NEW YORK (GenomeWeb News) – Knowledge about genetic bottlenecks in HIV-1 can be used to forensically unravel the direction of viral transmission and source of infection, researchers have shown.
In a paper appearing online last night in the Proceedings of the National Academy of Science, researchers from Baylor College of Medicine and the University of Texas at Austin described their phylogenetic strategy for tracing HIV infections back to their source. The team's analyses contributed to convictions of two men, one in Washington and one in Texas, who were accused of knowingly exposing women to the virus.
"Phylogenetic analysis allows us to reconstruct the history of the infection events," corresponding author David Hillis, an integrative biology researcher at the University of Texas at Austin, said in a statement. "We can identify the source in a cluster of infections because some isolates of HIV from the source will be related to HIV isolates in each of the recipients."
"This is the first case study to establish the direction of transmission," senior author Michael Metzker, a genetics researcher at the Baylor College of Medicine's Human Genome Sequencing Center, added in a statement.
Due to factors such as HIV mutation and recombination and the loss of some strains as a consequence of host defenses and/or antiretroviral treatment, it is more difficult to trace the route of viral transmission and infection between individuals than it is to assess typical DNA samples, the researchers explained.
Nevertheless, because HIV exists as a population of strains within each infected individual, it's sometimes possible to glean information about transmission based on the genetic bottlenecks that occur when a sub-group of viruses from one person sets up shop in another.
"Within a given person, there is not just one strain but a population of strains because HIV mutates all the time when it makes new virions," Metzker explained in a statement. "During transmission, however, there is a genetic bottleneck in which only one or two viruses get transmitted to the recipient."
The researchers exploited this so-called paraphyly during their forensic assessment of HIV samples from two criminal trials in which individuals were charged, among other things, with causing bodily harm or injury by knowingly exposing others to HIV.
In Washington, a defendant was accused of exposing 17 women to HIV through unprotected sex and infecting five of them. And in Texas, another defendant was similarly accused of infecting six women.
To determine whether each of the accused men was the index case or source of infection, the researchers used PCR amplification and Sanger sequencing to sequence pol and env gene regions of HIV-1 viruses isolated from each of the men and women they were suspected of infecting.
They then did phylogenetic analyses, incorporating information from HIV strains in GenBank and from unrelated HIV samples from the same geographic regions. Together, this phylogenetic data helped to not only discern relationships between HIV strains in each of the criminal cases, but also allowed the team to determine the direction of viral transmission between individuals involved.
For instance, they explained, HIV samples each formed a monophyletic group with other samples tested for the same trial. The team also found evidence of paraphyly between HIV samples in each case.
The researchers remained blinded to the actual identities of individuals whose samples were tested. But when the samples were re-identified at trial, the paraphyletic relationships between HIV samples pointed to the accused individuals as the sources of HIV infection in both the Washington and Texas cases.
"These independent cases support the use of phylogenetic analysis to test a priori transmission hypotheses," the researchers wrote, "both by linking epidemiologically related individuals and by providing evidence of the direction of transmission between individuals."
The team cautioned that "phylogenetic trees remain statistical estimates, subject to several key assumptions, and do not carry the same degree of certainty as human DNA profiling technology, which does not require the need to model sequence changes."
Consequently, they emphasized the need to consider and test as many potential routes of infection as possible. In addition, they explained, because paraphyly can decrease over time, absence of paraphyly between strains can't be used to rule out certain HIV transmission routes.
Even so, the authors noted, when paraphyly is present and strongly supported by genetic data, it serves as a valuable tool for forensically tracking HIV infection routes.
Finally, the researchers noted that their findings offer insights into the route of HIV transmission, but do not speak to the motives of the individuals who were accused of infecting others with the virus.
"In each case, the defendant was charged with intentionally exposing and, in some instances, infecting his female partners with HIV, with the motivation of each defendant being weighed alongside other evidence presented at trial," they wrote.