Abstract
The crown-like outline of the virions of coronaviruses will long endure as the iconic image of 2020 – the year of the COVID-19 pandemic. This major human health emergency has been caused by a betacoronavirus, as have others in the past. In this chapter, we outline the taxonomy of betacoronaviruses and their properties, both genetic and biological. We discuss their recombinational and mutational histories separately to show that the sequence of the RaTG13 bat virus isolate is the closest currently known full-length genetic homolog of that of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). However, the RaTG13 bat virus and SARS-CoV-2 have probably diverged over 20 years. We discuss the ecology of their pangolin and bat hosts and conclude that, like other recent viral pandemics, the underlying cause of the SARS-CoV-2 emergence is probably the relentless growth of the world’s human population and the overexploitation and disturbance of the environment.
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References
Afelt A, Frutos R, Devaux C (2018) Bats, coronaviruses, and deforestation: toward the emergence of novel infectious diseases? Front Microbiol 9:702. https://doi.org/10.3389/fmicb.2018.00702
Agrios GN (2005) Plant pathology, 5th edn. Elsevier Academic Press, Burlington
Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, Hanafi NS, Kamarulzaman A, Tee KK (2016) Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia. Virol J 13:33. https://doi.org/10.1186/s12985-016-0488-4
Almeida JD, Tyrrell DA (1967) The morphology of three previously uncharacterized human respiratory viruses that grow in organ culture. J Gen Virol 1(2):175–178. https://doi.org/10.1099/0022-1317-1-2-175
Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF (2020) The proximal origin of SARS-CoV-2. Nat Med 26(4):450–452. https://doi.org/10.1038/s41591-020-0820-9
Anthony SJ, Johnson CK, Greig DJ, Kramer S, Che X, Wells H, Hicks AL, Joly DO, Wolfe ND, Daszak P, Karesh W, Lipkin WI, Morse SS, Mazet JAK, Goldstein T, Consortium P (2017) Global patterns in coronavirus diversity. Virus Evol 3(1):vex012. https://doi.org/10.1093/ve/vex012
Ashokkumar M, Valsarajan D, Suresh MA, Kaimal AR, Chandy G (2017) Stomach contents of the Indian Pangolin Manis crassicaudata (Mammalia: Pholidota: Manidae) in tropical forests of southern India. J Threat Taxa 9(5):10246–10248
Azhar EI, El-Kafrawy SA, Farraj SA, Hassan AM, Al-Saeed MS, Hashem AM, Madani TA (2014) Evidence for camel-to-human transmission of MERS coronavirus. N Engl J Med 370(26):2499–2505
Baric RS, Fu K, Schaad MC, Stohlman SA (1990) Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups. Virology 177(2):646–656. https://doi.org/10.1016/0042-6822(90)90530-5
Baroja U, Garin I, Aihartza J, Arrizabalaga-Escudero A, Vallejo N, Aldasoro M, Goiti U (2019) Pest consumption in a vineyard system by the lesser horseshoe bat (Rhinolophus hipposideros). PLoS One 14(7):e0219265. https://doi.org/10.1371/journal.pone.0219265
Beaudette F (1937) Cultivation of the virus of infectious bronchitis. J Am Vet Med Assoc 90:51–60
Belshaw R, Sanjuán R, Pybus OG (2011) Viral mutation and substitution: units and levels. Curr Opin Virol 1(5):430–435. https://doi.org/10.1016/j.coviro.2011.08.004
Boni MF, Lemey P, Jiang X, Lam TT-Y, Perry B, Castoe T, Rambaut A, Robertson DL (2020) Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. bioRxiv
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ (2019) BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 15(4):e1006650. https://doi.org/10.1371/journal.pcbi.1006650
Bukhari K, Mulley G, Gulyaeva AA, Zhao L, Shu G, Jiang J, Neuman BW (2018) Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 524:160–171. https://doi.org/10.1016/j.virol.2018.08.010
Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T (2006) Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev 19(3):531–545. https://doi.org/10.1128/CMR.00017-06
