Virus variant quantification with Orthanq

Background Existing tools for virus variant identification can pinpoint the most abundant virus variant in a sequencing sample. However, patients can be infected by more than one variant of the same virus species or strain, for example by multiple variants of SARS-CoV-2. This leads to the more complicated problem of virus variant quantification from samples with virus mixtures. Results We report on improvements of Orthanq, our generic tool for haplotype quantification, and show how it can be applied to perform uncertainty aware quantification of virus variants. We evaluate this ability on simulated and real SARS-CoV-2 and HIV-1 virus mixture datasets. Conclusions Orthanq is the first tool to accurately quantify multiple virus variants in co-infected SARS-CoV-2 samples. But it is not limited to SARS-CoV-2 and can be used for an uncertainty-aware quantification of virus variants in any virus mixture.