Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing.

ABSTRACT: Discrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events. We developed a tool (GNU-based Virus IDentification [GNUVID]) that integrates whole-genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to all high-quality genomes available from GISAID. STs were clustered into clonal complexes (CCs) and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events and to estimate effective viral diversity across locations and over time in 16 US states. GNUVID is a highly scalable tool for viral genotype classification (https://github.com/ahme

SUBMITTER: Moustafa AM 

PROVIDER: S-EPMC8449825 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature