Introduction The study was aimed at assessing frequencies of neutralising antibodies in individuals affected with the commonest HIV-1 clades A and D in Uganda.

Methods This was a cross- sectional study of 83 HIV-1 chronically infected Anti- Retroviral Therapy (ART) naïve adults who were enrolled from Medical Research Council (MRC) cohort and The AIDS Support Organisation (TASO) Clinic in Entebbe. Samples of Plasma were tested for the neutralisation activity against a panel of 3 clade A and D viruses using the Neutralisation Assays. Neutralisation assays were performed using Env pseudovirus viruses in the TZM-bl cell- based assay. Neutralisation values were obtained as the plasma dilutions at which virus entry was inhibited by 50% compared to that in the absence of plasma (IC50). A plasma sample was scored as displaying neutralising activity against a particular virus if at least 50% inhibition of infection was recorded at the lowest plasma dilution tested (1: 20) in at least two independent neutralisation assays.

Results Clade A viruses are better neutralised compared to clade D viruses. Individuals whose titers were above 1080 (labelled red required further sample dilution. 51.81% of the participants had their antibody neutralisation titers above 40. There was a significant difference between the proportion of clade A viruses neutralised and those of clade D as obtained statistically using the Mann- Whitney test with a p- value <0.0001. The neutralisation titers obtained for the individual clade A viruses Q23.17, Q769.d22 and Q842.d12 were much higher than those for clade D viruses QA013.H1, Q857.B3 and QD435.5B.

Conclusion Generally, the frequency of neutralising antibodies was found to be much higher in Clade A compared to Clade D. This implies that in case of a vaccine design, emphasis should be put on Clade D subtype since it’s harder to neutralise naturally.