Virologica Sinica

, Volume 31, Issue 1, pp 31–40 | Cite as

Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft

  • Xing-Yi Ge
  • Ning Wang
  • Wei Zhang
  • Ben Hu
  • Bei Li
  • Yun-Zhi Zhang
  • Ji-Hua Zhou
  • Chu-Ming Luo
  • Xing-Lou Yang
  • Li-Jun Wu
  • Bo Wang
  • Yun Zhang
  • Zong-Xiao Li
  • Zheng-Li Shi
Research Article

Abstract

Since the 2002–2003 severe acute respiratory syndrome (SARS) outbreak prompted a search for the natural reservoir of the SARS coronavirus, numerous alpha- and betacoronaviruses have been discovered in bats around the world. Bats are likely the natural reservoir of alpha- and betacoronaviruses, and due to the rich diversity and global distribution of bats, the number of bat coronaviruses will likely increase. We conducted a surveillance of coronaviruses in bats in an abandoned mineshaft in Mojiang County, Yunnan Province, China, from 2012–2013. Six bat species were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus fuliginosus, and Miniopterus fuscus. By sequencing PCR products of the coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high frequency of infection by a diverse group of coronaviruses in different bat species in the mineshaft. Sequenced partial RdRp fragments had 80%–99% nucleic acid sequence identity with well-characterized Alphacoronavirus species, including BtCoV HKU2, BtCoV HKU8, and BtCoV1, and unassigned species BtCoV HKU7 and BtCoV HKU10. Additionally, the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species. Furthermore, coronavirus co-infection was detected in all six bat species, a phenomenon that fosters recombination and promotes the emergence of novel virus strains. Our findings highlight the importance of bats as natural reservoirs of coronaviruses and the potentially zoonotic source of viral pathogens.