Clark WH, Blom PE (1991) Observations of ants (Hymenoptera: Formicidae: Myrmicinae, Formicinae, Dolichoderinae) utilizing carrion. Southwest Nat 36(1):140–142
Corman VM, Eckerle I, Memish ZA, Liljander AM, Dijkman R, Jonsdottir H, Ngeiywa KJJ, Kamau E, Younan M, Al Masri M (2016) Link of a ubiquitous human coronavirus to dromedary camels. Proc Natl Acad Sci 113(35):9864–9869
Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ, Assiri A, Al-Tawfiq JA, Alhakeem RF, Madani H, AlRabiah FA, Al Hajjar S, Al-nassir WN, Albarrak A, Flemban H, Balkhy HH, Alsubaie S, Palser AL, Gall A, Bashford-Rogers R, Rambaut A, Zumla AI, Memish ZA (2013) Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet 382(9909):1993–2002. https://doi.org/10.1016/S0140-6736(13)61887-5
Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, Al Rabeeah AA, Alhakeem RF, Assiri A, Al-Tawfiq JA (2014) Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. MBio 5(1):e01062–01013
Cuevas JM, Duffy S, Sanjuán R (2009) Point mutation rate of bacteriophage ΦX174. Genetics 183(2):747–749
Cui J, Li F, Shi Z-L (2019) Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 17(3):181–192
Decaro N, Mari V, Campolo M, Lorusso A, Camero M, Elia G, Martella V, Cordioli P, Enjuanes L, Buonavoglia C (2009) Recombinant canine coronaviruses related to transmissible gastroenteritis virus of Swine are circulating in dogs. J Virol 83(3):1532–1537. https://doi.org/10.1128/JVI.01937-08
Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS (2011) Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity. RNA Biol 8(2):270–279. https://doi.org/10.4161/rna.8.2.15013
Domingo E (2019) Virus as populations: composition, complexity, quasi species, dynamics, and biological implications. Academic Press, New York
Drake JW (1991) A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A 88(16):7160–7164. https://doi.org/10.1073/pnas.88.16.7160
Drake JW, Holland JJ (1999) Mutation rates among RNA viruses. Proc Natl Acad Sci 96(24):13910–13913
Drosten C, Günther S, Preiser W, Van Der Werf S, Brodt H-R, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RA (2003) Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348(20):1967–1976
Duchêne S, Holmes EC, Ho SY (2014) Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates. Proc Biol Sci 281(1786):20140732. https://doi.org/10.1098/rspb.2014.0732
Dudas G, Carvalho LM, Rambaut A, Bedford T (2018) MERS-CoV spillover at the camel-human interface. Elife 7. https://doi.org/10.7554/eLife.31257
Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9(4):267–276. https://doi.org/10.1038/nrg2323
Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR (2010) Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing. PLoS Pathog 6(5):e1000896. https://doi.org/10.1371/journal.ppat.1000896
Eckrich M, Neuweiler G (1988) Food habits of the sympatric insectivorous bats Rhinolophus rouxi and Hipposideros lankadiva from Sri Lanka. J Zool 215(4):729–737
Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O’Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J, Group -nS (2020) An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol 6(1):veaa027. https://doi.org/10.1093/ve/veaa027
El-Duah P, Meyer B, Sylverken A, Owusu M, Gottula LT, Yeboah R, Lamptey J, Frimpong YO, Burimuah V, Folitse R, Agbenyega O, Oppong S, Adu-Sarkodie Y, Drosten C (2019) Development of a whole-virus ELISA for serological evaluation of domestic livestock as possible hosts of human coronavirus NL63. Viruses 11(1):43. https://doi.org/10.3390/v11010043
Fabricant J (1998) The early history of infectious bronchitis. Avian Dis 42(4):648–650
Fenner F (1975) The classification and nomenclature of viruses. Summary of results of meetings of the International Committee on Taxonomy of Viruses in Madrid, September 1975. Intervirology 6(1):1–12. https://doi.org/10.1159/000149448
Forni D, Cagliani R, Clerici M, Sironi M (2017) Molecular evolution of human coronavirus genomes. Trends Microbiol 25(1):35–48. https://doi.org/10.1016/j.tim.2016.09.001
