{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T01:19:43Z","timestamp":1776734383591,"version":"3.51.2"},"reference-count":26,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T00:00:00Z","timestamp":1766102400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CovarrNet","award":["ARR-175622"],"award-info":[{"award-number":["ARR-175622"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,19]]},"abstract":"<jats:p>Ongoing viral evolution is a key driver of global pandemics, such as COVID-19, contributing to the repeated emergence and spread of new variants of concern. Identifying emerging viral variants is crucial for controlling the spread of infection; however, patient testing is not always feasible, and clinical samples are not routinely sequenced. As a result, new approaches, such as environmental-based surveillance, are needed for monitoring genetic diversity. Floor swabs provide greater spatial resolution than other environmental sampling approaches, but pose challenges for genomic analyses due to microbial RNA\/DNA yields. We investigate the potential of obtaining whole-genome diversity data from floor swab samples to detect circulating lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Floor swabs (n=23) were collected and sequenced from public locations in Ottawa, Canada, during December 2022, and were compared with contemporaneous human samples. Low biomass recovery remained a challenge, as approximately half of the swabs did not yield sufficient genetic material for analysis. The most commonly identified lineages from the floor swabs were XBB, while B (12.5%) and BA (12.5%) lineages appeared less frequently. In contrast, swab results from humans most often identified BQ (49.3%), BA (23.8%) and BF (17.8%), with XBB detected at a lower prevalence (2.7%). XBB became the dominant lineage in the region in the month following floor swab collection, suggesting that floor swabs may offer early signals of emerging outbreaks in comparison with hospital-based clinical sampling. This may suggest a role for floor swabs in outbreak prediction; however, larger studies are needed to validate this approach.<\/jats:p>","DOI":"10.1099\/mgen.0.001575","type":"journal-article","created":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T17:17:03Z","timestamp":1766164623000},"source":"Crossref","is-referenced-by-count":1,"title":["Sequencing and variant calling of SARS-CoV-2 from floor swabs: a potential tool for identifying emergent lineages"],"prefix":"10.1099","volume":"11","author":[{"given":"Benazir","family":"Hodzic-Santor","sequence":"first","affiliation":[{"name":"Division of General Internal Medicine, Sinai Health System, Toronto, ON, Canada"},{"name":"Department of Medicine, University of Toronto, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron","family":"Hinz","sequence":"additional","affiliation":[{"name":"Department of Biology, McGill University, Montreal, QC, Canada"},{"name":"Department of Biology, Carleton 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