Bioinformatics Framework for Wastewater-based Surveillance of SARS-CoV-2

National Library Of Medicine

Investigators

Linked publications, trials & patents

Abstract

As seen during the SARS-CoV-2 pandemic, epidemiological surveillance systems are essential tools for informing health decisions during disease outbreaks. Although most surveillance focused on clinical cases, once it was determined that SARS-CoV-2 could be shed through the feces and urine of infected patients, wastewater-based epidemiology (WBE) became a supporting approach that offered a non-invasive and cost-effective way to monitor viral population changes. To fully take advantage of WBE data, new bioinformatic approaches that account for the population heterogeneity and facilitate the comparison of wastewater samples are needed. In this project, we developed a bioinformatics framework to process high-throughput sequencing data from wastewater. We developed a tool called Cov-Dist for viral diversity analysis that computes viral similarity between wastewater samples and SARS-CoV-2 lineages by assessing SNV frequency differences at each position of the SARS-CoV-2 genome. Using Cov-Dist, we could observe temporal and spatial trends for lineages from major variants of concern in our wastewater samples, such as the Delta wave being displaced by Omicron. We also developed a pipeline to identify defining SNVs, insertions, and deletions for each SARS-CoV-2 VOC clade, which we then compare with the wastewater results to identify the VOCs present in each sample. In this more detailed approach, we observed the defining variants present in the transition periods of Delta and Omicron and the replacement of Delta lineages by Omicron lineages. After the shift to Omicron, we observed that Delta-associated SNVs were still present at low frequencies, indicating that the Delta variant was still present and was being missed in clinical samples or that new recombinant strains were present. This work helps to discern viral diversity trends and the presence of SARS-CoV-2 VOCs that are circulating in wastewater collection sites. This information can help local authorities and healthcare decision-makers act in response to changes in viral populations detected through WWBE. Wastewater surveillance is now even more critical with the decrease in clinical testing and genome sequencing from SARS-CoV-2 patients. This work was published in Science of the Total Environment in June of 2023 and will serve as a valuable tool for applying WBE to SARS-CoV-2 and future viral outbreaks.