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


The polyphyletic picture of HIV-1 infection in Cyprus is a fact, as new variants and unique recombinant forms were found in the recent past. As part of a growing effort to monitor any changes in the molecular epidemiology of HIV we studied two notable cohorts of the known HIV-1 population diagnosed in 2010 to 2011. Near full-length genome sequencing and phylogenetic analysis was carried out to determine the heterogeneity among HIV-1 strains isolated from patients, 10 originated from eastern European countries (mostly Romania) and 8 young Cypriots (<25 yrs), all men who have sex with men (MSM).

Materials and methods

Sequence of the near full-length genome was amplified by RT-nested PCR from all HIV-1 seropositives and sequenced. Detailed phylogenetic and bootscanning analyses were performed by MEGA v5.0 to determine phylogenetic associations and subtype assignments. To explore putative recombination patterns in the sequences we performed a bootscanning analysis using Simplot, version 3.5.1.


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.


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.

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Correspondence to Ioanna Kousiappa.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Kousiappa, I., Lazarou, Y., Othonos, K.M. et al. Influx of uncommon HIV-1 strains from Eastern Europe and identification of a new unique recombinant strain among young Cypriot MSM in Cyprus. Retrovirology 9 (Suppl 1), P98 (2012).

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