Science China Life Sciences

, Volume 59, Issue 6, pp 604–614 | Cite as

Genetic diversity of coronaviruses in Miniopterus fuliginosus bats

  • Jiang Du
  • Li Yang
  • Xianwen Ren
  • Junpeng Zhang
  • Jie Dong
  • Lilian Sun
  • Yafang Zhu
  • Fan Yang
  • Shuyi Zhang
  • Zhiqiang WuEmail author
  • Qi JinEmail author
Open Access
Research Paper


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.


coronavirus Miniopterus fuliginosus bat co-infection recombination 


  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., and Zdobnov, E.M. (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 29, 37–40.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. (2002). The Pfam protein families database. Nucleic Acids Res 30, 276–280.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bosch, B.J., van der Zee, R., de Haan, C.A., and Rottier, P.J. (2003). The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol 77, 8801–8811.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Chen, L.L., Ou, H.Y., Zhang, R., and Zhang, C.T. (2003). 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 307, 382–388.CrossRefPubMedGoogle Scholar
  5. Chu, D.K., Peiris, J.S., Chen, H., Guan, Y., and Poon, L.L. (2008). Genomic characterizations of bat coronaviruses (1A, 1B and HKU8) and evidence for co-infections in Miniopterus bats. J Gen Virol 89, 1282–1287.CrossRefPubMedGoogle Scholar
  6. Cui, J., Han, N., Streicker, D., Li, G., Tang, X., Shi, Z., Hu, Z., Zhao, G., Fontanet, A., Guan, Y., Wang, L., Jones, G., Field, H.E., Daszak, P., and Zhang, S. (2007). Evolutionary relationships between bat coronaviruses and their hosts. Emerg Infect Dis 13, 1526–1532.CrossRefPubMedPubMedCentralGoogle Scholar
  7. King, A.M.Q., Adams, M.J., Carstens, E.B. (2011). Virus Taxonomy, Classification and Nomenclature of Viruses. Ninth Report of the International Committee on Taxonomy of Viruses, International Union of Microbiological Societies, Virology Division. London: Elsevier Academic Press, 806–828.Google Scholar
  8. Dveksler, G.S., Pensiero, M.N., Cardellichio, C.B., Williams, R.K., Jiang, G.S., Holmes, K.V., and Dieffenbach, C.W. (1991). Cloning of the mouse hepatitis virus (MHV) receptor: expression in humaaan and hamster cell lines confers susceptibility to MHV. J Virol 65, 6881–6891.PubMedPubMedCentralGoogle Scholar
  9. Gonzalez, J.M., Gomez-Puertas, P., Cavanagh, D., Gorbalenya, A.E., and Enjuanes, L. (2003). A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch Virol 148, 2207–2235.CrossRefPubMedGoogle Scholar
  10. Graham, R.L., and Baric, R.S. (2010). Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol 84, 3134–3146.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59, 307–321.CrossRefPubMedGoogle Scholar
  12. Herrewegh, A.A., Smeenk, I., Horzinek, M.C., Rottier, P.J., and de Groot, R.J. (1998). Feline coronavirus type IIstrains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J Virol 72, 4508–4514.PubMedPubMedCentralGoogle Scholar
  13. Holmes, K.V., and Enjuanes, L. (2003). Virology. The SARS coronavirus: a postgenomic era. Science 300, 1377–1378.PubMedGoogle Scholar
  14. Jonassen, C.M., Kofstad, T., Larsen, I.L., Lovland, A., Handeland, K., Follestad, A., and Lillehaug, A. (2005). Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos). J Gen Virol 86, 1597–1607.CrossRefPubMedGoogle Scholar
  15. Kosakovsky Pond, S.L., Posada, D., Gravenor, M.B., Woelk, C.H., and Frost, S.D. (2006). GARD: a genetic algorithm for recombination detection. Bioinformatics 22, 3096–3098.CrossRefPubMedGoogle Scholar
  16. Lai, M.M. (1990). Coronavirus: organization, replication and expression of genome. Annu Rev Microbiol 44, 303–333.CrossRefPubMedGoogle Scholar
  17. Lai, M.M., and Cavanagh, D. (1997). The molecular biology of coronaviruses. Adv Virus Res 48, 1–100.CrossRefPubMedGoogle Scholar
  18. Lai, M.M.C., and Holmes, K.V. (2001). Coronaviruses. In: Knipe, D.M., Howley, P.M., Griffin, D.E., Lamb, R.A., Martin, M.A., Roizman, B., and Straus, S.E., eds. Fields Virology. Philadelphia: Lippincott Williams & Wilkins 1163–1185.Google Scholar
  19. Lau, S.K., Li, K.S., Tsang, A.K., Shek, C.T., Wang, M., Choi, G.K., Guo, R., Wong, B.H., Poon, R.W., Lam, C.S., Wang, S.Y., Fan, R.Y., Chan, K.H., Zheng, B.J., Woo, P.C., and Yuen, K.Y. (2012a). Recent trans mission of a novel alphacoronavirus, bat coronavirus HKU10, from Leschenault’s rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders. J Virol 86, 11906–11918.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Lau, S.K., Woo, P.C., Li, K.S., Huang, Y., Tsoi, H.W., Wong, B.H., Wong, S.S., Leung, S.Y., Chan, K.H., and Yuen, K.Y. (2005). Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA 102, 14040–14045.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Lau, S.K., Woo, P.C., Li, K.S., Huang, Y., Wang, M., Lam, C.S., Xu, H., Guo, R., Chan, K.H., Zheng, B.J., and Yuen, K.Y. (2007). Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology 367, 428–439.CrossRefPubMedGoogle Scholar
  22. Lau, S.K., Woo, P.C., Yip, C.C., Fan, R.Y., Huang, Y., Wang, M., Guo, R., Lam, C.S., Tsang, A.K., Lai, K.K., Chan, K.H., Che, X.Y., Zheng, B.J., and Yuen, K.Y. (2012b). Isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14, from domestic rabbits. J Virol 86, 5481–5496.CrossRefPubMedPubMedCentralGoogle Scholar
  23. Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J.H., Wang, H., Crameri, G., Hu, Z., Zhang, H., Zhang, J., McEachern, J., Field, H., Daszak, P., Eaton, B.T., Zhang, S., and Wang, L.F. (2005). Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679.CrossRefPubMedGoogle Scholar
  24. Liu, S., Chen, J., Kong, X., Shao, Y., Han, Z., Feng, L., Cai, X., Gu, S., and Liu, M. (2005). Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas). J Gen Virol 86, 719–725.CrossRefPubMedGoogle Scholar
  25. Makino, S., Keck, J.G., Stohlman, S.A., and Lai, M.M. (1986). High-frequency RNA recombination of murine coronaviruses. J Virol 57, 729–737.PubMedPubMedCentralGoogle Scholar
  26. Miller-Butterworth, C.M., Jacobs, D.S., and Harley, E.H. (2003). Strong population substructure is correlated with morphology and ecology in a migratory bat. Nature 424, 187–191.CrossRefPubMedGoogle Scholar
  27. Rest, J.S., and Mindell, D.P. (2003). SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infect Genet Evol 3, 219–225.CrossRefPubMedGoogle Scholar
  28. Shirato, K., Maeda, K., Tsuda, S., Suzuki, K., Watanabe, S., Shimoda, H., Ueda, N., Iha, K., Taniguchi, S., Kyuwa, S., Endoh, D., Matsuyama, S., Kurane, I., Saijo, M., Morikawa, S., Yoshikawa, Y., Akashi, H., and Mizutani, T. (2012). Detection of bat coronaviruses from Miniopterus fuliginosus in Japan. Virus Genes 44, 40–44.CrossRefPubMedGoogle Scholar
  29. Song, H.D., Tu, C.C., Zhang, G.W., Wang, S.Y., Zheng, K., Lei, L.C., Chen, Q.X., Gao, Y.W., Zhou, H.Q., Xiang, H., Zheng, H.J., Chern, S.W., Cheng, F., Pan, C.M., Xuan, H., Chen, S.J., Luo, H.M., Zhou, D.H., Liu, Y.F., He, J.F., Qin, P.Z., Li, L.H., Ren, Y.Q., Liang, W.J., Yu, Y.D., Anderson, L., Wang, M., Xu, R.H., Wu, X.W., Zheng, H.Y., Chen, J.D., Liang, G., Gao, Y., Liao, M., Fang, L., Jiang, L.Y., Li, H., Chen, F., Di, B., He, L.J., Lin, J.Y., Tong, S., Kong, X., Du, L., Hao, P., Tang, H., Bernini, A., Yu, X.J., Spiga, O., Guo, Z.M., Pan, H.Y., He, W.Z., Manuguerra, J.C., Fontanet, A., Danchin, A., Niccolai, N., Li, Y.X., Wu, C.I., and Zhao, G.P. (2005). Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci USA 102, 2430–2435.CrossRefPubMedPubMedCentralGoogle Scholar
  30. Sonnhammer, E.L., von Heijne, G., and Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6, 175–182.PubMedGoogle Scholar
  31. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731–2739.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Tang, X.C., Zhang, J.X., Zhang, S.Y., Wang, P., Fan, X.H., Li, L.F., Li, G., Dong, B.Q., Liu, W., Cheung, C.L., Xu, K.M., Song, W.J., Vijaykrishna, D., Poon, L.L., Peiris, J.S., Smith, G.J., Chen, H., and Guan, Y. (2006). Prevalence and genetic diversity of coronaviruses in bats from China. J Virol 80, 7481–7490.CrossRefPubMedPubMedCentralGoogle Scholar
  33. van Boheemen, S., de Graaf, M., Lauber, C., Bestebroer, T.M., Raj, V.S., Zaki, A.M., Osterhaus, A.D., Haagmans, B.L., Gorbalenya, A.E., Snijder, E.J., and Fouchier, R.A. (2012). Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. MBio doi: 10.1128/mBio.00473-12.Google Scholar
  34. Vijaykrishna, D., Smith, G.J., Zhang, J.X., Peiris, J.S., Chen, H., and Guan, Y. (2007). Evolutionary insights into the ecology of coronaviruses. J Virol 81, 4012–4020.CrossRefPubMedPubMedCentralGoogle Scholar
  35. Weiss, S.R., and Navas-Martin, S. (2005). Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol Mol Biol Rev 69, 635–664.CrossRefPubMedPubMedCentralGoogle Scholar
  36. Woo, P.C., Lau, S.K., Lam, C.S., Lai, K.K., Huang, Y., Lee, P., Luk, G.S., Dyrting, K.C., Chan, K.H., and Yuen, K.Y. (2009). Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus. J Virol 83, 908–917.CrossRefPubMedPubMedCentralGoogle Scholar
  37. Woo, P.C., Lau, S.K., Lam, C.S., Lau, C.C., Tsang, A.K., Lau, J.H., Bai, R., Teng, J.L., Tsang, C.C., Wang, M., Zheng, B.J., Chan, K.H., and Yuen, K.Y. (2012). Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol 86, 3995–4008.CrossRefPubMedPubMedCentralGoogle Scholar
  38. Woo, P.C., Lau, S.K., Li, K.S., Poon, R.W., Wong, B.H., Tsoi, H.W., Yip, B.C., Huang, Y., Chan, K.H., and Yuen, K.Y. (2006a). Molecular diversity of coronaviruses in bats. Virology 351, 180–187.CrossRefPubMedGoogle Scholar
  39. Woo, P.C., Lau, S.K., Yip, C.C., Huang, Y., Tsoi, H.W., Chan, K.H., and Yuen, K.Y. (2006b). Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1. J Virol 80, 7136–7145.CrossRefPubMedPubMedCentralGoogle Scholar
  40. Woo, P.C., Lau, S.K., and Yuen, K.Y. (2006c). Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections. Curr Opin Infect Dis 19, 401–407.CrossRefPubMedGoogle Scholar
  41. Woo, P.C., Lau, S.K., Huang, Y., and Yuen, K.Y. (2009). Coronavirus diversity, phylogeny and interspecies jumping. Exp Biol Med 234, 1117–1127.CrossRefGoogle Scholar
  42. Woo, P.C., Lau, S.K., and Yuen, K.Y. (2006). Infectious diseases emerging from Chinese wet-markets: zoonotic origins of severe respiratory viral infections. Curr Opin Infect Dis 19, 401–407.CrossRefPubMedGoogle Scholar
  43. Wu, Z., Yang, L., Ren, X., He, G., Zhang, J., Yang, J., Qian, Z., Dong, J., Sun, L., Zhu, Y., Du, J., Yang, F., Zhang, S., and Jin, Q. (2015). Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J 10, 609–620.CrossRefPubMedGoogle Scholar
  44. Zeng, Q., Langereis, M.A., van Vliet, A.L., Huizinga, E.G., and de Groot, R.J. (2008). Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution. Proc Natl Acad Sci USA 105, 9065–9069.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© The Author(s) 2016

Authors and Affiliations

  • Jiang Du
    • 1
  • Li Yang
    • 1
  • Xianwen Ren
    • 1
  • Junpeng Zhang
    • 4
  • Jie Dong
    • 1
  • Lilian Sun
    • 1
  • Yafang Zhu
    • 1
  • Fan Yang
    • 1
  • Shuyi Zhang
    • 3
  • Zhiqiang Wu
    • 1
    Email author
  • Qi Jin
    • 1
    • 2
    Email author
  1. 1.MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
  2. 2.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhouChina
  3. 3.College of Animal Science and Veterinary MedicineShenyang Agricultural UniversityShenyangChina
  4. 4.State Key Laboratory of Estuarine and Coastal Research, Institute of Estuarine and Coastal ResearchEast China Normal UniversityShanghaiChina

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