Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)

In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China causing severe morbidity and mortality. Since then, the virus has swept across the globe causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, provided to us by the Arizona Department of Health Services, and at Arizona State University and the University of Arizona, collected as part of community surveillance projects. Phylogenetic analysis of 79 genomes we generated from across Arizona revealed a minimum of 9 distinct introductions throughout February and March. We show that >80% of our sequences descend from clades that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related cases in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported in part by funds provided by The NARBHA Institute, The Flinn Foundation, The Virginia G. Piper Charitable Trust, and Blue Cross and Blue Shield of Arizona (DME, JRB) as well as the National Institutes of Health (NIH grant: R00 DK107923) (ESL), and David and Lucile Packard Foundation as well as the University of Arizona College of Science, BIO5 Institute and Office of Research Innovation and Impact (MW). Computational analyses were run on Northern Arizona University’s Monsoon computing cluster, funded by Arizona’s Technology and Research Initiative Fund. Additional analysis effort was funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. The Cowden Endowment for Microbiology provided funds to support salaries. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes 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 sequences have been deposited into the GISAID repository. The software developed for our sequence collection sampling workflow is available at https://github.com/caporaso-lab/az-covid-1 under the BSD 3-clause license. Supplementary Tables 1 and 2 can be found at https://github.com/caporaso-lab/az-covid-1/tree/preprint.v1/paper1