Serving the Society Since 1986
Advanced Search
Volume 36 Issue 3
June 2021
    Citation: Wentao Zhu, Jing Yang, Shan Lu, Ruiting Lan, Dong Jin, Xue-lian Luo, Ji Pu, Shusheng Wu, Jianguo Xu. Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China .VIROLOGICA SINICA, 2021, 36(3) : 402-411.  http://dx.doi.org/10.1007/s12250-020-00325-z
    shu

    Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China

    cstr: 32224.14.s12250-020-00325-z
    • 1.

      State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China

    • 2.

      Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China

    • 3.

      Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China

    • 4.

      School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia

    • 5.

      Yushu Prefecture Center for Disease Control and Prevention, Yushu 815000, China

    • 6.

      Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing 100191, China

    • Corresponding author: Jianguo Xu, xujianguo@icdc.cn, ORCID: 0000-0003-3649-8229
    • Received Date: 03 August 2020
      Accepted Date: 27 September 2020
      Published Date: 01 December 2020
      Available online: 01 June 2021

    • Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.

    • 加载中

      1. Chen Q, Gauger P, Stafne M, Thomas J, Arruda P, Burrough E, Madson D, Brodie J, Magstadt D, Derscheid R, Welch M, Zhang J (2015) Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets. Virology 482:51–59
          doi: 10.1016/j.virol.2015.03.024

      2. Chen Q, Wang L, Yang C, Zheng Y, Gauger PC, Anderson T, Harmon KM, Zhang J, Yoon KJ, Main RG, Li G (2018) The emergence of novel sparrow deltacoronaviruses in the United States more closely related to porcine deltacoronaviruses than sparrow deltacoronavirus HKU17. Emerg Microbes Infect 7:105

      3. Dai X, Shang G, Lu S, Yang J, Xu J (2018) A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau. China Emerg Microbes Infect 7:74

      4. Drosten C, Günther S, Preiser W, van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RA, Berger A, Burguière AM, Cinatl J, Eickmann M, Escriou N, Grywna K, Kramme S, Manuguerra JC, Müller S, Rickerts V, Stürmer M, Vieth S, Klenk HD, Osterhaus AD, Schmitz H, Doerr HW (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967–1976
          doi: 10.1056/NEJMoa030747

      5. Ge P, Xi J, Ding J, Jin F, Zhang H, Guo L, Zhang J, Li J, Gan Z, Wu B, Liang J, Wang X, Wang X (2015) Primary case of human pneumonic plague occurring in a Himalayan marmot natural focus area Gansu Province, China. Int J Infect Dis 33:67–70
          doi: 10.1016/j.ijid.2014.12.044

      6. Ge XY, Yang WH, Zhou JH, Li B, Zhang W, Shi ZL, Zhang YZ (2017) Detection of alpha- and betacoronaviruses in rodents from Yunnan. China Virol J 14:98
          doi: 10.1186/s12985-017-0766-9

      7. Ge Y, Yang J, Lai XH, Zhang G, Jin D, Lu S, Wang B, Huang Y, Huang Y, Ren Z, Zhang X, Xu J (2020) Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content. Int J Syst Evol Microbiol 70:2493–2498

      8. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652
          doi: 10.1038/nbt.1883

      9. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321
          doi: 10.1093/sysbio/syq010

      10. Herrewegh AA, Smeenk I, Horzinek MC, Rottier PJ, de Groot RJ (1998) Feline coronavirus type Ⅱ strains 79–1683 and 79–1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J Virol 72:4508–4514
          doi: 10.1128/JVI.72.5.4508-4514.1998

      11. Jung K, Hu H, Eyerly B, Lu Z, Chepngeno J, Saif LJ (2015) Pathogenicity of 2 porcine deltacoronavirus strains in gnotobiotic pigs. Emerg Infect Dis 21:650–654
          doi: 10.3201/eid2104.141859

      12. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
          doi: 10.1093/molbev/mst010

      13. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6:29
          doi: 10.1186/1471-2148-6-29

      14. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360
          doi: 10.1038/nmeth.3317

      15. Lai MM, Cavanagh D (1997) The molecular biology of coronaviruses. Adv Virus Res 48:1–100

      16. Lau SK, Wernery R, Wong EY, Joseph S, Tsang AK, Patteril NA, Elizabeth SK, Chan KH, Muhammed R, Kinne J, Yuen KY, Wernery U, Woo PC (2016) Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates. Emerg Microbes Infect 5:e128

      17. Lau SK, Woo PC, Li KS, Tsang AK, Fan RY, Luk HK, Cai JP, Chan KH, Zheng BJ, Wang M, Yuen KY (2015) Discovery of a novel coronavirus, China Rattus coronavirus HKU24, from Norway rats supports the murine origin of Betacoronavirus 1 and has implications for the ancestor of Betacoronavirus lineage A. J Virol 89:3076–3092
          doi: 10.1128/JVI.02420-14

      18. Lau SK, Woo PC, Yip CC, Fan RY, Huang Y, Wang M, Guo R, Lam CS, Tsang AK, Lai KK, Chan KH, Che XY, Zheng BJ, Yuen KY (2012) Isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14, from domestic rabbits. J Virol 86:5481–5496
          doi: 10.1128/JVI.06927-11

