Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2.
Amino Acid Sequence
Animals
Betacoronavirus
/ classification
COVID-19
Chiroptera
/ virology
Coronavirus Infections
/ epidemiology
Eutheria
/ virology
Evolution, Molecular
Genome, Viral
Host Specificity
Humans
Pandemics
Phylogeny
Pneumonia, Viral
/ epidemiology
SARS-CoV-2
Sequence Alignment
Sequence Homology, Amino Acid
Spike Glycoprotein, Coronavirus
/ classification
COVID-19
SARS-CoV-2
TMRCA
cross-species transmission
evolutionary rate
potential intermediate animal host
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
15
02
2020
accepted:
24
02
2020
pubmed:
28
2
2020
medline:
1
7
2020
entrez:
28
2
2020
Statut:
ppublish
Résumé
To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10
Identifiants
pubmed: 32104911
doi: 10.1002/jmv.25731
pmc: PMC7228310
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
602-611Subventions
Organisme : K.C. Wong Magna Fund in Ningbo University
Pays : International
Organisme : National Natural Science Foundation of China
ID : 31470268
Pays : International
Informations de copyright
© 2020 Wiley Periodicals, Inc.
Références
Emerg Infect Dis. 2014 Jun;20(6):1049-53
pubmed: 24856660
N Engl J Med. 2012 Nov 8;367(19):1814-20
pubmed: 23075143
J Virol. 1999 Jan;73(1):152-60
pubmed: 9847317
Chembiochem. 2004 Dec 3;5(12):1653-61
pubmed: 15526330
Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6
pubmed: 18428792
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5
pubmed: 15258291
Lancet. 2020 Feb 15;395(10223):514-523
pubmed: 31986261
J Mol Evol. 1980 Dec;16(2):111-20
pubmed: 7463489
Lancet. 2020 Feb 22;395(10224):565-574
pubmed: 32007145
N Engl J Med. 2003 May 15;348(20):1953-66
pubmed: 12690092
Lancet. 2013 Dec 14;382(9909):1993-2002
pubmed: 24055451
J Virol. 2013 Jul;87(14):7790-2
pubmed: 23678167
N Engl J Med. 2020 Mar 26;382(13):1199-1207
pubmed: 31995857
mBio. 2014 Feb 18;5(1):
pubmed: 24549846
J Med Virol. 2020 Jun;92(6):602-611
pubmed: 32104911
Nat Methods. 2012 Jul 30;9(8):772
pubmed: 22847109
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
Science. 2003 Oct 10;302(5643):276-8
pubmed: 12958366
Science. 2004 Mar 12;303(5664):1666-9
pubmed: 14752165
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
BMC Evol Biol. 2004 Jun 28;4:21
pubmed: 15222897
Virus Evol. 2018 Jan 08;4(1):vex042
pubmed: 29340210
J Biol Chem. 1994 Apr 22;269(16):12240-7
pubmed: 8163529
J Vis Exp. 2019 Jan 9;(143):
pubmed: 30688313
PLoS Biol. 2006 May;4(5):e88
pubmed: 16683862
J Virol. 2010 Mar;84(6):2808-19
pubmed: 20071579
Mol Biol Evol. 2006 Feb;23(2):254-67
pubmed: 16221896
N Engl J Med. 2003 May 15;348(20):1967-76
pubmed: 12690091
Mol Biol Evol. 1987 Jul;4(4):406-25
pubmed: 3447015
Bioinformatics. 2002 Mar;18(3):502-4
pubmed: 11934758
J Med Virol. 2020 May;92(5):501-511
pubmed: 32027035
Viruses. 2019 Oct 24;11(11):
pubmed: 31652964
Mol Biol Evol. 2012 Aug;29(8):1969-73
pubmed: 22367748
Virus Res. 1999 Mar;60(1):55-65
pubmed: 10225274
Bioinformatics. 2009 Jun 1;25(11):1370-6
pubmed: 19369496
Trends Microbiol. 2016 Jun;24(6):490-502
pubmed: 27012512
Lancet. 2003 Oct 25;362(9393):1353-8
pubmed: 14585636
J Mol Evol. 1984;20(1):86-93
pubmed: 6429346
Biochim Biophys Acta. 2000 Nov 10;1469(3):121-32
pubmed: 11063880
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):14040-5
pubmed: 16169905
Sci Rep. 2018 Nov 9;8(1):16597
pubmed: 30413791
Virus Evol. 2016 Apr 09;2(1):vew007
pubmed: 27774300
Evolution. 1985 Jul;39(4):783-791
pubmed: 28561359
Glob Chall. 2017 Jan 10;1(1):33-46
pubmed: 31565258
Mol Biol Evol. 2018 Jul 1;35(7):1812-1819
pubmed: 29401317
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
J Med Virol. 2020 Apr;92(4):448-454
pubmed: 31997390
Emerg Infect Dis. 2005 Dec;11(12):1860-5
pubmed: 16485471
Emerg Infect Dis. 2014 Dec;20(12):2093-5
pubmed: 25425139
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2430-5
pubmed: 15695582
J Virol. 2015 Aug;89(15):8077-81
pubmed: 25972540
Science. 2005 Oct 28;310(5748):676-9
pubmed: 16195424
Syst Biol. 2010 May;59(3):307-21
pubmed: 20525638