Coronavirus Infections (transmission)</term><term>Coronavirus Infections (veterinary)</term><term>Coronavirus Infections (virology)</term><term>Evolution, Molecular</term><term>Gene Expression</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Phylogeography</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (metabolism)</term><term>RNA, Viral (genetics)</term><term>RNA, Viral (metabolism)</term><term>Recombination, Genetic</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>SARS Virus (metabolism)</term><term>Sequence Alignment</term><term>Sequence Homology, Nucleic Acid</term><term>Severe Acute Respiratory Syndrome (genetics)</term><term>Severe Acute Respiratory Syndrome (metabolism)</term><term>Severe Acute Respiratory Syndrome (transmission)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Viral Matrix Proteins (genetics)</term><term>Viral Matrix Proteins (metabolism)</term><term>Viverridae (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>ARN messager (métabolisme)</term><term>ARN viral (génétique)</term><term>ARN viral (métabolisme)</term><term>Alignement de séquences</term><term>Animaux</term><term>Chine</term><term>Chiroptera (virologie)</term><term>Données de séquences moléculaires</term><term>Expression des gènes</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (génétique)</term><term>Infections à coronavirus (médecine vétérinaire)</term><term>Infections à coronavirus (transmission)</term><term>Infections à coronavirus (virologie)</term><term>Phylogénie</term><term>Phylogéographie</term><term>Protéines de la matrice virale (génétique)</term><term>Protéines de la matrice virale (métabolisme)</term><term>Recombinaison génétique</term><term>Similitude de séquences d'acides nucléiques</term><term>Syndrome respiratoire aigu sévère (génétique)</term><term>Syndrome respiratoire aigu sévère (métabolisme)</term><term>Syndrome respiratoire aigu sévère (transmission)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (métabolisme)</term><term>Viverridae (virologie)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Viral</term><term>Viral Matrix Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Viral</term><term>Viral Matrix Proteins</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>China</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus Infections</term><term>SARS Virus</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>ARN viral</term><term>Infections à coronavirus</term><term>Protéines de la matrice virale</term><term>Syndrome respiratoire aigu sévère</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>SARS Virus</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN messager</term><term>ARN viral</term><term>Protéines de la matrice virale</term><term>Syndrome respiratoire aigu sévère</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Coronavirus Infections</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Chiroptera</term><term>Infections à coronavirus</term><term>Syndrome respiratoire aigu sévère</term><term>Viverridae</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chiroptera</term><term>Coronavirus Infections</term><term>Severe Acute Respiratory Syndrome</term><term>Viverridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Base Sequence</term><term>Evolution, Molecular</term><term>Gene Expression</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Phylogeography</term><term>Recombination, Genetic</term><term>Sequence Alignment</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Animaux</term><term>Chine</term><term>Données de séquences moléculaires</term><term>Expression des gènes</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus</term><term>Phylogénie</term><term>Phylogéographie</term><term>Recombinaison génétique</term><term>Similitude de séquences d'acides nucléiques</term><term>Syndrome respiratoire aigu sévère</term><term>Séquence d'acides aminés</term><term>Séquence nucléotidique</term><term>Virus du SRAS</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>République populaire de Chine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26269185</PMID><DateCompleted><Year>2015</Year><Month>12</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1098-5514</ISSN><JournalIssue CitedMedium="Internet"><Volume>89</Volume><Issue>20</Issue><PubDate><Year>2015</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Journal of virology</Title><ISOAbbreviation>J. Virol.</ISOAbbreviation></Journal><ArticleTitle>Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination.</ArticleTitle><Pagination><MedlinePgn>10532-47</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1128/JVI.01048-15</ELocationID><Abstract><AbstractText Label="UNLABELLED">Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS-CoV ORF8 originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.</AbstractText><AbstractText Label="IMPORTANCE" NlmCategory="OBJECTIVE">Although horseshoe bats are the primary reservoir of SARS-related coronaviruses (SARSr-CoVs), it is still unclear how these bat viruses have evolved to cross the species barrier to infect civets and humans. Most human SARS-CoV epidemic strains contain a signature 29-nucleotide deletion in ORF8, compared to civet SARSr-CoVs, suggesting that ORF8 may be important for interspecies transmission. However, the origin of SARS-CoV ORF8 remains obscure. In particular, SARSr-Rs-BatCoVs from Chinese horseshoe bats (Rhinolophus sinicus) exhibited <40% amino acid identities to human/civet SARS-CoV in the ORF8 protein. We detected diverse alphacoronaviruses and betacoronaviruses among various bat species in Yunnan, China, including two SARSr-Rf-BatCoVs from greater horseshoe bats that possessed ORF8 proteins with exceptionally high amino acid identities to that of human/civet SARSr-CoVs. We demonstrated recombination events around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. Our findings offer insight into the evolutionary origin of SARS-CoV ORF8 protein, which was likely acquired from SARSr-CoVs of greater horseshoe bats through recombination.</AbstractText><CopyrightInformation>Copyright © 2015, American Society for Microbiology. All Rights Reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lau</LastName><ForeName>Susanna K P</ForeName><Initials>SK</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Yun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Honglin</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luk</LastName><ForeName>Hayes K H</ForeName><Initials>HK</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wei-Hong</ForeName><Initials>WH</Initials><AffiliationInfo><Affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Kenneth S M</ForeName><Initials>KS</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yu-Zhen</ForeName><Initials>YZ</Initials><AffiliationInfo><Affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Zhi-Zhong</ForeName><Initials>ZZ</Initials><AffiliationInfo><Affiliation>Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan, China Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chow</LastName><ForeName>Wang-Ngai</ForeName><Initials>WN</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-1275-2464</Identifier><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Rachel Y Y</ForeName><Initials>RY</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ahmed</LastName><ForeName>Syed Shakeel</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yeung</LastName><ForeName>Hazel C</ForeName><Initials>HC</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lam</LastName><ForeName>Carol S F</ForeName><Initials>CS</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cai</LastName><ForeName>Jian-Piao</ForeName><Initials>JP</Initials><AffiliationInfo><Affiliation>Department of Microbiology, The University of Hong Kong, Hong Kong, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Samson S 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