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

Abstract

Herpes-Simplex Virus 1 (HSV-1) infects most humans when they are young, sometimes with fatal consequences. Gene expression occurs in a temporal order upon lytic HSV-1 infection: immediate early (IE) genes are expressed, then early (E) genes, followed by late (L) genes. During this infection cycle, the HSV-1 genome has the potential for exposure to APOBEC3 (A3) proteins, a family of cytidine deaminases that cause C>U mutations on single-stranded DNA (ssDNA), often resulting in a C>T transition. We developed a computational model for the mutational pressure of A3 on the lytic cycle of HSV-1 to determine which viral kinetic gene class is most vulnerable to A3 mutations. Using in silico stochastic methods, we simulated the infectious cycle under varying intensities of A3 mutational pressure. We found that the IE and E genes are more vulnerable to A3 than L genes. We validated this model by analyzing the A3 evolutionary footprints in 25 HSV-1 isolates. We find that IE and E genes have evolved to underrepresent A3 hotspot motifs more so than L genes, consistent with greater selection pressure on IE and E genes. We extend this model to two-step infections, such as those of polyomavirus, and find that the same pattern holds for over 25 human Polyomavirus (HPyVs) genomes. Genes expressed earlier during infection are more vulnerable to mutations than those expressed later. The APOBEC family of cytidine deaminases are a component of innate immunity that can bind to viral DNA and cause mutations. We developed a computational model of the lytic life cycle of herpes simplex virus 1 (HSV-1), a large double-stranded DNA virus, to evaluate the potential effects of APOBEC on the virus and its evolution. The model considered three types of viral genes: Immediate Early (IE), Early (E) and Late (L). We found that genes expressed earliest in the lytic life cycle, E and particularly IE, are the most vulnerable to APOBEC-mediated mutations, because even low levels of mutation were sufficient to disrupt the infection process. We were able to validate the predictions of the computational model by analyzing published HSV-1 genomes, in particular by using software tools that quantify the extent to which each genome has evolved to reduce the number of DNA motifs (also known as “mutational hotspots”) that are preferred by APOBEC for mutation. Our analysis suggested that the IE and E genes have evolved to avoid APOBEC3 targeting. We extended our modeling and genomic analysis to human Polyomaviruses, which are smaller double-stranded DNA viruses with a simpler life cycle than HSV-1 and found similar results. These studies highlight the vulnerability to APOBEC of genes expressed early during viral infection and may suggest these genes as therapeutic targets.