Tracking SARS-CoV-2 variants in wastewater in San Pedro de la Paz, Chile

Various studies have shown the presence of SARS-CoV-2 RNA in the feces of patientswith COVID-19, both symptomatic and asymptomatic. This allowed determining theviral load in wastewater samples from Wastewater Treatment Plants (WWTPs),carrying out wastewater-based surveillance (WBS) of the virus in the community, as acomplement to person-to-person testing. The appearance of SARS-CoV-2 variants,which can increase transmissibility and/or immune evasion, creates an imperativeneed to implement specific and permanent surveillance methods to control the COVID19 pandemic. For variant detection, we performed a real-time RT-qPCR assay with acommercial kit to detect five virus variants (Alpha, Beta, Gamma, Lambda, and Delta)in the municipality of San Pedro de la Paz, Chile, from January to November 2021.Detection of variants in wastewater was consistent with available clinical data andprovided additional information for community surveillance, identifying lambda anddelta variants as the most frequently detected during the second and third wave ofinfections in the population of this area. Furthermore, in some cases we detectedspecific variants in wastewater before local authorities confirmed the first clinical cases.The study demonstrates that WBS is a tool that allows a rapid and cost-effectivedetection of specific mutations associated with SARS-CoV-2 variants using RT-qPCR.However, Illumina amplicon sequencing confirms that there are more optimal methodsto sequence this type of matrices. This method can be used to complement clinicaldata during outbreaks and is especially useful when clinical care is insufficient orcollapsed and/or cost is very high, as is the case in many countries