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

Ilinca I. Ciubotariu; Jack Dorman; Nicole M. Perry; Lev Gorenstein; Jobin J. Kattoor; Abebe A. Fola; Amy Zine; G. Kenitra Hendrix; Rebecca P. Wilkes; Andrew Kitchen; Giovanna Carpi

doi:10.1093/ofid/ofac268

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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

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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

Ilinca I. Ciubotariu, Jack Dorman, Nicole M. Perry, Lev Gorenstein, Jobin J. Kattoor, Abebe A. Fola, Amy Zine, G. Kenitra Hendrix, Rebecca P. Wilkes, Andrew Kitchen, …

Open forum infectious diseases, Vol.9(7), ofac268

05/26/2022

DOI: 10.1093/ofid/ofac268

PMID: 35818365

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Abstract

Abstract Background 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. Methods 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. Results 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. Conclusions 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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Title: Subtitle: Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant
Creators: Ilinca I. Ciubotariu - Purdue University West Lafayette
Jack Dorman - Purdue University West Lafayette
Nicole M. Perry - Purdue University West Lafayette
Lev Gorenstein - Purdue University West Lafayette
Jobin J. Kattoor - Purdue University West Lafayette
Abebe A. Fola - Purdue University West Lafayette
Amy Zine - University of Iowa
G. Kenitra Hendrix - Purdue University West Lafayette
Rebecca P. Wilkes - Purdue University West Lafayette
Andrew Kitchen - University of Iowa
Giovanna Carpi - Purdue University West Lafayette
Resource Type: Journal article
Publication Details: Open forum infectious diseases, Vol.9(7), ofac268
DOI: 10.1093/ofid/ofac268
PMID: 35818365
NLM abbreviation: Open Forum Infect Dis
ISSN: 2328-8957
eISSN: 2328-8957
Publisher: Oxford University Press
Grant note: name: Purdue Department of Biological Sciences
Language: English
Date published: 05/26/2022
Academic Unit: Anthropology; International Programs
Record Identifier: 9984274823302771

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