Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2

• Published in: Biomolecules (Basel, Switzerland) Vol. 12; no. 5; p. 631
• Main Authors: Goh, Gerard Kian-Meng, Dunker, A Keith, Foster, James A, Uversky, Vladimir N
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 25.04.2022; MDPI
• Subjects: Animals; Artificial intelligence; Bronchus; Chiroptera; coronavirus; Coronaviruses; COVID-19; Dengue fever; Disease transmission; Ebola virus; intrinsic disorder; membrane; Mucosa; Mutation; Neural networks; nucleocapsid; nucleoprotein; Pandemics; Phylogenetics; Phylogeny; Proteins; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Virions; Virulence; Viruses; China; membrane; nucleoprotein; coronavirus; mucus; severe acute respiratory syndrome; spread; COVID-19; lung; nucleocapsid; saliva; bronchus; transmission; virulence; shell; pangolin; Omicron; intrinsic disorder
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom12050631

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. The 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 and pangolin-CoV-2017 (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 the higher contagiousness of SARS-CoV-2 and Omicron, since hard outer shell protects the virion from salivary/mucosal antimicrobial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan-Hu-1 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 e.g., the presence of fewer infectious particles in the lungs than in the bronchi upon infection.