Exploring cross-neutralizing anti-SARS-CoV-2 antibody responses among the general population

By Pooja Toshniwal PahariaMay 20 2022Reviewed by Aimee Molineux

In a recent study posted to the bioRxiv* preprint server, researchers performed a molecular analysis of cross-reactive antibodies targeted against the receptor-binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains among the general population.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Background

As SARS-CoV-2 strains continue to emerge, cross-neutralizing antibody responses are essential for the development of a universal SARS-CoV-2 vaccine that would neutralize the antigenically distinct SARS-CoV-2 strains with high potency.

Studies have reported that IGHV2-5/IGLV2-14 (immunoglobulin heavy chain variable region 2-5/ immunoglobulin lambda variable cluster 2-14)-encoded RBD antibodies have a wide breadth of SARS-CoV-2 neutralization and can even neutralize Omicron and its sublineages. The antibodies are a general population antibody clonotype and therefore, they underpin the rationale and scheme for the development of a more universal coronavirus disease 2019 (COVID-19) vaccine.

The representative monoclonal antibody of the authors for the present study was the IGHV2-5/IGLV2-14 -encoded LY-CoV1404 (Bebtelovimab) which has demonstrated cross-neutralization potency against all SARS-CoV-2 strains including Omicron and its sublineages.

About the study

In the present study, researchers elucidated the molecular basis for the development of heterogeneous cross-reactive RBD antibodies against SARS-CoV-2 and the mechanistic basis for their allelic preferences among the general population.

The titers of 11 IGHV2-5/IGLV2-14-encoded-RBD antibodies from a minimum of seven donor individuals were assessed. A structural analysis was performed to uncover the sequence determinants of IGHV2- 75 5/IGLV2-14-encoded antibodies for engagement of RBD. The team also assessed the somatic hypermutations (SHMs) in the IGHV2-5/IGLV2-14-encoded antibodies.

In addition, sequence analysis was performed to determine the allelic preferences of the antibodies and the mechanistic basis for the allelic preferences was elucidated. Further, the complementarity-determining region (CDR) H3 sequences of the IGHV2-5/IGLV2-14-encoded antibodies were analyzed and further subjected to an IgBlast analysis. The B lymphocyte repertoires among the healthy donor individuals were also assessed.  

Results

The structural analysis showed that all the IGHV2-5/IGLV2-14-encoded antibodies demonstrated the same RBD binding mode. The majority of the paratope’s amino acid side chains were germline-encoded and formed the key RBD interactions. For e.g., the germline-encoded V_H S32 of the CDR H1 was inserted into a polar pocket within the RBD.

The germline-encoded V_H Y52, R58, D54, and D56 of the CDR H2 assembled into an elaborate network of hydrogen (H)-bonds with electrostatic RBD interactions. Further, two main paratope residues of the light chain VL viz. Y91 and Y32 also demonstrated germline-encoding. This indicated that the determinants of RBD-binding were encoded within the germline sequences of IGLV2-14 and IGHV2-5.

Many IGHV2-5/IGLV2-14-encoded antibodies possessed only a few SHMs, for e.g., S24-223 had one SHM only, whereas COV2-2268 had only four SHMs. Notably, the SHMs did not demonstrate overlapping.

The sequence analysis showed that IGHV2-5/IGLV2-14-encoded antibodies preferred the IGHV2-5*02 allele. Out of 11 IGHV2-5/IGLV2-14-encoded antibodies, eight were assigned to IGHV2-5*02, while the allelic preference of the remaining three antibodies was not clear. The IGHV2-5*02 allele preference of the antibodies was due to an allelic polymorphism at the amino-acid residue 54 of IGHV2-5, which was located at the paratope.

B lymphocyte repertoire analysis among 13 healthy donor individuals showed high frequencies of use of the IGHV2-5*01 and IGHV2-5*02 allele usage, which were 33% and 64%, respectively, by the IGHV2-5 RBD antibodies. Out of nine IGHV2-5/IGLV2-14-encoded antibodies, eight demonstrated aspartic acid (Asp) at V_H residue 54, while the remaining one demonstrated glutamic acid (Glu) at V_H residue 54. The observations provide a mechanistic explanation for the IGHV2-5*01 allele preference, despite its prevalence among the general population. As a coincidence, a similar finding was noted for the IGHV2-5-encoded human immunodeficiency virus (HIV) antibody, in which V_H D54 demonstrated a more robust binding than V_H N54.

In the CH3 sequence analysis, out of 10, eight IGHV2-5/IGLV2-14-encoded antibodies preferred a CDR H3 length of 11 amino acids and shared the HxIxxI motif or its HxVxxI and HxIxxL variants. The HxIxxI motif comprised V_H I100, H95, and I97, and was not commonly observed in the CDR H3 sequences of IGHV2-5-encoded RBD antibodies among the B lymphocyte repertoires. V_H I100, H95, and I97 of the HxIxxI motif were necessary to stabilize the RBD binding and loop-type conformations.

The IgBlast analysis showed that the conserved HxIxxI motif was mainly encoded by the addition of N-nucleotide, although V_H I97 was also encoded by the immunoglobulin heavy constant delta (IGHD) gene. Notably, although the CDR H3 of XG005 comprised 12 amino acids, it adopted an 11-amino-acid conformation. The findings indicate that IGHV2-5/IGLV2-14-encoded antibodies with an 11-amino acid-CDR H3 length possessed converging CDR H3 sequences, and therefore, could be categorized as a clonotype of the general population.

The healthy donor 112 was most probably IGHV2-5*01 homozygous as 94% of the donor’s IGHV2-5-encoded RBD antibodies had been assigned to IGHV2-5*01. Furthermore, the conserved HxIxxI motif within the CDR H3 of the IGHV2-5/IGLV2-14-encoded antibodies was largely encoded by the addition of N-nucleotide, which explains the comparative rarity of the IGHV2-5/IGLV2-14-encoded antibody producing-B lymphocyte germline clones. The findings justify the genetic heterogenicity of the neutralizing antibody responses against SARS-CoV-2 strains among different individuals.

Overall, the study findings showed that the combination of germline genes IGHV2-5/IGLV2-14 represents a public antibody response to the receptor-binding domain (RBD) that potently cross-neutralizes all SARS-COV-2 strains to date, including Omicron and its sublineages.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources