Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.
SARS-CoV-2
pandemic
phylogenomics
Journal
Journal of virology
ISSN: 1098-5514
Titre abrégé: J Virol
Pays: United States
ID NLM: 0113724
Informations de publication
Date de publication:
31 08 2020
31 08 2020
Historique:
received:
27
05
2020
accepted:
07
07
2020
pubmed:
10
7
2020
medline:
15
9
2020
entrez:
10
7
2020
Statut:
epublish
Résumé
The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.
Identifiants
pubmed: 32641486
pii: JVI.01056-20
doi: 10.1128/JVI.01056-20
pmc: PMC7459550
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
Copyright © 2020 American Society for Microbiology.
Références
N Engl J Med. 2020 Mar 26;382(13):1199-1207
pubmed: 31995857
Appl Environ Microbiol. 2018 May 17;84(11):
pubmed: 29625974
PLoS One. 2014 Nov 20;9(11):e113570
pubmed: 25412469
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
J Virol. 2012 Jan;86(1):11-8
pubmed: 22013031
AIDS. 2017 Jun 1;31(9):1211-1222
pubmed: 28353537
Bioinformatics. 2006 Dec 15;22(24):3096-8
pubmed: 17110367
BMC Bioinformatics. 2004 Aug 19;5:113
pubmed: 15318951
Emerg Infect Dis. 2020 Jun;26(6):1320-1323
pubmed: 32125269
Nat Commun. 2020 Nov 2;11(1):5511
pubmed: 33139731
Science. 2020 Oct 30;370(6516):571-575
pubmed: 32913002
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Cell Res. 2017 Jan;27(1):119-129
pubmed: 28008928
Methods Mol Biol. 2012;856:239-72
pubmed: 22399462
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Arch Virol. 2020 Sep;165(9):2095-2098
pubmed: 32556599
PLoS One. 2010 Jun 10;5(6):e11057
pubmed: 20548780
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Bioinformatics. 2009 May 1;25(9):1189-91
pubmed: 19151095
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508