Keeping an Eye on Phylogenetics

June 12, 2015

Heeyoung Sohn is an AVAC staff member.

Last week, the New York Academy of Sciences brought together researchers and public policy makers for a conference on phylogenetics. As someone who is not a biologist or researcher, I quickly learned that phylogenetics is using genetic sequences to tell a story about how groups or organisms evolved from a common ancestor and/or how they are related to one another. In fact, we hear about phylogenetics all the time when scientists talk about the evolution of humans or even when we draw a family tree. But it isn’t just human genetic material that gets run through phylogenetic analyses. Viruses have genomes, too. The purpose of this conference was to discuss the state of the art in the ongoing investigation of how phylogenetic analyses are being used in the context of HIV.

Phylogenetic analyses of HIV use sequenced viral genomes, along with a complex set of assumptions and statistics to develop “family trees” for groups of viruses. This approach has been used to pinpoint the strains of SIV—the simian form of HIV—that likely made the leap from non-human primates to humans, to begin the epidemic many decades ago. And it is being used now to understand the origins and geography of particular strains, study drug resistance and so much more.

HIV is highly genetically variable. It copies itself over and over again and makes countless small errors. This means that evolutionary trees don’t stretch over decades, but over weeks or months. Scientists can use phylogenetics to track clusters of new cases of HIV, even potentially identifying the individual who is the source of the virus that was then passed on to others in the community. It’s important to remember, though, that phylogenetic analysis isn’t fool proof. It generates viral “family trees” based on a set of assumptions and statistical analyses, and these can be wrong.

On one level, phylogenetics sounds like a powerful tool for fighting the virus. In geographic areas where HIV testing has identified high rates of new cases, researchers can pinpoint the specific locales and even individuals associated with these “hot spots.” (HIV testing gives you an idea of where a hot spot is, but because people can travel to testing centers and may even intentionally choose to go somewhere other than where they live, the sites that find many new cases may not always reveal where the new transmissions are happening.) Researchers propose that phylogenetics could be used to project incidence rates in a given area and even calculate the likelihood of an individual from that area acquiring HIV.

So far, most phylogenetic analyses are focused on understanding what has happened in a community—not predicting the future. For instance, one phylogenetic study presented at the conference focused on HIV transmission in the Netherlands, which has seen a resurgence in HIV despite the widespread use of antiretroviral therapy. The study mapped and tracked HIV transmission in gay men and men who have sex with men, and found that both well-established networks and the continual addition of new networks drive the HIV epidemic.

However, phylogenetics is a double-edged sword and advocates at the meeting pointed out that there are issues to track closely as the field develops. Joanne Csete of Columbia University highlighted the potential risks to and violations of human rights that could happen if phylogenetics was used to pinpoint specific areas and/or at-risk populations. Mark Harrington, from the Treatment Action Group, discussed the importance of language and how dangerous the phrase “who infected who” can be when talking about phylogenetics, as people or groups can become targets for abuse.

This erroneous linking of people is a real threat as the world recently saw Michael Johnson, a university student, accused of infecting others with HIV, without any evidence. Although phylogenetics was not used, Johnson’s case shows how quick people are to link HIV infections to specific individuals despite the lack of evidence. As the UNAIDS guidance on HIV criminalization writes, “HIV phylogenetic evidence alone is not sufficient to establish, to the required criminal law standard, that one person did infect another person with HIV.”

Phylogenetics also has the potential to drive funding to only certain areas or groups and cause others to fall through the cracks that also are in need of prevention, treatment and testing. The science behind phylogenetics is complex, leaving room for potential misinterpretation of results.

It is no doubt that phylogenetics will play an important role in the future of HIV/AIDS. Advocates and their allies need to track this evolving field to ensure that efforts to pinpoint genetically linked cases don’t end up putting targets on specific communities or even individuals. It’s essential, as always, to ensure that research and methods which can be used for improving the fight against HIV/AIDS do not violate human rights and are clearly explained, so that the overall response stays on track. To read a phylogenetic case study, click here.