A team of scientists from Japan has recently investigated the neutralizing potency of convalescent sera against currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike mutations.

The study’s findings reveal that the variants containing Y543F or N501Y spike mutations are capable of evading neutralization by SARS-CoV-2-induced antibodies. However, no such immune evading potency has been observed for the variants with only the E484K spike mutation.

The study is currently available on the medRxiv* preprint server.

Background

According to the World Health Organization (WHO) report, a significant increase in daily infection rates has been observed in many countries during this latter phase of the coronavirus disease 2019 (COVID-19) pandemic.

The emergence of novel SARS-CoV-2 variants with multiple spike protein mutations, including the UK, South African, and Brazilian variants, and the more recent Indian variant, are primarily responsible for such an exponential rise in new COVID-19 cases worldwide.

The acquisition of mutations is a basic step of viral evolution. During continuous proliferation inside host cells, viruses acquire mutations under positive selection to improve their host adaptability and fitness. Increased infectivity, virulence, and immune evasion ability observed in newly emerged SARS-CoV-2 variants clearly validate the ongoing process of viral evolution.

In Tokyo, Japan, a novel SARS-CoV-2 variant with E484K spike mutation has been observed in one-third of all confirmed COVID-19 cases. This Tokyo-type E484K variant is different from the UK, South African, and Brazilian variants.  

In the current study, the scientists have investigated the affinity and neutralizing potency of IgG-specific antibodies obtained from COVID-19 patients against the original spike receptor-binding domain (RBD) and the mutant RBDs.

Study design

The study was conducted on 41 SARS-CoV-2-positive patients and 20 SARS-CoV-2. Using enzyme-linked immunosorbent assay (ELISA), the plasma samples collected from the participants were analyzed for IgG-specific antibodies against original RBD and RBD variants containing Y453F, N501Y, or E484K mutation.

Moreover, by conducting three-dimensional structural analysis, the binding affinity of six neutralizing monoclonal antibodies for Y453F, N501Y, and E484K RBD variants of SARS-CoV-2 was also determined in the study.

Important observations

The structural analysis results revealed that the original three-dimensional structure of spike protein is not altered by the Y453F, N501Y, and E484K RBD mutations. Moreover, compared to the original RBD, only a slight increase in affinity of the E484K RBD was observed for the human angiotensin-converting enzyme 2 (ACE2) receptor.

Regarding antibody binding, three out of six tested antibodies showed a relatively weaker affinity for the E484K RBD compared to that for the original RBD. In contrast, one antibody showed a stronger binding affinity for the mutant RBD compared to the original RBD.

Regarding the Regeneron Pharmaceuticals-developed antibody cocktail therapy, REGN-COV2, which contains two neutralizing antibodies, Casirivimab and Imdevimab, a weaker affinity was observed for E484K RBD compared to that for the original RBD.

The glutamic acid to lysine substitution at position 484 is primarily responsible for the lack of hydrogen bonding between the mutant RBD and certain amino acid residues of the antibody Fab fragment heavy chain. This could be a potential reason for lower affinity.

Affinity of neutralizing antibodies

In 29 out of 41 COVID-19 positive patients, serum IgG-specific antibodies showed strong neutralizing affinity toward original RBD. Similarly, strong and moderate levels of neutralizing affinities for E484K RBD were observed in 16 and 10 COVID-19 patients, respectively.

Regarding RBD Y453F mutant, serum IgG-specific antibodies with strong and moderate neutralizing affinities were detected in 1 and 6 COVID-19 patients, respectively. Similarly, a moderate neutralizing affinity of serum IgGs toward the RBD N501Y mutant was observed in 8 out of 41 patients.

Taken together, these observations indicate that Y453F and N501Y mutations in the spike RBD have a higher impact than the E484K RBD mutation in reducing the neutralizing potency of IgG-specific antibodies developed in response to natural SARS-CoV-2 infection.

Study significance

According to the available literature, the South African and Brazilian SARS-CoV-2 variants with N501Y and E484K spike mutations and the UK variant with N501Y mutation exhibit significantly higher infectivity compared to the previously circulating variants. These variants are also associated with a higher mortality rate. The lower sensitivity of N501Y-bearing variants to antibody-mediated neutralization could be a potential reason for higher infectivity and virulence.

In contrast, no evidence of increased infectivity or virulence has yet been documented for the Tokyo-type SARS-CoV-2 variant, which contains only a single E484K spike mutation. This could be due to the comparatively lower impact of the E484K mutation on immune evasion.

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.