Optimal combinations of broadly neutralizing antibodies for prevention and treatment of HIV-1 clade C infection.

CAPRISA, 2016.Abstract available in PDF file

Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition : implications for active and passive immunization.

CAPRISA, 2016.Abstract available in PDF file

An investigation of HIV-1 diversity in Southern Africans, and characterisation of viral populations in recently infected women

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Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments

ABSTRACT In the search for effective immunologic interventions to prevent and treat HIV-1 infection, standardized reference reagents are a cost-effective way to maintain robustness and reproducibility among immunological assays. To support planned and ongoing studies where clade C predominates, here we describe three virus panels, chosen from 200 well-characterized clade C envelope (Env)-pseudotyped viruses from early infection. All 200 Envs were expressed as a single round of replication pseudoviruses and were tested to quantify neutralization titers by 16 broadly neutralizing antibodies (bnAbs) and sera from 30 subjects with chronic clade C infections. We selected large panels of 50 and 100 Envs either to characterize cross-reactive breadth for sera identified as having potent neutralization activity based on initial screening or to evaluate neutralization magnitude-breadth distributions of newly isolated antibodies. We identified these panels by downselection after hierarchical clustering of bnAb neutralization titers. The resulting panels represent the diversity of neutralization profiles throughout the range of virus sensitivities identified in the original panel of 200 viruses. A small 12-Env panel was chosen to screen sera from vaccine trials or natural-infection studies for neutralization responses. We considered panels selected by previously described methods but favored a computationally informed method that enabled selection of viruses representing diverse neutralization sensitivity patterns, given that we do not a priori know what the neutralization-response profile of vaccine sera will be relative to that of sera from infected individuals. The resulting 12-Env panel complements existing panels. Use of standardized panels enables direct comparisons of data from different trials and study sites testing HIV-1 clade C-specific products. IMPORTANCE: HIV-1 group M includes nine clades and many recombinants. Clade C is the most common lineage, responsible for roughly half of current HIV-1 infections, and is a focus for vaccine design and testing. Standard reference reagents, particularly virus panels to study neutralization by antibodies, are crucial for developing cost-effective and yet rigorous and reproducible assays against diverse examples of this variable virus. We developed clade C-specific panels for use as standardized reagents to monitor complex polyclonal sera for neutralization activity and to characterize the potency and breadth of cross-reactive neutralization by monoclonal antibodies, whether engineered or isolated from infected individuals. We chose from 200 southern African, clade C envelope-pseudotyped viruses with neutralization titers against 16 broadly neutralizing antibodies and 30 sera from chronic clade C infections. We selected panels to represent the diversity of bnAb neutralization profiles and Env neutralization sensitivities. Use of standard virus panels can facilitate comparison of results across studies and sites

Comparison of Additive and Bliss-Hill models for predicting bnAb combination neutralization scores.

<p>Additive and Bliss-Hill models were used to analyze bnAb combination IC₈₀ scores for the Clade C Panel. In (A), BH model predictions are plotted against observed IC₈₀ values for 20 viruses, with different bnAb combinations (n = 10) shown by different colors and/or symbols. (B) For each bnAb combination tested, the absolute difference between the predicted and the observed Log₁₀ IC₈₀ values for each virus was calculated using both BH and additive models (Fig D in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005520#ppat.1005520.s001" target="_blank">S1 Text</a>). Median Log₁₀ differences using BH model are shown as blue bars and using additive model are shown as green bars, with vertical grey bars representing half the interquartile range. Wilcoxon paired rank test was used to determine whether the Bliss Hill model provides a statistically significantly smaller prediction error for this panel of viruses. Fig D in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005520#ppat.1005520.s001" target="_blank">S1 Text</a> illustrates each of the paired model predictions for the Envs and antibody combinations tested. The additive model often slightly underestimates the observed combination potency, while BH model estimates are closer to the observed. Combinations of bnAbs for which the p-value was smaller than the threshold established by a false discovery rate of q<0.1 are indicated. See Figs C and E in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005520#ppat.1005520.s001" target="_blank">S1 Text</a> for equivalent analysis using the Kong et al. dataset [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005520#ppat.1005520.ref060" target="_blank">60</a>].</p

BH predicted IC₈₀ potency-breadth curves scores for all candidate 2, 3 and 4 bnAb combinations against the clade C virus panel.

<p>Potency-breadth curves for all candidate 2 (A), 3 (B) and 4 (C) bnAb combinations are shown for a total of 1,622 bnAb combinations (81 double-, 431 triple-, 1,110 quadruple-bnAb combinations), using BH model predicted IC₈₀ scores. Each combination’s potency-breadth curve is color coded according to the number of bnAbs of different specificities in the combination, e.g. all 4-bnAb combinations that had two V2g bnAbs, and 1 each of other specificities, were assigned to the same category and were color coded blue in (C). The best-in-category bnAb combinations are highlighted in darker colors in A-C, and the others are shown by matched lighter colors. In (B) and (C), “0/1” indicates combinations in which the indicated epitope may or may not have been covered by a representative bnAb. Combinations with a given total number of bnAbs that have 2 bnAbs targeting a single epitope and up to one bnAb targeting other epitopes were grouped together into categories. Such categories are represented as e.g. “2 CD4bs + 0/1 V2g + 0/1V3g + 0/1 MPER” in the figure, which in the case of 4 bnAb combinations, are composed of combination types “2 CD4bs + V2g + V3g”, “2CD4bs + V2g + MPER” and “2CD4bs + V3g + MPER.</p