Detection of genetic diversity of SARS-CoV-2 in wastewater to monitor COVID-19 transmission

Abstract

Coronavirus Disease 2019 (COVID-19), an infectious respiratory disease caused by the viral strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a distinct cause of the global burden and a rising concern to global public health. It has single-handedly destroyed economies of every country it has affected. Despite the policy makers trying to tackle this virus, SARS-CoV-2 having a rapid mutation rate makes it difficult to monitor and create effective therapeutics to completely avoid fatalities. Since the only way to detect presence of COVID-19 and circulating strain was by testing every individual, it was a tedious and very inefficient method as it required a significant amount of time. This study aims to provide an alternate method of detecting the genetic diversity of SARS-CoV-2 and the strain currently circulating in an area by wastewater monitoring. Collecting samples from community wastewater as well as hospital discharge is faster and does not require testing hundreds of individual. This method provides an understanding of the strains currently present in a selected area as the virus is present in fecal discharge of affected individuals. We carried out RNA extraction of over 300 samples and selected the samples with positive RT PCR values and performed whole genome sequencing using Oxford Nanopore Technology. The sequences were then analyzed and the data were compared. It was seen that the most abundant variant of Omicron was of clades XBB and XBB.1 with majority of the mutations taking place in the Non-Structural Proteins and Spike Proteins of the virus, these are responsible for the cell attachments and play a key role in pathogenesis of the virus. This study further helps in understanding how despite mass vaccination against COVID-19, this virus seems to be present in significant concentrations in the community.