VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.

ABSTRACT:

Background

The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.1.617.2 or Omicron variant B.1.1.529). Proportions of these variants circulating in a human population are typically estimated by large-scale sequencing of individual patient samples. Sequencing a mixture of SARS-CoV-2 RNA molecules from wastewater provides a cost-effective alternative, but requires methods for estimating variant proportions in a mixed sample.

Results

We propose a new method based on a probabilistic model of sequencing reads, capturing sequence diversity present within individual variants, as well as sequencing errors. The algorithm is implemented in an open source Python program called VirPool. We evaluate the accur

SUBMITTER: Gafurov A 

PROVIDER: S-EPMC9761630 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature