Fig 1.
Maximum likelihood phylogenetic Tree of Spike protein gene obtained from IQTREE.
Table 1.
High frequency amino acid substitutions of Spike protein coding gene. Frequency higher than 10% in at least one variant (Alpha, Delta, Omicron, XBB*, EG*, BA*) were considered to prioritize the substitutions. Each a.a. replacement was attributed to the functional Spike subunits and the corresponding subdomain. Frequencies are reported in percentage scale.
Fig 2.
High frequency Spike gene amino acid deletions sites.
Table 2.
Insertions detected in Spike gene amino acid sequences with their corresponding positions and frequencies. All insertions belong to NTD functional subdomain of S1 subunit.
Table 3.
Selection pressure results obtained from spike protein coding gene with HYPHY software of a) XBB*, b) EG* and c) BA* datasets. The frequencies of amino acids mutation found under selection pressure are reported in the same order and separated by semi-colon. The predicted ΔΔG and the resulting effect on protein stability (+ for increased, – for decreased) are given for each corresponding mutation. The green colour indicates the sites involved in binding affinity to ACE2 (BAA) or Immune Escape (IE) according to deep-mutational scanning studies. The conserved mutation in the variant of interest, which appeared subsequently, according outbreak.info (namely JN.1 and its 949 sub-lineages) are signed with an asterisk (*).