Phylogenetic Viral Linkage: A Tool for Evaluating HIV Prevention Efforts

Graphics showing Phylogenetic Viral Linkage

Major HIV prevention trials are underway in African countries, including Botswana, Kenya, South Africa, Uganda, and Zambia. These trials involve hundreds of thousands of people and cost hundreds of millions of dollars. But how will we know if they work?

The Botswana Combination Prevention Project (BCPP) is an HIV prevention study taking place in 30 pair-matched villages in Botswana. Half of the villages receive scaled-up combination prevention measures and half of the villages act as controls. The study was designed to test whether a combination of HIV prevention measures could significantly reduce the number of new HIV infections within a community.

At the start of the BCPP, the field team rapidly scaled up HIV testing and counseling in the 15 intervention communities. Participants who tested positive were urged to begin antiretroviral treatment (ART) as soon as possible, both to improve their own health and to make them significantly less likely to infect others.

When the field work ends in 2018, the research team’s next challenge is to make sense out of the huge amount of data and thousands of blood samples collected from those enrolled during the study. Some participants were HIV+ at the start of the study. Others became infected during the course of the study, despite increased prevention efforts.

From the blood samples collected, the virus of each HIV-infected participant will be sequenced. By the end of the study, researchers expect to have up to 7000 near full-length HIV genome sequences.

Melissa Zahralban-Steele, Max Essex and Vlad Novitsky. Photo by Ken Dayton
BCPP team members: Melissa Zahralban-Steele, Max Essex, and Vlad Novitsky. Photo by Kent Dayton

What Sequencing Reveals

When a person becomes infected with HIV, their virus is similar to the virus of the person who infected them. Because HIV mutates quickly, each infected person’s virus evolves differently over time.

HIV Phylogenetic Tree
HIV Phylogenetic Tree

By sequencing the HIV genome of every infected study participant in a village, researchers can create what is known as a phylogenetic tree. HIV phylogenetics is the study of the evolutionary history and relationships among transmitted viruses. A phylogenetic tree is an illustration of those relationships and HIV transmission dynamics.

To insure every participant’s privacy, the sequenced HIV genomes are analyzed at a population (community) level. With the data, researchers can create a map that shows all sampled HIV infections in a village, as well as patterns of clustering between closely related infections. For the BCPP, a cluster is defined as two or more closely related infections.

Targeted Response

By analyzing where clusters exist and where new infections occur, researchers can pinpoint HIV transmission chains, or distinct sub-epidemics. If performed in real time, this analysis will allow healthcare workers to quickly target HIV prevention efforts to high-risk groups and geographic areas.

“The goal from a public health perspective is to identify hot spots—the viral transmission chains that are feeding and fueling the epidemic—and target interventions to prevent new transmissions,” said Dr. Vlad Novitsky, the Harvard AIDS Initiative (HAI) Research Scientist leading the BCPP genetic sequencing team.

Report Card

The primary endpoint of the BCPP is the number of new HIV infections. The hope is that in the 15 villages that receive the interventions, there will be a minimal number of new infections. “But people don’t restrict interactions to their own village,” said Novitsky. “They work and socialize between communities.”

When HIV testing reveals that an individual in a village is newly infected with HIV, researchers will be able to tell if that infection is related or unrelated to viral lineages circulating within the community. If it is not related, the newly infected individual is more likely to have been infected from someone outside of the community who is not receiving the scaled-up prevention interventions.

“Basically, viral linkage tells us whether the interventions are working—whether new infections are coming from inside or outside of the community,” said Novitsky. “If there is a new infection and we have built a phylogenetic tree and see that there are 25 circulating viruses within this community, but the person does not cluster with any of those, it would be a strong confirmation that the person was infected somewhere outside of this community and interventions within this community would not prevent this infection, no matter what.”

Besides helping to gauge how well HIV prevention efforts work, phylogenetic viral linkage will also help researchers understand why different HIV lineages behave differently. HIV transmission clusters are not all the same. Some grow quickly; other are relatively stable over time. “Why are particular viral lineages still spreading despite high levels of ART? Is the answer biological or social and behavioral?” asks Novitsky.

With the powerful tool of phylogenetics, researchers are gaining a better understanding of how and where HIV spreads, allowing public health officials to rapidly target their treatment and preventions efforts to quell the epidemic.