Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil

Abstract

Wastewater-based epidemiology can be a complementary approach for monitoring SARS-CoV-2 prevalence, diversity, and geographic distribution. It is a complementary approach regarding its prevalence and diversity, and geographic distribution. The study aimed to evaluate the genetic diversity of SARS-CoV-2 in two wastewater treatment plants (WWTPs) in Rio de Janeiro, Brazil. Samples were collected over a period of January to December 2021 and were concentrated with PEG8000 and the presence of SARS-CoV-2 was detected using E and N1 genes. Partial sequencing of the SARS-CoV-2 genomes resulted in the identification of variants of concern and variants of interest throughout the collection period. It was possible to identify the Mu, Delta, Gamma and Omicron variants in WWTP1; on the contrary, no variants were observed in WWTP2. To the best of our knowledge, we detected the variant Mu (B.1.621) containing characteristic mutations (S:E484K, S:N501Y) from WWTP, for the first time, in Brazil. Another Mu variant detected from clinical surveillance was announced one month after our finding. The detection of SARS-CoV-2 in wastewater can serve as a tool to monitor the prevalence and epidemiology in each community, helping to understand the spread of the virus among the population. HIGHLIGHTS Sequencing analysis showed the circulation of the Mu variant from the wastewater one month before being detected in the clinical surveillance in Rio de Janeiro city.; Wastewater-based epidemiology (WBE) revealed Delta variant AY.32, Mu, B.1618, B.1469, XD presenting characteristic mutations by the WHO.; The potential for WBE to track the emergence and spread of variants of concern in wastewater before being detected through clinical surveillance in Rio de Janeiro city.;

Keywords

• sars-cov-2
• environmental genomic surveillance
• wastewater-based epidemiology