Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data

Abstract

Herpes simplex virus 2 is a human herpesvirus found worldwide that causes genital lesions and more rarely causes encephalitis. This pathogen is most common in Africa, and particularly in central and east Africa, an area of particular significance for the evolution of modern humans. Unlike HSV1, HSV2 has not simply co-speciated with humans from their last common ancestor with primates. HSV2 jumped the species barrier between 1.4 and 3 MYA, most likely through intermediate but unknown hominin species. In this paper, we use probability-based network analysis to determine the most probable transmission route between intermediate hosts of HSV2, from the ancestors of chimpanzees to the ancestors of modern humans, using paleo-environmental data on the distribution of African tropical rainforest over the last 3 million years and data on the age and distribution of fossil species of hominin present in Africa between 1.4 and 3 MYA. Our model identifies Paranthropus boisei as the most likely intermediate host of HSV2, while Homo habilis may also have played a role in the initial transmission of HSV2 from the ancestors of chimpanzees to P. boisei.

Migrating microbes: what pathogens can tell us about population movements and human evolution

“…The issue is further complicated by the high human-to-virus DNA ratios experienced when trying to sequence herpesviruses from living humans, meaning only a tiny proportion of the total DNA within a sample would come from HSV2 (Houldcroft et al 2017) if samples from archaeological specimens were available; explicit enrichment of HSV2 DNA by PCR or target capture would be required (Houldcroft & Breuer 2015;Depledge et al 2011;Ebert et al 2013). Computational modelling and knowledge of areas of Africa with particular important for the understanding of human evolution would allow for more HSV2 genomes to be collected from humans and ChHV in an evolutionarily informed manner and the potential transmission route reconstructed (Underdown et al 2017). This could mean focusing on areas of Africa where particularly ancient HSV2 lineages are predicted to be found; sequencing of a bonobo herpes simplex genome would also aid in reconstructions of the history of ChHV1 and HSV2.…”