Dataset Information

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

ABSTRACT: The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new 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) 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 see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.

SUBMITTER: Muller NF

PROVIDER: S-EPMC7536883 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Müller Nicola F NF Wagner Cassia C Frazar Chris D CD Roychoudhury Pavitra P Lee Jover J Moncla Louise H LH Pelle Benjamin B Richardson Matthew M Ryke Erica E Xie Hong H Shrestha Lasata L Addetia Amin A Rachleff Victoria M VM Lieberman Nicole A P NAP Huang Meei-Li ML Gautom Romesh R Melly Geoff G Hiatt Brian B Dykema Philip P Adler Amanda A Brandstetter Elisabeth E Han Peter D PD Fay Kairsten K Llcisin Misja M Lacombe Kristen K Sibley Thomas R TR Truong Melissa M Wolf Caitlin R CR Boeckh Michael M Englund Janet A JA Famulare Michael M Lutz Barry R BR Rieder Mark J MJ Thompson Matthew M Duchin Jeffrey S JS Starita Lea M LM Chu Helen Y HY Shendure Jay J Jerome Keith R KR Lindquist Scott S Greninger Alexander L AL Nickerson Deborah A DA Bedford Trevor T

medRxiv : the preprint server for health sciences 20200930

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new 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) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineag ...[more]

PMID: 33024981

Similar Datasets

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in Wuhan, China in December of 2019 and has since caused a global pandemic resulting in millions of deaths and tens of millions of patients testing positive for infection. Analysis of different viral strains has identified a D614G change in the spike protein that is correlated with the virus becoming more transmissible. While studies have shown G614 viruses to be more transmissible, the effects of this mutation on the host response, especially on the cellular level, are yet to be fully elucidated. In this experiment we infected NHBE cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at three different time points to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes, enriched Gene Ontology terms and dysregulated signaling pathways. We detected over 2,000 differentially expressed genes, over 600 Gene Ontology terms, and 29 affected pathways between the two treatments. Many of these entities play a role in immune signaling and response. When comparing the different strains and different time points we found more overall similarities between matched time points than across different time points with the same strain. When specifically comparing the affected pathways, we saw that the 24hr time point of the New York strain was more similar to the 12hr time point of the Washington strain with a large number of pathways related to translation being inhibited in both strains at these time points. These results suggest that D614G substitution in the spike protein, combined with other nonsynonymous changes in the viral gene products cause distinct responses in infected host cells, especially relating to how quickly translation is dysregulated after infection. These observed differences in the intracellular host response to infection could play a role in driving the increase in pathogenicity and mortality seen in the New York outbreaks versus the Washington outbreaks at the beginning of the SARS-CoV-2 pandemic.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets