Optimised use of passive samplers enabled early detection of SARS-CoV-2 variants BA.4 and BA.5 in sewage water

Abstract

Wastewater-based epidemiology emerged as a valuable method to monitor the COVID-19 epidemic and the dynamic of SARS-CoV-2 variants. Because of its ease of deployment and low cost, membrane-based passive sampling is a prime alternative for deploying a monitoring network in wastewater, especially when automatic samplers cannot be used. However, the performance of these strategies for the identification of low-abundance viruses needs to be evaluated. Passive sampling using nylon membranes and grab sampling were carried out in parallel in the sewers of two French cities in April and May 2022, for the detection of norovirus GII (NoV GII) and SARS-CoV-2. SARS-CoV-2 sequencing was performed to compare the performance of passive samplers and their paired grab sampler in identifying Omicron sub-lineages. Direct lysis and elution methods from nylon membranes were equally effective for virus recovery and SARS-CoV-2 sequencing. For all sites, the virus concentrations in passive and grab samples were very similar. A near-complete genome coverage at a depth of 30 was obtained for most samples, using ARTIC multiplex PCR (V4.1) and Illumina MiSeq. There was a high proportion of low-frequency mutations for both methods and rare mutations in the S gene were detected, which could reflect the presence of cryptic lineages. Even though a large proportion of BA.2 lineage was detected in sewage, most importantly this study provides the first evidence that the use of passive sampling enables early detection of SARS-CoV-2 variants BA.4 and BA.5, that is, before they are identified in the population.