The Pandemic is in Progress: Long Covid, Omicrons, Vaccination and Vaccines

Abstract

The article discusses the residual effects of survivors of COVID-19, referred to as long-term covid, a short list of their manifestations, their possible causes and difficulties of recognition. Changes in the primary structure of emerging coronaviruses from the Wuhan strain to new omicron strains are analyzed. Among the features of their evolution, there is an increase in the content of arginine and lysine, especially in the S1 subunit, and a decrease in the proportion of aspartic and glutamic amino acids. The receptorbinding domain of omicrons is characterized by a tendency to decrease the content of threonine, serine and glutamine. Mutations in the S protein are characterized by asymmetry in relation to both substitutable and substitutive amino acids. Isoleucine and cysteine are not replaced. Certain trends and limitations in the mutations of their S protein and especially the unusual ratio transversion: transitions in them argue for the version of the artificial origin of the SARS-Cov-2 variants. At the level of the S protein genes, there are prohibitions regarding the use of certain codons. To assess the effectiveness of vaccines and the sensitivity of coronaviruses to them during a pandemic, it is useful to divide pandemic coronaviruses into two groups: omicrons and pre-omicrons. This division is justified by the fact that these groups differ sharply in the number of mutations and changes in the composition of immune epitopes, especially in the receptor-binding domain. The specific tendency of changes in its amino acid composition, apparently, is associated with a consistent decrease in pathogenicity in BA.1, BA.2, BA.4 and BA.5 variants. Taking into account these features makes it possible to predict the sensitivity of coronavirus strains to the vaccines used and rationally design vaccines with a wide range of specificity.