      19. Lau SKP, Wong EYM, Tsang CC, Ahmed SS, Au-Yeung RKH, Yuen KY, Wernery U, Woo PCY (2018) Discovery and sequence analysis of four deltacoronaviruses from birds in the middle east reveal interspecies jumping with recombination as a potential mechanism for avian-to-avian and avian-to-mammalian transmission. J Virol 92:e00265-18

      20. Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242-245
          doi: 10.1093/nar/gkw290

      21. Luo XL, Lu S, Jin D, Yang J, Wu SS, Xu J (2018) Marmota himalayana in the Qinghai-Tibetan plateau as a special host for bi-segmented and unsegmented picobirnaviruses. Emerg Microbes Infect 7:20

      22. Ma Y, Zhang Y, Liang X, Lou F, Oglesbee M, Krakowka S, Li J (2015) Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. mBio 6:e00064

      23. Moreno A, Franzo G, Massi P, Tosi G, Blanco A, Antilles N, Biarnes M, Majó N, Nofrarías M, Dolz R, Lelli D, Sozzi E, Lavazza A, Cecchinato M (2017) A novel variant of the infectious bronchitis virus resulting from recombination events in Italy and Spain. Avian Pathol 46:28–35
          doi: 10.1080/03079457.2016.1200011

      24. Phan LT, Nguyen TV, Luong QC, Nguyen TV, Nguyen HT, Le HQ, Nguyen TT, Cao TM, Pham QD (2020) Importation and human-to-human transmission of a novel coronavirus in Vietnam. N Engl J Med 382:872–874
          doi: 10.1056/NEJMc2001272

      25. Phan MVT, Ngo Tri T, Hong Anh P, Baker S, Kellam P, Cotten M (2018) Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Virus Evol 4: vey035

      26. Saetre GP, Borge T, Lindell J, Moum T, Primmer CR, Sheldon BC, Haavie J, Johnsen A, Ellegren H (2001) Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers. Mol Ecol 10:737–749

      27. Shi ZL, Guo D, Rottier PJ (2016) Coronavirus: epidemiology, genome replication and the interactions with their hosts. Virol Sin 31:1–2
          doi: 10.1007/s12250-016-3746-0

      28. Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phylogenet Evol 12:105–114
          doi: 10.1006/mpev.1998.0602

      29. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 110. Virus Evol 4: vey016

      30. Wang L, Byrum B, Zhang Y (2014) Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014. Emerg Infect Dis 20:1227–1230

      31. Wang W, Lin XD, Guo WP, Zhou RH, Wang MR, Wang CQ, Ge S, Mei SH, Li MH, Shi M, Holmes EC, Zhang YZ (2015) Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China. Virology 474:19–27
          doi: 10.1016/j.virol.2014.10.017

      32. 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 (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
          doi: 10.1128/JVI.06540-11

      33. Woo PC, Lau SK, Yip CC, Huang Y, Tsoi HW, Chan KH, Yuen KY (2006) Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1. J Virol 80:7136–7145
          doi: 10.1128/JVI.00509-06

      34. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265–269
          doi: 10.1038/s41586-020-2008-3

      35. Wu Z, Lu L, Du J, Yang L, Ren X, Liu B, Jiang J, Yang J, Dong J, Sun L, Zhu Y, Li Y, Zheng D, Zhang C, Su H, Zheng Y, Zhou H, Zhu G, Li H, Chmura A, Yang F, Daszak P, Wang J, Liu Q, Jin Q (2018) Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases. Microbiome 6:178
          doi: 10.1186/s40168-018-0554-9

      36. Xu L, Zhang F, Yang W, Jiang T, Lu G, He B, Li X, Hu T, Chen G, Feng Y, Zhang Y, Fan Q, Feng J, Zhang H, Tu C (2016) Detection and characterization of diverse alpha- and betacoronaviruses from bats in China. Virol Sin 31:69–77
          doi: 10.1007/s12250-016-3727-3

      37. 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
          doi: 10.1056/NEJMoa1211721

      38. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270–273
          doi: 10.1038/s41586-020-2012-7

    • 加载中

    Figures(5) / Tables(3)

    PDF

    Article Metrics

    Article views(22578) PDF downloads(27) Cited by()

    Related
    Proportional views

      Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China

        Corresponding author: Jianguo Xu, xujianguo@icdc.cn
      • 1. State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
      • 2. Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
      • 3. Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China
      • 4. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
      • 5. Yushu Prefecture Center for Disease Control and Prevention, Yushu 815000, China
      • 6. Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing 100191, China
      • Received Date: 03 August 2020
      • Accepted Date: 27 September 2020
      • Published Date: 01 December 2020

      Abstract: 

      Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2). Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus (beta-CoV) genome and a novel delta-coronavirus (delta-CoV) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-CoV shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-CoV (MtCoV) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-CoV showed highest amino acid identity to Sparrow coronavirus HKU17 (73.1%). Interestingly, our results identified a novel host (Montifringilla taczanowskii) for the novel delta-CoV and the potential cross-species transmission. The most recent common ancestor (tMRCA) of MtCoVs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-CoVs and delta-CoVs, and also provides a new perspective of the coronavirus hosts.

        HTML

      Introduction