Identification and detailed characterization of mixed SARS-CoV-2 populations in Argentina - PAIS Project

In this work we present VICOS (VIral COinfection Surveillance), a novel integrated bioinformatic pipeline that allows the characterization of iSNVs in SARS-CoV-2 sequences obtained by Illumina technology. Through the analysis of 1,097 SARS-CoV-2 sequences from clinical samples, obtained between March 2020 and August 2021 for genomic surveillance in Argentina by the Argentine Inter-Institutional SARS-CoV-2 Genomic Project (PAIS Project), VICOS allowed the identification and detailed characterization of mixed SARS-CoV-2 populations in 2% of the samples. Our results not only add a new powerful bioinformatic tool for viral genomic analysis but also provide important evidence of SARS-CoV-2 diversity and intra-host evolution. A total of 1,097 nasopharyngeal swabs from symptomatic patients testing positive for COVID-19 from March 2020 to August 2021 in Argentina underwent SARS-CoV-2 genome sequencing using ARTIC v3 protocol and Illumina technology (MiSeq and NextSeq 500 platforms) [ARTIC V3].