The virus under study, herpes simplex virus type 1 (HSV-1), usually causes nothing more severe than cold sores around the mouth, says Curtis Brandt, a professor of medical microbiology and ophthalmology at the University of Wisconsin-Madison. Brandt is senior author of the study, now online in the journal PLOS ONE.
When Brandt and co-authors Aaron Kolb and Cécile Ané compared 31 strains of HSV-1 collected in North America, Europe, Africa and Asia, "the result was fairly stunning," says Brandt.
"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," he says.
"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."
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. "Scientists have come to realize that the relationships you get back from a single gene, or a small set of genes, are not very accurate."
The PLOS ONE study used high-capacity genetic sequencing and advanced bioinformatics to analyze the massive amount of data from the 31 genomes.
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."
The PLOS ONE paper is available at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0076267. These studies were supported by grants from the National Institutes of Health: R01EY07336 and R01EY018597.
—David Tenenbaum, 608-265-8549, email@example.com
Curtis Brandt | EurekAlert!
The importance of biodiversity in forests could increase due to climate change
17.11.2017 | Deutsches Zentrum für integrative Biodiversitätsforschung (iDiv) Halle-Jena-Leipzig
Win-win strategies for climate and food security
02.10.2017 | International Institute for Applied Systems Analysis (IIASA)
The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.
Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...
Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.
That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...
Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.
During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....
The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.
Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...
Pillared graphene would transfer heat better if the theoretical material had a few asymmetric junctions that caused wrinkles, according to Rice University...
15.11.2017 | Event News
15.11.2017 | Event News
30.10.2017 | Event News
17.11.2017 | Physics and Astronomy
17.11.2017 | Health and Medicine
17.11.2017 | Studies and Analyses