Genomic heterogeneity and clinical characterization of SARS CoV 2 in Oregon

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. ### Competing Interest Statement KM, ML and GS are employees of and hold a vested interest in Omics Data Automation, Inc. ### Funding Statement This work was supported by a grant from Providence Foundations of Oregon. Omics Data Automation employees (KM, ML and GS) were supported by a grant from the National Science Foundation under award #1721343. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Providence St Joseph Health Institutional Review Board reviewed and approved this study (IRB protocol number 2020000127). All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All SARS-CoV-2 sequences generated for this manuscript are publicly available through GISAID.org (under originating laboratory Providence St. Joseph Health Molecular Genomics Laboratory or by author filter for Dowdell et al.). Deidentified clinical data are available upon request.