Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples.

ABSTRACT: Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple

SUBMITTER: Pipek OA 

PROVIDER: S-EPMC10789779 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature