SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community

Valesano, Andrew L; Fitzsimmons, William J.; Blair, Christopher; Woods, Robert J.; Gilbert, Julie; Rudnik, Dawn; Mortenson, Lindsey; Friedrich, Thomas C.; O’Connor, David H.; MacCannell, Duncan; Petrie, Joshua G.; Martin, Emily T.; Lauring, Adam S.

doi:10.1093/ofid/ofab518

Cited by 25 publications

(20 citation statements)

References 31 publications

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“…Overall, we were able to successfully achieve viral genomic sequencing of an average of 32% of weekly cases confirmed SARS-CoV-2 positive by RT-PCR throughout the study period. This percentage is consistent with other studies conducted in a university setting, and higher than other studies done in a similarly localized population or state-level sequencing efforts in states like New York which aims to sequence 15% of weekly samples to pick up trends over time [16,19,20,45]. A total of 677 whole-genomes were successfully sequenced from the Purdue campus over the course of the 18-week study period, taking into account differences in actual case number positivity and testing per week in the community.…”

Section: Discussionsupporting

confidence: 89%

“…While rapid implementation of SARS-CoV-2 genome sequencing has proven useful in the investigation of COVID-19 dynamics in other institutional settings like healthcare, few studies have been conducted on university campuses [15][16][17][18][19][20][21][22][23]. Some studies in the university setting have evaluated testing programs to understand control of SARS-CoV-2 transmission, while others used modeling approaches to infer SARS-CoV-2 transmission or estimate the introduction and growth rate of particular variants [17,[24][25][26].…”

Section: Introductionmentioning

confidence: 99%

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Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant

Ciubotariu

Dorman

Gorenstein

et al. 2022

Preprint

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Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis we tracked the spread and introduction events of SARS-CoV-2 variants focusing on a large university community. Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame. Our analysis of circulating SARS-CoV-2 variants over time revealed periods when Variant of Concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20,000 previously published P.1 genomes revealed ten independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread. We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.

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Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant

Ciubotariu

Dorman

Gorenstein

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Furthermore, unlike the report by Valesano, et al (2021) [32] which found that university cases in Michigan did not contribute enhanced transmission in the community, the viral clone discussed here was identified in more than 40% of cases with no known association with the university (i.e., community). This may in part be due to the relatively small size of the surrounding city (estimated population of ~75,000) and its tourism-based economy.…”

Section: (Which Was Not Certified By Peer Review)contrasting

confidence: 96%

One Health Genomic Surveillance and Response to a University-Based Outbreak of the SARS-CoV-2 Delta AY.25 Lineage, Arizona, 2021

Yaglom

Maurer

Collins

et al. 2022

Preprint

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Large scale outbreaks of the SARS-CoV-2 Delta variant have occurred in numerous settings, including universities. An outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus with multiple transmission events was identified; genomic analyses characterized this outbreak and complemented contract tracing and wastewater surveillance strategies that strengthened overall public health response actions. Epidemiologic and clinical data routinely gathered through contact tracing and public health investigations was matched to genomic sequencing of SARS-CoV-2 positive samples belonging to a suspect cluster identified through ongoing phylogenomic analyses. Continued phylogenetic analyses were conducted to 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 during "move-in", 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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“…The outbreak in students was asynchronous with the outbreak in non-students in Centre County and led the reported cases in the non-student residents of Centre County. Other studies of university populations also noted little genomic evidence for spread between student populations with high incidence and surrounding non-student communities 19 , 20 . The outbreak in Centre County’s non-students was synchronous with outbreaks in surrounding counties.…”

Section: Discussionmentioning

confidence: 99%

Large university with high COVID-19 incidence is not associated with excess cases in non-student population

Bharti

Lambert

Exten

et al. 2022

Sci Rep

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Large US colleges and universities that re-opened campuses in the fall of 2020 and the spring of 2021 experienced high per capita rates of COVID-19. Returns to campus were controversial because they posed a potential risk to surrounding communities. A large university in Pennsylvania that returned to in-person instruction for Fall 2020 and Spring 2021 semesters reported high incidence of COVID-19 among students. However, the co-located non-student resident population in the county experienced fewer COVID-19 cases per capita than reported in neighboring counties. Activity patterns from mobile devices indicate that the non-student resident population near the university restricted their movements during the pandemic more than residents of neighboring counties. Respiratory virus prevention and management in student and non-student populations requires different, specifically targeted strategies.

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SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community

Cited by 25 publications

References 31 publications

Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant

Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant

One Health Genomic Surveillance and Response to a University-Based Outbreak of the SARS-CoV-2 Delta AY.25 Lineage, Arizona, 2021

Large university with high COVID-19 incidence is not associated with excess cases in non-student population

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