Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron.

ABSTRACT: Concomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections. Here we present a metagenomic pipeline based on the inference of multiple fragments similar to amplicon sequence variant (ASV-like) from sequencing data and a custom SARS-CoV-2 database to identify the concomitant presence of divergent SARS-CoV-2 genomes, i.e., variants of concern (VOCs). This approach was compared to

SUBMITTER: Molina-Mora JA 

PROVIDER: S-EPMC9172093 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature