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Volume 10, Issue 2

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

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genomic surveillance , Omicron , phylodynamics , SARS-CoV-2 , sequencing and university population
Funding
This study was supported by the:
  • Graduate School, Purdue University
    • Principle Award Recipient: IlincaI. Ciubotariu
  • Purdue University
    • Principle Award Recipient: RebeccaP. Wilkes
  • Department of Biological Sciences, Purdue University
    • Principle Award Recipient: GiovannaCarpi
  • University of Iowa
    • Principle Award Recipient: AndrewKitchen
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-02-09
2024-05-09
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Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population
M Gen 10, 001194 (2024); https://doi.org/10.1099/mgen.0.001194
/content/journal/mgen/10.1099/mgen.0.001194
/content/journal/mgen/10.1099/mgen.0.001194
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