The impact of interspecies recombination on human herpes simplex virus evolution and host immune recognition

Abstract

Among the most ubiquitous of human pathogens, HSV-1 and HSV-2 are distinct viral species that diverged about six million years ago. At least four ancient HSV-1 x HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and non-recombinants at each locus circulating today. Though interspecies recombination has occurred in the past, its importance in HSV evolution remains incompletely defined. Using 255 newly-sequenced and 219 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. The novel recombinants we identify demonstrate that the sizes and locations of interspecies recombination events in HSV-2 are more variable than previously appreciated. One novel recombinant arose in its current host, showing for the first time that interspecies recombination occurs in contemporary HSV populations. We also demonstrate that interspecies recombination affects T-cell recognition of HSV. Our findings indicate that interspecies recombination can significantly influence genetic variation in and host immunologic response to HSV-2.

Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome

“…Only a very few HSV-2 complete genomic sequences are currently available: laboratory strain HG52 [12,13] and clinical isolates such as SD90e [13], among others [14]. There are also numerous partial genome sequences containing poorly covered regions and gaps at the frequently unresolved repeated regions [14][15][16][17][18]. By using Illumina and Pacific Biosciences (PacBio) sequencing technologies in combination, we successfully reported the complete genomic sequence of the widely used laboratory strain HSV-2 333 [19].…”