Phylogenetic analysis of the timing of SARS-CoV-2 introductions into washington state

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.