US genotyping survey finds rapid HIV infection rate in young and Latino gay men

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.


transmission cluster

By comparing the genetic sequence of the virus in different individuals, scientists can identify viruses that are closely related. A transmission cluster is a group of people who have similar strains of the virus, which suggests (but does not prove) HIV transmission between those individuals.

person years

In a study “100 person years of follow-up” could mean that information was collected on 100 people for one year, or on 50 people for two years each, or on ten people over ten years. In practice, each person’s duration of follow-up is likely to be different.


A unit of heredity, that determines a specific feature of the shape of a living organism. This genetic element is a sequence of DNA (or RNA, for viruses), located in a very specific place (locus) of a chromosome.

anonymised data

Information about a patient from which the name, address and other identifying information has been removed.


A variant characterised by a specific genotype.


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.

Priority clusters

During the period December 2015 to December 2016, which involved five quarterly collections of data, the CDC identified 60 priority clusters. These clusters ranged in size from 5 to 42 persons.

Clusters were identified in all regions of the country, and involved all 20 states in the programme. Not all clusters are connected by geographical location: nine of the 60 did not have more than 50% of the persons in the cluster in any single state.

On average, it is calculated that one in 25 people with HIV in the US transmits their HIV to another person in the course of a year – four transmissions per 100 person-years.

In these 60 clusters, the ongoing transmission rate was 44 per 100 person-years – eleven times the national average. Rates in individual clusters ranged from 21 to 132 transmission events per 100 person-years, meaning that in the cluster with the highest rate it was more likely than not that a member of the cluster would transmit HIV to another person within a year.

Members of these priority clusters were more likely than people in non-priority clusters, or who were not in clusters, to be men who had sex with men (MSM). In the whole database 59% of individuals were MSM, 15% were heterosexual and 3% people who injected drugs. In priority clusters 83% were MSM.

Priority cluster members were on average younger too: 70% were under 30 compared with 42% on average. This implies, as would be expected, that they were in general more recently infected.

What was more of a surprise was that Hispanic people were over-represented in the priority clusters and black people under-represented. Thirty-eight per cent of priority cluster members were Hispanic compared to 27% in non-priority clusters or not in clusters; in contrast 31% were black in priority clusters compared with 41% non-priority. The proportion who were white was the same in both (24%).

This could possibly indicate the beginnings of a change in the racial makeup of those in the US at the highest risk of HIV infection.

Using the data to guide prevention

By agreement with the jurisdictions, the CDC does not publish their location and other identifying details. However, they did confidentially notify affected jurisdictions and provided support for further investigation and interventions if needed.

“These findings suggest rapid transmission in networks involving young MSM, especially young Hispanic MSM,” the CDC’s Anne Marie France told the conference.

“We will be using these data to guide future prevention interventions,” she added. “Prioritizing these clusters for public health intervention may have increased potential to reduce future infections.”

She told ”Although we do not publish location, I can say that we only had a few clusters in the south-eastern states [where HIV prevalence is highest] because several key states such as Mississippi and Georgia have so far not participated. So we may find more now they have joined the programme.

“But we did get surprises, and not all priority clusters are where you’d expect or contain who you’d expect. Rapidly growing clusters were not all in urban areas, for instance.”


France AM et al. Rapidly growing HIV transmission clusters in the United States, 2013–2016. Conference on Retroviruses and Opportunistic Infections (CROI 2018), Boston, abstract 40, 2018.

View the abstract on the conference website.

Watch the webcast of this presentation on the conference website.