2.2. Annotation of mutations in SARS-CoV-2 spike variants of
concern
SARS-CoV-2 spike mutation details corresponding to the five variants of
concern were collected from WHO on 17th February 2022. Independent
mutations in each variant were manually represented on the schematic of
SARS-CoV-2 spike glycoprotein. Substitutions were represented as yellow
circles, deletions with red triangles and insertions with green
triangles. Common mutations to multiple VOC have been connected through
a standard line at that residue position. The spike subdomains
(N-terminal domain -dark blue, receptor binding domain- green, fusion
peptide- dark yellow, heptad repeat sequence 1- light yellow, heptad
repeat sequence 2- light blue, transmembrane domain- brown) were
represented with unique colors.
The Protein Data Bank (PDB) structure of SARS-CoV-2 S-ACE2 complex
(7DF4) was used to annotate the mutations in five variants of concern
(VOC) based on the WHO classification. All the mutations in the VOCs
were manually highlighted in the spike glycoprotein using PyMOL (The
PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC). The
receptor binding domain (RBD) of spike glycoprotein in open conformation
was highlighted in orange color and N-terminal domain (NTD) in green,
while the regions excluding NTD and RBD of spike protein was colored in
grey. All the mutated residues were shown in sphere representation
highlighted in red color and spike monomer was shown in cartoon
representation on chain B of the structure.
2.3. Acquisition of SARS-CoV-2 spike epitopes of neutralizing
monoclonal antibodies Experimentally validated 74 SARS-CoV-2
neutralizing mAbs with varying ranges of efficacy (modest to highly
neutralizing) were selected from previous published articles for
generating a map of individual antibody binding sites. Data on epitope
residues was collected from the pre-analyzed crystal structure of
monoclonal neutralizing antibodies in complex with
SARS-CoV-2 spike glycoprotein and were retrieved manually for epitope
annotation. Independent mAb binding residues were tabulated in an excel
sheet which was further used for generating the map of SARS-CoV-2 spike
glycoprotein mAb binding residues.
2.4. Generation of monoclonal antibody epitope heat mapThe python library Seaborn was used to visualize the heatmap displaying
epitopes of the antibodies. Briefly, the number of antibodies containing
a given epitope residue were divided by the total number of antibodies
to generate the strength of the given epitope. These strengths were then
represented in the form of a heatmap, with the colours with highest
intensity representing highly represented epitopes.