Etiology of epidemic outbreaks COVID-19 in Wuhan, Hubei province, Chinese People Republic associated with 2019-nCoV (Nidovirales, Coronaviridae, Coronavirinae, Betacoronavirus, Subgenus Sarbecovirus): lessons of SARS-CoV outbreak
- Authors: Lvov D.K.1, Alkhovsky S.V.1, Kolobukhina L.V.1, Burtseva E.I.1
-
Affiliations:
- D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
- Issue: Vol 65, No 1 (2020)
- Pages: 6-15
- Section: REVIEWS
- URL: https://journals.rcsi.science/0507-4088/article/view/118015
- DOI: https://doi.org/10.36233/0507-4088-2020-65-1-6-15
- ID: 118015
Cite item
Full Text
Abstract
Results of analysis of phylogenetic, virological, epidemiological, ecological, clinical data of COVID-19 outbreaks in Wuhan, China (PRC) in comparison with SARS-2002 and MERS-2012 outbreaks allow to conclude:
– the etiological agent of COVID-19 is coronavirus (2019-CoV), phylogenetically close to the SARS-CoV, isolated from human, and SARS-related viruses isolated from bats (SARS-related bat CoV viruses). These viruses belong to the Sarbecovirus subgenus, Betacoronavirus genus, Orthocoronavirinae subfamily, Coronaviridae family (Cornidovirinea: Nidovirales). COVID-19 is a variant of SARS-2002 and is different from MERS-2012 outbreak, which were caused by coronavirus belonged to the subgenus Merbecovirus of the same genus;
– according to the results of phylogenetic analysis of 35 different betacoronaviruses, isolated from human and from wild animals in 2002-2019, the natural source of COVID-19 and SARS-CoV (2002) is bats of Rhinolophus genus (Rhinolophidae) and, probably, some species of other genera. An additional reservoir of the virus could be an intermediate animal species (snakes, civet, hedgehogs, badgers, etc.) that are infected by eating of infected bats. SARS-like coronaviruses circulated in bats in the interepidemic period (2003-2019);
– seasonal coronaviruses (subgenus Duvinacovirus, Alphacoronavirus) are currently circulating (November 2019
– January 2020) in the European part of Russia, Urals, Siberia and the Far East of Russia, along with the influenza viruses A(H1N1)pdm09, A(H3N2), and В, as well as six other respiratory viruses (HPIV, HAdV, HRSV, HRV, HBoV, and HMPV)
Keywords
Full Text
##article.viewOnOriginalSite##About the authors
D. K. Lvov
D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
Author for correspondence.
Email: dk_lvov@mail.ru
ORCID iD: 0000-0001-8176-6582
Dmitry K. Lvov, Doctor of Medical Sciences, Professor, Academician of RAS, Head of the Department of Ecology of Viruses, Head of Ecology and Epidemiology of Influenza Center.
Moscow, 123098
Russian FederationS. V. Alkhovsky
D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
Email: fake@neicon.ru
ORCID iD: 0000-0001-6913-5841
Moscow, 123098 Russian Federation
L. V. Kolobukhina
D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
Email: fake@neicon.ru
ORCID iD: 0000-0001-5775-3343
Moscow, 123098 Russian Federation
E. I. Burtseva
D.I. Ivanovsky Institute of Virology of National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya
Email: fake@neicon.ru
ORCID iD: 0000-0003-2518-6801
Moscow, 123098 Russian Federation
References
- de Groot R.J., Baker S.C., Baric R., Enjuanes L., Gorbalenya A.E., Holmes K.V., et al. Family Coronaviridae. In: King A.M., Adams M.J., Carstens E.B., Lefkowitz E.J., eds. Virus Taxonomy: Classification and Nomenclature of Viruses. Ninth Report of the International Committee on Taxonomy of Viruses. London: Elsevier; 2012: 806-28.
- Львов Д.К., Щелканов М.Ю. Коронавирусы (Coronaviridae). В кн.: Львов Д.К., ред. Руководство по вирусологии. Вирусы и вирусные инфекции человека и животных. М.: МИА; 2013: 211-8.
- Perlman S., Gallagher T., Snijder E.J. Nidoviruses. Washington: ASM press; 2008.
