Background
A recent study demonstrated that combined administration of N-803 (IL15 agonist) and the 10-1074 and 3BNC117 broadly neutralizing antibodies (bNAbs) results in durable virologic remission following ART cessation in SHIV-infected, ART-suppressed rhesus macaques (RM). Here, we investigate the impact of this curative intervention on viral population genetics to identify SHIV genetic features associated with durable remission.
Methods
Plasma samples were collected during analytical treatment interruption (ATI) from SHIV-AD8-infected ART-suppressed RM treated with N-803 and the 10-1074 and 3BNC117 bNAbs (N=8) and SHIV-AD8-infected ART-suppressed RM control animals (N=8). Viral RNA was extracted, and multiple SHIV env gene sequences were obtained using single genome amplification (SGA). Phylogenetic reconstruction, pairwise distance calculations, entropy calculations, and highlighter plots were used to compare viral genetics and protein features between groups. Signatures of natural selection were analyzed using SNAP and HyPhy software (maximum likelihood method).
Results
A total of 306 SHIV env gene sequences (152 from controls and 156 from treated animals) were generated (Figure 1). Viral genetic diversity was higher in immunotherapy-treated animals with respect to controls (p<0.0001, t test). Genetic divergence from the SHIV-AD8 ancestral inoculum sequence was additionally higher in treated animals (p<0.0191) (Figure 1). Although the cumulative ratios of non-synonymous to synonymous substitutions (dN/dS) across the env sequence did not differ significantly between groups (p=0.4933), four codon sites (HXB2 positions 224, 260, 529, 593) were found to be under positive selection and 8 sites (30, 33, 71, 475, 539, 575, 813, 850) under purifying selection were identified in the treated group (none of these sites were under selection in control animals. Exclusively in the treated group, Shannon entropy was elevated at specific sites in V1, V3 and fusion peptide regions, and a loss of N-glycosylation at position 130 was observed.
Conclusions
Combined administration of N-803 and the 10-1074 and 3BNC117 bNAbs modulated SHIV population genetics, resulting in increased viral genetic diversity, divergence, and selection at specific sites within Env. Observed mutational patterns and glycosylation site disruption likely reflect evolutionary responses to pressure from neutralizing antibodies. Phenotypic characterization of the induced SHIV Env mutants will inform the development of HIV cure approaches.