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. 2021 Sep:1:100018.
doi: 10.1016/j.lana.2021.100018. Epub 2021 Jul 13.

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

Diana M Tordoff  1   2 , Alexander L Greninger  3 , Pavitra Roychoudhury  3 , Lasata Shrestha  3 , Hong Xie  3 , Keith R Jerome  3   4 , Nathan Breit  3 , Meei-Li Huang  3 , Mike Famulare  2 , Joshua T Herbeck  2   5
Affiliations

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

Diana M Tordoff et al. Lancet Reg Health Am. 2021 Sep.

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 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: 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: 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: None.

Keywords: Genomic analysis; Molecular epidemiology; Phylogeography; SARS-CoV-2.

PubMed Disclaimer

Conflict of interest statement

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.

Figures

Figure 1
Figure 1
Geographic variation in confirmed SARS-CoV-2 cases, genome sequences, and sampling coverage in WA
Figure 2
Figure 2
Estimates number and proportion of SARS-CoV-2 introductions and exports by lineage.
Figure 3
Figure 3
Temporal trends in SARS-CoV-2 sampling coverage, introductions and exported lineages for Washington State
Figure 4
Figure 4
Size and duration of Washington state subclades resulting from an out-of-state introduction of SARS-CoV-2
See this image and copyright information in PMC

Update of

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