Epistasis leads to reduced genetic barriers to evasion of COVID-19 neutralizing antibodies

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, has undergone genomic mutations leading to the emergence of new variants.

On characterization, these mutants were found to differ from ancestral strains with respect to virulence, infection rate and ability to evade immune responses induced by natural infection or COVID-19 vaccination.

Background

The surge in COVID-19 cases is due to the continuous emergence of new resistant SARS-CoV-2 variants. Neutralizing antibodyHowever, prolonged exposure to antigen leads to the development of diverse memory B cells that produce affinity-matured receptor-binding domain (RBD)-specific antibodies, thereby protecting individuals from severe infection.

RBD-specific antibodies generated by COVID-19 vaccination or natural infection fall into four prototype classes. Two antibodies belonging to classes 1 and 2 bind epitopes that overlap with the ACE-2 binding site. Class 3 and 4 antibodies bind outside the ACE-2 binding site on the opposite side of the RBD.

The advent of SARS-CoV-2 Omicron BA.1 and BA.2 has led to numerous RBD substitutions, efficacy of Neutralizing antibody. Subsets of plasma and memory antibodies induced from previous infection or COVID-19 vaccine based on ancestral strain spike protein BA.1, BA.2, and other subvariants.

About research

Recent research posted on Bio Rxiv*The preprint server addresses the key question of how the SARS-CoV-2 virus may evolve in the future and escape the diverse and broadly neutralizing antibodies mentioned above.

A total of 40 antibodies were isolated from memory B cells from multiple cohorts of volunteers, and each participant was exposed to SARS-CoV-2 to varying degrees. Antibodies were isolated from a participant who had received one or two doses of his mRNA-based COVID-19 vaccine and had previously been infected with the ancestral Wuhan-Hu-1 RBD. Neutralizing antibodies were also isolated from an individual who had received his three doses of mRNA vaccine and had no history of COVID-19. Additionally, antibodies were obtained from a participant who had an Omicron BA.1 breakthrough infection after his three doses of the COVID-19 vaccine.

Broadly neutralizing antibodies were selected for this study. They neutralized both Wuhan-Hu-1 and Omicron (BA.1) pseudotype viruses. 35 antibodies also he neutralized BA.2.

A replication-competent recombinant vesicular stomatitis virus encoding spike protein SARS-CoV-2 ancestral strains and Omicron (BA.1 or BA.2) variants were utilized to select antibody escape mutants. Diverse groups of rVSV/SARS-CoV-2 containing 106 infectious units were incubated with neutralizing antibodies prior to infection of target cells. Based on selection experiments, 39 antibodies produced substitutions at 34 different positions in the RBD. Substitution positions were either spatially close to the ACE2 binding site or within the ACE2 binding site.

Twenty-three substitutions were selected and used to construct spiked plasmids. Infection was quantified on the basis of uninhibited virus, but there was her 5-fold increase in infection-defined antibody escape compared to antibody-inhibited parental pseudotypes. Most of the substitutions were associated with resistance to one or more antibodies of the same class. Importantly, some class 4 antibodies were found to be less effective against BA.2. Most of the substitutions showed class-specific antibody resistance, but two RBD-based substitutions showed reduced antibody susceptibility (Y369F).

Epistasis and decreased antibody efficacy

Overall, extensive epistatic interactions were observed between antibody resistance substitutions and mutations in BA.1 or BA.2 proteins. Interestingly, C099 (antibody) resistance was generated by single amino acid substitutions in the BA.1 and BA.2 genomes. Two substitutions within or near the target epitope, namely D420 and N460, were essential to confer resistance to C099 against Wuhan-Hu-1. Nevertheless, the F486S or N487D substitutions conferred complete resistance of C099 to BA.1 and/or BA.2.

Taken together, we confirm that SARS-CoV-2 Omicron BA.1 and BA.2 variants can easily evade broadly neutralizing antibodies (such as C099 and C080) due to many subset target epitope substitutions essential for antibody resistance. It was

Based on selected mutation in vitro, observed that substitutions altered during the transition from BA.2 to BA.5 were responsible for the resistance of multiple classes of antibodies. Importantly, 7 out of 14 antibodies showed resistance to his L452 or F486 substitutions.

Meaning of research

This study describes that epistatic interactions between newly acquired and pre-existing substitutions help evade neutralizing antibodies. Most antibodies tolerated single mutations but not multiple mutations.

Analysis of antibodies in plasma suggested that BA.1 breakthrough infection selectively enhanced a subset of vaccine-induced neutralizing antibodies present in memory. Some memory antibodies, including Omicron BA.5, have been shown to neutralize SARS-CoV-2 variants, but most failed to neutralize variants containing three substitutions at the target site .

This study demonstrated that differences in antigen exposure contribute to significant heterogeneity in antibody neutralization breadth and potency. In addition to population diversity, epistatic interactions between new viral mutations and existing ones will influence the future course of SARS-CoV-2 variant emergence.

*Important Notices

bioRxiv publishes non-peer-reviewed, preliminary scientific reports and should not be considered conclusive, to guide clinical practice/health-related actions, or to be treated as established information .