Molecular Epidemiology of Early and Acute HIV Type 1 Infections in the United States Navy and Marine Corps, 2005–2010

Abstract

The U.S. military represents a unique population within the human immunodeficiency virus 1 (HIV-1) pandemic. The last comprehensive study of HIV-1 in members of the U.S. Navy and Marine Corps (Sea Services) was completed in 2000, before large-scale combat operations were taking place. Here, we present molecular characterization of HIV-1 from 40 Sea Services personnel who were identified during their seroconversion window and initially classified as HIV-1 negative during screening. Protease/reverse transcriptase (pro/rt) and envelope (env) sequences were obtained from each member of the cohort. Phylogenetic analyses were carried out on these regions to determine relatedness within the cohort and calculate the most recent common ancestor for the related sequences. We identified 39 individuals infected with subtype B and one infected with CRF01_AE. Comparison of the pairwise genetic distance of Sea Service sequences and reference sequences in the env and pro/rt regions showed that five samples were part of molecular clusters, a group of two and a group of three, confirmed by single genome amplification. Real-time molecular monitoring of new HIV-1 acquisitions in the Sea Services may have a role in facilitating public health interventions at sites where related HIV-1 infections are identified.

Molecular epidemiology of a primarily MSM acute HIV‐1 cohort in Bangkok, Thailand and connections within networks of transmission in Asia

“…Here, the connection of RV254 sequences with the rest of Asia was investigated by a transmission network analysis that clustered similar env sequences with a pairwise distance of 3% or less. In known transmission pairs, divergence in the env gp160 gene has been reported to be less than 3% or approximately 75 nucleotides in the 2.5‐kb gene . At this relatively strict threshold, we identified five pairs of potential transmission linkages within RV254, and a total of 123 clusters within the larger Asia region.…”

Significant contribution of subtype G to HIV-1 genetic complexity in Nigeria identified by a newly developed subtyping assay specific for subtype G and CRF02_AG

“…Complementary DNA was synthesized from extracted plasma RNA and subjected to a nested PCR using the method previously described. [36] Sequence data were manually edited using Sequencher 5.0 (Gene Codes Corporation, Ann Arbor, MI).…”

Centralized HIV Program Oversight

“… 12 Pairwise genetic distances of sequences were performed using the Kimura 2-parameter substitution model against all incident Army sequences acquired from this base in the period 2001 to 2013 (n = 29). To confirm networking in another region of the virus, the HIV-1 envelope sequences encompassing HXB2 5984–9063 were generated and analyzed using methods previously described 13 , 14 for individuals who were networked (less than 2.0% divergence between sequences) in pro-RT sequence analysis.…”