CROI 2024 Abstract eBook

Abstract eBook

Poster Abstracts

Methods: To demonstrate feasibility towards the consistent, broad, and potent neutralizing responses, we combined vaccination targeting the fusion peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). Results: In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45-77% breadth on a cross-clade panel of 208 strains with geometric mean ID 50 titers of ~100, a level of potency recently shown to protect against mucosal SHIV challenge from fusion peptide directed antibodies. Neutralization fingerprinting identified epitope-specific signatures in plasma and observed higher estimates for fusion peptide-directed specificity versus other known specificities. By longitudinally plasma viral RNA sequencing, we observed evidence of strong viral selection by post-SHIV week 16 at the N terminus of the fusion peptide and at the structural adjacent regions, including residues nearby glycan 88. Molecular dissection of these responses into component antibody specificities by antibody isolation and cryo-EM structure determination revealed 15 of 16 isolated antibodies with cross clade neutralization breadth to be directed towards the fusion peptide-site of vulnerability. In each macaque, isolated monoclonal antibodies recapitulated the plasma-neutralizing response (r =0.71-0.97), with fusion peptide-binding antibodies reaching breadths of 40- 60% (IC 50 <50 μg/ml) on a 208 strains panel. Longitudinal phylogenetic analysis revealed each of the top macaques to have only 1-2 broadly neutralizing fusion peptide-binding lineages, each induced before SHIV infection. Conclusion: These results provide explicit in-vivo molecular examples for one or few B-cell lineages affording potent cross-reactive plasma-neutralizing responses. While increased titers in the current study resulted from SHIV infection boosting, it will be interesting to test fusion peptide-Env trimer immunogens not only with altered boosting regimens, but also with altered priming regimens, such as with the escalating prime, extended- boost regimen. Maturation Pathway of Rhesus V3-Glycan Broadly Neutralizing Antibody Lineage Mitchell Martin 1 , Tyler Evangelous 1 , Madison Berry 1 , Bhavna Hora 1 , Chuangcang Jiang 1 , Katayoun Mansouri 1 , Robert J. Edwards 1 , Hui Li 2 , George M. Shaw 2 , Priyamvada Acharya 1 , Kevin O. Saunders 1 , Kevin Wiehe 1 , Barton F. Haynes 1 , Wilton Williams 1 1 Duke Human Vaccine Institute, Durham, NC, USA, 2 University of Pennsylvania, Philadelphia, PA, USA Background: We previously isolated clonally-related HIV-1 envelope (Env)-reactive broadly neutralizing antibodies (bnAbs), termed DH1030, from a pathogenic SHIV-infected rhesus macaque (RM08N021). Rhesus DH1030 targeted the V3-glycan bnAb-epitope on HIV-1 Env using an arginine (R) residue acquired via an improbable mutation from glycine (G) in the HCDR2. Engineering HCDR2-G56R mutation into the DH1030 unmutated common ancestor (UCA) alone was insufficient to achieve neutralization activity. We hypothesized that DH1030 lineage maturation included a series of mutations that preceded G56R in the HCDR2. Defining mutations associated with maturation of DH1030 will inform prime-boosting strategies to select for key mutations that confer maturation to bnAb status. Methods: We isolated 62 clonally-related DH1030 Abs from RM08N021 via Env-reactive B cell flow cytometry sorting and 10X Genomics single cell immune profiling assays. DH1030 Abs clustered into three phylogenetic clades. The majority of clade 1 Abs had HCDR2-G56; all clade 2 Abs had HCDR2-G56; and all clade 3 Abs had HCDR2-R56. Monoclonal (m) Abs were tested for binding specificities, structure, and function. We expressed 26 mAbs representative of all three clades, including the inferred intermediates and UCA. Results: Of 8 mAbs tested from clade 1, two containing HCDR2-G56 neutralized only autologous HIV-1 strains, but two that contained HCDR2-R56 did not neutralize HIV-1 strains tested. None of six mAbs tested from clade 2 neutralized HIV-1. In contrast to results from clades 1 and 2, all 10 mAbs tested from clade 3 with HCDR2-R56 neutralized CH848 10.17DT and up to 6/9 heterologous tier 2 HIV-1 from the global panel. Sequence analysis of DH1030 Abs along the path to clade 3 bnAbs revealed mutations in the HCDRs that preceded G56R. All the clade 3 bnAbs had a serine-to-proline mutation at position 114 (S114P) in the HCDR3. Mutating S114P into an intermediate Ab (IA59) along the clade 3 bnAb path conferred Ab binding at similar levels to the clade 3 bnAbs in contrast with wild-type IA59 which showed no binding. Computational modeling of S114P on DH1030.1-Env complex suggested favorable neighboring contact residues facilitated by this mutation. Additionally, the light chain (VL) of DH1030UCA

