Evolution of SARS-COV2 Entry-point Residues Interacting with ACE2 Receptor
K31-493Q and K353-501N attachment site of human ACE2-SARS-COV2 respectively are the most efficient virus-host entry-point and civet cat experiment suggests that K353-501N is most crucial entry-point between these two attachment site (7). In RaTG13 of bat from where SARS-COV2 is believed to be originated, the homologue at 501N position is aa D (code GAU). Thus, an amino acid changes from D (code GAU) to N (code AAU) at this position in SARS-COV2 enables them to infect human host. D is also present at the same homologous position in pangolin virus Pan_SL_COV_GD. Thus, a single substitution in 1stcodon from G>A nucleotide could give rise aa N from aa D at the 501 position in the RBD of SARS-COV2 for K353-501N salt bridge formation and gave the important attachment site to entry into human host.
Similarly, 493Q residue in SARS-COV2 for K31-493Q interaction, which is the second most important entry-point attachment is evoluted from amino acid Y, which is present in both RaTG13 of bat and Pan_SL_COV_GD of pangolin and can come from either of these two virus. However, Y is coded by UAU in both animals and to become Q (code CAA) of SARS-COV2, the codon needs to mutate at least twice i.e. mutation in two nucleotides in 1st and 3rd codon. The 1st codon must be U>C mutation and the second mutation at the 3rd codon could be U>A. If the 3rd codon mutation occurred earlier than 1st codon mutation in the bat or pangolin virus, it would lead to nonsense (stop) code (UAA) and immaturely terminate S protein formation. Thus, 1st codon mutation (U>C) had to be created earlier than 3rd codon mutation for survival of this present-day virus. Eventually, 1st codon mutation (U>C) would create intermediate code CAU in ancestors of SARS-COV2 virus that would code for H (Histidine) at this position. Thus, the conversion of Y > Q had to be in the course of pathway Y >H>Q. In that case, 493H carrying intermediate ancestor virus must be existed in any of the related virus strain. Until now sequences from twenty-six types of bat and eight types of pangolin COV virus are known and analyzed (4, 8, 15, 16) but no such ancestral viral strain was identified with a 493H in RBD. Thus, besides these two animals, there must be an intermediate host with SARS-COV2 ancestors carrying 493H virus that remains to be identifiedunless the existence of such an ancestor virus still could be explored in bat or Pangolin.