# Virus variant quantification with Orthanq

## TL;DR

Orthanq improves the ability to quantify multiple virus variants in a sample, especially when multiple variants are present.

## Contribution

Orthanq introduces uncertainty-aware quantification of virus variants in mixed infections.

## Key findings

- Orthanq outperforms state-of-the-art methods in quantifying virus variants from mixed samples.
- The tool provides detailed visualizations and reports to assess result uncertainty.

## Abstract

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 containing virus mixtures.

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 and show that Orthanq outperforms other state of the art approaches.

Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, in particular also in samples with mixed infections. With extensive built-in visualizations and reporting of alternative solutions with posterior densities, users can easily evaluate the uncertainty of the results.