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

National Library Of Medicine

Investigators

Linked publications & trials

Abstract

As seen during the SARS-CoV-2 pandemic, epidemiological surveillance systems are important tools to inform health decision during disease outbreaks. Although most surveillance focused on clinical cases, once it was determined that SARS-CoV-2 can be shed through the feces and urine of infected patients, wastewater became another avenue for surveillance. Wastewater-based epidemiology (WWBE) can act as a support to clinical epidemiology, but also has many advantages since it provides an anonymous, non-invasive, cost-effective sampling opportunity able to capture viral genomes from both symptomatic and asymptomatic individuals. However, SARS-CoV-2 genomic analysis from wastewater has its challenges since samples are obtained at a population level, and is composed of multiple genomes. Hence, there is a need to develop new approaches to support wastewater analysis. In this project we developed a bioinformatics framework to process high-through put sequencing data from wastewater and analyzed the data to obtain viral diversity analysis, major circulating VOCs and identify novel single nucleotide variants (SNVs) not yet detect in clinical data. 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 were able to 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 were able to observe 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. Overall, 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 health care decision makers to act in response to changes in viral populations detected through WWBE. Wastewater surveillance it is now even more important with the decrease in clinical testing and genome sequencing from SARS-CoV-2 patients. We are currently writing a manuscript about our results including and the analysis that should be submitted soon.