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

ABSTRACT

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.

KEYWORDS:

• Human immunodeficiency virus type 1
• circulating recombinant forms
• unique recombinant forms
• HIV-1 genetic diversity
• HIV-1 phylogeny
• HIV-1 molecular epidemiology
• Cyprus

Acknowledgments

We thank all participating study subjects from the Grigorios HIV Clinic of Larnaca General Hospital, Dr. George Siakalis, Andri Demetriou, the Cyprus Ministry of Health, and the Cyprus National Bioethics Committee for valuable assistance.

Disclosure statement

No potential conflict of interest was reported by the authors.

Bioethics statement

Bioethical approval under approval number EEBK EΠ 2017.01.23 on February 20, 2017 was obtained for the period from March 9, 2017 to October 13, 2019, and bioethical approval under approval number EEBK ΕΠ 2019 71 on September 2, 2019 was obtained for the period from October 14, 2019 to October 14, 2021.

Data availability statement

The DNA nucleotide sequence data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21505594.2022.2106021.

Additional information

Funding

This work was co-funded by the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation (Project: EXCELLENCE/0918/0093), the Ministry of Health of the Republic of Cyprus (Contract No 240/2019), the University of Cyprus and the Cyprus Academy of Sciences, Letters, and Arts through internal funds awarded to Professor Leondios G. Kostrikis.