HIV-1 Subtype Diversity in Morocco: Signals of Change and Implications for National Surveillance

Limited molecular surveillance continues to constrain Morocco's HIV response, leaving subtype dynamics largely underreported. Once characterized by a predominance of subtype B, the Moroccan epidemic now appears to reflect shifting patterns shaped by regional and international connectivity. This study aimed to investigate HIV-1 molecular diversity, monitor circulating HIV-1 genetic variants, and inter-gene recombination in a cohort of people living with HIV in Morocco.

We conducted an analysis of individuals diagnosed with HIV-1 infection or receiving follow-up care. Demographic and clinical data were extracted. Genotypic testing was performed on the protease/reverse transcriptase (PR/RT) and integrase (IN) regions of the pol gene using the HIV-1 Genotyping Kit with Integrase. Subtypes were assigned via Stanford HIVdb and HIV Blast, and phylogenetic relationships were analyzed using MEGA 12.

Of the 73 individuals enrolled, 64 were successfully sequenced. The median age was 43 years (IQR 35-51.3), with over half aged 25-44, and 85.9% were male. Heterosexual transmission was the main route (87.5%), and 59.4% were ART-naïve. Non-B subtypes predominated (87.5%), led by CRF02_AG (73.4%), followed by B (12.5%), C (7.8%), and A3 (3.1%). The cohort showed significant genetic diversity, including multiple CRFs such as CRF45_cpx (1.6%), CRF01_AE (1.6%), B/CRF02_AG (7.8%), G/CRF02_AG (3.1%), C/CRF02_AG (1.6%), CRF02_AG/CRF45_cpx (1.6%) and CRF02_AG/CRF22_01A1 (1.6%).

This study provides updated insight into HIV-1 diversity in Morocco, showing a predominance of non-B subtypes, particularly CRF02_AG, and signals of increasing heterogeneity compared with reports from more than a decade ago that described subtype B predominance. These findings suggest a viral transition shaped in part by regional connectivity and highlight a gap in Morocco's HIV strategy, underscoring the need to implement nationwide molecular surveillance to inform future HIV control efforts.