Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
03
01
2023
accepted:
13
04
2023
medline:
1
5
2023
pubmed:
28
4
2023
entrez:
28
4
2023
Statut:
epublish
Résumé
In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.
Identifiants
pubmed: 37115761
doi: 10.1371/journal.pone.0285042
pii: PONE-D-23-00183
pmc: PMC10146508
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0285042Informations de copyright
Copyright: © 2023 Leiser et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
China CDC Wkly. 2021 Dec 3;3(49):1049-1051
pubmed: 34934514
Innovation (Camb). 2021 Nov 28;2(4):100150
pubmed: 34401863
Neurol Sci. 2021 Dec;42(12):4903-4907
pubmed: 34523082
Nat Rev Cardiol. 2022 May;19(5):332-341
pubmed: 34686843
BMJ Open. 2021 May 13;11(5):e044684
pubmed: 33986052
Open Forum Infect Dis. 2020 Dec 28;8(2):ofaa638
pubmed: 33553477
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Nature. 2020 Apr;580(7803):E7
pubmed: 32296181
Mol Biol Evol. 2020 Apr 1;37(4):1237-1239
pubmed: 31904846
Sci Rep. 2021 Aug 9;11(1):16144
pubmed: 34373540
J Mol Diagn. 2022 Feb;24(2):112-119
pubmed: 34826637
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Lancet Microbe. 2020 Jul;1(3):e99-e100
pubmed: 32835336
Hum Mol Genet. 2018 Feb 15;27(4):732-741
pubmed: 29228364
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Brain Sci. 2021 Apr 02;11(4):
pubmed: 33918426
Glob Chall. 2017 Jan 10;1(1):33-46
pubmed: 31565258
Nat Med. 2022 Mar;28(3):583-590
pubmed: 35132265
Nat Genet. 2021 Jun;53(6):809-816
pubmed: 33972780
Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72
pubmed: 26590407