- Woo P.C., Lau S.K., Huang Y., Yuen K.Y. Coronavirus diversity, phylogeny and interspecies jumping. Exp. Biol. Med. (Maywood). 2009; 234(10): 1117-27. doi: 10.3181/0903-MR-94
- Cowley J.A., Dimmock C.M., Spann K.M., Walker P.J. Gill-associated virus of Penaeus monodon prawns: an invertebrate virus with ORF1a and ORF1b genes related to arteri– and coronaviruses. J. Gen. Virol. 2000; 81(Pt. 6): 1473-84. doi: 10.1099/0022-1317-81-6-1473
- Decaro N., Buonavoglia C. An update on canine coronaviruses: viral evolution and pathobiology. Vet. Microbiol. 2008; 132(3-4): 221-34. doi: 10.1016/j.vetmic.2008.06.007
- Cavanagh D. Coronaviruses in poultry and other birds. Avian Pathol. 2005; 34(6): 439-48. doi: 10.1080/03079450500367682
- Chu D.K., Leung C.Y., Gilbert M., Joyner P.H., Ng E.M., Tse T.M., et al. Avian coronavirus in wild aquatic birds. J. Virol. 2011; 85(23): 12815-20. doi: 10.1128/JVI.05838-11
- Traavik T., Mehl R., Kjeldsberg E. “Runde” viurs, a coronaviruslike agent associated with seabirds and ticks. Arch. Virol. 1977; 55(1-2): 25-38. http://doi.org/10.1007/bf01314476
- Gagneur A., Vallet S., Talbot P.J., Legrand-Quillien M.C., Picard B., Payan C., et al. Outbreaks of human coronavirus in a pediatric and neonatal intensive care unit. Eur. J. Pediatr. 2008; 167(12): 1427-34. http://doi.org/10.1007/s00431-008-0687-0
- Колобухина Л.В., Львов Д.К. Коронавирусная инфекция, тяжелый острый респираторный синдром. В кн.: Львов Д.К., ред. Руководство по вирусологии. Вирусы и вирусные инфекции человека и животных. М.: МИА; 2013: 588-92.
- Xu J., Hu J., Wang J., Han Y., Hu Y., Wen J., et al. Genome organization of the SARS-CoV. Genomics Proteomics Bioinformatics. 2003; 1(3): 226-35. http://doi.org/10.1016/s1672-0229(03)01028-3
- Li W., Shi Z., Yu M., Ren W., Smith C., Epstein J.H., et al. Bats are natural reservoirs of SARS-like coronaviruses. Science. 2005; 310(5748): 676-9. http://doi.org/10.1126/science.1118391
- Woo P.C., Lau S.K., Lam C.S., Lau C.C., Tsang A.K., Lau J.H., et al. 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. 2012; 86(7): 3995-4008. http://doi.org/10.1128/JVI.06540-11
- Guan Y., Zheng B.J., He Y.Q., Liu X.L., Zhuang Z.X., Cheung C.L., et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003; 302(5643): 276-8. http://doi.org/10.1126/science.1087139
- Annan A., Baldwin H.J., Corman V.M., Klose S.M., Owusu M., Nkrumah E.E., et al. Human betacoronavirus 2c EMC/2012-related viruses in bats, Ghana and Europe. Emerg. Infect. Dis. 2013; 19(3): 456-9. http://doi.org/10.3201/eid1903.121503
- Balboni A., Battilani M., Prosperi S. The SARS-like coronaviruses: the role of bats and evolutionary relationships with SARS coronavirus. New Microbiol. 2012; 35(1): 1-16.
- Wang L.F., Shi Z., Zhang S., Field H., Daszak P., Eaton B.T. Review of bats and SARS. Emerg. Infect. Dis. 2006; 12(12): 1834-40. http://doi.org/10.3201/eid1212.060401
- Dominguez S.R., O’Shea T.J., Oko L.M., Holmes K.V. Detection of group 1 coronaviruses in bats in North America. Emerg. Infect. Dis. 2007; 13(9): 1295-300. http://doi.org/10.3201/eid1309.070491
- Gloza-Rausch F., Ipsen A., Seebens A., Gottsche M., Panning M., Drexler J.F., et al. Detection and prevalence patterns of group I coronaviruses in bats, northern Germany. Emerg. Infect. Dis. 2008; 14(4): 626-31. http://doi.org/10.3201/eid1404.071439
- Lau S.K., Woo P.C., Li K.S., Huang Y., Tsoi H.W., Wong B.H., et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc. Natl. Acad. Sci. USA. 2005; 102(39): 14040-5. http://doi.org/10.1073/pnas.0506735102
- Tong S., Conrardy C., Ruone S., Kuzmin I.V., Guo X., Tao Y., et al. Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg. Infect. Dis. 2009; 15(3): 482-5. http://doi.org/10.3201/eid1503.081013
- Zhou P., Li H., Wang H., Wang L.F., Shi Z. Bat severe acute respiratory syndrome-like coronavirus ORF3b homologues display different interferon antagonist activities. J. Gen. Virol. 2012; 93(Pt. 2): 275-81. http://doi.org/10.1099/vir.0.033589-0
- Summary table of SARS cases by country, 1 November 2002 – 7 August 2003. Available at: https://www.who.int/csr/sars/country/2003_08_15/en/
- Покровский В.И., Малеев В.В., Киселев О.И. Коронавирус SARS – возбудитель атипичной пневмонии. Временые методические рекомендации. М.; 2003.
- Чучалин А.Г. Синдром острого повреждения легких. РМЖ. 2006; 14(22): 1582.
