ArticleFrontiers in microbiology2025
Evaluation of sampling methods for genomic surveillance of SARS-CoV-2 variants in aircraft wastewater: advancing global early-warning systems for future pandemics.
Article in Frontiers in microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of aircraft wastewater was adopted at an early stage of the pandemic to track importation of emerging variants into the country. However, the acute need to determine the presence of emerging SARS-CoV-2 sublineages meant that the sampling methods utilized were not adequately validated. Here, we compared two different sampling methods for genomic surveillance of SARS-CoV-2 VOCs in aircraft sewage samples. Methods: Eighty-eight composite wastewater samples were collected over 9 weeks using both autosampler and passive torpedo samplers at the same location. SARS-CoV-2 nucleic acid in the samples was quantified using RT-qPCR. RNA samples were extracted and sequenced with the MiniSeq system using the tiled-amplicon sequencing approach with ARTIC V4.1 primer sets. Raw reads were preprocessed and SARS-CoV-2 mutations, variants lineages, and other sequence metrics from the two sampling methods were compared. Results: The two sampling methods yielded comparable viral load by RT-qPCR, but the autosampler produced higher genome coverage relative to the passive samplers. The Omicron lineages identified differed by sampling method. BQ.1* and BA.5.2*, which were the predominant lineages in wastewater and clinical samples at the time, were identified as dominant in the autosampler and passive sampler, respectively. Additionally, the autosampler captured higher diversity and relative abundance of VOCs, including emerging variants (XBB* and CH.1* lineages), as well as more clinically relevant mutations (S:K444T, T22942A, S:R346T) relative to passive sampler. Overall, the passive samplers produced concordant results with the autosampler for measuring SARS-CoV-2 load with RT-qPCR in aircraft wastewater. Conclusion: Taken together, our results suggest underestimation of the diversity and abundance of SARS-CoV-2 VOCs and mutations in aircraft sewage using passive torpedo samplers. These data can be used to optimize genomic surveillance approaches for SARS-CoV-2 VOCs in aircraft wastewater samples.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.