{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:44:39Z","timestamp":1760150679706,"version":"build-2065373602"},"reference-count":38,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,12,21]],"date-time":"2023-12-21T00:00:00Z","timestamp":1703116800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation","award":["EXCELLENCE\/0918\/0093","240\/2019"],"award-info":[{"award-number":["EXCELLENCE\/0918\/0093","240\/2019"]}]},{"name":"Ministry of Health of the Republic of Cyprus","award":["EXCELLENCE\/0918\/0093","240\/2019"],"award-info":[{"award-number":["EXCELLENCE\/0918\/0093","240\/2019"]}]},{"name":"University of Cyprus","award":["EXCELLENCE\/0918\/0093","240\/2019"],"award-info":[{"award-number":["EXCELLENCE\/0918\/0093","240\/2019"]}]},{"name":"Cyprus Academy of Sciences, Letters, and Arts","award":["EXCELLENCE\/0918\/0093","240\/2019"],"award-info":[{"award-number":["EXCELLENCE\/0918\/0093","240\/2019"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Molecular investigations of the HIV-1 pol region (2253\u20135250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790\u20138795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.<\/jats:p>","DOI":"10.3390\/v16010019","type":"journal-article","created":{"date-parts":[[2023,12,22]],"date-time":"2023-12-22T01:19:42Z","timestamp":1703207982000},"page":"19","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9641-7737","authenticated-orcid":false,"given":"Cicek","family":"Topcu","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasilis","family":"Georgiou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johana Hezka","family":"Rodosthenous","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Georgios","family":"Siakallis","sequence":"additional","affiliation":[{"name":"AIDS Clinic, Larnaca General Hospital, 6043 Larnaca, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena Katerina","family":"Gavala","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4857-7561","authenticated-orcid":false,"given":"Christiana Reveka","family":"Dimitriou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evgenia","family":"Zeniou","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1086-0296","authenticated-orcid":false,"given":"Brian Thomas","family":"Foley","sequence":"additional","affiliation":[{"name":"T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5340-7109","authenticated-orcid":false,"given":"Leondios G.","family":"Kostrikis","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Cyprus, 1 University Avenue, Aglantzia, 2109 Nicosia, Cyprus"},{"name":"Cyprus Academy of Sciences, Letters, and Arts, 60\u201368 Phaneromenis Street, 1011 Nicosia, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,21]]},"reference":[{"key":"ref_1","unstructured":"Joint United Nations Programme on HIV\/AIDS (UNAIDS) (2023, November 03). 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