Publication date: Dec 01, 2025
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.
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Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | COVID-19 |
| disease | MESH | infection |
| disease | MESH | severe acute respiratory syndrome |
| disease | MESH | included |
| drug | DRUGBANK | Water |