A US study of HIV gene sequences in networks with a particularly high HIV infection rate has found the highest rates in groups containing more young gay men, which is not unexpected, but also in more Latino than black men, which may signal a shift in the demographics of those most at risk of HIV.
Anne Marie France of the US Centers for Disease Control and Prevention (CDC) told the 25th Conference on Retroviruses and Opportunistic Infections (CROI 2018) that since 2013, the US National HIV Surveillance System (NHSS) has started to routinely analyse the gene sequences of HIV viruses in newly diagnosed people. Such phylogenetic analysis can identify clusters of infection – groups of two or more people whose viruses are so similar that they must share a common origin.
Clusters have often been analysed retrospectively to trace the growth of an epidemic, to analyse viral load in transmission pairs, or to to see when different HIV strains first arrived in a population and how long they persist. But because the NHSS is receiving so much data, and receives it quarterly, the genetic data can also be used prospectively. This means that the ongoing rate of new infections in clusters can be determined, and clusters that are unusually ‘active’, in other words where new infections turn up particularly frequently, can be identified and used to identify HIV ‘hot spots’. Since late 2015, the CDC has been identifying such clusters and calculating infection rates in ones with five or more members.
The first 15 months’ of data have been analysed in 27 jurisdictions in the USA – in 20 states, the District of Columbia and Puerto Rico, and five individual cities such as New York and Houston. From January this year the NHSS has collected phylogenetic data from every state, so the CDC will be able to build up a fuller picture. At present, there are viral gene sequences available for over 280,000 people living with HIV, of whom 51,750 have been diagnosed since December 2013.
The phylogenetic tests are anonymised. But the tests can still be used to ensure people with diagnosed infections are actually in care and to provide pre-exposure prophylaxis (PrEP) and other focused, community-level interventions to connected communities.