Data from: Ancient recombination events between human herpes simplex viruses

Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are seen as close relatives but also unambiguously considered as evolutionary independent units. Here, we sequenced the genomes of 18 HSV-2 isolates characterized by divergent UL30 gene sequences to further elucidate the evolutionary history of this virus. Surprisingly, genome-wide recombination analyses showed that all HSV-2 genomes sequenced to date contain HSV-1 fragments. Using phylogenomic analyses, we could also show that two main HSV-2 lineages exist. One lineage is mostly restricted to subSaharan Africa whereas the other has reached a global distribution. Interestingly, only the worldwide lineage is characterized by ancient recombination events with HSV-1. Our findings highlight the complexity of HSV-2 evolution, a virus of putative zoonotic origin which later recombined with its human-adapted relative. They also suggest that coinfections with HSV-1 and 2 may have genomic and potentially functional consequences and should therefore be monitored more closely.Annotated HSV-2v genomesPutative coding sequences were annotated with Geneious 10.0.5 using a conservative similarity threshold of 60% to coding sequences annotated in the HSV-2 reference genome (NC_001798). GFF3 format.annotated_genomes.zipMutliple sequence alignments including HSV-2v sequencesThis archive contains the following alignments: Whole genome 1, 2 and 3; Whole genome de novo 2 and 3; Non recombinant 1 to 10; UL15 non recombinant and recombinant, UL29 non recombinant and recombinant, UL30 non recombinant and recombinant, UL39 non recombinant and recombinant. Whole genome 2 and 3 and Whole genome de novo 2 and 3 are provided as NEXUS files and include site masks pinpointing the recombinant regions (Whole genome 2 and Whole genome de novo 2 and 3) and large non recombinant fragments (Whole genome 3). All other alignments are provided as FASTA files.alignments.zi