ABSTRACT
The evolution of the two herpes simplex virus (HSV) species, HSV-1 and HSV-2, falls naturally into two main components. This chapter deals with HSV-1 and HSV-2, which belong to the Simplexvirus genus or α1 group of the Alphaherpesvirinae. Four major lineages are recognized in the Alphaherpesvirinae. Two of these are populated sparsely and exclusively by avian viruses, namely Mardivirus and Iltovirus. The mammalian viruses in the subfamily lie in a clade with the avian virus lineages as outgroups, and with two genera, Simplexvirus and Varicellovirus. The complexity concerns the relationship between the HSV species. HSV-1 and HSV-2 are each other's closest known relative, but their genomes are actually quite diverged. Homologous recombination, mediated by the viral deoxyribonucleic acid replication machinery, has long been recognized as the mechanism underlying HSV genome isomerization. Patterns of population variability are the key to characterizing contemporary molecular evolution in HSV.
