Emergence of HIV-1 C/A1 and C/A1/D circulating recombinant forms, and dominance of subtype C and R5 use from whole genome sequence analysis in Addis Ababa

Abstract Background The HIV pandemic in Ethiopia is dominated by subtype C with sporadic A and D epidemiology. The presence of subtypes A and D may result in emergence of recombinant viruses, and increase the genetic diversity that makes monitoring the HIV epidemic, and the development of vaccines and therapeutics difficult. This study is aimed at determining subtypes, circulating recombinant forms (CRFs), and the dominant coreceptor use in Addis Ababa, Ethiopia. Methods Participants with a range of purposely selected CD4+ T-cell counts were included. Chi-square and Mann-Whitney tests were used. Whole genome next-generation sequencing (NGS) of HIV was performed using a PCR amplification method and Illumina MiSeq. Subtyping and scanning of recombination were done by the REGA subtyping tool version 3.0. Prediction of coreceptor usage was performed using Geno2Pheno clonal-model and PhenoSeq. Signature amino acids and positive charges were also used in the tropism prediction. Phylogenetic analyses were conducted with MEGA version 6 using maximum likelihood with the neighbor-joining (N-J) methods. Results Sixty participants were included with a median age of 34.5 [interquartile range (IQR) 30.0-40.0]. Seven (11.7%) of the study participants were at WHO clinical stage 3/4 and 13 (21.7%) were at AIDS stage with CD4+ T cell count <200 cells/uL. Among the total 60 HIV genomes sequenced, 49 were subtype C (81.7%), one was subtype A1 (1.7%), six were recombinant C/A1 (10%), three were recombinant C/A1/D (5.0%), and one was unassigned. From 50 of the sequences where coreceptor usage was determined by PhenoSeq, 44 (88.0%) were CCR5-tropic and six (12.0%) used CXCR4. Conclusion The study confirmed that the dominant subtype in Addis Ababa is HIV-1 subtype C. In addition, HIV-1 subtype A1, CRFs C/A1 and C/A1/D were also identified. The dominance of R5-tropic viruses was detected and these were associated with a higher CD4 T-cell count and lower viral load. Further studies on HIV subtypes and CRFs will be essential to fully understand HIV/AIDS epidemiology. In addition, the tropism information is important in Ethiopia if the use of the co-receptor antagonist maraviroc is planned.