Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data.

ABSTRACT: High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-n

SUBMITTER: Roder AE 

PROVIDER: S-EPMC10470513 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature