Highlights d Neutralizing mAbs against SARS-CoV-2 are isolated from two convalescent patients d Efficacy of antibodies is maintained against B.1.1.7 and mink cluster 5 variants d B.1.351 from South Africa and P.1 from Brazil are resistant to mAbs and plasmas d mAbs with high affinity for the RBD efficiently crossneutralize B.

As of July 2023, EG.5.1 (a.k.a. XBB.1.9.2.5.1), a XBB subvariant bearing the S:Q52H and S:F456L substitutions, alongside the S:F486P substitution (Figure S1A), has rapidly spread in some countries. On July 19, 2023, the WHO classified EG.5 as a variant under monitoring. First, we showed that EG.5.1 exhibits a higher effective reproduction number compared with XBB.1.5, XBB.1.16, and its parental lineage (XBB.1.9.2), suggesting that EG.5.1 will spread globally and outcompete these XBB subvariants in the near future. We then addressed whether EG.5.1 evades from the antiviral effect of the humoral immunity induced by breakthrough infection (BTI) of XBB subvariants and performed a neutralization assay using XBB BTI sera. However, the 50% neutralization titer (NT50) of XBB BTI sera against EG.5.1 was comparable to those against XBB.1.5/1.9.2 and XBB.1.16. Moreover, the sensitivity of EG.5.1 to convalescent sera of XBB.1- and XBB.1.5-infected hamsters was similar to those of XBB.1.5/1.9 and XBB.1.16. These results suggest that the increased Re of EG.5.1 is attributed to neither increased infectivity nor immune evasion from XBB BTI, and the emergence and spread of EG.5 is driven by the other pressures. We previously demonstrated that Omicron BTI cannot efficiently induce antiviral humoral immunity against the variant infected. In fact, the NT50s of the BTI sera of Omicron BA.1, BA.2, and BA.5 against the variant infected were 3.0-, 2.2-, and 3.4-fold lower than that against the ancestral B.1.1 variant, respectively. However, strikingly, we found that the NT50 of the BTI sera of XBB1.5/1.9 and XBB.1.16 against the variant infected were 8.7- and 8.3-fold lower than that against the B.1.1 variant. These results suggest that XBB BTI cannot efficiently induce antiviral humoral immunity against XBB subvariants.

Monoclonal antibody 1C10 targets the V3 loop of HIV-1 and neutralizes a broad range of clade B viruses. However, the mode of interaction between 1C10 and the V3 loop remains unclear, because the crystallization of 1C10 and the V3 peptide was unsuccessful because of the flexible nature of 1C10 and the V3 peptide. In this study, we predicted which amino acid residues of 1C10 contact the V3 loop using a deep learning (DL)-based method. Inputs from ROSIE for docking simulation and FastContact, Naccess, and PDBtools, to approximate interactions were processed by Chainer for DL, and outputs were obtained as probabilities of contact residues. Using this DL algorithm, D95, D97, P100a and D100b of CDRH3, D53 and D56 of CDRH2, and D61 of FR3 were highly ranked as contact residues of 1C10. Substitution of these residues to alanine significantly decreased the affinity of 1C10 to the V3 peptide. Moreover, the higher the rank of residue, the more the binding activity was diminished. This study demonstrates that the prediction of contact residues using a DL-based approach is precise and useful for the analysis of antibody-antigen interactions.

Background Recent data suggest the importance of non-neutralizing antibodies (nnAbs) in the development of vaccines against HIV-1 because two types of nnAbs that recognize the coreceptor binding site (CoRBS) and the C1C2 region mediate antibody-dependent cellular-cytotoxicity (ADCC) against HIV-1-infected cells. However, many studies have been conducted with nnAbs obtained from subtype B-infected individuals, with few studies in patients with non-subtype B infections. Results We isolated a monoclonal antibody 1E5 from a CRF02_AG-infected individual and constructed two forms of antibody with constant regions of IgG1 or IgG3. The epitope of 1E5 belongs to the C1C2 of gp120, and 1E5 binds to 27 out of 35 strains (77 %) across the subtypes. The 1E5 showed strong ADCC activity, especially in the form of IgG3 in the presence of small CD4-mimetic compounds (CD4mc) and 4E9C (anti-CoRBS antibody), but did not show any neutralizing activity even against the isolates with strong binding activities. The enhancement in the binding of A32, anti-C1C2 antibody isolated from a patient with subtype B infection, was observed in the presence of 1E5 and the combination of 1E5, A32 and 4E9C mediated a strong ADCC activity. Conclusions These results suggest that anti-C1C2 antibodies that are induced in patients with different HIV-1 subtype infections have common functional modality and may have unexpected interactions. These data may have implications for vaccine development against HIV-1. Graphical abstract

The V3 loop of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) is one of the conserved immunogenic regions targeted by neutralizing antibodies (nAb). Two different binding modes of anti-V3 abs have been reported in studies using two V3 mimotopes: the ladle-type and cradle-type. We previously isolated a ladle-type nAb, 1C10, that potently and broadly neutralized clade B viruses. Despite its potent neutralization activity, 1C10 possesses no unique features in its amino acid sequence. We hypothesized that the neutralization potency of 1C10 is derived from its antigen-binding characteristics, which are not a consequence of the two previously reported binding modes of anti-V3 nAbs. To analyze epitope-paratope interactions between 1C10 and the V3 loop, we produced five anti-idiotypic antibodies (anti-Id abs) from mice immunized with 1C10 nAb. The idiotopes of the anti-Id Abs on the 1C10 heavy chain were estimated by alanine scanning, germline reversion mutagenesis, and a 1C10 sibling clone. Next-generation sequencing combined with homology modeling revealed contact between R315 at the tip of the V3 loop and 1C10 by D53 of CDRH2 and Phe/Asp of CDRH3. These amino acids were enriched in the anti-Id-ab-reactive B cell receptors encoded by the IGHV3-30 gene. We also found that 20% of HIV-infected individuals had abs specific to the anti-Id abs, as well as both of the V3 mimotopes, that did not respond to the linear V3 peptide. Our findings showed that the anti-Id abs induced by 1C10 recognized a key amino acid formation essential for steric interactions between the ladle-type nAb and the V3 loop. We also revealed the coexistence of anti-V3 ab reactivity to V3 loop mimotopes and to the anti-Id abs in HIV-positive individuals.