Transmission dynamics and evolutionary history of 2019-nCoV

Journal of Medical Virology

Volumn 92, Issue 5, 2020, Pages 501-511

  Li, Xingguang ^a   Wang, Wei ^b   Zhao, Xiaofang ^c   Zai, Junjie ^d   Zhao, Qiang ^e   Li, Yi ^a   Chaillon, Antoine ^f  

^a Wuhan University of Bioengineering   (China)

^b THE FIRST AFFILIATED HOSPITAL OF GUANGXI UNIVERSITY OF CHINESE MEDICINE   (China)

^c RUIKANG HOSPITAL AFFILIATED TO GUANGXI UNIVERSITY OF CHINESE MEDICINE   (China)

^d NINGBO UNIVERSITY   (China)

^e KEY LABORATORY OF CANCER PREVENTION AND THERAPY   (China)

^f UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

2019 nCoV; evolutionary rate; phylogenetic cluster; time to most recent common ancestor; TMRCA; transmission cluster

Indexed keywords

ARTICLE; CHINA; CLINICAL ARTICLE; CORONAVIRUS DISEASE 2019; EVOLUTIONARY RATE; GENETIC VARIABILITY; HUMAN; NONHUMAN; PUBLIC HEALTH; SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2; THAILAND; VIRUS GENOME; VIRUS STRAIN; BAYES THEOREM; BETACORONAVIRUS; BIOLOGICAL MODEL; CORONAVIRUS INFECTION; EPIDEMIC; GENETICS; MUTATION RATE; PHYLOGENY; STATISTICAL MODEL; UNITED STATES; VIRUS PNEUMONIA;

COVID-19; SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2;

BAYES THEOREM; BETACORONAVIRUS; CHINA; CORONAVIRUS INFECTIONS; DISEASE OUTBREAKS; GENOME, VIRAL; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION RATE; PHYLOGENY; PNEUMONIA, VIRAL; THAILAND; UNITED STATES;

EID: 85079436157     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.25701     Document Type: Article

References (37)

1. Chan JFW, Yuan S, Kok KH, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020. https://doi.org/10.1016/S0140-6736(20)30154-9
2. Li Q, Guan X, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med. 2020. https://doi.org/10.1056/NEJMoa2001316
3. Su S, Wong G, Shi W, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24:490-502. https://doi.org/10.1016/j.tim.2016.03.003
4. Drosten C, Günther S, Preiser W, et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003;348:1967-1976. https://doi.org/10.1056/NEJMoa030747
5. Ksiazek TG, Erdman D, Goldsmith CS, et al. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003;348:1953-1966. https://doi.org/10.1056/NEJMoa030781
6. Zhong N, Zheng B, Li Y, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February 2003. Lancet. 2003;362:1353-1358. https://doi.org/10.1016/s0140-6736(03)14630-2
7. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814-1820. https://doi.org/10.1056/NEJMoa1211721
8. de Groot RJ, Baker SC, Baric RS, et al. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group. J Virol. 2013;87:7790-7792. https://doi.org/10.1128/JVI.01244-13
9. Lau SKP, Li KSM, Huang Y, et al. 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. 2010;84:2808-2819. https://doi.org/10.1128/JVI.02219-09
10. Guan Y, Zheng BJ, He YQ, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302:276-278. https://doi.org/10.1126/science.1087139
11. Lau SKP, Woo PCY, Li KSM, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci USA. 2005;102:14040-14045. https://doi.org/10.1073/pnas.0506735102
12. Li W, Shi Z, Yu M, et al. Bats are natural reservoirs of SARS-like coronaviruses. Science. 2005;310:676-679. https://doi.org/10.1126/science.1118391
13. Song HD, Tu CC, Zhang GW, et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A. 2005;102:2430-2435. https://doi.org/10.1073/pnas.0409608102
14. Chinese SARS Molecular Epidemiology Consortium. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004;303:1666-1669. https://doi.org/10.1126/science.1092002
15. Wang M, Yan M, Xu H, et al. SARS-CoV infection in a restaurant from palm civet. Emerg Infect Dis. 2005;11:1860-1865. https://doi.org/10.3201/eid1112.041293
16. Müller MA, Corman VM, Jores J, et al. MERS coronavirus neutralizing antibodies in camels, Eastern Africa, 1983-1997. Emerg Infect Dis. 2014;20:2093-2095. https://doi.org/10.3201/eid2012.141026
17. Chu DKW, Poon LLM, Gomaa MM, et al. MERS coronaviruses in dromedary camels, Egypt. Emerg Infect Dis. 2014;20:1049-1053. https://doi.org/10.3201/eid2006.140299
18. Zhou P, Yang XL, Wang XG, et al. Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. BioRxiv. 2020. https://doi.org/10.1101/2020.01.22.914952
19. Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020. https://doi.org/10.1016/S0140-6736(20)30251-8
20. Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall. 2017;1:33-46. https://doi.org/10.1002/gch2.1018
21. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772-780. https://doi.org/10.1093/molbev/mst010
22. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95-98. https://doi.org/citeulike-article-id:691774
23. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254-267. https://doi.org/10.1093/molbev/msj030
24. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9:772. https://doi.org/10.1038/nmeth.2109
25. Schmidt HA, von Haeseler A. Maximum-likelihood analysis using TREE-PUZZLE. Curr Protoc Bioinformatics. 2007;1:6.6.1-6.6.23.
26. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18:502-504. https://doi.org/10.1093/bioinformatics/18.3.502
27. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307-321. https://doi.org/10.1093/sysbio/syq010
28. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:vew007. https://doi.org/10.1093/ve/vew007
29. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969-1973. https://doi.org/10.1093/molbev/mss075
30. Suchard MA, Rambaut A. Many-core algorithms for statistical phylogenetics. Bioinformatics. 2009;25:1370-1376. https://doi.org/10.1093/bioinformatics/btp244
31. Zhao Z, Li H, Wu X, et al. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol. 2004;4:21. https://doi.org/10.1186/1471-2148-4-21
32. Cotten M, Watson SJ, Kellam P, et al. Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study. Lancet. 2013;382:1993-2002. https://doi.org/10.1016/S0140-6736(13)61887-5
33. Cotten M, Watson SJ, Zumla AI, et al. Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. mBio. 2014;5, https://doi.org/10.1128/mBio.01062-13
34. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:901-904. https://doi.org/10.1093/sysbio/syy032
35. Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens. Mol Biol Evol. 2018;35:1812-1819. https://doi.org/10.1093/molbev/msy016
36. Li X, Zai J, Wang X, Li Y. Potential of large 'first generation' human-to-human transmission of 2019-nCoV. J Med Virol. 2020. https://doi.org/10.1002/jmv.25693
37. Muth D, Corman VM, Roth H, et al. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission. Sci Rep. 2018;8:15177. https://doi.org/10.1038/s41598-018-33487-8