Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

doi:10.1007/s11427-016-5039-0

. 2016 Jun;59(6):604-14.

doi: 10.1007/s11427-016-5039-0. Epub 2016 Apr 28.

Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

Jiang Du¹, Li Yang¹, Xianwen Ren¹, Junpeng Zhang², Jie Dong¹, Lilian Sun¹, Yafang Zhu¹, Fan Yang¹, Shuyi Zhang³, Zhiqiang Wu⁴, Qi Jin^{5

6}

Affiliations

¹ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China.
² State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China.
³ College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
⁴ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China. wuzq2009@ipbcams.ac.cn.
⁵ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China. zdsys@vip.sina.com.
⁶ Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China. zdsys@vip.sina.com.

PMID: 27125516
PMCID: PMC7089092
DOI: 10.1007/s11427-016-5039-0

Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

Jiang Du et al. Sci China Life Sci. 2016 Jun.

. 2016 Jun;59(6):604-14.

doi: 10.1007/s11427-016-5039-0. Epub 2016 Apr 28.

Authors

Jiang Du¹, Li Yang¹, Xianwen Ren¹, Junpeng Zhang², Jie Dong¹, Lilian Sun¹, Yafang Zhu¹, Fan Yang¹, Shuyi Zhang³, Zhiqiang Wu⁴, Qi Jin^{5

6}

Affiliations

¹ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China.
² State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China.
³ College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
⁴ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China. wuzq2009@ipbcams.ac.cn.
⁵ MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China. zdsys@vip.sina.com.
⁶ Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China. zdsys@vip.sina.com.

PMID: 27125516
PMCID: PMC7089092
DOI: 10.1007/s11427-016-5039-0

Abstract

Coronaviruses, such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, pose significant public health threats. Bats have been suggested to act as natural reservoirs for both these viruses, and periodic monitoring of coronaviruses in bats may thus provide important clues about emergent infectious viruses. The Eastern bent-wing bat Miniopterus fuliginosus is distributed extensively throughout China. We therefore analyzed the genetic diversity of coronaviruses in samples of M. fuliginosus collected from nine Chinese provinces during 2011-2013. The only coronavirus genus found was Alphacoronavirus. We established six complete and five partial genomic sequences of alphacoronaviruses, which revealed that they could be divided into two distinct lineages, with close relationships to coronaviruses in Miniopterus magnater and Miniopterus pusillus. Recombination was confirmed by detecting putative breakpoints of Lineage 1 coronaviruses in M. fuliginosus and M. pusillus (Wu et al., 2015), which supported the results of topological and phylogenetic analyses. The established alphacoronavirus genome sequences showed high similarity to other alphacoronaviruses found in other Miniopterus species, suggesting that their transmission in different Miniopterus species may provide opportunities for recombination with different alphacoronaviruses. The genetic information for these novel alphacoronaviruses will improve our understanding of the evolution and genetic diversity of coronaviruses, with potentially important implications for the transmission of human diseases.

Keywords: Miniopterus fuliginosus; bat; co-infection; coronavirus; recombination.

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[1] Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001;29:37–40. doi: 10.1093/nar/29.1.37. - DOI - PMC - PubMed

[2] Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001;29:37–40. doi: 10.1093/nar/29.1.37. - DOI - PMC - PubMed

[3] Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 2002;30:276–280. doi: 10.1093/nar/30.1.276. - DOI - PMC - PubMed

[4] Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 2002;30:276–280. doi: 10.1093/nar/30.1.276. - DOI - PMC - PubMed

[5] Bosch B.J., van der Zee R., de Haan C.A., Rottier P.J. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol. 2003;77:8801–8811. doi: 10.1128/JVI.77.16.8801-8811.2003. - DOI - PMC - PubMed

[6] Bosch B.J., van der Zee R., de Haan C.A., Rottier P.J. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol. 2003;77:8801–8811. doi: 10.1128/JVI.77.16.8801-8811.2003. - DOI - PMC - PubMed

[7] Chen L.L., Ou H.Y., Zhang R., Zhang C.T. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun. 2003;307:382–388. doi: 10.1016/S0006-291X(03)01192-6. - DOI - PMC - PubMed

[8] Chen L.L., Ou H.Y., Zhang R., Zhang C.T. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun. 2003;307:382–388. doi: 10.1016/S0006-291X(03)01192-6. - DOI - PMC - PubMed

[9] Chu D.K., Peiris J.S., Chen H., Guan Y., Poon L.L. Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats. J Gen Virol. 2008;89:1282–1287. doi: 10.1099/vir.0.83605-0. - DOI - PubMed

[10] Chu D.K., Peiris J.S., Chen H., Guan Y., Poon L.L. Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats. J Gen Virol. 2008;89:1282–1287. doi: 10.1099/vir.0.83605-0. - DOI - PubMed

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Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

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Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

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