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

PLoS One. 2022 Oct 31;17(10):e0272830. doi: 10.1371/journal.pone.0272830. eCollection 2022.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arizona / epidemiology
  • COVID-19* / epidemiology
  • Disease Outbreaks
  • Genomics
  • Humans
  • One Health*
  • Phylogeny
  • SARS-CoV-2 / genetics
  • Universities
  • Wastewater
  • Wastewater-Based Epidemiological Monitoring

Substances

  • Waste Water

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

The NARBHA Institute (#AOTHNARBHA3640C) and the Arizona Department of Health Services (#CTR049427) provided financial support for this work, mainly the genomic sequencing efforts.” These agencies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No authors received a salary from any of the funders.