A7 Co-receptor tropism determined by genotypic assay in HIV-1 non-B subtypes circulating in Cuba: Implications for pathogenesis and Maraviroc resistance

The V3 loop of the HIV-1 envelope (env) gene is involved in binding to the chemokine receptors CCR5 and CXCR4, thus determining viral tropism. With the aim of genetically characterizing the C2V3 env region of HIV-1 samples from Cuban patients, naive to Maraviroc (MVC) therapy, 115 plasma samples were taken in the period of 2014–6 and analyzed by sequencing of the C2V3 region. HIV-1 subtyping was performed using COMET V.2 and Rega subtyping toolV.3 software. Subtypes were confirmed by phylogenetic analyses using Mega-6. Prediction of co-receptor tropism was performed using the geno2pheno algorithm. The viral mutations associated to MVC resistance were analyzed, as well as the association of the subtype with clinical, epidemiological, virological, and immunological variables. The subtypes detected using the C2V3 region were CRF20, 23, 24_BG (35 patients, 30.4%); Subtype B (33 patients, 28.7%); CRF19_cpx (30 patients, 26.1%); CRF18_cpx (10 patients, 8.7%); and others (7 patients, 6.1%). Overall, 60 per cent of the viruses exhibited R5 phenotype, 14.8 per cent were R5X4 and 25.2 per cent were X4. Interestingly, CRF19_cpx virus was associated with having phenotype X4 [46.7%, P = 0.0047, odds ratio (OR): 3.96, 95% confidence interval (95% CI): 1.59–9.84], with infection in young individuals (39.1%, P = 0.025, OR: 3,548; 95% CI: 1,136–11,077) and with higher values of viral load (P ≤ 0.05). The comparison of the amino acid sequences of the V3 loop showed differences between the B and non-B subtypes (P = 0.0001). Mutations reported to be associated with MVC resistance, were detected in 75.7 per cent of the samples, in positions 11 (6.1%), 13 (49.6%), 25 (6.1%), 316 (7.0%), 323 (11.3%), and 319 (3.5%) of Gp120, particularly in the recombinant forms CRF19_cpx and CRF_BGs. HIV variants that use the CXCR4 co-receptor were associated with more than 10 years of diagnosis, with older individuals, in the AIDS stage, with low CD4 counts and higher viral load levels (P < 0.05). The results support the hypothesis previously stated that CRF19_cpx viruses could be more pathogenic and would have limitations for the use of MVC. The high rate of mutations associated to MVC among non-B Cuban subtypes should be further studied.