Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

• Published in: Lancet Regional Health - Americas (Online) Vol. 1; p. 100018
• Main Authors: Tordoff, Diana M., Greninger, Alexander L., Roychoudhury, Pavitra, Shrestha, Lasata, Xie, Hong, Jerome, Keith R., Breit, Nathan, Huang, Meei-Li, Famulare, Mike, Herbeck, Joshua T.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.09.2021; The Authors. Published by Elsevier Ltd; Elsevier
• Subjects: Genomic analysis; Molecular epidemiology; Phylogeography; Research Paper; SARS-CoV-2; Molecular epidemiology; SARS-CoV-2; Genomic analysis; Phylogeography
• ISSN: 2667-193X; 2667-193X
• DOI: 10.1016/j.lana.2021.100018

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.