Longitudinal genomic surveillance of SARS-CoV-2 in a university microcosm reflects global evolutionary trends

SARS-CoV-2 transmission has declined, yet ongoing viral evolution continues to pose public health challenges. This study conducted long-term (2020-2024) genomic surveillance within a large and globally diverse university community. Viral genomes obtained from clinical (n = 1,786) and surveillance (n = 888) testing samples were classified under clade, lineage, and variant systems, and compared with global genomic data sets. Local patterns broadly paralleled global evolutionary trends, including the phased emergence of major variants, episodic introductions of new lineages, and shifts in dominant clades. Lineage diversity peaked during fall semesters and was highest among undergraduate-aged individuals, with similar distributions across sexes. Phylogenetic analyses revealed transmission patterns characteristic of semi-contained, high-contact environments. These findings illustrate how large university communities can serve as microcosms of broader SARS-CoV-2 evolution. They also demonstrate the value of targeted genomic surveillance in generating epidemiologic intelligence to support early detection, track viral diversification, and inform public health preparedness.

This study highlights the public health and epidemiological value of academic laboratories and campus‑based testing programs in variant monitoring, outbreak detection, and pandemic preparedness. It also demonstrates how locally generated genomic data can effectively complement national and global surveillance networks.