Fouchier RA, Hartwig NG, Bestebroer TM, Niemeyer B, de Jong JC, Simon JH, Osterhaus AD (2004) A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci U S A 101(16):6212–6216. https://doi.org/10.1073/pnas.0400762101
Fox J, Castella J-C (2013) Expansion of rubber (Hevea brasiliensis) in Mainland Southeast Asia: what are the prospects for smallholders? J Peasant Stud 40(1):155–170
Fox J, Castella J-C, Ziegler AD, Westley SB (2014) Rubber plantations expand in mountainous Southeast Asia: what are the consequences for the environment? East-West Center, Honolulu
Fox J, Castella JC, Hurni K (2018) As rubber plantations expand in the highlands of Southeast Asia, what happens to local farmers? East-West Center, Honolulu
Frutos R, Lopez Roig M, Serra-Cobo J, Devaux CA (2020) COVID-19: the conjunction of events leading to the coronavirus pandemic and lessons to learn for future threats. Front Med 7:223
Ge X, Li Y, Yang X, Zhang H, Zhou P, Zhang Y, Shi Z (2012) Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J Virol 86(8):4620–4630. https://doi.org/10.1128/JVI.06671-11
Gibbs MJ, Wayper P, Fourment ML, Wood JT, Ohshima K, Armstrong JS, Gibbs AJ (2007) The variable codons of H3 influenza A virus haemagglutinin genes. Arch Virol 152(1):11–24. https://doi.org/10.1007/s00705-006-0834-8
González-Candelas F, Patiño-Galindo JÁ, Valiente-Mullor C (2018) Population genomics of human viruses. In: Population genomics: microorganisms. Springer, Cham, pp 267–296
Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ (2006) Nidovirales: evolving the largest RNA virus genome. Virus Res 117(1):17–37. https://doi.org/10.1016/j.virusres.2006.01.017
Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LLM, Samborskiy DV, Sidorov IA, Sola I, Ziebuhr J, Coronaviridae Study Group of the International Committee on Taxonomy of V (2020a) The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 5(4):536–544. https://doi.org/10.1038/s41564-020-0695-z
Gorbalenya AE, Krupovic M, Mushegian AR, Kropinski AM, Siddell SG, Varsani A, Adams MJ, Davison AJ, Dutilh BE, Harrach B (2020b) The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol 5(5):668–674
Gribble J, Pruijssers AJ, Agostini ML, Anderson-Daniels J, Chappell JD, Lu X, Stevens LJ, Routh AL, Denison MR (2020) The coronavirus proofreading exoribonuclease mediates extensive viral recombination. BioRxiv
Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, Luo SW, Li PH, Zhang LJ, Guan YJ, Butt KM, Wong KL, Chan KW, Lim W, Shortridge KF, Yuen KY, Peiris JS, Poon LL (2003) Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 302(5643):276–278. https://doi.org/10.1126/science.1087139
Gunnell GF, Simmons NB (2005) Fossil evidence and the origin of bats. J Mamm Evol 12(1–2):209–246
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, vol 41. London: Information Retrieval Ltd., c1979-c2000, pp 95–98
Han HJ, Yu H, Yu XJ (2016) Evidence for zoonotic origins of Middle East respiratory syndrome coronavirus. J Gen Virol 97(2):274–280. https://doi.org/10.1099/jgv.0.000342
Hanada K, Suzuki Y, Gojobori T (2004) A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol 21(6):1074–1080. https://doi.org/10.1093/molbev/msh109
Henry R (2020) Etymologia: coronavirus. Emerg Infect Dis 26(5):1027
Heo CC, Mohamad AR, Rosli H, Nurul Ashikin A, Chen CD, John J, Hiromu K, Baharudin O (2009) Ants (Hymenoptera: Formicidae) associated with pig carcasses in Malaysia. Trop Biomed 26(1):106–109
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(5):4508–4514
Holmes EC (2009) The evolution and emergence of RNA viruses. Oxford University Press, New York
Hon CC, Lam TY, Shi ZL, Drummond AJ, Yip CW, Zeng F, Lam PY, Leung FC (2008) Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol 82(4):1819–1826. https://doi.org/10.1128/JVI.01926-07
Jenkins GM, Rambaut A, Pybus OG, Holmes EC (2002) Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54(2):156–165. https://doi.org/10.1007/s00239-001-0064-3
