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Results Phylogenetic analyses of the obtained viral sequences showed genetic diversity. In the eastern European cohort, subtype F1 was the dominant subtype (40%), followed by subtype C (20%), A1, A2, CRF02_AG, and CRF03_AB (10% each). In the young MSM cohort subtype B was the main subtype (50%), followed by subtype A1 (25%), CRF01_AE (12.5%) and one HIV-1 isolate that was not classified in any known subtype or recombinant form (12.5%). Complete recombination analysis revealed that this isolate had a new recombinant pattern, comprising segments of subtypes A1 and B, and is distinct from any reported recombinant. Conclusions These findings exhibit an influx of infrequent HIV-1 genetic forms from eastern European countries in Cyprus, and a stable circulation of B and A1 subtype among the young Cypriot MSM cohort. A unique recombination event between A1 and B subtypes has occurred and the parental strains seem to be formerly characterized Cypriot MSM patients. For the first time, these data show an impact on the evolutionary progress of HIV-1 epidemic of the island. The significance of this study along with the earlier variable epidemiological status of HIV-1 infection in Cyprus reflects the contribution to HIV classification, and the important implications for HIV-1 disease control and surveillance.

Influx of uncommon HIV-1 strains from Eastern Europe and identification of a new unique recombinant strain among young Cypriot MSM in Cyprus