Phylogenetic analysis of the Latvian HIV-1 epidemic

Abstract

The Latvian HIV-1 outbreak among intravenous drug users (IDUs) in 1997-1998 involved subtype A1. To obtain a more complete picture of the Latvian HIV-1 epidemic, 315 HIV-1-infected patients diagnosed in 1990-2005 representing different transmission groups and geographic regions were phylogenetically characterized using env V3 and gag p17 sequences. Subtypes A1 and B infections were found in 76% and 22% of the patients, respectively. The subtype A1 sequences formed one large cluster, which also included sequences from other parts of the former Soviet Union (FSU), whereas most subtype B sequences formed three distinct clusters. We estimated that subtype A1 was introduced from FSU around 1997 and initially spread explosively among IDUs in Riga. A recent increase of heterosexually infected persons did not form a separate subepidemic, but had multiple interactions with the IDU epidemic. Subtype B was introduced before the collapse of the Soviet Union and primarily has spread among men who have sex with men.

FIG. 1.

Number of newly HIV-1 diagnosed individuals in different transmission groups in Latvia from 1987 to 2008. HET, heterosexual; MSM, men who have sex with men; VERT, mother-to-child transmission; IDU, intravenous drug use; Unkn, unknown transmission route.

FIG. 2.

Maximum likelihood trees of V3 sequences from Latvia and closely related database sequences for subtype A1 (A) and subtype B (B). The color of each branch represents the transmission route of Latvian sequences, while sequences from other countries are colored black. The scale at the bottom indicates nucleotide substitutions per site according to a GTR+G+I model. The subtype A1 tree was rooted using subtype A1 sequences SE8538 (AF069669), SE7253 (AF069670), and SE7535 (AF069671) and the subtype B tree was rooted using the subtype D sequence D.CD.84.84ZR085 (U88822). Three sequence clusters (1–3) in the subtype B tree are indicated. HET, heterosexual; MSM, men who have sex with men; VERT, mother-to-child transmission; IDU, intravenous drug use; Unkn, unknown transmission route.