Behind the bars: Wastewater-based surveillance of SARS-CoV-2, and its variants in prison wastewater

Droplet-borne infectious diseases can spread quickly in overcrowded, poorly ventilated prisons, making it difficult to monitor diseases like COVID-19. Therefore, wastewater-based surveillance (WBS) is essential for tracking the spread of SARS-CoV-2 and its variants. We aimed to compare how different sampling methods and assays impact WBS in prisons, focusing on their effect on genomic sequencing to monitor SARS-CoV-2 variants in a prison sewage system in Selangor, Malaysia. Raw sewage samples were collected between February, and August 2023, using both grab and composite sampling. The SARS-CoV-2 ribonucleic acid (RNA) concentration was quantified via reverse transcription digital polymerase chain reaction (RT-dPCR) followed by sequencing using nanopore technology. Among the 90 paired samples, 84 (93.3 %) and 85 (94.4 %) tested positive for SARS-CoV-2 RNA in grab and composite samples, respectively. There were no significant differences in RNA concentrations between grab and composite samples for N1 (z = -0.885, p = 0.376) and N2 (z = −1.032, p = 0.302). Moderate positive correlations were observed between composite and grab samples, with Pearson's r values of 0.67 and 0.56 for nucleoproteins 1 and 2 (N1 and N2 genes), respectively. Wastewater genomic surveillance consistently identified the same dominant circulating sublineages of the Omicron variant in the prison community via both sampling methods. Moreover, our study highlights the benefits of using different methods to capture variant diversity and assess environmental susceptibility to external sources. This study provides a comprehensive analysis of WBS methods that allow the detection of SARS-CoV-2, its variant, mutation and transmission in carceral settings.