Abstract
BackgroundUnderstanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Sequence variation may affect antiviral drug resistance development, disease progression, evolutionary rates and transmission routes.ResultsWe investigated the subtype distribution of HIV-1 in Europe and Israel in a representative sample of patients diagnosed between 2002 and 2005 and related it to the demographic data available. 2793 PRO-RT sequences were subtyped either with the REGA Subtyping tool or by a manual procedure that included phylogenetic tree and recombination analysis. The most prevalent subtypes/CRFs in our dataset were subtype B (66.1%), followed by sub-subtype A1 (6.9%), subtype C (6.8%) and CRF02_AG (4.7%). Substantial differences in the proportion of new diagnoses with distinct subtypes were found between European countries: the lowest proportion of subtype B was found in Israel (27.9%) and Portugal (39.2%), while the highest was observed in Poland (96.2%) and Slovenia (93.6%). Other subtypes were significantly more diagnosed in immigrant populations. Subtype B was significantly more diagnosed in men than in women and in MSM > IDUs > heterosexuals. Furthermore, the subtype distribution according to continent of origin of the patients suggests they acquired their infection there or in Europe from compatriots.ConclusionsThe association of subtype with demographic parameters suggests highly compartmentalized epidemics, determined by social and behavioural characteristics of the patients.
Highlights
Understanding Human immunodeficiency virus type 1 (HIV-1) subtype distribution and epidemiology can assist preventive measures and clinical decisions
Subtype B accounts for 70% of HIV-1 infections in newly diagnosed patients living in Europe Of the 2730 sequences included in the study, 2469 (90.4%) were successfully subtyped using the REGA Subtyping Tool version 2, while 261 (9.6%) were unclassified, of which 137 sequences (5.0%) remained untypable even after manual analysis
When adjusting for oversampling in some countries (Additional file 1: Figure S1), the proportion of new diagnoses with subtype B increased to 70.2%; subtypes C and A decreased to 5.0 and 3.6% respectively; CRF02_AG and subtype G increased to 4.9% and 4.8% respectively; CRF01_AE decreased to 1.9%; and U/Unique Recombinant Forms (URFs) increased to 5.8% (Additional file 2: Figure S2)
Summary
Understanding HIV-1 subtype distribution and epidemiology can assist preventive measures and clinical decisions. Human immunodeficiency virus type 1 (HIV-1) is characterized by extensive genetic diversity. HIV-1 strains are divided in four groups (M, N, O and P), originating from four separate cross-species transmissions from chimpanzees and/or gorillas to humans. HIV-1 group M has been further classified into 9 distinct subtypes, sub-subtypes and inter-subtype circulating recombinant forms (CRFs). Subtypes and subsubtypes arose from founder effects at different time points in the past, and inter-subtype recombinants can arise in patients co-infected with strains from two different subtypes. If these newly recombined strains have a significant epidemic spread, they are called Circulating Recombinant Forms (CRFs) [5]
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