HIV Care Prioritization using Phylogenetic Branch Length

AO_SCPLOWBSTRACTC_SCPLOWIn HIV epidemics, the structure of the transmission network can be dictated by just a few individuals. Public health intervention, such as ensuring people living with HIV adhere to antiretroviral therapy (ART) and are continually virally-suppressed, can help control the spread of the virus. However, such intervention requires utilizing the limited public health resource allocations. As a result, the ability to determine which individuals are most at-risk of transmitting HIV could allow public health officials to focus their limited resources on these individuals. Molecular epidemiology suggests an approach: prioritizing people living with HIV based on patterns of transmission inferred from their sampled viral sequences. In this paper, we introduce ProACT (Prioritization using AnCesTral edge lengths), a phylogenetic approach for prioritizing individuals living with HIV. ProACT uses a simple idea: ordering individuals by their terminal branch length in the phylogeny of their virus. In simulations and also on a dataset of HIV-1 subtype B pol sequences obtained in San Diego, we show that this simple strategy improves the effectiveness of prioritization compared to state-of-the-art methods that rely on monitoring the growth of transmission clusters defined based on genetic distance.