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

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

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)
Creator	Keim, Paul Engelthaler, David Ladner, Jason Bokulich, Nicholas Bolyen, Evan Bowers, Jolene Caporaso, J Folkerts, Megan Hepp, Crystal Kaelin, Emily Komatsu, Kenneth Larsen, Brendan Lemmer, Darrin Lim, Efrem Maqsood, Rabia Pfeiffer, Ashlyn Quirk, Grace Sahl, Jason Sheridan, Krystal Waddell, Victor Watts, Thomas Worobey, Michael Yaglom, Hayley
Source	MedRxiv
abstract	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.
has issue date	2020-05-13(xsd:dateTime)
bibo:doi	10.1101/2020.05.08.20095935
has license	medrxiv
sha1sum (hex)	092a7d7d64e92791f6d38cf10abb0cda4de9f62c
schema:url	https://doi.org/10.1101/2020.05.08.20095935
resource representing a document's title	Defining the Pandemic at the State Level: Sequence-Based Epidemiology of the SARS-CoV-2 virus by the Arizona COVID-19 Genomics Union (ACGU)
resource representing a document's body	covid:092a7d7d64e92791f6d38cf10abb0cda4de9f62c#body_text
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