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 patients
with COVID-19, both symptomatic and asymptomatic. This allowed determining the
viral load in wastewater samples from Wastewater Treatment Plants (WWTPs),
carrying out wastewater-based surveillance (WBS) of the virus in the community, as a
complement to person-to-person testing. The appearance of SARS-CoV-2 variants,
which can increase transmissibility and/or immune evasion, creates an imperative
need to implement specific and permanent surveillance methods to control the COVID19 pandemic. For variant detection, we performed a real-time RT-qPCR assay with a
commercial 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 and
provided additional information for community surveillance, identifying lambda and
delta variants as the most frequently detected during the second and third wave of
infections in the population of this area. Furthermore, in some cases we detected
specific 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-effective
detection of specific mutations associated with SARS-CoV-2 variants using RT-qPCR.
However, Illumina amplicon sequencing confirms that there are more optimal methods
to sequence this type of matrices. This method can be used to complement clinical
data during outbreaks and is especially useful when clinical care is insufficient or
collapsed and/or cost is very high, as is the case in many countries.