identified by negative values of Tajima's D, revealed complex evolutionary scenarios, and suggested the existence of several adaptive mutations in each host. Furthermore, epistasis between positions is likely, due to existence of low frequency combinations, of the adaptive alleles, that do not grow in frequency. In two individuals, subpopulation structure correlating with sequence signatures of cell tropism is associated with different escape mutations. Conclusion: These results suggest diverse adaptive pathways to bNAb escape among different individuals. While some mutations are easily identified as adaptive, multiple escape mutations, epistasis and tropism associated mutation are more challenging to identify and interpret. A Rare Molecular Signature in HIV-1 Env V1 Associates With bNAb Evolution Maria C Hesselman 1 , Marius Zeeb 2 , Peter Rusert 1 , Jennifer Mamrosh 3 , Samuel Kariuki 4 , Hugh Murrell 4 , Nonhlanhla N. Mkhize 5 , Kshitij Wagh 3 , Penny Moore 5 , Carolyn Williamson 4 , Huldrych F. Günthard 2 , Roger Kouyos 2 , Alexandra Trkola 1 1 University of Zurich, Zurich, Switzerland, 2 University Hospital Zurich, Zurich, Switzerland, 3 Los Alamos National Laboratory, Los Alamos, NM, USA, 4 University of Cape Town, Cape Town, South Africa, 5 University of the Witwatersrand, Johannesburg, South Africa Background: Identifying traits of HIV-1 Envelope (Env) linked with broadly neutralizing antibody (bnAb) development is critical for designing bnAb vaccines. Here we report a rare twin cysteine (Cys) motif in the variable loop 1 (V1) region that is enriched among Env of bnAb inducers. Methods: V1 Cys insertions were functionally characterized in vitro and quantified in Env sequence datasets from bnAb inducer cohorts (Swiss 4.5K), longitudinal cohorts (ZPHI, SHCS, CAPRISA) and the LANL sequence database. Factors associated with frequency of V1 Cys insertions were analyzed using logistic regression. Results: Studying Env from 35 bnAb inducers from the Swiss 4.5K screen we noted a high overall neutralization resistance and observed a rare twin Cys motif in V1 in several Envs. Functional studies with bnAb inducer Envs and analysis of the CATNAP database showed that Envs with the V1 Cys motif had a modestly increased neutralization resistance pointing towards a compensatory stabilizing effect. Analyzing Env sequences from 1,105 Swiss 4.5K participants, we observed an independent association with neutralization where >20% of elite neutralizers carried the motif compared to 5% of non-neutralizers. Sequence simulations and comparison to >6000 Env sequences of the LANL database showed that the observed frequency of Env with two extra Cys in V1 is unlikely to occur by chance. Twin V1 Cys occur in recent transmission, suggesting no transmission bias, and show peak frequencies in later infection. Longitudinal Env profiles of 57 CAPRISA donors showed fluctuating frequencies of variants with extra V1 Cys, suggesting the motif alone provides a limited fitness advantage. Notably, a high proportion of Env with twin V1 Cys was transmitted in the AMP trial placebo arms (15% and 9% of participants in HVTN703 and 704, respectively) while breakthrough viruses showed a VRC01 treatment dose dependent reduction in twin V1 Cys, suggesting a fitness deficit of transmitted twin V1 Cys viruses. Conclusion: Our data support a role of the V1 Cys motif in optimizing V1 stabilization and epitope shielding during neutralization escape. Gains in neutralization resistance and viral fitness through the motif may vary depending on the extent of virus nAb co-evolution. BnAb-experienced viruses are likely optimized for both fitness and resistance, while recently escaped variants may, despite twin V1 Cys insertions, still have fitness deficits and are rapidly counter-selected when new pressure arises as in the case of VRC01 prophylaxis. Potent Cross-Reactive HIV-1 Neutralization in Fusion Peptide-Primed SHIV-Infected Macaques Hua Wang 1 , Cheng Cheng 1 , James L. Dal Santo 1 , Chen-Hsiang Shen 1 , Tatsiana Bylund 1 , Amy R. Henry 1 , Colin A. Howe 1 , Juyun Hwang 1 , Nicholas C. Morano 1 , Daniel J. Morris 2 , Sergei Pletnev 1 , Ryan S. Roark 1 , Tongqing Zhou 1 , Theodore C. Pierson 1 , Peter D. Kwong 1 1 National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA, 2 University of Pennsylvania, Philadelphia, PA, USA Background: An effective antibody-based HIV-1 vaccine will require the consistent induction of potent cross- reactive HIV-1-neutralizing responses. Epitope-focusing approaches have elicited consistent, but low titer, cross- clade neutralizing responses against multiple sites of vulnerability. However, consistent, broad, and potent neutralizing responses against HIV-1 have not been achieved by vaccination.

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CROI 2024