COVID-19: evolution of the pandemic in Russia. Report II: dynamics of the circulation of SARS-CoV-2 genetic variants

Акимкин, В. Г.; Popova, A. Yu.; Khafizov, K.; Дубоделов, Д. В.; Углева, С. В.; Semenenko, Т. A.; Плоскирева, А.А.; Gorelov, А.V.; Pshenichnaya, N.; Ежлова, Е. Б.; Letyushev, A. N.; Demina, Yu. V.; Кутырев, Владимир; Максютов, Р. А.; Govorun, Vadim M.; Dyatlov, I. A.; Тотолян, Арег А.; Куличенко, А. Н.; Balakhonov, S. V.; Рудаков, Н. В.; Троценко, О. Е.; Носков, А. К.; Zaitseva, N.N.; Топорков, А. В.; Lioznov, Dmitry; Andreeva, E. E.; Микаилова, О. М.; Komarov, A. G.; Ananyev, V. Yu.; Молдованов, В В; Logunov, Denis Y.; Gushchin, Vladimir A.; Dedkov, Vladimir; Cherkashina, Anna S.; Кузин, С. Н.; Тиванова, Е. В.; Kondrasheva, L. Yu.; Kaptelova, V.V.; Selezov, S. Yu.; Gasanov, Gasan A.; Svanadze, Nino Kh.; Glazov, M. B.; Остроушко, А. А.; Миронов, К. О.; Esman, A. S.; Осина, Н. А.; Боднев, С. А.; Komissarov, Andrey; Danilenko, Daria; Богун, А. Г.; Skryabin, Yury P.; Lopatovskaya, K. V.; Штрек, С. В.; Волынкина, А. С.; Гладких, А. С.; Котова, В. О.; Водопьянов, А. С.; Новикова, Н. А.; Speranskaya, A.S.; Samoilov, Andrei E.; Neverov, Alexey D.; Шпак, И. М.

doi:10.36233/0372-9311-295

Cited by 25 publications

(10 citation statements)

References 15 publications

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“…In addition to the Delta (AY.122), variant B.1.1 (20B) was still detected; however, the small number of sequences for this period does not allow us to say what other variants could have circulated at that time. The fourth wave, according to our data, was completely caused by the Delta variant, which is in good agreement with the situation in Russia during this period [27,28].…”

Section: The Diversity Of Genetic Variants Of Sars-cov-2 In the Siber...supporting

confidence: 91%

“…In all other regions of the Siberian Federal District, immediately after the plateau of the third wave, a new increase in the incidence began in the middle of September 2021. However, we cannot associate this rise with the arrival of the Omicron variant, since it appeared in Russia only at the end of December 2021 [ 27 , 28 ]. Most likely, the rise after the start of the decrease is associated with the beginning of the school year.…”

Section: Resultsmentioning

confidence: 99%

“…In Russia, European descendants of the Wuhan strain were dominant in the first wave of incidence [ 15 ], its subsequent genovariants in wave 2, then AY.122 in the third and fourth, and Omicron in the fifth and sixth [ 27 , 28 ]. The variety of SARS-CoV-2 variants we have considered shows that, due to restrictions, not all possible variants entered the Siberian Federal District, while many variants of SARS-CoV-2 circulated in Russia.…”

Section: Discussionmentioning

confidence: 99%

“…Instead, educational institutions opened when the number of cases in the community was still quite high. As we know that Omicron displaced Delta very quickly [ 27 , 28 ], maintaining restrictions until Omicron arrived in the region could have saved a huge number of lives. The incidence would still be very high, but the people who died from the Delta could survive the Omicron as it is less lethal [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

“…The maximum mortality occurred at the beginning and middle of the pandemic, when the most pathogenic variants of the virus were circulating. In Russia [27,28], as well as throughout the world [29], mortality was low in the first wave of incidence, and it was maximal in the third and fourth waves with the AY.122 dominating variant, and minimal during circulation of exclusively the Omicron genovariants. In contrast to incidence, mortality in all regions of the Siberian Federal District, except for the Irkutsk region, looks like three waves, not six.…”

Section: Covid-19 Mortality In the Siberian Federal Districtmentioning

confidence: 99%

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The Development of the SARS-CoV-2 Epidemic in Different Regions of Siberia in the 2020–2022 Period

Palyanova,

Sobolev,

Palyanov

et al. 2023

Viruses

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The comparison of the development of the SARS-CoV-2 epidemic in several neighboring regions can help researchers to assess the risks and develop more effective strategies and approaches in the field of preventive medicine. We analyzed the infection and mortality statistics for the 2020–2022 period in ten individual regions of the Siberian Federal District of Russia. We also sequenced complete genomes, which allowed us to analyze the genetic diversity of SARS-CoV-2 circulated in each of the ten regions and to build a phylogenetic dendrogram for the virus variants. The ParSeq v.1.0 software was developed to automate and speed up the processing and analysis of viral genomes. At the beginning of the pandemic, in the first two waves, the B.1.1 variant (20B) dominated in all regions of the Siberian Federal District. The third and fourth waves were caused by the Delta variant. Mortality during this period was at a maximum; the incidence was quite high, but the number of deposited genomes with GISAID during this period was extremely low. The maximum incidence was at the beginning of 2022, which corresponds to the arrival of the Omicron variant in the region. The BA.5.2 variant became the dominant one. In addition, by using NextClade, we identified three recombinants in the most densely populated areas.

