Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny
Author:
Leiser Owen P.ORCID, Auberry Deanna L., Bakker Erica, Chrisler Will, Engbrecht Kristin, Engelmann Heather, Fansler Sarah, Gerbasi Vincent, Hansen JoshuaORCID, Hutchinson Chelsea, Hutchison Janine, Lancaster Mary J., Lawrence Kathleen, Melville Angela, Mobberley Jennifer, O’Bryon Isabelle, Oxford Kristie L., Oxford Tessa, Phillips Shelby, Rodda Kabrena E., Sanford James A., Schepmoes Athena, Staley Brian E., Terrell Kelcey, Victry Kristin, Warner Cynthia, Omberg Kristin M.ORCID
Abstract
In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.
Funder
US Department of Energy Office of Science National Virtual Biotechnology Laboratory
Publisher
Public Library of Science (PLoS)
Subject
Multidisciplinary
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