Herpes simplex virus type 1 (HSV-1) is a common human virus, you get a cold sore near the mouth, but a study of the full genetic code of HSV-1 shows a dramatic confirmation of the "out-of-Africa" pattern of human migration., according to their paper.

Geneticists explore how organisms are related by studying changes in the sequence of bases, or "letters" on their genes. From knowledge of how quickly a particular genome changes, they can construct a "family tree" that shows when particular variants had their last common ancestor.

Studies of human genomes have shown that our 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 herpes simplex virus type 1 by looking at a single gene, or a small cluster of genes, but Brandt notes that this approach can be misleading. Relationships from a single gene, or a small set of genes, are not very accurate.

Phylogenetic network generated from 500, maximum likelihood bootstrap replicates. The HSV-1 strains in the network form the same six clades as in Figure 1. Clade I includes European/North American strains, Clade II comprises East Asian strains and III, IV, V and VI are East African. HSV-2 was used as an outgroup. Splitstree 4 was used to generate the network. The viral isolates are colored according to country of origin and are as follows: U.S.A: light blue, U.K.: dark blue, China: red, South Korea: purple, Japan: orange, and Kenya: green. 
doi:10.1371/journal.pone.0076267

"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,"   says senior author Curtis Brandt, a professor of medical microbiology and ophthalmology at the University of Wisconsin-Madison about their comparison of 31 strains of HSV-1 collected in North America, Europe, Africa and Asia. "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."

The technology of simultaneously comparing the entire genomes of related viruses could also be useful in exploring why certain strains of a virus are so much more lethal than others. In a tiny percentage of cases, for example, HSV-1 can cause a deadly brain infection, Brandt notes.

"We'd like to understand why these few viruses are so dangerous, when the predominant course of herpes is so mild. We believe that a difference in the gene sequence is determining the outcome, and we are interested in sorting this out," he says.

For studies of influenza virus in particular, Brandt says, "people are trying to come up with virulence markers that will enable us to predict what a particular strain of virus will do."

The researchers broke the HSV-1 genome into 26 pieces, made family trees for each piece and then combined each of the trees into one network tree of the whole genome, Brandt says. "Cécile Ané did a great job in coming up with a new way to look at these trees, and identifying the most probable grouping." It was this grouping that paralleled existing analyses of human migration.

The new analysis 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?" Kolb asks. Either the sample had come from someone who had travelled 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.

"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. Brandt says. "The dates match, so we postulate that this was an Amerindian virus."

Herpes simplex virus type 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 HSV-1 is spread by close contact, kissing or saliva, it tends to run in families. "You can think of this as a kind of external genome," Brandt says.

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, Brandt says, "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."

The correspondence with anthropology even extends, as before, to the details. In the virus, as in human genomes, a small human population entered the Middle East from Africa. "There is a population bottleneck between Africa and the rest of the world; very few people were involved in the initial migration from Africa," Brandt says. "When you look at the phylogenetic tree from the virus, it's exactly the same as what the anthropologists have told us."

Citation: Kolb AW, Ané C, Brandt CR (2013) Using HSV-1 Genome Phylogenetics to Track Past Human Migrations. PLoS ONE 8(10): e76267. doi:10.1371/journal.pone.0076267