- Riley S., Fraser C., Donnelly C.A., Ghani A.C., Abu-Raddad L.J., Hedley A.J., et al. Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions. Science. 2003; 300(5627): 1961-6. http://doi.org/10.1126/science.1086478
- Lipsitch M., Cohen T., Cooper B., Robins J.M., Ma S., James L., et al. Transmission dynamics and control of severe acute respiratory syndrome. Science. 2003; 300(5627): 1966-70. http://doi.org/10.1126/science.1086616
- Wang J.T., Sheng W.H., Fang C.T., Chen Y.C., Wang J.L., Yu C.J., et al. Clinical manifestations, laboratory findings, and treatment outcomes of SARS patients. Emerg. Infect. Dis. 2004; 10(5): 818-24. http://doi.org/10.3201/eid1005.030640
- Drosten C., Gunther S., Preiser W., van der Werf S., Brodt H.R., Becker S., et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N. Engl. J. Med. 2003; 348(20): 1967-76. http://doi.org/10.1056/NEJMoa030747
- Tan E.L., Ooi E.E., Lin C.Y., Tan H.C., Ling A.E., Lim B., et al. Inhibition of SARS coronavirus infection in vitro with clinically approved antiviral drugs. Emerg. Infect. Dis. 2004; 10(4): 581-6. http://doi.org/10.3201/eid1004.030458
- Дерябин П.Г., Зарубаев В.В. К вопросу о коронавирусной инфекции и перспективах профилактики и лечения препаратами интерферона альфа-2в человеческого рекомбинантного. Инфекционные болезни. 2014; 12(3): 32-4.
- de Groot R.J., Baker S.C., Baric R.S., Brown C.S., Drosten C., Enjuanes L., et al. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group. J. Virol. 2013; 87(14): 7790-2. http://doi.org/10.1128/JVI.01244-13
- Reusken C.B., Haagmans B.L., Muller M.A., Gutierrez C., Godeke G.J., Meyer B., et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. Lancet Infect. Dis. 2013; 13(10): 859-66. http://doi.org/10.1016/S1473-3099(13)70164-6
- Perera R.A., Wang P., Gomaa M.R., El-Shesheny R., Kandeil A., Bagato O., et al. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt, June 2013. Euro Surveill. 2013; 18(36): pii20574. http://doi.org/10.2807/1560-7917.es2013.18.36.20574
- Стрелков П.П. Отряд Chiroptera, Blumenbach, 1779 – Рукокрылые. В кн.: Громов И.М., Баранова Г.И., ред. Каталог млекопитающих СССР. Плиоцен – современность. Ленинград: Наука; 1981: 31-53.
- Surveillance case definitions for human infection with novel coronavirus (nCoV). Available at: https://www.who.int/internal-publications-detail/surveillance-case-definitions-for-human-infectionwithnovel-coronavirus-(ncov)
- Disease commodity package – Novel Coronavirus (nCoV). Available at: https://www.who.int/publications-detail/disease-commodity-package---novel-coronavirus-(ncov)
- WHO recommendations to reduce risk of transmission of emerging pathogens from animals to humans in live animal markets. Available at: https://www.who.int/health-topics/coronavirus/who-recommendations-to-reduce-risk-of-transmission-of-emerging-pathogens-from-animals-to-humans-in-live-animal-markets
- Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases. Available at: https://www.who.int/publications-detail/laboratory-testing-for-2019-novel-coronavirus-insuspected-human-cases-20200117
- European surveillance for human infection with novel coronavirus (2019-nCoV). Available at: https://www.ecdc.europa.eu/en/european-surveillance-human-infection-novel-coronavirus-2019-ncov
- European Virus Archive – GLOBAL. Available at: https://www.european-virus-archive.com/
- Diagnostic detection of Wuhan coronavirus 2019 by realtime RTPCR. Available at: https://www.who.int/docs/defaultsource/coronaviruse/wuhan-virus-assay-v1991527e5122341d99287a1b17c111902.pdf?sfvrsn=d381fc88_2
- Novel Coronavirus (2019-nCoV) situation reports (WHO). Available at: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
- WHO, Western Pacific Region. Avian Influenza Weekly Update 2019. Available at: https://iris.wpro.who.int/handle/10665.1/14328
- Львов Д.К. Грипп и другие новые и возвращающиеся инфекции Северной Евразии: глобальные последствия. В кн.: Федеральный справочник здравоохранения России. Том 11. М.; 2010: 209-19.
- Львов Д.К., Борисевич С.В., Альховский С.В., Бурцева Е.И. Актуальные подходы анализа вирусных геномов в интересах биобезопасности. Инфекционные болезни: новости, мнения, обучение. 2019; 8(2): 96-101. http://doi.org/10.24411/2305-3496-2019-12012
- Lvov D.K., Shchelkanov M.Y., Alkhovsky S.V., Deryabin P.G. Zoonotic Viruses of Northern Eurasia. Taxonomy and Ecology. London: Academic Press, Elsevier; 2015.
- WHO. Coronavirus disease 2019 (COVID-19). Sitation report - 40 (29 February 2020).