Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2

Abstract

Despite extensive worldwide vaccination, the current COVID-19 pandemic caused by SARS-CoV-2 continues. The Omicron variant is a recently emerged variant of concern and is now taking over the Delta variant. To characterize the potential antigenicity of the Omicron variant, we examined the distributions of SARS-CoV-2 nonself mutations (in reference to the human proteome) as 5 amino acid stretches of short constituent sequences (SCSs) in the Omicron and Delta proteomes. The number of nonself SCSs did not differ much throughout the Omicron, Delta, and Reference Se-quence (RefSeq) proteomes but markedly increased in the receptor binding domain (RBD) of the Omicron spike protein compared to those of the Delta and RefSeq proteins. In contrast, the number of nonself SCSs decreased in non-RBD regions in the Omicron spike protein, compensating for the increase in the RBD. Several nonself SCSs were tandemly present in the RBD of the Omicron spike protein, likely as a result of selection for higher binding affinity to the ACE2 receptor (and hence higher infectivity and transmissibility) at the expense of increased antigenicity. Taken together, the present results suggest that the Omicron variant has evolved to have higher antigenicity and less virulence in humans despite increased infectivity and transmissibility.

Emerging evidence on Omicron (B.1.1.529) SARS‐CoV‐2 variant

“…While this is a positive aspect, a reasonably high rate of transmission could quickly exhaust existing healthcare ability, resulting in more deaths than predicted. Such healthcare stress may also lead to an increase in mortalities that are not linked to COVID‐19 62 . Omicron multiplies 70 times faster in tissues that line airway passages than the earlier Delta variant, potentially facilitating person‐to‐person spread, according to the researchers.…”

“…Such healthcare stress may also lead to an increase in mortalities that are not linked to COVID‐19. 62 Omicron multiplies 70 times faster in tissues that line airway passages than the earlier Delta variant, potentially facilitating person‐to‐person spread, according to the researchers. However, Omicron replicates 10 times slower in lung tissues than the original coronavirus, which could contribute to less severe illness.…”

Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2

“…Our first results on the Omicron variant were obtained immediately after the emergence of the variant and were released as of 3 January 2022 [70]. At that time, only preliminary data were presented about this variant in the literature database.…”

SVEIRS Mathematical Model on Stability Analysis of HIV-1 Coronavirus CO-Infection

“…The analysis suggested that COVID-19 only prevention strategy is the most effective strategy and it averted about 10,500 new co-infection cases. Further, [18,19,20,21,22] studied analysis of COVID-19 and comorbidity specifically diabetes mellitus co-infection model with optimal control. The model showed backward bifurcation caused by parameter accounting for susceptibility for Covid-19 and rate of reinfection.…”

“…The results showed that preventive measures such as number of chlorine water tablets, lockdown, social distancing and number of tests played a key role in reducing spread of the disease. COVID-19 and tuberculosis co-dynamics model with optimal control strategies carried out by [30,13,31,22] suggested that COVID-19 prevention, treatment and control of co-infection yields a better outcome in terms in terms of the number of COVID-19 cases prevented at a lower percentage of the total cost of this strategy. Ordinary differential equations constructed by [32,33,34,35] modeled bifurcation and optimal control analysis of HIV/AIDS and COVID-19 co-infection model with numerical simulation.…”