Fine structure of a partition in the spike glycoprotein encoded in the SARS-CoV-2 genome

Abstract

The gene encoding the spike glycoprotein of the SARS-CoV-2 virus that causes COVID-19 disease, was analyzed through two types of periodic tables (standard and cube) of the genetic code to discover the internal fine structure of the spike (S) protein. The analysis was performed on the Wuhan-Hu-1 SARS-CoV-2 sequence (GenBank accession number NC_045512.2). A partition was detected between codon numbers (three-letter code numbers) 47 and 48 that code amino acids in the S-protein. The population distribution of organized codes and amino acid replacements in the S-protein showed large differences between two regions of the cube-type periodic table. The genetic codes of codon numbers 48–63 (4th plane of the cube table) had a higher frequency than the genetic codes of each of the other three planes (1st–3rd planes). Planes-linkage structures involved in the partition were also analyzed and a simplified model for the S-protein gene was obtained where a planes-linkage of the 4th plane and another planes-linkage of the 1st–3rd planes were linked together in alternate shifts. Most of the code population in the 4th plane and their planes-linkage multiformity gave additional support to the partition between codon numbers 47 and 48 in the S-protein gene. Analysis of real lineages of the SARS-CoV-2 virus through the cube-type periodic table identified distinguishing features of the Omicron lineage that included not only a large code population within the receptor-binding domain of the S-protein, but also large percentage rises in the population of amino acid replacements in the 1st and 2nd planes.