Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations

Following our recent report of high levels of recombination and geographic structuring amongst isolates from two populations, we have investigated global patterns of herpes simplex virus type 1 (HSV-1) molecular diversity using population samples from six countries in Europe, Asia and Africa. Sequence comparisons show that HSV-1 from Kenya is both highly diverse and distinct from either European or Asian HSV-1. HSV-1 populations are much more highly differentiated than human populations at the same geographic scales, with 35% of total variation at the level of inter-population comparisons, a difference likely to be due to higher rates of both mutation and genetic drift in HSV-1 than in equivalent human data. There is substantial differentiation between northwestern European HSV-1 populations and those from East Asia, and while patterns of British and Swedish HSV-1 variation were indistinguishable, differentiation was detectable amongst Chinese, Korean and Japanese HSV-1 samples, in spite of their lower overall diversity. The program Structure was used to reconstruct ancestral Eurasian lineages, which we estimated to have originated ∼60,000 years ago. A specific pattern detected amongst East Asian HSV-1 isolates is currently best explained by the two waves of migration responsible for the peopling of Japan.