Deletions in antigenic sites in SARS-CoV-2 increase transmission and ability to evade immunity

A new study published in the journal Scientific Reports analyzed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole genome data to identify deletion mutations around the spike protein region associated with increased transmission of the virus and identified an increase in deletion-prone spike protein regions, indicating an evolution of an immune escape strategy.

Studies: Expanding repertoire of SARS-CoV-2 deletion mutations contributes to the evolution of highly infectious variants. Image Credit: WildMedia/Shutterstock

Background

Although coronavirus disease 2019 (COVID-19) vaccines have succeeded in slowing the rapid transmission and severity of SARS-CoV-2 infections worldwide, the increasing number of sudden infections indicates the increased ability of emerging SARS-CoV-2 variants to evade immunity. responses induced by vaccines and previous infections.

Studies using neutralizing antibodies from COVID-19 patients have identified the receptor binding domain (RBD) and N-terminal domain (NTD) of spike protein as the main targets of neutralizing antibodies. NTD, the antigenic supersite targeted by multiple neutralizing antibodies, was also found to contain deletions with four regions having repetitive deletions. It is important to understand the role these deletions may also play in enhancing the transmission capabilities of SARS-CoV-2, as studies have shown that such deletion mutations reduce the neutralizing effectiveness of neutralizing antibodies targeting NTD.

about the study

In this study, the researchers used whole genome sequences and SARS-CoV-2 whole genome sequences, totaling approximately 2.3 million stored in the Global Initiative on Sharing Avian Influenza Data (GISAID) database worldwide. It was produced from 102 patients with breakthrough SARS-CoV-2 infections. Epidemiological data including SARS-CoV-2 positivity rates were obtained from Our World in Data (OWID) and other databases.

Monthly mutation prevalence and SARS-CoV-2 test positivity rates were assessed at quarterly intervals to identify mutations associated with spikes in COVID-19 cases. Mutations that showed a monotonous increase in prevalence corresponding to monotonous increases in SARS-CoV-2 positive tests were considered fluctuation-related mutations.

Mutations identified as associated with increases in COVID-19 cases were then compared with mutations in four related variants and seven related variants identified by the United States (US) Centers for Disease Control and Prevention (CDC). Related variants consisted of Alpha, Beta, Delta, and Gamma variants, while related variants consisted of Epsilon, Eta, Iota, Kappa, and Zeta sub-variants.

In addition, various types of mutations such as insertions, deletions and substitutions were evaluated to determine their enrichment in fluctuation-associated mutations. Sites of repetitive deletion in the spike protein NTD were also identified. The researchers also created a time series tile plot to study the temporal expansion of regions with repetitive deletions.

Results

Results reported 1045 spike protein amino acid mutations including insertions, deletions and missense mutations found in a minimum of 100 sequences in the GISAID database. Substitution mutations accounted for a large percentage of 95.21% (995) of these mutations. Deletions and insertions were 4.3% (45) and 0.48% (5), respectively. The number of mutations associated with monotonically increasing fluctuation with a monotonous increase in positive SARS-CoV-2 tests at three-month intervals was 92, of which 42 were also found in CDC-defined variants of interest or concern. .

The repertoire of deletions in the spike protein N-terminal domain is expanding throughout the pandemic. (a) Frequency of occurrence of deletion mutations in the N-terminal domain in 2.13 million Spike protein sequences (as of June 30, 2021). Both known and novel repetitive deletion sites are schematically shown and mapped onto the structure of the Spike protein. Positions corresponding to deletion mutations in the spike protein are shown as colored spheres and the neutralizing antibody is indicated using a gray surface representation. (b) Heatmap showing the expansion of «erasable» regions during the pandemic, where rows show residue positions in the Spike protein and columns show the course of the pandemic (in months). Each box indicates the frequency of a particular deletion mutation worldwide during that month. The color of the boxes corresponds to a frequency of 1 to 100,000 sequences shown on the log10 scale. (c) Regions of deletion mutations associated with fluctuations in different regions of the world are shown as spheres in the 3D structure of the Spike protein complexed with neutralizing antibody 4A8 (PDB identifier: 7C2L as described by Chi et al., from PDB).

When fluctuation-associated mutations were analyzed by mutation type, deletions were found to be associated with infection fluctuations at frequencies higher than expected by chance. The fluctuations were associated with 40% of the deletion mutations identified, compared to non-deleting mutations accounting for only 12% of all non-deletion mutations identified in the SARS-CoV-2 genome. These deletions were also found only in the NTD region of the spike protein, suggesting a correlation between NTD-associated deletion mutations and increased virus transmission.

A temporal assessment of the prevalence of deletion mutations also showed that regions containing deletion mutations flanking the antigenic region in the NTD were also expanded; this may contribute to the evolution of variants with immune avoidance and increased transmission. Annotated whole-genome sequences of SARS-CoV-2 from patients with breakthrough infections revealed 107 unique mutations, including 29 deletions and 78 substitutions. between 85 deletions^pearl and 90^pearl Residues in the B-cell epitope region were identified in five patients and are thought to have appeared since December 2020.

solution

Overall, the results suggested that expanding regions and increased deletion frequencies, particularly in the antigenic regions surrounding the NTD spike protein, may drive the evolution of SARS-CoV-2 variants with increased transmission and immune-escaping abilities.