Evidence for HIV in humans in distant past

By Will Parker on December 19, 2012 in Genetics, News

HIV may have affected humans for much longer than is currently believed, according to a scientist who says that the genomes of an isolated West African human population provide important clues about how the disease has evolved.

HIV-1 Type M, which accounts for 90 percent of human infections, is thought to have crossed the species barrier into human populations between 1884 and 1924. But Alfred Roca, from the University of Illinois, believes that it may have crossed much earlier, and on many occasions, selecting for genetic resistance in isolated rural populations while remaining undetected.

“Some of the scientific literature suggests that the persistence of HIV in humans required population densities typical of the larger cities that appeared in West Central Africa during the colonial era,” Roca explained. “[But] perhaps an even more important factor is that, before modern medicine and vaccinations, infectious diseases such as smallpox killed large numbers of people. People with compromised immune systems may have succumbed first, preventing the immunodeficiency virus from spreading.”

If HIV crossed the species barrier many times, it is possible that selection favored protective genetic variants in the affected populations. Roca and his co-investigators looked for evidence of this selection in the genomes of the Biaka people.

The Biaka inhabit forests in the range of the chimpanzee subspecies believed to be the source of the current HIV pandemic. The researchers compared Biaka genomes with the genomes of four other African populations who live outside the chimpanzee’s range.

Specifically, the researchers looked at the 26 genomic locations known to be involved in resistance to HIV. Researcher Kai Zhao examined these locations, comparing selection signatures across the 5 human populations to see if there was any overlap with the selection signatures. Eight of the comparisons showed overlap and seven of these were linked to the Biaka people.

The researchers identified four genes in these overlaps that code for proteins affecting either the ability of HIV to infect the host cell or the disease progression. The researchers also found that for several genes, genomic variations with protection against HIV-1 were common among the Biaka.

Roca cautions that these results should not be considered definitive. “You may detect a signature of selection, but it doesn’t necessarily mean that selection has caused it. It’s just a good sign that selection may have occurred,” he explained. “Also, the signature of selection may span several genes, of which only one is actually protective against HIV-1.”

However, he said that the results are intriguing and indicate that this line of research is worth pursuing. “If additional studies confirm that these genes have undergone selection and that human populations in the region have some genetic resistance to HIV-1, one could try to find additional genes in the population that may also be protective against HIV but have not yet been identified,” he said. “It could open up a new line of research for fighting retroviruses.”