Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil.

The genomic monitoring of SARS-CoV-2 variants of concern (VOCs) in riverine and sewage water has been widely used as an epidemiological tool worldwide. But its utility for epidemiological assessments still needs to be evaluated in some areas. Our study encompassed thirteen Brazilian rivers spanning a vast urban expanse across the states of Rio de Janeiro, São Paulo, and Paraná. The sampled rivers in Rio de Janeiro are heavily contaminated with sewage. Meanwhile, the Indian samples were all wastewater before joining the water bodies from urban regions (Andhra Pradesh and Telangana). The viral copies were quantified using quantitative polymerase chain reaction (qPCR) in all examined samples (N = 91). The abundance of viral particles varied from 567 to 85,700,000 copies/ml. Subsequently, Illumina CovidSeq was applied to identify the major variants. In Brazil, while a single SARS-CoV-2 VOC was identified for just a few samples (6/50, 12 %), most samples harbored multiple VOCs (44/50, 88 %). In India only one probed sample had a single variant identified. Gamma (2021) and Omicron (2021 and 2022) were the most abundant variants. Delta and Omicron genetic material were detected in Rio de Janeiro city rivers before Brazil's first cases of these variants. Several negative samples in the Real-Time RT-PCR (qPCR) turned out to have SARS-CoV-2 sequences suggesting CovidSeq was more sensitive than RT-PCR for virus detection in environmental samples. Sewage surveillance holds promise for early detection of emerging variants driving pandemic waves, exemplified by the Delta and Omicron variants, potentially offering a preemptive advantage over clinical sample reports.