Keywords

coronavirus bat coinfection mineshaft 

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References

  1. Anthony SJ, Ojeda-Flores R, Rico-Chavez O, Navarrete-Macias I, Zambrana-Torrelio CM, Rostal MK, Epstein JH, Tipps T, Liang E, Sanchez-Leon M, Sotomayor-Bonilla J, Aguirre AA, Avila-Flores R, Medellin RA, Goldstein T, Suzan G, Daszak P, Lipkin WI. 2013. Coronaviruses in bats from Mexico. J Gen Virol, 94: 1028–1038.PubMedCentralCrossRefPubMedGoogle Scholar
  2. Baker ML, Schountz T, Wang LF. 2013. Antiviral immune responses of bats: a review. Zoonoses Public Health, 60: 104–116.CrossRefPubMedGoogle Scholar
  3. Bruckova M, McIntosh K, Kapikian AZ, Chanock RM. 1970. The adaptation of two human coronavirus strains (OC38 and OC43) to growth in cell monolayers. Proc Soc Exp Biol Med, 135: 431–435.CrossRefPubMedGoogle Scholar
  4. Cavanagh D, Britton P. 2012. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Family Coronaviridae. In: International Committee on Taxonomy of Viruses. Andrew M.Q. King MJA, Eric B. Carstens, and Elliot J. Lefkowitz (eds). Cambridge: Academic Press Elsevier, pp. 770–792.Google Scholar
  5. Chu DK, Peiris JS, Chen H, Guan Y, Poon LL. 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. Chu DK, Poon LL, Chan KH, Chen H, Guan Y, Yuen KY, Peiris JS. 2006. Coronaviruses in bent-winged bats (Miniopterus spp.). J Gen Virol, 87: 2461–2466.CrossRefPubMedGoogle Scholar
  7. Corman VM, Ithete NL, Richards LR, Schoeman MC, Preiser W, Drosten C, Drexler JF. 2014. Rooting the phylogenetic tree of Middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat. J Virol, 88: 11297–11303.PubMedCentralCrossRefPubMedGoogle Scholar
  8. De Benedictis P, Marciano S, Scaravelli D, Priori P, Zecchin B, Capua I, Monne I, Cattoli G. 2013. Alpha and lineage C beta-CoV infections in Italian bats. Virus Genes, 48: 366–371.CrossRefPubMedGoogle Scholar
  9. de Souza Luna LK, Heiser V, Regamey N, Panning M, Drexler JF, Mulangu S, Poon L, Baumgarte S, Haijema BJ, Kaiser L, Drosten C. 2007. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray. J Clin Microbiol, 45: 1049–1052.PubMedCentralCrossRefPubMedGoogle Scholar
  10. Drexler JF, Corman VM, Wegner T, Tateno AF, Zerbinati RM, Gloza-Rausch F, Seebens A, Muller MA, Drosten C. 2011. Amplification of emerging viruses in a bat colony. Emerg Infect Dis, 17: 449–456.PubMedCentralCrossRefPubMedGoogle Scholar
  11. Drexler JF, Gloza-Rausch F, Glende J, Corman VM, Muth D, Goettsche M, Seebens A, Niedrig M, Pfefferle S, Yordanov S, Zhelyazkov L, Hermanns U, Vallo P, Lukashev A, Muller MA, Deng H, Herrler G, Drosten C. 2010. Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. J Virol, 84: 11336–11349.PubMedCentralCrossRefPubMedGoogle Scholar
  12. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C, Zhang YJ, Luo CM, Tan B, Wang N, Zhu Y, Crameri G, Zhang SY, Wang LF, Daszak P, Shi ZL. 2013. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature, 503: 535–538.CrossRefPubMedGoogle Scholar
  13. Geldenhuys M, Weyer J, Nel LH, Markotter W. 2013. Coronaviruses in South african bats. Vector Borne Zoonotic Dis, 13: 516–519.CrossRefPubMedGoogle Scholar
  14. Goes LG, Ruvalcaba SG, Campos AA, Queiroz LH, de Carvalho C, Jerez JA, Durigon EL, Davalos LI, Dominguez SR. 2013. Novel bat coronaviruses, Brazil and Mexico. Emerg Infect Dis, 19: 1711–1713.PubMedCentralCrossRefPubMedGoogle Scholar
  15. Gouilh MA, Puechmaille SJ, Gonzalez JP, Teeling E, Kittayapong P, Manuguerra JC. 2011. SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory. Infect Genet Evol, 11: 1690–1702.CrossRefPubMedGoogle Scholar
  16. Graham RL, Donaldson EF, Baric RS. 2013. A decade after SARS: strategies for controlling emerging coronaviruses. Nat Rev Microbiol, 11: 836–848.CrossRefPubMedGoogle Scholar
  17. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser (Oxf), 41: 95–98.Google Scholar
  18. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754–755.CrossRefPubMedGoogle Scholar
