Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon

Publication Title

medRxiv

Authors

Alexa K Dowdell, Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, OR, USA.Follow
Kevin Matlock
Fred L. Robinson, Providence St. Joseph Health
Roshanthi Weerasinghe, Providence St Joseph Health, Renton, WA.Follow
Rogan Rattray, Providence St. Joseph HealthFollow
Marina Pukay, Providence St. Joseph HealthFollow
Melvin Lathara
Anastacia Harlan, Providence St. Joseph HealthFollow
Thomas R. Ward, Providence St. Joseph HealthFollow
Mary Campbell, Providence St. Joseph HealthFollow
Walter Urba, Earle A. Chiles Research InstituteFollow
Ganapati Srinivasa
Carlo Bifulco, Earle A. Chiles Research Institute, Robert W. Franz Cancer Research Center, Providence Portland Medical Center, Portland, ORFollow
Brian D. Piening, Molecular Genomics Laboratory, Providence Portland Medical Center, Portland, OR; Earle A. Chiles Research Institute, Robert W. Franz Cancer Research Center, Providence Portland Cancer Center, Portland, OR.Follow

Document Type

Article

Publication Date

8-4-2020

Keywords

2019-nCoV; genomics

Abstract

The first reported case of COVID-19 in the State of Oregon occurred in late February 2020, with subsequent outbreaks occurring in the populous Portland metro area but also with significant outbreaks in less-populous and rural areas. Here we report viral sequences from 188 patients across the hospitals and associated clinics in the Providence Health System in the State of Oregon dating back to the early days of the outbreak. We show a significant shift in dominant clade lineages over time in Oregon, with the rapid emergence and dominance of Spike D614G-positive variants. We also highlight significant diversity in SARS-CoV-2 sequences in Oregon, including a large number of rare mutations, indicative that these genomes could be utilized for outbreak tracing. Lastly, we show that SARS-CoV-2 genomic information may offer additional utility in combination with clinical covariates in the prediction of acute disease phenotypes.

Specialty/Research Institute

Earle A. Chiles Research Institute

Specialty/Research Institute

Infectious Diseases

Comments

This article is a preprint and has not been certified by peer review. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.