New computational method helps trace HIV outbreak

November 23, 2010—Thomas Leitner of the Laboratory's Theoretical Biology & Biophysics group and collaborators at the Karolinska Institute in Sweden analyzed a recent outbreak of HIV among injecting drug users in Stockholm, Sweden using a new computational method developed by Lietner for genetic analyses. This method measures the relative rate of an epidemic, such as the one in Stockholm, which was caused by the HIV-1 (CRF01) variant.

Tracing the outbreak

The results showed that the rate of HIV spread increased momentarily by a factor 12 from what is normal in the population. The genetic analysis also showed that the epidemic spread from nearby Finland, where a previous outbreak had occurred. The scientists learned that the particular HIV strain had entered Stockholm several times. However, only one introduction set off the outbreak once HIV entered a so-called "standing social network," that consisted of previously uninfected injecting drug users with risky behavior.

The novelty of the research is the ability to convert the virus genetic information in a phylogenetic tree to epidemiological information about the infected human population. A phylogenetic tree is a diagram (dendrogram) that shows the genetic relationships between the investigated DNA sequences of HIV. The horizontal branches show how much the HIV sequences have evolved, and the vertical branches that connect the horizontal branches together show how lineages have evolved from common ancestor viruses. The shape of the tree, both in terms of how branches connect to each other and how long they are, give information regarding how HIV spread in these populations.

Creating a powerful tool

The scientists estimated the relative rate of spread among injecting drug users from DNA data of the virus that infected them. The analysis shows the evolutionary history of HIV in this outbreak and how it is related to the Finnish outbreak. Hard data on prevalence and incidence are difficult to retrieve by other methods, especially during an outbreak in a population that is marginalized in society. Combining phylogenetics and epidemiological data creates a powerful tool to investigate outbreaks of HIV and other infectious diseases that could improve surveillance and prevention.

The Journal of Virology published the research. The National Institutes of Health supported the LANL work.