High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection.

Herpes simplex virus type 1 (HSV-1) is highly prevalent in all human populations and has been presumed to evolve in a clonal manner because of a lack of evidence for significant levels of co-infection. Different HSV-1 populations have distinct distributions of strains and the long timescale evident from HSV-1 population diversity has led to the suggestion that studies of virus variability may yield information about host population history. In this sequencing study of three segments of the HSV-1 genome in population samples from the UK and Korea, evidence of recombination was widespread both at the level of reassortment between widely separated loci and within shorter contiguous sequences and the estimated rate of recombination was comparable to that of mutation. Since recombination requires the coexistence of two viral genomes, these results suggest that co-infection by genetically distinct strains may be a more important aspect of HSV-1 epidemiology than previously realized. With its capacity to make new combinations of variants available for selection, substantial recombination requires a radically revised model for the rate and mode of evolution of the virus.