Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.

ABSTRACT:

Background

The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, these sets of viral mutations provide distinct genetic fingerprints that reveal the patterns of transmission and have utility in contract tracing.

Methods

Leveraging thousands of sequenced SARS-CoV-2 genomes, we performed a viral pangenome analysis to identify conserved genomic sequences. We used a rapid and highly efficient computational approach that relies on k-mers, short tracts of sequence, instead of conventional sequence alignment. Using this method,

SUBMITTER: Lau BT 

PROVIDER: S-EPMC7654905 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature