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

被引：28

作者：

Mueller, Nicola F. ^{[1
]}

Wagner, Cassia ^{[1
,2
]}

Frazar, Chris D. ^{[2
]}

Roychoudhury, Pavitra ^{[1
,3
]}

Lee, Jover ^{[1
]}

Moncla, Louise H. ^{[1
]}

Pelle, Benjamin ^{[2
]}

Richardson, Matthew ^{[2
]}

Ryke, Erica ^{[2
]}

Xie, Hong ^{[3
]}

Shrestha, Lasata ^{[3
]}

Addetia, Amin ^{[3
]}

Rachleff, Victoria M. ^{[1
,3
]}

Lieberman, Nicole A. P. ^{[3
]}

Huang, Meei-Li ^{[3
]}

Gautom, Romesh ^{[4
]}

Melly, Geoff ^{[4
]}

Hiatt, Brian ^{[4
]}

Dykema, Philip ^{[4
]}

Adler, Amanda ^{[5
]}

Brandstetter, Elisabeth ^{[6
]}

Han, Peter D. ^{[2
]}

Fay, Kairsten ^{[1
]}

Llcisin, Misja ^{[1
]}

Lacombe, Kristen ^{[5
]}

Sibley, Thomas R. ^{[1
]}

Truong, Melissa ^{[2
]}

Wolf, Caitlin R. ^{[6
]}

Boeckh, Michael ^{[1
,6
,7
]}

Englund, Janet A. ^{[5
,8
]}

Famulare, Michael ^{[9
]}

Lutz, Barry R. ^{[7
,10
]}

Rieder, Mark J. ^{[7
]}

Thompson, Matthew ^{[11
]}

Duchin, Jeffrey S. ^{[6
,12
]}

Starita, Lea M. ^{[2
,7
]}

Chu, Helen Y. ^{[6
,7
]}

Shendure, Jay ^{[2
,7
,13
]}

Jerome, Keith R. ^{[1
,3
]}

Lindquist, Scott ^{[4
]}

Greninger, Alexander L. ^{[1
,3
]}

Nickerson, Deborah A. ^{[2
,7
]}

Bedford, Trevor ^{[1
,2
,7
]}

机构：

[1] Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, Seattle, WA 98109 USA

[2] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[3] Univ Washington, Dept Lab Med & Pathol, Seattle, WA 98195 USA

[4] Washington State Dept Hlth, Shoreline, WA 98155 USA

[5] Seattle Childrens Res Inst, Seattle, WA 98101 USA

[6] Univ Washington, Dept Med, Div Allergy & Infect Dis, Seattle, WA 98195 USA

[7] Brotman Baty Inst Precis Med, Seattle, WA 98195 USA

[8] Univ Washington, Dept Pediat, Seattle, WA 98105 USA

[9] Inst Dis Modeling, Bellevue, WA 98105 USA

[10] Univ Washington, Dept Bioengn, Seattle, WA 98105 USA

[11] Univ Washington, Dept Global Hlth, Seattle, WA 98195 USA

[12] Publ Hlth Seattle & King Cty, Seattle, WA 98121 USA

[13] Howard Hughes Med Inst, Seattle, WA 98195 USA

来源：

SCIENCE TRANSLATIONAL MEDICINE | 2021年 / 13卷 / 595期

基金：

瑞士国家科学基金会;

关键词：

COALESCENT;

D O I：

10.1126/scitranslmed.abf0202

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected 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 (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, 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 affects clinical severity or patient outcomes. Overall, this suggests that with regard 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.

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