Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Ilinca I Ciubotariu; Rebecca P Wilkes; Jobin J Kattoor; Erin N Christian; Giovanna Carpi; Andrew Kitchen

doi:10.1099/mgen.0.001194

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Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Journal article

Open access

Peer reviewed

Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Ilinca I Ciubotariu, Rebecca P Wilkes, Jobin J Kattoor, Erin N Christian, Giovanna Carpi and Andrew Kitchen

Microbial genomics, Vol.10(2), 001194

02/2024

DOI: 10.1099/mgen.0.001194

PMCID: PMC10926704

PMID: 38334271

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Abstract

Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.

SARS-CoV-2

Omicron

university population

phylodynamics

genomic surveillance

sequencing

Details

Title: Subtitle: Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population
Creators: Ilinca I Ciubotariu - Purdue University West Lafayette
Rebecca P Wilkes - Purdue University West Lafayette
Jobin J Kattoor - Purdue University West Lafayette
Erin N Christian - Purdue University West Lafayette
Giovanna Carpi - Purdue University West Lafayette
Andrew Kitchen - University of Iowa
Resource Type: Journal article
Publication Details: Microbial genomics, Vol.10(2), 001194
DOI: 10.1099/mgen.0.001194
PMID: 38334271
PMCID: PMC10926704
NLM abbreviation: Microb Genom
eISSN: 2057-5858
Grant note: DOI: 10.13039/100008893, name: University of Iowa; DOI: 10.13039/100011623, name: Department of Biological Sciences, Purdue University; DOI: 10.13039/100006377, name: Purdue University; DOI: 10.13039/100007290, name: Graduate School, Purdue University
Language: English
Date published: 02/2024
Academic Unit: Anthropology; International Programs
Record Identifier: 9984557838702771

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