Shell Disorder Models Detect that Attenuated Omicron has Harder Shells but is not a Descendant of the Wuhan (SARS-CoV-2) Strain

Before the SARS-CoV-2 Omicron variant emergence, Shell Disorder Models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell-disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9% - lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer-shell) among all CoVs. This is likely to be responsible for higher contagiousness of SARS-CoV-2 and Omicron, since the hard outer-shell protects the virion from salivary/mucosal anti-microbial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan strain closely related to pangolin-CoVs. M, being evolutionarily conserved in COVID-19, is most ideal for COVID-19 phylogenetic study. Omicron may have been hiding among burrowing animals (e.g. pangolins) that provide optimal evolutionary environments for attenuation and increase shell hardness, which is essential for fecal-oral-respiratory transmission via buried feces. Incoming data support SDM showing the presence of fewer infectious particles in the lungs than in the bronchi upon infection.