One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021

Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to S...

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Bibliographic Details
Published in:	PloS one Vol. 17; no. 10; p. e0272830
Main Authors:	Yaglom, Hayley D, Maurer, Matthew, Collins, Brooke, Hojnacki, Jacob, Monroy-Nieto, Juan, Bowers, Jolene R, Packard, Samuel, Erickson, Daryn E, Barrand, Zachary A, Simmons, Kyle M, Brock, Breezy N, Lim, Efrem S, Smith, Sandra, Hepp, Crystal M, Engelthaler, David M
Format:	Journal Article
Language:	English
Published:	San Francisco Public Library of Science 31-10-2022 Public Library of Science (PLoS)
Subjects:	Biology and Life Sciences College campuses Colleges & universities Computer and Information Sciences Contact tracing Coronaviruses COVID-19 Dormitories Epidemiology Genomes Genomics Infectious diseases Medicine and health sciences Mitigation Mutation Outbreaks Phylogeny Public health Safety and security measures Severe acute respiratory syndrome coronavirus 2 Surveillance Undergraduate study United States Universities and colleges Viral diseases Wastewater Water sampling United States United States > US Arizona
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Summary:	Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to SARS-CoV-2 genomes belonging to an outbreak of AY.25 identified through ongoing phylogenomic analyses. Continued phylogenetic analyses were conducted to further describe the AY.25 outbreak. Wastewater collected twice weekly from sites across campus was tested for SARS-CoV-2 by RT-qPCR, and subsequently sequenced to identify variants. The AY.25 outbreak was defined by a single mutation (C18804T) and comprised 379 genomes from SARS-CoV-2 positive cases associated with the university and community. Several undergraduate student gatherings and congregate living settings on campus likely contributed to the rapid spread of COVID-19 across the university with secondary transmission into the community. The clade defining mutation was also found in wastewater samples collected from around student dormitories a week before the semester began, and 9 days before cases were identified. Genomic, epidemiologic, and wastewater surveillance provided evidence that an AY.25 clone was likely imported into the university setting just prior to the onset of the Fall 2021 semester, rapidly spread through a subset of the student population, and then subsequent spillover occurred in the surrounding community. The university and local public health department worked closely together to facilitate timely reporting of cases, identification of close contacts, and other necessary response and mitigation strategies. The emergence of new SARS-CoV-2 variants and potential threat of other infectious disease outbreaks on university campuses presents an opportunity for future comprehensive One Health genomic data driven, targeted interventions.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 HDY and MM contributed equally to this work and co-first authors. Competing Interests: The authors have declared that no competing interests exist.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0272830