Neutralization diversity of HIV-1 Indian subtype C envelopes obtained from cross sectional and followed up individuals against broadly neutralizing monoclonal antibodies having distinct gp120 specificities

Abstract

Background: The potential use of the broadly neutralizing monoclonal antibodies (bnAbs) towards prophylaxis and treatment to HIV-1 is currently being explored. While a number of promising bnAbs have been discovered and a few of them have progressed towards clinical development, their extent of neutralization coverage with respect to global HIV-1 variants given the existence of genetically distinct subtypes and recombinants circulating globally is not clearly known. In the present study, we examined the variation in the neutralization susceptibility of pseudoviruses expressing 71 full length primary HIV-1 subtype C envs obtained from limited cross-sectional individuals over different time points against four bnAbs that target gp120 with distinct specificities: VRC01, CAP256-VRC26.25, PGDM1400 and PGT121.

Results: We found significant variations in the susceptibility of Indian clade C to these four bnAbs. These variations were found to be distinct to that observed in African subtype C based on the existing datasets and concordant with their sequence diversity. Trend analysis indicated an increasing neutralization resistance observed over time with CAP25-VRC26.25, PGDM1400 and PGT121 when tested on pseudoviruses expressing envs obtained from 1999 to 2016. However, inconsistent trend in neutralization susceptibility was observed, when pseudoviruses expressing envs obtained from three followed up individuals were examined. Finally, through predictive analysis of the 98 Indian subtype C including those assessed in the present study by employing additive model implemented in CombiNAber ( http://www.hiv.lanl.gov ), we observed two possibilities where combinations of three bnAbs (VRC01/CAP56-VRC26.25/PGT121 and PGDM1400/CAP256-VRC26.25/PGT121) could achieve near 100% neutralization coverage.

Conclusions: Our findings not only indicate disparate intra-clade C genetic vis-à-vis neutralization diversities but also warrant the need for more comprehensive study using additional isolates towards comparing inter and intra-clade neutralization diversities which will be necessary for selecting the bnAb combinations suitable for optimal coverage of the region-specific HIV-1 circulating subtypes. Expanding these efforts is imperative for designing efficacious bnAb based intervention strategies for India as well as subtype C in general.

Keywords: CAP256-VRC26.25; Clade C; Envelope; HIV-1; India; Neutralizing antibodies; PGDM1400; PGT121; VRC01.

Fig. 1

Association of phylogenetic relatedness of env and their responses when expressed as pseudoviruses to the four bnAbs: a A phylogenetic tree was constructed for gp160 amino acid sequences of viral clones reported in the present study along with those reported in the CATNAP database (Total N = 1020). The terminal branches of the tree were color-coded based on the subtype as depicted in the color legend. Four heatmaps based on their responses to bnAbs PGDM1400, PGT121, VRC01 and CAP256.-VRC26.25 were overlayed on the phylogenetic tree in the form of concentric tracks one for each bnAb to assess phylogenetic clustering of their IC50 values. IC50 value of 5 µg/mL were considered as neutralization sensitivity threshold. b Neutralization potency (scatter plot against left Y axis) was plotted for pseudoviruses expressing 98 subtype C envs (71 from the present study) from India against the four bnAbs. Pink lines indicate median IC50 values. Orange dots represent data generated in the present study while the black dots indicate data retrieved from the CATNAP database. Potency against all the pairs of bnAbs were compared using Mann–Whitney test. p values were illustrated as follows: > 0.05-non-significant, 0.05–0.01- *, 0.01–0.001-** and < 0.001-***. Percent neutralization coverage of all the bnAbs were plotted as a bar chart against the right Y axis. c Year matched randomly selected equal number viral clone datasets were retrieved from CATNAP database and their IC50 values to 4 bnAbs (PGT121, PGDM1400, VRC01 and CAP256-VRC26.25 were compared between Subtype C from India, Subtype C pan Africa and Other subtypes (All except C). IC50 value of 5 µg/mL was considered as a threshold of neutralization sensitivity. Statistical comparisons were made between each pair for every antibody using Mann–Whitney test

Fig. 2

Comparison of trend in bnAb sensitivity across time against VRC01, CAP256-VRC26.25, PGDM1400 and PGT121. Top panel. Scatter plots of IC50 values for clones reported in the CATNAP database were grouped as 1990–2000, 2001–2010 and 2011–2016 for viruses from India along with those reported in the present study (indicated by larger dots). Bottom panel. Scatter plots of IC50 values for Env-pseudotyped viruses reported in the CATNAP database were grouped as 1990–2000, 2001–2005 and 2006–2010 for envs from Pan-Africa. Data points were color-coded based on the disease stage at sampling of the respective viruses. IC50 value of 5 µg/mL was considered as a threshold of neutralization sensitivity. Statistical assessment of increase in the IC₅₀ values was performed with Jonckheere-Terpstra test (JTT)

Fig. 3

Progression of bnAb responses of pseudoviruses expressing envs obtained from longitudinally followed up individuals. Mean IC₅₀ values against bnAbs VRC01, CAP256-VRC26.25, PGDM1400 and PGT121 were plotted for viral clones prepared from longitudinally collected samples from three HIV-1 subtype C infected individuals (NARI IVC-2, NARI IVC-3 and NARI IVC-11). IC₅₀ value of 5 µg/ml were considered as a threshold of neutralization sensitivity

Fig. 4

Predictive analysis of effect of bnAb combinations on neutralization breadth and potency of HIV-1 Indian clade C. a Cumulative coverage of the virus panel (a fraction between 0 & 1) of 98 clones reported in the present study and CATNAP database from India at various IC50 values for single mAbs and/or mAb combinations with a target Ab concentration of 5 µg/ml. Dashed curve in each of the plots indicates four bnAb combinations. All other combinations are depicted according to the given color codes. Vertical dashed lines in each plot indicate the expected final Ab concentration of four bnAb combination (pink line) and combination under assessment (black line). b Predicted geometric IC₅₀ values against each bnAb/combination based on experimental IC50 values for viruses from India (N-98, left boxplot in each group) vs Viruses from Africa retrieved from CATNAP (N = 250, right boxplot in each group). Black lines in each plot indicate Median IC50 values. Statistical comparison within each group was performed with Mann–Whitney test