Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.
SARS-CoV-2
molecular epidemiology
phylogenetics
phylogeography
transmission lineages
Journal
Virus evolution
ISSN: 2057-1577
Titre abrégé: Virus Evol
Pays: England
ID NLM: 101664675
Informations de publication
Date de publication:
2021
2021
Historique:
received:
01
04
2021
revised:
12
05
2021
accepted:
03
06
2021
entrez:
16
9
2021
pubmed:
17
9
2021
medline:
17
9
2021
Statut:
epublish
Résumé
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
Identifiants
pubmed: 34527281
doi: 10.1093/ve/veab051
pii: veab051
pmc: PMC8244811
doi:
Types de publication
Journal Article
Langues
eng
Pagination
veab051Subventions
Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : FIC NIH HHS
ID : D43 TW010540
Pays : United States
Organisme : Medical Research Council
ID : MR/S019510/1
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : U01 AI151788
Pays : United States
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press.
Références
N Engl J Med. 2020 Jun 11;382(24):2302-2315
pubmed: 32289214
Emerg Infect Dis. 2021 Feb;27(2):612-615
pubmed: 33496228
Cell. 2015 Jun 18;161(7):1516-26
pubmed: 26091036
Nat Med. 2020 Nov;26(11):1714-1719
pubmed: 32943787
Nature. 2017 Jun 15;546(7658):406-410
pubmed: 28538727
J Virol. 2021 Jan 13;95(3):
pubmed: 33127745
Science. 2021 Feb 12;371(6530):708-712
pubmed: 33419936
PLoS Negl Trop Dis. 2021 Jan 4;15(1):e0008958
pubmed: 33395425
Nat Microbiol. 2019 Jan;4(1):10-19
pubmed: 30546099
Virus Evol. 2020 Aug 19;6(2):veaa061
pubmed: 33235813
Virus Evol. 2016 Apr 09;2(1):vew007
pubmed: 27774300
Nat Microbiol. 2020 Jul;5(7):876-877
pubmed: 32427978
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
Emerg Infect Dis. 2020 Dec;26(12):2854-2862
pubmed: 33219646
J Math Biol. 2008 Mar;56(3):391-412
pubmed: 17874105
PLoS Genet. 2015 Aug 12;11(8):e1005421
pubmed: 26267488
Infect Genet Evol. 2016 Dec;46:248-255
pubmed: 27262354
Syst Biol. 2018 Sep 1;67(5):901-904
pubmed: 29718447
Science. 2020 Oct 30;370(6516):564-570
pubmed: 32912998
Nature. 2021 Apr;592(7854):438-443
pubmed: 33690265
Mol Ecol Resour. 2015 Jul;15(4):785-94
pubmed: 25431227
Nat Commun. 2021 Jan 19;12(1):434
pubmed: 33469026
Mol Biol Evol. 2017 Nov 1;34(11):2982-2995
pubmed: 28981709
Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):20198-20201
pubmed: 32723824
PLoS Comput Biol. 2021 Jan 6;17(1):e1008561
pubmed: 33406072
Nat Commun. 2020 Dec 11;11(1):6351
pubmed: 33311501
Nat Med. 2020 Sep;26(9):1405-1410
pubmed: 32678356
Virus Evol. 2020 Nov 10;6(2):veaa082
pubmed: 33335743
Microbiol Resour Announc. 2020 Jun 25;9(26):
pubmed: 32586872
PLoS Curr. 2009 Aug 18;1:RRN1003
pubmed: 20025195
Cell. 2019 Aug 22;178(5):1057-1071.e11
pubmed: 31442400
Mol Biol Evol. 2013 Mar;30(3):713-24
pubmed: 23180580
Nature. 2005 Nov 17;438(7066):355-9
pubmed: 16292310
Science. 2021 May 21;372(6544):815-821
pubmed: 33853970
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Lancet Infect Dis. 2020 Nov;20(11):1263-1271
pubmed: 32679081
Science. 2020 Sep 4;369(6508):1255-1260
pubmed: 32703910
Infect Dis Model. 2021 Jan 07;6:232-243
pubmed: 33506154
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
PLoS Pathog. 2014 Feb 20;10(2):e1003932
pubmed: 24586153
Mol Biol Evol. 2021 Jan 4;38(1):307-317
pubmed: 32722797
Virus Evol. 2021 Mar 14;7(1):veaa102
pubmed: 33747543
Emerg Microbes Infect. 2021 Dec;10(1):51-65
pubmed: 33306459
Science. 2020 May 1;368(6490):493-497
pubmed: 32213647
Sci Transl Med. 2020 Dec 9;12(573):
pubmed: 33229462
Nat Commun. 2020 Oct 9;11(1):5110
pubmed: 33037213
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nat Commun. 2020 Nov 3;11(1):5558
pubmed: 33144575
Nature. 2021 May;593(7858):266-269
pubmed: 33767447
Cell. 2020 May 28;181(5):997-1003.e9
pubmed: 32359424
PLoS Comput Biol. 2009 Sep;5(9):e1000520
pubmed: 19779555
Syst Biol. 2010 May;59(3):307-21
pubmed: 20525638
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508