Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa

• Published in: Nature communications 2022-09, Vol.13 (1), p.5477-5477, Article 5477
• Main Authors: Havens, Jennifer L., Calvignac-Spencer, Sébastien, Merkel, Kevin, Burrel, Sonia, Boutolleau, David, Wertheim, Joel O.
• Format: Article
• Language: English
• Subjects: 631/114/739; 631/181; 631/326/596/1553; 631/553/1745; Adult; Africa; Base Sequence; Dispersal; Dispersion; DNA viruses; Genome; Genomes; Geography; Herpes simplex; Herpes viruses; Herpesvirus 2, Human - genetics; Humanities and Social Sciences; Humans; Hypotheses; Life Sciences; Migration; multidisciplinary; Phylogeography; Science; Science (multidisciplinary); Viruses; Young Adult
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-33214-y

Human herpes simplex virus 2 (HSV-2) is a ubiquitous, slowly evolving DNA virus. HSV-2 has two primary lineages, one found in West and Central Africa and the other found worldwide. Competing hypotheses have been proposed to explain how HSV-2 migrated out-of-Africa (i)HSV-2 followed human migration out-of-Africa 50-100 thousand years ago, or (ii)HSV-2 migrated via the trans-Atlantic slave trade 150-500 years ago. Limited geographic sampling and lack of molecular clock signal has precluded robust comparison. Here, we analyze newly sequenced HSV-2 genomes from Africa to resolve geography and timing of divergence events within HSV-2. Phylogeographic analysis consistently places the ancestor of worldwide dispersal in East Africa, though molecular clock is too slow to be detected using available data. Rates 4.2 × 10 −8 −5.6 × 10 −8 substitutions/site/year, consistent with previous age estimates, suggest a worldwide dispersal 22-29 thousand years ago. Thus, HSV-2 likely migrated with humans from East Africa and dispersed after the Last Glacial Maximum. There are competing hypotheses for human herpes simplex virus 2’s migration out-of-Africa. Here, the authors sequence 65 new herpes simplex virus 2 genomes with a focus on under-sampled sub-Saharan African countries, suggesting an Eastern African origin for global dispersal the virus between 22-29 thousand years ago.