tetano
Editor, Senior Moderator
Microb Genom
. 2025 Dec;11(12):001575.
doi: 10.1099/mgen.0.001575. Sequencing and variant calling of SARS-CoV-2 from floor swabs: a potential tool for identifying emergent lineages
Benazir Hodzic-Santor[SUP] 1 2 [/SUP], Aaron Hinz[SUP] 3 4 [/SUP], Rees Kassen[SUP] 4 [/SUP], Ju-Ling Liu[SUP] 5 6 [/SUP], Haig Djambazian[SUP] 5 6 [/SUP], Sally Lee[SUP] 5 6 [/SUP], Alexandra Hicks[SUP] 7 [/SUP], Calvin Sjaarda[SUP] 8 9 10 [/SUP], Henry Wong[SUP] 8 9 10 [/SUP], Prameet M Sheth[SUP] 8 9 10 [/SUP], Caroline Nott[SUP] 11 12 [/SUP], Derek R MacFadden[SUP] 11 12 [/SUP], Anne-Marie Roy[SUP] 5 6 [/SUP], Jiannis Ragoussis[SUP] 5 6 [/SUP], Lucas Castellani[SUP] 13 14 [/SUP], Michael Fralick[SUP] 1 15 [/SUP], Alex Wong[SUP] 3 [/SUP]
Affiliations
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.
Keywords: built environment; environmental surveillance; viral diversity.
. 2025 Dec;11(12):001575.
doi: 10.1099/mgen.0.001575. Sequencing and variant calling of SARS-CoV-2 from floor swabs: a potential tool for identifying emergent lineages
Benazir Hodzic-Santor[SUP] 1 2 [/SUP], Aaron Hinz[SUP] 3 4 [/SUP], Rees Kassen[SUP] 4 [/SUP], Ju-Ling Liu[SUP] 5 6 [/SUP], Haig Djambazian[SUP] 5 6 [/SUP], Sally Lee[SUP] 5 6 [/SUP], Alexandra Hicks[SUP] 7 [/SUP], Calvin Sjaarda[SUP] 8 9 10 [/SUP], Henry Wong[SUP] 8 9 10 [/SUP], Prameet M Sheth[SUP] 8 9 10 [/SUP], Caroline Nott[SUP] 11 12 [/SUP], Derek R MacFadden[SUP] 11 12 [/SUP], Anne-Marie Roy[SUP] 5 6 [/SUP], Jiannis Ragoussis[SUP] 5 6 [/SUP], Lucas Castellani[SUP] 13 14 [/SUP], Michael Fralick[SUP] 1 15 [/SUP], Alex Wong[SUP] 3 [/SUP]
Affiliations
- PMID: 41417279
- PMCID: PMC12716492
- DOI: 10.1099/mgen.0.001575
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.
Keywords: built environment; environmental surveillance; viral diversity.