The analyses restricted to plasma samples yielded similar results, with PSSM score strongly associated with stage 4 infection (β = 8.54, p<0.0001), intermediate (200–500 cells/ml) and low (<200 cells/ml) CD4 counts (β = 1.67, p = 0.03 and β = 8.83; p<0.0001, respectively) compared to those with CD4 counts above 500 cells/ml, and PSSM score weakly associated with increased V1V2 length (β = 0.07; p = 0.12 per one amino acid increase in V1V2 length). Here, CD4 is linked to infection.