Sublines of Omicron Genovariant of SARS-CoV-2 Virus as Potential Dominant Agents of New Rises of COVID-19 Morbidity in Russia

The analysis of existing information about invasion of COVID-19 in Russia shows that that one of leading reason of  existing of new rises of covid-19 morbidity is distribution of new genovariants of SARS-CoV-2 virus. The omicron  genovariant of SARS-CoV-2 virus was a dominant agent of fifth and subsequent rises of COVID-19 morbidity in  Russia. The aim of this work – the estimation of sublines of omicron genovariant of SARS-CoV-2 virus as potential  dominant agents of new rises of COVID-19 morbidity in Russia. The source base of the study. Data published in  Russian and English-language scientific publications available via the Internet (RSCI, PubMed, Google Scholar). The  research method is analytical. Results. The basic properties of omicron genovariant of SARS-CoV-2 virus, epidemical  characteristics of the rises of COVID-19 morbidity in Russia, caused by new sublines of omicron variant, estimation  ofsublines of omicron genovariant as potential dominant agent of new rises of COVID-19 morbidity in Russia are  viewed. It is shown that basic direction of SARS-CoV-2 virus evolution is existing of sublines of omicron genovariant,  which are characterized by increased transmissivity but with less severity of the disease caused compared to previously  circulated variants of COVID-19agent. The main distinguishing feature of the new subvariants («Kraken», «Czerber»,  «Centaur», «Arktur», «Pirola») are multiple amino acid exchanges in structural glycoprotein S. The maximum level  of variability of this structural protein compared to the original variant of SARS-CoV-2 virus is marked for Pirola  subvariant. Onle Kraken subvariant was dominant agent of rise of COVID-19 morbidity in Russia. Conclusion. New  rises of COVID-19 morbidity in Russia will not be connected with existing of new subvariants of omicron genovariant,  but only with season factor.

1. Sizikova TE, Lebedev VN, Borisevich SV. Environmental, biological and social factors contributing to new rises in COVID-19 morbidity in Russia. Biological Products. Prevention, Diagnosis, Treatment. 2022;22(4):351–60 (in Russian). https://doi.org/10.30895/2221-996X-2022-22-4-351-360

2. Sizikova TE, Chukhralya OV, Lebedev VN, Borisevich SV. The Omicron Variant of SARS-CoV-2 Virus: the Ability to Cause Disease in Persons with Immunity against COVID-19. Journal of NBC Protection Corps. 2022;6(1):44–55 (in Russian). https://doi.org/10.35825/2587-5728-2021-6-1-44-55

3. Onishchenko GG, Sizikova TE, Lebedev VN, Borisevich SV. The Omicron Variant of the Sars-Cov-2 Virus As the Dominant Agent of a New Risk of Disease amid the COVID-19 Pandemic. Herald Russ Acad Sci. 2022;92(4):381– 91 (in Russian). https://doi.org/10.1134/S1019331622040074

4. Thakur S, Sasi S, Pillai SG, Nag A, Shukla D, Singhal R, et al. SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Front. Med. 2022;9:815389. https://doi.org/10.3389/fmed.2022.815389

5. Roemer C, Sheward DJ, Hisner R, Gueli F, Sakaguchi H, Frohberg N, et al. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol. 2023;8:1952–59. https://doi.org/10.1038/s41564-023-01504-w

6. Guo Y, Han J, Zhang Y, He J, Yu W, Zhang X, et al. SARS-CoV-2 Omicron Variant: Epidemiological Features, Biological Characteristics, and Clinical Significance. Front Immunol. 2022;13:877101. https://doi.org/10.3389/fimmu.2022.877101

7. Morris CP, Eldesouki RE, Fall A, Gaston DC, Norton JM, Gallagher ND, et al. SARS-CoV-2 reinfections during the Delta and Omicron waves. JCI Insight. 2022;7(20):e162007. https://doi.org/10.1172/jci.insight.162007

8. Zhang J, Chen N, Zhao D, Zhang J, Hu Z, Tao Z. Clinical Characteristics of COVID-19 Patients Infected by the Omicron Variant of SARS-CoV-2. Front Med. 2022;9:912367. https://doi.org/10.3389/fmed.2022.912367

9. Tanasa IA, Manciuc C, Carauleanu A, Navolan DB, Bohiltea RE, Nemescu D. Anosmia and ageusia associated with coronavirus infection (COVID-19) – what is known? Exp Ther Med. 2020;20(3):2344–7. https://doi.org/10.3892/etm.2020.8808

10. Wu Y, Kang L, Guo Z, Liu J, Liu M, Liang W. Incubation Period of COVID-19 Caused by Unique SARS-CoV-2 Strains: A Systematic Review and Meta-analysis. JAMA Netw Open. 2022;5(8):e2228008. https://doi.org/10.1001/jamanetworkopen.2022.28008