Jianchu X, Fox J, Melick D, Fujita Y, Jintrawet A, Jie Q, Thomas D, Weyerhaeuser H (2006) Land use transition, livelihoods, and environmental services in Montane Mainland Southeast Asia. Mt Res Dev 26(3):278–284
Johnson CK, Hitchens PL, Pandit PS, Rushmore J, Evans TS, Young CCW, Doyle MM (2020) Global shifts in mammalian population trends reveal key predictors of virus spillover risk. Proc Biol Sci 287(1924):20192736. https://doi.org/10.1098/rspb.2019.2736
Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P (2008) Global trends in emerging infectious diseases. Nature 451(7181):990–993. https://doi.org/10.1038/nature06536
Kahn JS, McIntosh K (2005) History and recent advances in coronavirus discovery. Pediatr Infect Dis J 24 (11 Suppl):S223–227, discussion S226. https://doi.org/10.1097/01.inf.0000188166.17324.60
Kan B, Wang M, Jing H, Xu H, Jiang X, Yan M, Liang W, Zheng H, Wan K, Liu Q, Cui B, Xu Y, Zhang E, Wang H, Ye J, Li G, Li M, Cui Z, Qi X, Chen K, Du L, Gao K, Zhao YT, Zou XZ, Feng YJ, Gao YF, Hai R, Yu D, Guan Y, Xu J (2005) Molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms. J Virol 79(18):11892–11900. https://doi.org/10.1128/JVI.79.18.11892-11900.2005
Karawita H, Perera P, Gunawardane P, Dayawansa N (2018) Habitat preference and den characterization of Indian Pangolin (Manis crassicaudata) in a tropical lowland forested landscape of Southwest Sri Lanka. PLoS One 13(11):e0206082. https://doi.org/10.1371/journal.pone.0206082
Karawita H, Perera P, Dayawansa N, Dias S (2020) Dietary composition and foraging habitats of the Indian Pangolin (Manis crassicaudata) in a tropical lowland forest-associated landscape in Southwest Sri Lanka. Glob Ecol Conserv 21:e00880
Knipe DM, Howley P (2013) Fields virology. Lippincott Williams & Wilkins, Philadelphia
Lai MM (1996) Recombination in large RNA viruses: coronaviruses. In: seminars in virology, vol 6. Academic, pp 381–388
Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, Wei W, Cheung WY, Li WJ, Li LF, Leung GM, Holmes EC, Hu YL, Guan Y (2020) Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature 583:282. https://doi.org/10.1038/s41586-020-2169-0
Lau SK, Li KS, Huang Y, Shek CT, Tse H, Wang M, Choi GK, Xu H, Lam CS, Guo R, Chan KH, Zheng BJ, Woo PC, Yuen KY (2010) Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events. J Virol 84(6):2808–2819. https://doi.org/10.1128/JVI.02219-09
Lau SK, Lee P, Tsang AK, Yip CC, Tse H, Lee RA, So LY, Lau YL, Chan KH, Woo PC, Yuen KY (2011) Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. J Virol 85(21):11325–11337. https://doi.org/10.1128/JVI.05512-11
Lau SK, Luk HK, Wong AC, Li KS, Zhu L, He Z, Fung J, Chan TT, Fung KS, Woo PC (2020) Early release-possible bat origin of severe acute respiratory syndrome coronavirus 2
Leung K, Wu JT, Liu D, Leung GM (2020) First-wave COVID-19 transmissibility and severity in China outside Hubei after control measures, and second-wave scenario planning: a modelling impact assessment. Lancet 395(10233):1382–1393. https://doi.org/10.1016/S0140-6736(20)30746-7
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(5748):676–679. https://doi.org/10.1126/science.1118391
Lim N (2008) Ecological research and conservation of Sunda pangolin Manis javanica in Singapore. In: Proceedings of the workshop on trade and conservation of Pangolins Native to South and Southeast Asia. TRAFFIC Southeast Asia, Singapore Zoo, Singapore, pp 90–93
Luk HKH, Li X, Fung J, Lau SKP, Woo PCY (2019) Molecular epidemiology, evolution and phylogeny of SARS coronavirus. Infect Genet Evol 71:21–30. https://doi.org/10.1016/j.meegid.2019.03.001
Mahase E (2020) Coronavirus covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate. BMJ 368:m641. https://doi.org/10.1136/bmj.m641
Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1(1):vev003. https://doi.org/10.1093/ve/vev003
