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One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021.
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.
  • Yaglom HD; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Maurer M; Coconino County Health and Human Services, Flagstaff, Arizona, United States of America.
  • Collins B; Coconino County Health and Human Services, Flagstaff, Arizona, United States of America.
  • Hojnacki J; Coconino County Health and Human Services, Flagstaff, Arizona, United States of America.
  • Monroy-Nieto J; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Bowers JR; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Packard S; Coconino County Health and Human Services, Flagstaff, Arizona, United States of America.
  • Erickson DE; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Barrand ZA; School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
  • Simmons KM; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
  • Brock BN; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Lim ES; School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
  • Smith S; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
  • Hepp CM; Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
  • Engelthaler DM; School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
PLoS One ; 17(10): e0272830, 2022.
Article in English | MEDLINE | ID: covidwho-2098733
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: One Health / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Journal.pone.0272830

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Full text: Available Collection: International databases Database: MEDLINE Main subject: One Health / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Journal.pone.0272830