Phylogenetic estimates of SARS-CoV-2 introductions into Washington State.
Genomic analysis
Molecular epidemiology
Phylogeography
SARS-CoV-2
Journal
Lancet regional health. Americas
ISSN: 2667-193X
Titre abrégé: Lancet Reg Health Am
Pays: England
ID NLM: 9918232503006676
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
received:
08
04
2021
revised:
24
06
2021
accepted:
24
06
2021
entrez:
11
1
2022
pubmed:
12
1
2022
medline:
12
1
2022
Statut:
ppublish
Résumé
The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. We conducted a molecular epidemiologic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state. We estimated a minimum 287 introductions (range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively. The SARS-CoV-2 epidemic in Washington was continually seeded by a large number of introductions. Our findings highlight the importance of genomic surveillance to monitor for emerging variants due to high levels of inter- and intra-state transmission of SARS-CoV-2. None.
Sections du résumé
BACKGROUND
BACKGROUND
The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington.
METHODS
METHODS
We conducted a molecular epidemiologic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state.
FINDINGS
RESULTS
We estimated a minimum 287 introductions (range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively.
INTERPRETATION
CONCLUSIONS
The SARS-CoV-2 epidemic in Washington was continually seeded by a large number of introductions. Our findings highlight the importance of genomic surveillance to monitor for emerging variants due to high levels of inter- and intra-state transmission of SARS-CoV-2.
FUNDING SOURCE
BACKGROUND
None.
Identifiants
pubmed: 35013735
doi: 10.1016/j.lana.2021.100018
pii: S2667-193X(21)00010-7
pmc: PMC8733893
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100018Subventions
Organisme : NIAID NIH HHS
ID : F31 AI152542
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI127232
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2021 The Authors. Published by Elsevier Ltd.
Déclaration de conflit d'intérêts
ALG reports personal fees from Abbott Molecular, grants from Merck, grants from Gilead, outside the submitted work. DMT, PR, LS, HX, KRJ, NB, MLH, MF and JTH have nothing to disclose.
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