Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California.
COVID-19
D614G lineage
SARS-CoV-2
epidemiology
public health surveillance
viral evolution
viral whole-genome sequencing
Journal
The Journal of infectious diseases
ISSN: 1537-6613
Titre abrégé: J Infect Dis
Pays: United States
ID NLM: 0413675
Informations de publication
Date de publication:
15 07 2021
15 07 2021
Historique:
received:
22
01
2021
accepted:
19
04
2021
pubmed:
25
4
2021
medline:
23
7
2021
entrez:
24
4
2021
Statut:
ppublish
Résumé
We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with coronavirus disease 2019, 101 genomes from 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 (n = 9; including the first 2 reported deaths in the United States, with postmortem diagnosis), D614G (n = 4), ancestral Wuhan Hu-1 (n = 21), and 13 others (n = 26). Public health intervention may have curtailed the persistence of lineages that appeared transiently during February and March. By August, only D614G lineages introduced after 21 March were circulating in Santa Clara County.
Identifiants
pubmed: 33893501
pii: 6242512
doi: 10.1093/infdis/jiab199
pmc: PMC8135363
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
207-217Subventions
Organisme : NIAID NIH HHS
ID : R21 AI129455
Pays : United States
Organisme : Innovative Genomics Institute
Organisme : NIH HHS
ID : R33-AI129455
Pays : United States
Organisme : CIHR
Pays : Canada
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.
Références
Nature. 2021 Apr;592(7852):116-121
pubmed: 33106671
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Open Forum Infect Dis. 2020 Sep 18;7(11):ofaa434
pubmed: 33200080
N Engl J Med. 2020 Mar 5;382(10):929-936
pubmed: 32004427
Nature. 2021 Apr;592(7852):122-127
pubmed: 33636719
Science. 2020 Jul 31;369(6503):582-587
pubmed: 32513865
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Emerg Infect Dis. 2020 Oct;26(10):2401-2405
pubmed: 32610037
Glob Chall. 2017 Jan 10;1(1):33-46
pubmed: 31565258
Nat Rev Genet. 2018 Jan;19(1):9-20
pubmed: 29129921
Science. 2020 Oct 30;370(6516):571-575
pubmed: 32913002
Genome Res. 2020 Dec;30(12):1781-1788
pubmed: 33093069
J Epidemiol Community Health. 2020 Oct;74(10):861-866
pubmed: 32576605
Cell. 2021 Jan 7;184(1):64-75.e11
pubmed: 33275900
MMWR Morb Mortal Wkly Rep. 2020 Mar 27;69(12):347-352
pubmed: 32214086
MMWR Morb Mortal Wkly Rep. 2020 Jun 05;69(22):680-684
pubmed: 32497028
MMWR Morb Mortal Wkly Rep. 2020 Apr 10;69(14):419-421
pubmed: 32271724
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Science. 2020 Jul 17;369(6501):297-301
pubmed: 32471856
Sci Rep. 2020 Aug 20;10(1):14031
pubmed: 32820179
MMWR Morb Mortal Wkly Rep. 2020 May 08;69(18):551-556
pubmed: 32379733
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Lancet Infect Dis. 2020 May;20(5):533-534
pubmed: 32087114
Nat Commun. 2020 Nov 25;11(1):5986
pubmed: 33239633
Cell. 2020 May 28;181(5):990-996.e5
pubmed: 32386545