Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men
- Univ. of Cyprus, Nicosia (Cyprus)
- Larnaca General Hospital, Larnaca (Cyprus)
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Univ. of Cyprus, Nicosia (Cyprus); Cyprus Academy of Sciences, Letters, and Arts, Nicosia (Cyprus)
Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.
- Research Organization:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Organization:
- USDOE
- Grant/Contract Number:
- 89233218CNA000001
- OSTI ID:
- 2470523
- Journal Information:
- Virulence, Journal Name: Virulence Journal Issue: 1 Vol. 13; ISSN 2150-5594
- Publisher:
- Taylor & FrancisCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Similar Records
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
Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola
Journal Article
·
Wed Dec 20 19:00:00 EST 2023
· Viruses
·
OSTI ID:2470549
Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola
Journal Article
·
Sun Oct 16 20:00:00 EDT 2022
· Frontiers in Microbiology
·
OSTI ID:2470548