Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning.

Area of Science:

• Virology
• Molecular Biology
• Epidemiology

Background:

• Human Immunodeficiency Virus type 1 (HIV-1) Subtype C is the most common globally.
• Previous research indicated a lack of clear phylogenetic structure in African HIV-1 Subtype C.
• Understanding HIV-1 Subtype C's genetic diversity is vital for effective control and prevention strategies.

Purpose of the Study:

• To investigate and define the phylogenetic structure of African HIV-1 Subtype C.
• To identify distinct clusters within HIV-1 Subtype C populations.
• To assess the implications of identified clusters for vaccine development.

Main Methods:

• Sequential pruning of ambiguously positioned taxa in phylogenetic analyses.
• Construction of phylogenetic trees using envelope gene sequences and full-length genomes.
• Analysis of recently transmitted viruses in South Africa to assess clustering and recombination.

Main Results:

• A well-defined intrasubtype C phylogenetic structure emerged after data pruning.
• 52% of African HIV-1 Subtype C isolates formed 11 distinct clusters with geographical associations.
• 70% of recently transmitted South African viruses clustered, with 15% identified as intercluster recombinants.

Conclusions:

• HIV-1 Subtype C exhibits a defined phylogenetic structure, contrary to previous beliefs.
• The identified clusters, particularly in South Africa, highlight specific circulating viral lineages.
• These findings have significant implications for designing subtype C-specific HIV vaccines for high-prevalence regions.