To investigate the rapid HIV epidemic in Latvia, 97 newly detected individuals were sampled in 2000-2001. To establish the molecular epidemiology we sequenced the env V3 and gag p17 regions of the HIV genome and compared them with reference sequences using phylogenetic analyses. As expected, the vast majority (n = 88; 91%) were intravenous drug users (IDUs) from the Riga region. Also, the majority of the investigated individuals (n = 93; 96%) were found to carry a subtype A1 virus that may have entered the Latvian IDU population several times. In addition, one IDU was infected with CRF03_AB and three other individuals, who had been infected through sexual contacts, carried subtype B virus. Thus, subtype A1 dominates the Latvian epidemic and is strongly associated with the IDU risk group. Although some spread of subtype A1 has occurred in the heterosexual group, subtype B dominates among homosexually and heterosexually infected individuals.

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.

Local, explosive outbreaks of HIV-1 infections among intravenous drug users (IDUs) caused by closely related variants have been reported in the Ukraine and Russia since 1996. Latvia experienced the start of a similar outbreak at the end of 1997 and already at the end of 1998 IDUs constituted approximately 50% of all known HIV cases (122 of 251). To investigate the molecular epidemiology of HIV-1 variants circulating among Latvian IDUs the V3 domain of the env gene was directly sequenced from samples of seven recently infected IDUs. Phylogenetic tree analysis showed that the seven Latvian HIV-1 variants had closely related subtype A genotypes that shared recent ancestry with each other as well as with variants involved in outbreaks in the Ukraine and southern Russia. There exists a clear risk for continued spread of HIV-1 in Latvia because the number of IDUs is increasing and needle sharing is common.

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