Descriptive Analysis of SARS-CoV-2 Genomics Data from Ambulatory Patients

Background: The COVID-19 pandemic has been characterized by ongoing evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with concomitant variation in viral transmissibility and morbidity. Within specific timeframes and geographic areas, multiple SARS-CoV-2 variants have coexisted in the human population, each characterized by distinct biologic and clinical features, such as varying susceptibility to neutralizing monoclonal antibodies (nMAbs), a major frontline treatment. As part of an observational real-world data study of the effectiveness of nMAbs for treatment of COVID-19, SARS-CoV-2 viral samples were obtained from patients under treatment, generating paired clinical and genomics data. This paper describes the processing pipeline and findings from the genomics portion of this combined data set. Methods: SARS-CoV-2 sequences were generated from 14,796 diagnostic samples from four large U.S. health systems between July 2020 and March 2022. Among nMAbs-treated patients, samples were collected on the same day as, or prior to, treatment with nMAbs. Thus, these samples represent a snapshot of SARS-CoV-2 variants circulating in the respective patient groups, as opposed to variants that arose in response to specific treatments. Health systems collected viral samples and performed library creation and sequencing according to local protocols, using tiled ARTIC amplicon primers. FASTQ files were submitted to a study data platform and processed through a common pipeline. This pipeline enabled a unified approach to quality control, assembly, and production of genomics features for downstream analysis. Results: Alpha and pre-Alpha SARS-CoV-2 lineages were predominant in the data set prior to June 2021. From June 2021 through November 2021, Delta was the dominant variant. Beginning in December 2021, Omicron was dominant. A variety of mutations associated with decreased nMAbs binding to the spike protein in vitro were detected, including lineage-defining mutations and non-lineage-defining mutations such as E340A, G446V, and S494P. Distinct patterns of sequence gaps and ambiguous base calls were associated with distinct variants. Conclusions: The distribution of SARS-CoV-2 variants, per WHO nomenclature, across epochs in this data set matched concurrent CDC genomic surveillance results across the U.S. Detection of putative nMAbs escape mutations within clinical samples was consistent with FDA decisions to amend EUAs as variants emerged. This genomics data set provides an opportunity to examine associations between SARS-CoV-2 genomic variation and clinical outcomes in the associated EHR data set. The expansion of real-world data sets such as this to study the relationship between viral sequence and treatment outcomes could provide the foundation for future efforts to achieve near-real-time understanding of clinical outcomes related to genomic variation over time, and evidence to update treatment decisions more rapidly and to greater effect during ongoing and future pandemics. ### Competing Interest Statement Dr Amin reported receiving grants from the University of California, Irvine, during the conduct of the study; grants from Alexion Pharmaceuticals, Blade Therapeutics, Eli Lilly and Company, Fulcrum Therapeutics, Humanigen, the National Institute of Allergy and Infectious Diseases, Novartis, NRx Pharmaceuticals, Octapharma, Pulmotect, PTC Therapeutics, and Takeda Pharmaceuticals; and personal fees from Achogen LaJolla, Alexion Pharmaceuticals, AseptiScope, AstraZeneca, Bayer, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lilly and Company, Ferring Pharmaceuticals, Gilead Sciences, HeartRite, Millennium Pharmaceuticals, Mylan, Nabriva Therapeutics, Novartis, Paratek Pharmaceuticals, Pfizer, Portola Pharmaceuticals, Salix Pharmaceuticals, Seres Therapeutics, Spero Therapeutics, Sprightly Health, Sunovion Pharmaceuticals, and Tetraphase Pharmaceuticals outside the submitted work. Dr Bertagnolli reported receiving personal fees from The MITRE Corporation during the conduct of the study. Dr Chow reported receiving personal fees from Canon Medical Systems outside the submitted work. Dr Drews reported receiving grants from The MITRE Corporation during the conduct of the study and outside the submitted work. Dr Jones reported receiving personal fees from The MITRE Corporation during the conduct of the study. Dr Lopansri reported receiving personal fees from Seegene outside the submitted work. Dr O'Horo reported receiving grants from The MITRE Corporation during the conduct of the study; grants from nference; and personal fees from Bates College outside the submitted work. Dr Piantadosi reported receiving personal fees from The MITRE Corporation during the conduct of the study and outside the submitted work. Dr Pritt reported receiving funding from The MITRE Corporation during the conduct of the study. Dr Razonable reported receiving grants from Gilead Sciences, Regeneron Pharmaceuticals, and Roche and personal fees from Novartis outside the submitted work. Dr Webb reported receiving grants from Gilead Sciences and Regeneron Pharmaceuticals outside the submitted work. No other disclosures were reported. ### Funding Statement This study was supported by funding from the Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, under contract 75FCMC18D0047, task order 75A50121F80012, with The MITRE Corporation. The funding organization was involved in the design of the study; interpretation of the data; preparation, review, and approval of the manuscript; and decision to submit the manuscript to a pre-print server. ### 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: Study design and methods were approved by the institutional review boards at the organization conducting the parent cohort study (The MITRE Corporation) and at the 4 health systems (University of California-Irvine Medical Center, Center for Individualized Medicine-Mayo Clinic Research [Minnesota], Houston Methodist [Texas], and Intermountain Healthcare [Utah]) participating in the study. The need for informed consent was waived because this study used deidentified data. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Deidentified data has been submitted to National COVID Cohort Collaborative (N3C). Available at https://ncats.nih.gov/n3c.