Minskaia E, Hertzig T, Gorbalenya AE, Campanacci V, Cambillau C, Canard B, Ziebuhr J (2006) Discovery of an RNA virus 3′->5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc Natl Acad Sci U S A 103(13):5108–5113. https://doi.org/10.1073/pnas.0508200103
Mohamed K, Rodríguez-Román E, Rahmani F, Zhang H, Ivanovska M, Makka SA, Joya M, Makuku R, Islam MS, Radwan N, Rahmah L, Goda R, Abarikwu SO, Shaw M, Zoghi S, Irtsyan S, Ling I, Cseprekal O, Faten AB, Hazar Sayar E, Soloukey C, Grancini G, Rezaei N (2020) Borderless collaboration is needed for COVID-19-a disease that knows no borders. Infect Control Hosp Epidemiol 41:1–2. https://doi.org/10.1017/ice.2020.162
Morse SS, Mazet JA, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P (2012) Prediction and prevention of the next pandemic zoonosis. Lancet 380(9857):1956–1965. https://doi.org/10.1016/S0140-6736(12)61684-5
Nielsen R, Wang H, Pipes L (2020) Synonymous mutations and the molecular evolution of SARS-Cov-2 origins. bioRxiv
Olival KJ, Hosseini PR, Zambrana-Torrelio C, Ross N, Bogich TL, Daszak P (2017) Host and viral traits predict zoonotic spillover from mammals. Nature 546(7660):646–650. https://doi.org/10.1038/nature22975
Pagán I (2018) The diversity, evolution and epidemiology of plant viruses: a phylogenetic view. Infect Genet Evol 65:187–199. https://doi.org/10.1016/j.meegid.2018.07.033
Perales C, Martín V, Domingo E (2011) Lethal mutagenesis of viruses. Curr Opin Virol 1(5):419–422. https://doi.org/10.1016/j.coviro.2011.09.001
Perera P, Karawita K, Pabasara M (2017) Pangolins (Manis crassicaudata) in Sri Lanka: a review of current knowledge, threats and research priorities. J Trop For Environ 7(1):1–14
Phommexay P, Satasook C, Bates P, Pearch M, Bumrungsri S (2011) The impact of rubber plantations on the diversity and activity of understorey insectivorous bats in southern Thailand. Biodivers Conserv 20(7):1441–1456
Prates ET, Garvin MR, Pavicic M, Jones P, Shah M, Alvarez C, Kainer D, Demerdash O, Amos BK, Geiger A (2020) Functional immune deficiency syndrome via intestinal infection in COVID-19. bioRxiv
Rocklöv J, Sjödin H (2020) High population densities catalyse the spread of COVID-19. J Travel Med 27(3). https://doi.org/10.1093/jtm/taaa038
Sanjuán R, Domingo-Calap P (2019) Genetic diversity and evolution of viral populations. Reference Module in Life Sciences
Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R (2010) Viral mutation rates. J Virol 84(19):9733–9748. https://doi.org/10.1128/JVI.00694-10
Shaw L, Wang A, Dylus D, Meier M, Pogacnik G, Dessimoz C (2019) The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol
Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ (2018) The evolutionary history of vertebrate RNA viruses. Nature 556(7700):197–202. https://doi.org/10.1038/s41586-018-0012-7
Simon-Loriere E, Holmes EC (2011) Why do RNA viruses recombine? Nat Rev Microbiol 9(8):617–626. https://doi.org/10.1038/nrmicro2614
Smith EC, Blanc H, Surdel MC, Vignuzzi M, Denison MR (2013) Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog 9(8):e1003565. https://doi.org/10.1371/journal.ppat.1003565
Sridhar K, Ashwini K, Seena S, Sreepada K (2006) Manure qualities of guano of insectivorous cave bat Hipposideros speoris. Trop Subtrop Agroecosyst 6(2):103–110
Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5(10):801–812. https://doi.org/10.1038/nrmicro1750
Swart J, Richardson P, Ferguson J (1999) Ecological factors affecting the feeding behaviour of pangolins (Manis temminckii). J Zool 247(3):281–292
Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, Kuzmin IV, Holmes EC, Tong S (2017) Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. J Virol 91(5):e01953. https://doi.org/10.1128/JVI.01953-16
Tu C, Crameri G, Kong X, Chen J, Sun Y, Yu M, Xiang H, Xia X, Liu S, Ren T, Yu Y, Eaton BT, Xuan H, Wang LF (2004) Antibodies to SARS coronavirus in civets. Emerg Infect Dis 10(12):2244–2248. https://doi.org/10.3201/eid1012.040520
