Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection
Fig 5
Hypermutation and SNV analysis shows that IE genes yield fewer mutations during HSV-1 infection.
A) hyperfreq, a Bayesian analysis tool to determine hypermutation, was used on the 26-genome alignment from [54]. The hyperfreq_fraction measure describes the fraction of analyzed genomes that were shown to be hypermutated in TC (blue) or GA (orange) motifs. This was run for each gene in HSV-1. Red is for IE genes, green for E genes, and black for L genes. B) SNVs determined from 10 clinical samples using a threshold for allelic fraction using bcftools (see Methods). Shown are transitions: A>G in blue, G>A in orange, C>T in green, and T>C in red. The x-axis in the top plot shows the 5-prime context for a given SNV, while the bottom shows the 3-prime context. C) The SNV counts were mapped to each gene and normalized by the gene length to determine the mutation % for Immediate Early genes (top), Early genes (middle), and Late genes (bottom).