  19. Irwin DM, Kocher TD, Wilson AC. 1991. Evolution of the Cytochrome-B Gene of Mammals. J Mol Evol, 32: 128–144.CrossRefPubMedGoogle Scholar
  20. Kusanagi K, Kuwahara H, Katoh T, Nunoya T, Ishikawa Y, Samejima T, Tajima M. 1992. Isolation and serial propagation of porcine epidemic diarrhea virus in cell cultures and partial characterization of the isolate. J Vet Med Sci, 54: 313–318.CrossRefPubMedGoogle Scholar
  21. Lai MMC, Perlman S, Anderson LJ. 2007. Coronaviridae. In: Fields Virology, Knipe DM, Howley PM (eds). Philadephia: Lippincott Williams & Wilkins, pp. 1305–1336.Google Scholar
  22. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23: 2947–2948.CrossRefPubMedGoogle Scholar
  23. Lau SK, Li KS, Tsang AK, Lam CS, Ahmed S, Chen H, Chan KH, Woo PC, Yuen KY. 2013. Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus. J Virol, 87: 8638–8650.PubMedCentralCrossRefPubMedGoogle Scholar
  24. Lau SK, Li KS, Tsang AK, Shek CT, Wang M, Choi GK, Guo R, Wong BH, Poon RW, Lam CS, Wang SY, Fan RY, Chan KH, Zheng BJ, Woo PC, Yuen KY. 2012. Recent transmission 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.PubMedCentralCrossRefPubMedGoogle Scholar
  25. Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, Wong SS, Leung SY, Chan KH, Yuen KY. 2005. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A, 102: 14040–14045.PubMedCentralCrossRefPubMedGoogle Scholar
  26. Lau SKP, Woo PCY, Li KSM, Huang Y, Wang M, Lam CSF, Xu HF, Guo RT, Chan KH, Zheng BJ, Yuen KY. 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
  27. Lelli D, Papetti A, Sabelli C, Rosti E, Moreno A, Boniotti MB. 2013. Detection of coronaviruses in bats of various species in Italy. Viruses, 5: 2679–2689.PubMedCentralCrossRefPubMedGoogle Scholar
  28. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang LF. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science, 310: 676–679.CrossRefPubMedGoogle Scholar
  29. Luis AD, Hayman DTS, O'Shea TJ, Cryan PM, Gilbert AT, Pulliam JRC, Mills JN, Timonin ME, Willis CKR, Cunningham AA, Fooks AR, Rupprecht CE, Wood JLN, Webb CT. 2013. A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci, 280: 20122753.PubMedCentralCrossRefPubMedGoogle Scholar
  30. Macnaughton MR, Madge MH. 1978. The genome of human coronavirus strain 229E. J Gen Virol, 39: 497–504.CrossRefPubMedGoogle Scholar
  31. Martin DP, Williamson C, Posada D. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics, 21: 260–262.CrossRefPubMedGoogle Scholar
  32. Mayer F, von Helversen O. 2001. Cryptic diversity in European bats. Proc Biol Sci, 268: 1825–1832.PubMedCentralCrossRefPubMedGoogle Scholar
  33. Mihindukulasuriya KA, Wu G, St Leger J, Nordhausen RW, Wang D. 2008. Identification of a novel coronavirus from a beluga whale by using a panviral microarray. J Virol, 82: 5084–5088.PubMedCentralCrossRefPubMedGoogle Scholar
  34. Mizutani T. 2001. The mechanism of MHV transcription. Uirusu, 51: 225–236. (In Janpanese)CrossRefPubMedGoogle Scholar
  35. Pedersen NC, Black JW, Boyle JF, Evermann JF, McKeirnan AJ, Ott RL. 1984. Pathogenic differences between various feline coronavirus isolates. Adv Exp Med Biol, 173: 365–380.CrossRefPubMedGoogle Scholar
  36. Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W, Nicholls J, Yee WK, Yan WW, Cheung MT, Cheng VC, Chan KH, Tsang DN, Yung RW, Ng TK, Yuen KY. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet, 361: 1319–1325.CrossRefPubMedGoogle Scholar
  37. Poon LL, Chu DK, Chan KH, Wong OK, Ellis TM, Leung YH, Lau SK, Woo PC, Suen KY, Yuen KY, Guan Y, Peiris JS. 2005. Identification of a novel coronavirus in bats. J Virol, 79: 2001–2009.PubMedCentralCrossRefPubMedGoogle Scholar
  38. Quan PL, Firth C, Street C, Henriquez JA, Petrosov A, Tashmukhamedova A, Hutchison SK, Egholm M, Osinubi MO, Niezgoda M, Ogunkoya AB, Briese T, Rupprecht CE, Lipkin WI. 2010. Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria. MBio, 1. doi: 10.1128/mBio.00208-10.Google Scholar
  39. Shi ZL. 2013. Emerging infectious diseases associated with bat viruses. Science China-Life Sciences, 56: 678–682.CrossRefPubMedGoogle Scholar
  40. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, Li G, Dong BQ, Liu W, Cheung CL, Xu KM, Song WJ, Vijaykrishna D, Poon LLM, Peiris JSM, Smith GJD, Chen H, Guan Y. 2006. Prevalence and genetic diversity of coronaviruses in bats from China. J Virol, 80: 7481–7490.PubMedCentralCrossRefPubMedGoogle Scholar
  41. Tong S, Conrardy C, Ruone S, Kuzmin IV, Guo X, Tao Y, Niezgoda M, Haynes L, Agwanda B, Breiman RF, Anderson LJ, Rupprecht CE. 2009. Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg Infect Dis, 15: 482–485.PubMedCentralCrossRefPubMedGoogle Scholar
  42. van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ, Fouchier RA. 2012. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. MBio, 3. doi: 10.1128/mBio.00473-12.Google Scholar
  43. van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJ, Wolthers KC, Wertheim-van Dillen PM, Kaandorp J, Spaargaren J, Berkhout B. 2004. Identification of a new human coronavirus. Nat Med, 10: 368–373.CrossRefPubMedGoogle Scholar
  44. Wacharapluesadee S, Duengkae P, Rodpan A, Kaewpom T, Maneeorn P, Kanchanasaka B, Yingsakmongkon S, Sittidetboripat N, Chareesaen C, Khlangsap N, Pidthong A, Leadprathom K, Ghai S, Epstein JH, Daszak P, Olival KJ, Blair PJ, Callahan MV, Hemachudha T. 2015. Diversity of coronavirus in bats from Eastern Thailand. Virol J, 12: 57.PubMedCentralCrossRefPubMedGoogle Scholar
  45. Watanabe S, Masangkay JS, Nagata N, Morikawa S, Mizutani T, Fukushi S, Alviola P, Omatsu T, Ueda N, Iha K, Taniguchi S, Fujii H, Tsuda S, Endoh M, Kato K, Tohya Y, Kyuwa S, Yoshikawa Y, Akashi H. 2010. Bat Coronaviruses and Experimental Infection of Bats, the Philippines. Emerg Infect Dis, 16: 1217–1223.PubMedCentralCrossRefPubMedGoogle Scholar
  46. Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol, 79: 884–895.PubMedCentralCrossRefPubMedGoogle Scholar
  47. Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY. 2012a. 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.PubMedCentralCrossRefPubMedGoogle Scholar
  48. Woo PC, Lau SK, Li KS, Poon RW, Wong BH, Tsoi HW, Yip BC, Huang Y, Chan KH, Yuen KY. 2006. Molecular diversity of coronaviruses in bats. Virology, 351: 180–187.CrossRefPubMedGoogle Scholar
  49. Woo PCY, Lau SKP, Huang Y, Yuen KY. 2009. Coronavirus Diversity, Phylogeny and Interspecies Jumping. Exp Biol Med (Maywood), 234: 1117–1127.CrossRefGoogle Scholar
  50. Woo PCY, Lau SKP, Li KSM, Tsang AKL, Yuen KY. 2012b. Genetic relatedness of the novel human group C betacoronavirus to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5. Emerg Microb Infect, 1: e35.CrossRefGoogle Scholar
  51. Wu ZQ, Yang L, Yang F, Ren XW, Jiang JY, Dong J, Sun LL, Zhu YF, Zhou HN, Jin Q. 2014. Novel Henipa-like Virus, Mojiang Paramyxovirus, in rats, China, 2012. Emerg Infect Dis, 20: 1064–1066.PubMedCentralPubMedGoogle Scholar
  52. Yuan J, Hon CC, Li Y, Wang D, Xu G, Zhang H, Zhou P, Poon LL, Lam TT, Leung FC, Shi Z. 2010. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol, 91: 1058–1062.CrossRefPubMedGoogle Scholar
  53. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. 2012. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med, 367: 1814–1820.CrossRefPubMedGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer Science+Business Media Singapore 2016

Authors and Affiliations

  • Xing-Yi Ge
    • 1
  • Ning Wang
    • 1
  • Wei Zhang
    • 1
  • Ben Hu
    • 1
  • Bei Li
    • 1
  • Yun-Zhi Zhang
    • 2
    • 3
  • Ji-Hua Zhou
    • 2
  • Chu-Ming Luo
    • 1
  • Xing-Lou Yang
    • 1
  • Li-Jun Wu
    • 1
  • Bo Wang
    • 1
  • Yun Zhang
    • 4
  • Zong-Xiao Li
    • 4
  • Zheng-Li Shi
    • 1
  1. 1.Key Laboratory of Special Pathogens, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina
  2. 2.Yunnan Provincial Key Laboratory for Zoonosis Control and PreventionYunnan Institute of Endemic Diseases Control and PreventionDaliChina
  3. 3.School of Public HealthDali UniversityDaliChina
  4. 4.Mojiang Center for Diseases Control and PreventionMojiangChina

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