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Section: The Diversity Of Genetic Variants Of Sars-cov-2 In the Siber...supporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Covid-19 Mortality In the Siberian Federal Districtmentioning

confidence: 99%

See 3 more Smart Citations

The Development of the SARS-CoV-2 Epidemic in Different Regions of Siberia in the 2020–2022 Period

Palyanova,

Sobolev,

Palyanov

et al. 2023

Viruses

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Treatment of COVID‐19 patients with a SARS‐CoV‐2‐specific siRNA‐peptide dendrimer formulation

Khaitov

Nikonova

Кофиади

et al. 2023

Allergy

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Background Severe acute respiratory syndrome corona virus (SARS‐CoV‐2) infection frequently causes severe and prolonged disease but only few specific treatments are available. We aimed to investigate safety and efficacy of a SARS‐CoV‐2‐specific siRNA‐peptide dendrimer formulation MIR 19® (siR‐7‐EM/KK‐46) targeting a conserved sequence in known SARS‐CoV‐2 variants for treatment of COVID‐19. Methods We conducted an open‐label, randomized, controlled multicenter phase II trial (NCT05184127) evaluating safety and efficacy of inhaled siR‐7‐EM/KK‐46 (3.7 mg and 11.1 mg/day: low and high dose, respectively) in comparison with standard etiotropic drug treatment (control group) in patients hospitalized with moderate COVID‐19 (N = 52 for each group). The primary endpoint was the time to clinical improvement according to predefined criteria within 14 days of randomization. Results Patients from the low‐dose group achieved the primary endpoint defined by simultaneous achievement of relief of fever, normalization of respiratory rate, reduction of coughing, and oxygen saturation of >95% for 48 h significantly earlier (median 6 days; 95% confidence interval [CI]: 5–7, HR 1.75, p = .0005) than patients from the control group (8 days; 95% CI: 7–10). No significant clinical efficacy was observed for the high‐dose group. Adverse events were reported in 26 (50.00%), 25 (48.08%), and 28 (53.85%) patients from the low‐, high‐dose and control group, respectively. None of them were associated with siR‐7‐EM/KK‐46. Conclusions siR‐7‐EM/KK‐46, a SARS‐CoV‐2‐specific siRNA‐peptide dendrimer formulation is safe, well tolerated and significantly reduces time to clinical improvement in patients hospitalized with moderate COVID‐19 compared to standard therapy in a randomized controlled trial.

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The Theory of Self-Regulation of Parasitary Systems and COVID-19

Akimkin,

Semenenko,

Dubodelov

et al. 2024

Annals RAMS

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Background. The COVID-19 pandemic once again confirmed the correctness of the theory of Academician V.D. Belyakov, according to which the basis for the development of the epidemic process is a phase change in the heterogeneity of the biological properties of the interacting populations of the pathogen and humans. In accordance with the theory of self-regulation of parasitic systems, changes are associated not only with genetic variability, but also with other polydeterminant characteristics of the pathogen: when new genovariants appeared, SARS-CoV-2 became less pathogenic for humans, but more contagious. This circumstance is important not only for theoretical, but also for practical epidemiology, as it makes it possible to predict the direction of development of the epidemic situation. Aims — to evaluate the manifestations of the epidemic process of the new coronavirus infection COVID-19 through the prism of the theory of self-regulation of parasitic systems. Methods. An epidemiological retrospective analysis of the incidence of COVID-19 was carried out, including the study of absolute and intensive incidence rates per 100,000 population, the dynamics of changes in the properties of the coronavirus population, and the identification of SARS-CoV-2 genovariants for the period from 03.2020 to 04.2023. To analyze SARS-CoV-2 genovariants at various stages of the pandemic, we used sequencing data presented on the SARS-CoV-2 genome information aggregation platform Virus Genome Aggregator of Russia (VGARus) — more than 248 thousand genetic sequences. Results. During the pandemic, there have been seven ups and downs in the incidence of COVID-19. During the period of circulation in the human population and adaptation to a new host, a significant amount of data has accumulated on the evolutionary changes in the SARS-CoV-2 genome, taking into account the trends in the acquisition of new epidemiological properties. Conclusion. An analysis of the manifestations of the epidemic process of COVID-19, as a classic aerosol anthroponosis, confirmed the correctness of the theory of Academician V.D. Belyakov, according to which the basis of its development is a phase change in the heterogeneity of the biological properties of the interacting populations of the pathogen and humans, based on negative feedback in the process of self-regulation.

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COVID-19: evolution of the pandemic in Russia. Report II: dynamics of the circulation of SARS-CoV-2 genetic variants

Cited by 25 publications

References 15 publications

The Development of the SARS-CoV-2 Epidemic in Different Regions of Siberia in the 2020–2022 Period

The Development of the SARS-CoV-2 Epidemic in Different Regions of Siberia in the 2020–2022 Period

Treatment of COVID‐19 patients with a SARS‐CoV‐2‐specific siRNA‐peptide dendrimer formulation

The Theory of Self-Regulation of Parasitary Systems and COVID-19

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