Biomics

The emergence of the new SARS-CoV-2 coronavirus has given rise to many enigmas, to which there are no answers yet. However, the degree of threat to humanity, due to the fact that by the beginning of February 2021, more than 100 million people were ill in the world, of which 2 million died, led to the fact that the efforts of many researchers were aimed at combating this disease, including massive sequencing of the complete genomes of SARS-CoV-2, as this is necessary for diagnostics and prediction of the epidemiological situation, including in the long term. Currently, a fairly high level of conservativeness of the SARS-CoV-2 genome is shown, but there is also a significant variability of intra-host viral RNA, confirming the concept of the existence of quasispecies for RNA-containing viruses. As of February 2021, the complete genomes of almost half a million coronavirus isolates have been sequenced worldwide, and a number of nomenclatures have been proposed to streamline their analysis, including the convenient dynamic nomenclature Pango lineage. Variations of SARS-CoV-2 genomes in the form of consensus SNPs (Single Nucleotide Polymorphism) and intra-host iSNVs (intra-host Single Nucleotide Variant) were demonstrated. Taking into account iSNV and minor mutations, about 85% of the 29.9 thousand nucleotides viral genome were changed at least once, but only a very few of them turned into major mutations due to certain features that ensure the predominant distribution of such strains. The example of the S-protein gene, taking into account iSNV, minor and major mutations, shows its significant variability, which is detected when sequencing hundreds of thousands of SARS-CoV-2 genomes. On the basis of the analysis of 400 complete SARS-CoV-2 genomes isolated on the territory of the Russian Federation during 2020, the dynamics of the circulation of individual strains with acquired major mutations, the representation of which is slightly different from the changes in the SARS-CoV-2 genome in the rest world, is estimated. The possibility of long-term persistence of the new coronavirus in the human body is note, while the reservoirs for the latent existence of SARS-CoV-2, in contrast, for example, to the herpes simple virus, remain unknown. There is no consensus on the possibility of reactivation of SARS-CoV-2 or reinfection. The latter is theoretically possible in cases where SARS-CoV-2 strains belonging to other genetic lineages and clades are found in the body of the "re-infected". This, however, does not exclude the possibility of mutating the virus within a single host. Despite significant progress in monitoring the spread of SARS-CoV-2, many questions remain, but as knowledge of the biology of the new coronavirus accumulates, they will also be answered.

coronavirus, SARS-CoV-2, quasispecies, genome, RNA, sequencing, S-protein, consensus mutations, intrahost mutations, SNP, iSNV, persistence, reinfection, COVID-19

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