Structure function analysis of potent antibodies against Beta SARS-CoV-2 variant

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance has revealed thousands of alterations in structural and non-structural proteins. However, by the end of 2020, viral variations had been identified that had quickly become the prevalent strains locally, leading to their classification as variants of concern (VoCs) Alpha, Beta, Gamma, and Delta.

Study: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Image Credit: Kateryna Kon/Shutterstock

Background

Multiple mutations in the SARS-CoV-2 spike (S) protein are present in all of these variants, including changes in the receptor-binding domain (RBD), N-terminal domain (NTD), and, in some cases, the furin cleavage site between S1 and S2. RBD mutations in Alpha (N501Y), Beta (K417N, E484K, N501Y), Gamma (K417T, E484K, N501Y), and Delta (L452R, T478K) are found at or close to the angiotensin-converting enzyme 2 (ACE2) interacting surface, where they can modify ACE2 interaction or disrupt neutralizing mAb binding.

Compared to neutralizing early pandemic strains, several studies suggest that vaccine efficacy against Beta is diminished, which correlates to significantly lower neutralization titers to Beta utilizing serum collected from early pandemic cases or vaccinees. The RBD mutations in Beta (K417N, E484K, N501Y) disrupt the binding of various effective neutralizing mAbs, including several that are being investigated for clinical use and likely explain the antigenic gap between Beta and early SARS-CoV-2 strains, together with changes in the NTD.

In a study published in Cell Host and Microbe, a team of researchers from UK and US institutions created a large panel of mAbs derived from memory B cells of convalescent Beta subjects to better understand the antigenic landscape of Beta. Twenty-seven of the 674 mAbs produced from five donors have significant neutralizing activity (50% Focus Reduction Neutralization Assay (FRNT50) 100ng/ml).

Neutralization experiments against a variety of viral isolates revealed that most mAbs only neutralized a subset of viruses. A thorough structure-function analysis involving twenty-two X-ray and cryo-EM structures for Sixteen Fabs, most of which are in complexes with RBD or S, is presented, allowing for a better understanding of the Beta S protein's antigenicity alterations.

The study

Many mAbs were shown to be particularly effective at neutralizing Beta, with FRNT50 values as low as 1ng/ml. Some mAbs, such as Beta-27, 32, 47, 48, 49, 50, and 53, showed full cross-reactivity with a 10-fold difference between FRNT50s, whereas others, such as Beta-27, 32, 47, 48, 49, 50, and 53, showed partial cross-reactivity with a 10-fold difference between FRNT50s.

The neutralization of Alpha, Beta, Gamma, and Alpha+ viruses was good with a large number of mAbs (Beta-6, 10, 23, 24, 30, 40, 54, 55, 56), but Victoria, B.1.525 (E484K), and Delta viruses were reduced or missing. We propose that the presence of the N501Y mutation produces an epitope for RBD identification in Beta infection and that this mutation is shared by Alpha, Beta, and Gamma.

The authors predicted Lys-484 to be detected by Beta-neutralizing mAbs since the E484K mutation impairs the binding of many potent mAbs developed from cases infected with early pandemic viruses. Six mAbs (Beta-26, 33, 34, 45, 51) show evidence of Lys-484 interaction, with reduced activity to Alpha but increased activity to Alpha+484K. Beta-20, 22, and 29 mAbs had the highest activity toward Beta and Gamma, indicating that they recognize an epitope associated with the K417N/T alterations in Beta and Gamma, respectively. Alpha and Alpha+484K were neutralized by mAbs Beta-22 and 29, indicating that they recognize an epitope consisting of Asn/Thr 417 + Tyr-501.

The researchers used a human ACE2 transgenic mouse model to assess the activity of mAbs generated against Beta in vivo. Four mAbs representing distinct epitope classes were chosen; Beta-20, which recognizes the K417N/T mutation and can effectively neutralize Beta and, to a lesser extent, Gamma; Beta-24, which recognizes the N501Y mutation found in Alpha, Beta, and Gamma; Beta-26, which recognizes the E484K mutation found in Beta and Gamma; Beta-27, the IgVH3-53 fully cross-reactive mAb, which neutralizes all variants in the same way.

Mice were injected with 103 FFU of Beta and then given a single 10mg/kg dose of mAb through i.p. injection 24 hours later. Over the six days following vaccination, all four Beta elicited mAbs, but not an isotype control mAb (hE16), prevented weight loss and reduced viral loads in the lung and brain, but not in nasal washes. These findings show that each of the mAbs evaluated can effectively lower infection severity and prevent systemic disease, but not viral infection in the upper respiratory tract.

Implications

An in-depth structure-function investigation of powerful mAbs from Beta-infected individuals has been presented. The anti-Beta reaction is significantly shifted towards the three altered residues discovered in the Beta RBD when using powerful neutralizing mAbs. The considerable antigenic gap between Beta and early pandemic strains used in modern vaccines is owing to differential targeting of these residues.

The majority of Beta-specific mAbs fail to neutralize Delta, which is consistent with the huge drops in the ability of Beta (and Gamma) infected sera to neutralize Delta and reflects the fact that the RBDs of Beta and Delta differ by five amino acids. Several companies are working on Beta booster vaccines. It will be fascinating to see how effective they are at triggering responses to the crucial altered residues in Beta in people vaccinated with Wuhan strains.