11. Parums DV. Editorial: The XBB.1.5 ('Kraken') Subvariant of Omicron SARS-CoV-2 and its Rapid Global Spread. Med Sci Monit. 2023;29:e939580 https://doi.org/10.12659/MSM.939580

12. Liu Z, Zheng H, Lin H, Li M, Yuan R, Peng J, et al. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020;94(17):e00790-20. https://doi.org/10.1128/JVI.00790-20

13. Pernet O, Weisenhaus M, Stafylis C, Williams C, Campan M, Pettersson J, et al. Variant Study Group. SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay. Sci Rep. 2023;13(1):7612. https://doi.org/10.1038/s41598-023-34188-7

14. Focosi D, Spezia PG, Maggi F. SARS-CoV-2 BA.2.86 ("Pirola"): Is it Pi or Just Another Omicron Sublineage? Vaccines (Basel). 2023;11(11):1634. https://doi.org/10.3390/vaccines11111634

15. Scarpa F, Sanna D, Benvenuto D, Borsetti A, Azzena I, Casu M, et al. Genetic and Structural Data on the SARS-CoV-2 Omicron BQ.1 Variant Reveal Its Low Potential for Epidemiological Expansion. Int J Mol Sci. 2022;23(23):15264. https://doi.org/10.3390/ijms232315264

16. Cobar O, Cobar S. What We Know about XBB. 1.16 (Arcturus) The Next Prevalent Variant of SARS-CoV-2. 2023 (Preprint). https://doi.org/10.13140/RG.2.2.25519.10409

17. Grein J, Ohmagari N, Shin D, Diaz G, Asperges E, Castagna A. Compassionate Use of Remdesivir for Patients with Severe Covid-19. N Engl J Med. 2020;382(24):2327–36. https://doi.org/10.1056/NEJMoa2007016

18. Painter WP, Holman W, Bush JA, Almazedi F, Malik H, Eraut NCJE, et al. Human Safety, Tolerability, and Pharmacokinetics of Molnupiravir, a Novel Broad-Spectrum Oral Antiviral Agent with Activity against SARS-CoV-2. Antimicrob Agents Chemother. 2021;65(5):e02428-20. https://doi.org/10.1128/AAC.02428-20

19. Wahl A, Gralinski LE, Johnson CE, Yao W, Kovarova M, Dinnon KH. SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801. Nature. 2021;591(7850):451–57. https://doi.org/10.1038/s41586-021-03312-w

20. Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, et al. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. N Engl J Med. 2020;382(13):1199–207. https://doi.org/10.1056/NEJMoa2001316

21. Riou J; Althaus CL. Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Euro Surveill. 2020;25(4):2000058. https://doi.org/10.2807/1560-7917.ES.2020.25.4.2000058

22. Wu JT, Leung K, Bushman M; Kishore N, Niehus R, de Salazar PM. Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China. Nat Med. 2020;26(4):506–10. https://doi.org/10.1038/s41591-020-0822-7

23. Sanches S, Lin YT, Xu C, Romero-Severson E, Hengartner N, Ke R. High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis. 2020;26(7):1470–7. https://doi.org/10.3201/eid2607.200282

24. Singanayagam A, Hakki S, Dunning J, Madon KJ, Crone MA, Koycheva A, et al. Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study. Lancet Infect Dis. 2022;22(2):183–95. https://doi.org/10.1016/S1473-3099(21)00648-4

25. Satish S, Sylvia J, Vasna J, Prabakaran M. Scientometric Research Mapping of OMICRON for Scientific Production: A Global Perception Analysis. National Journal of Community Medicine. 2023;14:187–93. https://doi.org/10.55489/njcm.140320232593

26. Shahhosseini N, Babuadze G, Wong G, Kobinger G. Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Microorganisms. 2021;9(5):926. https://doi.org/10.3390/microorganisms905092

27. Abas AH, Marfuah S, Idroes R, Kusumawaty D, Fatimawali, Park MN, et al. Can the SARS-CoV-2 Omicron Variant Confer Natural Immunity against COVID-19? Molecules. 2022;27(7):2221. https://doi.org/10.3390/molecules27072221

28. Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. 2022;603(7902):679–86. https://doi.org/10.1038/s41586-022-04411-y

29. Parums DV. Editorial: The XBB.1.5 ('Kraken') Subvariant of Omicron SARS-CoV-2 and its Rapid Global Spread. Med Sci Monit. 2023;29:e939580. https://doi.org/10.12659/MSM.939580

30. Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, et al. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods. 2023;20(4):512–22. https://doi.org/10.1038/s41592-023-01769-3