Detection of Omicron variant in November 2021: a retrospective analysis through wastewater in Halifax, Canada

Abstract

This study evaluates the efficacy of wastewater surveillance (WWS) for the early detection of the Omicron variant of SARS-CoV-2 in a university setting in Halifax, Canada. Utilizing an allele-specific RT-qPCR assay, that targets a distinctive Omicron–Lambda mutation (N: P13L; C28311T), we retrospectively analyzed wastewater samples collected from four university residences between 01 September and 31 December 2021. We analyzed 276 passive wastewater samples from four university residences and 51 composite wastewater samples from the wastewater treatment facility (WWTF) which is located downstream of the university. Our findings reveal the presence of the C28311T mutation in wastewater collected before the clinical identification of the Omicron variant in the province. Retrospective analysis of SARS-CoV-2-positive samples using the C28311T RT-qPCR assay showed detections in wastewater collected at the university on 05 November 2021 and 06 November 2021 and in the WWTF samples on 26 November 2021. SARS-CoV-2 N2 RNA was detected in 51 campus samples and 20 treatment facility samples (18 and 39% detection rate, respectively). The study emphasizes the utility of passive sampling for its cost-effectiveness and minimal maintenance, enabling rapid testing and prompt health interventions within an institutional setting. The comparison between the localized approach at the university and the broader community surveillance at the WWTF illustrates the nuanced understanding provided by targeted WWS. While the WWTF samples reflect a community-wide perspective with less variability, the university's targeted surveillance captures localized outbreaks, offering actionable insights for campus management. These findings underscore the strategic value of integrating passive wastewater sampling into public health strategies for variant detection and outbreak prevention, particularly in institutional settings with high-density populations.