Valitutto MT, Aung O, Tun KYN, Vodzak ME, Zimmerman D, Yu JH, Win YT, Maw MT, Thein WZ, Win HH, Dhanota J, Ontiveros V, Smith B, Tremeau-Brevard A, Goldstein T, Johnson CK, Murray S, Mazet J (2020) Detection of novel coronaviruses in bats in Myanmar. PLoS One 15(4):e0230802. https://doi.org/10.1371/journal.pone.0230802
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(4):368–373. https://doi.org/10.1038/nm1024
van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, Ortiz AT, Balloux F (2020) Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol 83:104351. https://doi.org/10.1016/j.meegid.2020.104351
Vandamme A-M (2009) Basic concepts of molecular evolution. In: The phylogenetic handbook, vol 2. Cambridge University Press, Cambridge, pp 3–32
Vijaykrishna D, Smith GJ, Zhang JX, Peiris JS, Chen H, Guan Y (2007) Evolutionary insights into the ecology of coronaviruses. J Virol 81(8):4012–4020. https://doi.org/10.1128/JVI.02605-06
Vijgen L, Keyaerts E, Moës E, Thoelen I, Wollants E, Lemey P, Vandamme AM, Van Ranst M (2005) Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol 79(3):1595–1604. https://doi.org/10.1128/JVI.79.3.1595-1604.2005
Weiss SR, Navas-Martin S (2005) Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. Microbiol Mol Biol Rev 69(4):635–664. https://doi.org/10.1128/MMBR.69.4.635-664.2005
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(2):884–895. https://doi.org/10.1128/JVI.79.2.884-895.2005
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(7):3995–4008. https://doi.org/10.1128/JVI.06540-11
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(7798):265–269. https://doi.org/10.1038/s41586-020-2008-3
Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, Zhang Z, Shu F, Huang W, Li Y, Chen RA, Wu YJ, Peng SM, Huang M, Xie WJ, Cai QH, Hou FH, Chen W, Xiao L, Shen Y (2020) Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 583:286. https://doi.org/10.1038/s41586-020-2313-x
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(19):1814–1820. https://doi.org/10.1056/NEJMoa1211721
Zhang YZ, Holmes EC (2020) A genomic perspective on the origin and emergence of SARS-CoV-2. Cell 181(2):223–227. https://doi.org/10.1016/j.cell.2020.03.035
Zhang X, Tan Y, Ling Y, Lu G, Liu F, Yi Z, Jia X, Wu M, Shi B, Xu S, Chen J, Wang W, Chen B, Jiang L, Yu S, Lu J, Wang J, Xu M, Yuan Z, Zhang Q, Zhao G, Wang S, Chen S, Lu H (2020) Viral and host factors related to the clinical outcome of COVID-19. Nature 583:437. https://doi.org/10.1038/s41586-020-2355-0
Zhao Z, Li H, Wu X, Zhong Y, Zhang K, Zhang YP, Boerwinkle E, Fu YX (2004) Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol 4:21. https://doi.org/10.1186/1471-2148-4-21
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(7798):270–273. https://doi.org/10.1038/s41586-020-2012-7
Websites
ASM Mammal Diversity Database, American Society of Mammalogist; Chiroptera: https://mammaldiversity.org/#Y2hpcm9wdGVyYSZnbG9iYWxfc2VhcmNoPXRydWUmbG9vc2U9dHJ1ZQ (consulted: May 21, 2020)
ICTV online: https://talk.ictvonline.org/. Consulted on May 21, 2020
Virological.: http://virological.org/. Consulted on May 21, 2020
WHO: WHO Director-General’s opening remarks at the media briefing on COVID-19—11 March 2020. World Health Organization website. https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-atthe-media-briefing-on-covid-19—11-march-2020. Published March 11, 2020. Accessed April 12, 2020
Worldometer.: https://www.worldometers.info/coronavirus/. Consulted on May 31, 2020
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The authors would like to thank Paul Scotti for constructive comments.
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Rodríguez-Román, E., Gibbs, A.J. (2021). Ecology and Evolution of Betacoronaviruses. In: Rezaei, N. (eds) Coronavirus Disease - COVID-19. Advances in Experimental Medicine and Biology, vol 1318. Springer, Cham. https://doi.org/10.1007/978-3-030-63761-3_3
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