Characterizing HIV-1 Tropism and Key Positions within the V3 Loop Using Random Forest Analysis

Abstract HIV-1 exhibits tropism for the CCR5 and/or CXCR4 receptors, which are essential for viral entry into CD4 cells. With the advent of coreceptor antagonists, understanding HIV-1 tropism has become crucial for patient management. The V3 loop, a highly variable region of approximately 35 amino acids, plays a key role in determining tropism. Due to the genetic diversity of HIV-1 subtypes, V3 loop sequences may vary in amino acid composition depending on tropism and subtype. This study aimed to identify critical positions within the V3 loop for defining CCR5, CXCR4, and R5X4 tropisms based on HIV-1 subtype. The random forest algorithm was employed to assess variable importance. CCR5 tropism was predominant, accounting for 80.06% of the sample, while 15% exhibited dual-tropism (R5X4) and 6.37% had CXCR4 tropism. The most prevalent subtype was B, representing 54.45% of the sample. Random forest analysis identified positions 2, 5, 8, 11, 12, 13, 18, 20, 21, 22, 24, 25, 32, and 34 as crucial for HIV-1 tropism. Most of these positions aligned with previous findings. Interestingly, the widely cited 11/25 rule was not universally applicable across subtypes, as recombinant forms exhibited different key positions. Position 25 was important across all subtypes, whereas position 11 ranked among the top five only in subtype B. The random forest algorithm effectively identified key positions for tropism characterization.