Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Meei-Li Huang, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. 2021. Sci Transl Med 13: eabf0202.
PDF
muller-ncov-wa-d614g.pdf
Supplement
muller-ncov-wa-d614g-supp.pdf
DOI
10.1126/scitranslmed.abf0202
GitHub
blab/ncov-wa-phylodynamics

Abstract

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) in early 2020 was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that with regards to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.