Herpes Virus Genetic Study Supports Out-of-Africa Theory of Human Migration

Oct 22, 2013 by Sci-News.com

Genomic sequences of 31 Herpes Simplex Virus Type 1 (HSV-1) strains collected in North America, Europe, Africa and Asia support the ‘out-of-Africa’ theory of human migration.

This image shows the phylogenetic tree for 31 HSV-1 strains and their 6 clades, based on geographic origin. The viral isolates are colored according to country of origin: the United States - light blue, UK - dark blue, China - red, South Korea - purple, Japan - orange, and Kenya - green. Image credit: Kolb AW et al.

This image shows the phylogenetic tree for 31 HSV-1 strains and their 6 clades, based on geographic origin. The viral isolates are colored according to country of origin: the United States – light blue, UK – dark blue, China – red, South Korea – purple, Japan – orange, and Kenya – green. Image credit: Kolb AW et al.

“The viral strains sort exactly as you would predict based on sequencing of human genomes. We found that all of the African isolates cluster together, all the virus from the Far East, Korea, Japan, China clustered together, all the viruses in Europe and America, with one exception, clustered together,” explained Prof Curtis Brandt from the University of Wisconsin-Madison, who is the senior author of the paper published in the open-access journal PLoS ONE.

“What we found follows exactly what the anthropologists have told us, and the molecular geneticists who have analyzed the human genome have told us, about where humans originated and how they spread across the planet.”

Studies of human genomes have shown that human ancestors emerged from Africa roughly 150,000 to 200,000 years ago, and then spread eastward toward Asia, and westward toward Europe.

Scientists have previously studied HSV-1 by looking at a single gene, or a small cluster of genes, but this approach can be misleading. The new study used high-capacity genetic sequencing and advanced bioinformatics to analyze the massive amount of data from the 31 HSV-1 genomes.

Prof Brandt’s team broke the genomes into 26 pieces, made family trees for each piece and then combined each of the trees into one network tree of the whole genome. And it was the grouping that paralleled existing analyses of human migration.

The results could even detect some intricacies of migration. Every HSV-1 sample from the United States except one matched the European strains, but one strain that was isolated in Texas looked Asian.

“How did we get an Asian-related virus in Texas? Either the sample had come from someone who had traveled from the Far East, or it came from a native American whose ancestors had crossed the land bridge across the Bering Strait roughly 15,000 years ago,” said lead author Dr Aaron Kolb from the University of Wisconsin-Madison.

This world map shows the geographic location of the 6 HSV-1 clades with respect to human migration: each clade is depicted by a roman numeral; land migration is depicted by yellow lines and sea migration is shown by the pink line. Image credit: Kolb AW et al.

This world map shows the geographic location of the 6 HSV-1 clades with respect to human migration: each clade is depicted by a roman numeral; land migration is depicted by yellow lines and sea migration is shown by the pink line. Image credit: Kolb AW et al.

“We found support for the land bridge hypothesis because the date of divergence from its most recent Asian ancestor was about 15,000 years ago. The dates match, so we postulate that this was an Amerindian virus,” Prof Brandt added.

HSV-1 was an ideal virus for the study because it is easy to collect, usually not lethal, and able to form lifelong latent infections. Because the virus is spread by close contact, it tends to run in families. Furthermore, HSV-1 is much simpler than the human genome, which cuts the cost of sequencing, yet its genome is much larger than another virus that also has been used for this type of study. Genetics often comes down to a numbers game; larger numbers produce stronger evidence, so a larger genome produces much more detail.

“But what really jumped out of the study was clear support for the out-of-Africa hypothesis. Our results clearly support the anthropological data, and other genetic data, that explain how humans came from Africa into the Middle East and started to spread from there,” Prof Brandt concluded.

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Bibliographic information: Kolb AW et al. 2013. Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS ONE 8 (10): e76267; doi: 10.1371/journal.pone.0076267