Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage

Abstract

The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.

Trends in HIV-1 pretreatment drug resistance and HIV-1 variant dynamics among antiretroviral therapy-naive Ethiopians from 2003 to 2018: a pooled sequence analysis

“…In addition, the NNRTI-associated PDRMs also increased over time (from 2.19% in 2003 to 7.84% in 2018) (Fig. 4 ), which is once again similar to observations from other studies around the world [ 23 – 28 , 39 ].…”

“…Protease inhibitor (PI) mutations are usually observed at lower frequencies in different studies [ 23 – 28 , 39 ]. Likewise, the frequency of PI mutations is low (0.8%) in this review.…”

HIV-1 drug resistance and genetic diversity in people with HIV-1 in Cape Verde

“…In terms of HIV-1 genetic diversity, we show that multiple subtypes and recombinant forms are still driving the current HIV-1 epidemic in Cape Verde, and that CRF02_AG has become the most common genetic form in Cape Verde, replacing subtype G [6,7]. Similar distribution of HIV-1 genetic forms is currently found in most West African countries [22,43–51]. CRF02_AG is the most prevalent recombinant HIV strain worldwide (7.7%) [52] and its spread in West and Central Africa has increased in recent years (2015–2020) while subtypes A and G are less common [53,54].…”

Genetic landscape for majority and minority HIV-1 drug resistance mutations in antiretroviral therapy naive patients in Accra, Ghana

“…The K103N mutation has also been detected in different studies as majority mutation in Ghana, with the CRF02_AG strain being the dominant subtype. This again, suggests how minority mutation can swiftly develop to become dominant in the viral population to cause virological failure [ 28 , 29 , 34 , [36] , [37] , [38] , [39] ].…”