An Extended Analysis of SARS-CoV-2 Using a Nonlinear Dynamics Chaotic Model

The two dimensional cellular automata (CA) picture is an alternative method to depict the nucleotide and amino acid sequences. Here we showed that the two dimensional CA pictures can vividly delineate the nucleotide sequences (base sequence) of the gene and the genomes of SARS-CoV-2, the pathogenic agent of the COVID-19 pandemic. If the genetic codon rules are strictly followed, the CA pictures can also depict the genetic codons and indirectly express the amino acid sequences of the proteins of SARS-CoV-2. CA pictures can reveal the overall and detailed differences between nucleotide or amino acid sequences and they are very sensitive to the sequence details, such as the cleavage recognition site of the host protease like TMPRSS2, and the receptor binding domain (RBD) of the spike protein of SARS-CoV-2, which are sensitive to even changes in only one amino acid or a nucleotide between the sequences from different strains of SARS-CoV2. We think that CA pictures can provide a mathematical basis for viral genetic and amino acid sequence messages or be applied to artificial intelligence when expressing the genetic messages of SARS-CoV2 and other viruses.