MMMVI: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Samples

Motivation SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Variants of Concern (VOCs) and Variants of Interest (VOIs) are lineages that represent a greater risk to public health, and can be differentiated from the wildtype virus based on unique profiles of signature mutations. Wastewater surveillance by metagenomic sequence analysis can capture signal for these variants that may not be detected by public health testing and/or sequencing initiatives. However, because multiple viral genomes are likely to be present in a metagenomic sample, additional analytical scrutiny of the sequencing reads beyond variant calling can provide more confident diagnostic determinations.

Results We have developed MMMVI to aggregate and report cases where multiple mutations are present on a given read. These reads can be used as enhanced biomarkers to more confidently confirm the presence of a VOC/VOI in the sample.