Phylogenetic analysis aided in categorizing HIV clusters in rural Idaho

**Nett RJ. Emerg Infect Dis. 2010;doi:10.3201/eid1611.100857.**

Issue: November 2010

Phylogenetic links were observed among 15 cases of HIV in two cities in rural southeastern Idaho, according to an analysis recently published.

There were 152 cases of HIV among Idaho residents from 2003 to 2007, resulting in an average of 30 cases per year (range 24-42 cases). Individuals living in rural areas — defined as areas with fewer than 75,000 residents living more than a 60-minute car ride from an urban area —composed 36% (n=54) of those cases.

Of the 54 rural cases in that time period, 35% were among men who have sex with men, 9% were injection drug users and 4% were both.

In March 2008, the Idaho Department of Health and Welfare received a report of a cluster (cluster A) of five newly identified HIV cases in a rural city in southeastern Idaho (city A).

Cluster B occurred from September to December 2008 among 10 men living either in a city fewer than 30 miles from the site of cluster A (city B) or within a 50-mile radius of city B.

Initial investigation

Each case was epidemiologically linked to at least one other case in the cluster, according to the findings. After initial investigation, health officials suspected that transmissions had occurred between the two clusters, but those suspicions were not immediately confirmed.

Health officials visited five commercial laboratories and obtained HIV-1 pol consensus sequence data for four of the five cases from cluster A, six of the 10 cases from cluster B and one patient with HIV residing in the city of cluster B who had received an HIV diagnosis in December 2008 that was not epidemiologically linked to either cluster. None of the patients had received antiretroviral therapy.

Samples from 34 patients with HIV within a 275-mile radius of city B were obtained for use as control sequences. The samples in the control group had not been treated with ART and had received resistance testing between 2005 and 2008.

There were 10 cases with nucleotide sequence data indicating HIV-1 subtype B, which further coalesced into two distinct phylogenetic-related groupings. There were four patients from cluster A in phylogenetic group 1 and five patients from cluster B in phylogenetic group two.

Genetic links

One patient had no known epidemiologic link to either cluster, which may indicate a previously unidentified epidemiologic link. One case associated with cluster B was not genetically similar to other cases from either cluster but similar to controls.

Among strains in phylogenetic group 1, the average pol genetic distance was 0.2% (median 0.1%, standard deviation [SD] 0.2%); for group 2 strains, the distance was 0.1% (median 0.1%, SD 0.1%); for controls, the average distance was 5.1% (median 5.2%, SD 1.2%).

An average pol genetic distance of 4.8% (median 4.8%, SD 0.2%) was observed between phylogenetic groups 1 and 2. The investigators noted that this distance suggests no linkage between the two groups.

The combination of epidemiologic investigation and molecular analysis indicated that transmission may have originated from two sources within the large group of MSM in southeastern Idaho. The results also suggest that a separate case previously considered to be unrelated may have had genetic similarity to cases from cluster A.

The use of phylogenetic analysis of the sequences “showed that Clusters A and B were not epidemiologically related and helped target appropriate and specific HIV prevention activities,” the investigators wrote.