One of the challenges in HIV epidemiology is the generation of reliable estimates of HIV incidence in cross-sectional surveys. Most tests for recent HIV infection measure either the magnitude or avidity of HIV-specific antibodies: both parameters are sensitive but not specific. Assays that quantify the epitope diversity of HIV-specific antibodies are a potential strategy to determine recent HIV infection. The hypothesis is that the greater the duration of HIV infection, the greater the epitope binding diversity of HIV-specific antibodies. We therefore used a novel assay, the global HIV peptide microarray, to define antibody epitope signatures associated with different stages of HIV infection.
Plasma samples from 3 groups were obtained from the Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA): ART-naïve individuals with recent HIV infection (<12 mos, N=17), ART-naïve individuals with non-recent infection (>12 mos, N=17) and ART-suppressed individuals with non-recent infection (N=15). Samples were incubated with the peptide microarray, a multiplex platform to measure antibody binding to 6,654 peptides from across the HIV proteome and covering the majority of global sequences. Positive peptide responses were tallied by protein, with fewer positive responses denoting a narrower antibody epitope signature.
ART-naïve individuals with recent HIV infection had significantly fewer positive HIV Env peptides than those with non-recent infection (median of 50 vs. 138, P=0.0002). The expansion of positive responses was observed at the V3 loop of Env, which is involved in coreceptor engagement. Positive Env responses were also significantly and strongly correlated with the duration of HIV infection (days from detectable infection) among ART-naïve participants (P<0.0001, R=0.67 by Spearman test). This positive association persisted when ART-suppressed participants were included in the analysis (P=0.0078, R=0.39).
Recent HIV infection was associated with a narrow epitope signature, while chronic HIV infection (even among persons with low HIV RNA) was associated with a broader and more diverse epitope signature. This data suggests that the global HIV peptide microarray can be used to measure epitope signatures associated with recent and non-recent HIV infection, independent of HIV RNA. Out data suggest that further optimization of the microarray in larger cohorts may allow for high throughput applications.