An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
AuthorLadner, Jason T
Larsen, Brendan B
Bowers, Jolene R
Hepp, Crystal M
Sahl, Jason W
Kaelin, Emily A
Bokulich, Nicholas A
Watts, Thomas D
Komatsu, Kenneth K
Lim, Efrem S
Caporaso, J Gregory
Engelthaler, David M
AffiliationUniv Arizona, Dept Ecol & Evolutionary Biol
MetadataShow full item record
PublisherAMER SOC MICROBIOLOGY
CitationLadner, J. T., Larsen, B. B., Bowers, J. R., Hepp, C. M., Bolyen, E., Folkerts, M., ... & Keim, P. (2020). An early pandemic analysis of SARS-CoV-2 population structure and dynamics in Arizona. MBio, 11(5).
RightsCopyright © 2020 Ladner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractIn 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, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains 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 case 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.IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.
NoteOpen access journal
VersionFinal published version
Except where otherwise noted, this item's license is described as Copyright © 2020 Ladner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
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