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1.
PubMed; 2021.
Preprint in English | PubMed | ID: ppcovidwho-333772

ABSTRACT

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: We conducted a phylogenetic 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 (e.g. 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. RESULTS: We estimated a minimum 287 separate introductions (median, 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. CONCLUSIONS: There is phylogenetic evidence that the SARS-CoV-2 epidemic in Washington is continually seeded by a large number of introductions, and that there was significant inter- and intra-state transmission. Due to incomplete sampling our data underestimate the true number of introductions.

2.
Topics in Antiviral Medicine ; 29(1):39, 2021.
Article in English | EMBASE | ID: covidwho-1250798

ABSTRACT

Background: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state (WA) on January 21, 2020. By October 1, 2020, there were 89,974 confirmed cases of SARS-CoV-2 in WA. To understand the role of epidemic seeding events, we estimated the number and timing of introductions of SARS-CoV-2 lineages in WA using phylogenetic methods. Methods: Our analysis used full genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. In order to incorporate phylogenetic uncertainty into our estimates, we generated 25 samples of sequences each with 5 random polytomy resolutions. Each sample contained 4918 high quality WA sequences and 6504 non-WA sequences, including 5056 non-WA sequences that were closest to WA sequences based on the raw number of mutations and a time-stratified random sample of 1448 additional non-WA sequences. Sequences were aligned using MAFFT and phylogenetic trees were reconstructed by lineage (GISAID clades S, L/V, G/GH and GR) using IQTREE. We then time-calibrated each phylogeny using the treedater algorithm assuming a strict molecular clock and used maximum parsimony ancestral state reconstruction to estimate the state (WA or non-WA) of each node. Internal node date for the MRCA of each subclade of two or more sequences or the date of sampling for singletons was assumed to be the date of SARS-CoV-2 introduction. Results: We estimated a median of 287 separate introductions (range 244-320) and 204 exported lineages (range 188-227) of SARS-CoV-2 into and out of WA through September 2020. Introductions began in mid-January 2020 and peaked in number on March 29, 2020 (Figure). Approximately 73% of introductions occurred prior to May 1, 2020. The majority of introductions were lineage G/ GH (72%), followed by lineage GR (16%), S (5%) and L/V (7%). The resulting WA subclades ranged in size from 1-2193 sequences: 71% included just one sampled sequence, 9% included 2 WA sequences, 12% included 3-10 WA sequences, 4% included 11-50 sequences, and 4% were large subclades that included more than 50 WA sequences and were suggestive of extended local transmission chains. Conclusion: We found phylogenetic evidence that the SARS-CoV-2 epidemic in WA was seeded by multiple ongoing introductions, although due to incomplete sampling our estimates underestimate the true number of introductions. In addition, lineages with the Spike 614G variant accounted for the majority (88%) of introductions.

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