Monitoring and assessment of SARS-CoV-2 evolution

Authors

DOI:

https://doi.org/10.14739/2310-1210.2022.1.241658

Keywords:

COVID-19, SARS-COV-2, genetic variability

Abstract

The aim of the study – systematization and analysis of information on the prevalence of SARS-CoV-2 virus variants according to information databases and own cross-sectional studies.

Materials and methods. The analysis was conducted in the period 2020–2021 using information databases and research resources: Google Scholar, Cochrane Library, Scirus, Springer, Medline, Embase, PubMed, Web of Science. Our own examination included a total of 80 nasopharyngeal swabs (at least two specimens in each case) collected from ARVI symptomatic or suspected COVID-19 patients, who were treated at the MNE KRC “Regional Clinical Infectious Diseases Hospital” from June to October 2021 and tested positive on SARS-CoV-2. The first study was performed in the inter-peak period, and the second one – on the rise of the disease. A real-time polymerase chain reaction (PCR) method was used for primary identification with the diagnostic kit “Biocore® SARS-CoV-2” (LLC “Biocor Technology Ltd.”, Ukraine) in accordance with the manufacturer’s instructions. Multiplex analysis SNPsig® VariPLEX Covid-19 (Primerdesign Ltd., UK) was used in the first cross-sectional study for secondary identification.

Results. Systematization and analysis of the prevalence of SARS-CoV-2 variants according to information databases were performed. According to the results of our cross-sectional studies on SARS-CoV2 variants circulating in the Kharkiv region in June – October 2021, the complete replacement of the alpha variant, which was dominant in June – 87.5 %, with the delta variant – 95.0 %. All patients had signs of respiratory failure, community-acquired pneumonia was visualized instrumentally (computed tomography, radiography, ultrasound) at the first study in 90 % of cases, and at the second – in 100 %. The median age of patients was 60.4 years (minimum – 25 years, maximum – 91 years) during the first study, but during the second – 52.6 years (minimum – 18 years, maximum – 84 years). Thus, the more aggressive and contagious delta variant has become dominant requiring thorough public health anti-epidemic measures.

Conclusions. Monitoring and control of the virus evolution using epidemiological studies, viral genetic sequence, as well as laboratory PCR are necessary to prevent the spread of COVID-19, to study the effectiveness of test systems and optimize diagnosis and etiotropic therapy as well as vaccine modifications.

 

Author Biographies

V. V. Miasoiedov, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Professor, Vice-Rector for Research

P. V. Nartov, Municipal Nonprofit Enterprise of Kharkiv Regional Council “Regional Clinical Infectious Hospital”, Ukraine

MD, PhD, DSc, Professor, Director

K. V. Yurko, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Professor, Head of the Department of Infectious Diseases

V. M. Lesovoy, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Professor, Head of Academic Council, Corresponding Member of the National Academy of Medical Sciences of Ukraine, Winner of the State Prize of Ukraine

V. A. Kapustnyk, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Professor, Rector, Honored Educator of Ukraine

A. V. Bondarenko, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Professor of the Department of Infectious Diseases

M. Ye. Cherniak, Kharkiv National Medical University, Ukraine

PhD, Assistant of the Department of Community Health and Health Protection Management

V. A. Yakushchenko, National University of Pharmacy, Kharkiv, Ukraine

PhD, Associate Professor of the Department of General Pharmacy and Drug Safety, Institute for Advanced Training of Pharmacy Specialist (IATPS)

V. V. Kucheriavchenko, Kharkiv National Medical University, Ukraine

MD, PhD, DSc, Associate Professor of the Department of Emergency Medicine, Anesthesiology and Intensive Care

V. S. Maslova, Kharkiv Regional Council “Regional Clinical Infectious Hospital”, Ukraine

MD, PhD, Deputy Chief Physician for Medical Work of the Municipal Nonprofit Enterprise

O. V. Bondarenko, Kharkiv Regional Council “Regional Clinical Infectious Hospital”, Ukraine

MD, Head of the Clinical and Diagnostic Laboratory of the Municipal Nonprofit Enterprise

References

Altmann, D. M., Boyton, R. J., & Beale, R. (2021). Immunity to SARS-CoV-2 variants of concern. Science, 371(6534), 1103-1104. https://doi.org/10.1126/science.abg7404

Challen, R., Brooks-Pollock, E., Read, J. M., Dyson, L., Tsaneva-Atanasova, K., & Danon, L. (2021). Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ, 372, Article n579. https://doi.org/10.1136/bmj.n579

Colson, P., Levasseur, A., Delerce, J., Pinault, L., Dudouet, P., Devaux, C., Fournier, P. E., La Scola, B., Lagier, J. C., & Raoult, D. (2021). Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Clinical Microbiology and Infection, 27(9), 1352.e1-1352.e5. https://doi.org/10.1016/j.cmi.2021.05.006

Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C., Russell, T. W., Tully, D. C., Washburne, A. D., Wenseleers, T., Gimma, A., Waites, W., Wong, K., van Zandvoort, K., Silverman, J. D., CMMID COVID-19 Working Group, COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz, K., Keogh, R., … Edmunds, W. J. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372(6538), Article eabg3055. https://doi.org/10.1126/science.abg3055

Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D., Mishra, S., Crispim, M., Sales, F., Hawryluk, I., McCrone, J. T., Hulswit, R., Franco, L., Ramundo, M. S., de Jesus, J. G., Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C., Manuli, E. R., Pereira, R., … Sabino, E. C. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 372(6544), 815-821. https://doi.org/10.1126/science.abh2644

Grint, D. J., Wing, K., Williamson, E., McDonald, H. I., Bhaskaran, K., Evans, D., Evans, S. J., Walker, A. J., Hickman, G., Nightingale, E., Schultze, A., Rentsch, C. T., Bates, C., Cockburn, J., Curtis, H. J., Morton, C. E., Bacon, S., Davy, S., Wong, A. Y., Mehrkar, A., … Eggo, R. M. (2021). Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February. Eurosurveillance, 26(11), Article 2100256. https://doi.org/10.2807/1560-7917.ES.2021.26.11.2100256

Singh, J., Rahman, S. A., Ehtesham, N. Z., Hira, S., & Hasnain, S. E. (2021). SARS-CoV-2 variants of concern are emerging in India. Nature Medicine, 27(7), 1131-1133. https://doi.org/10.1038/s41591-021-01397-4

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S. ... Ferguson, N. M. (2021). Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. medRxiv. https://doi.org/10.1101/2020.12.30.20249034

World Health Organization. (n.d.). Tracking SARS-CoV-2 variants. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants

CSSEGISandData. (2020). COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University. GitHub. https://github.com/CSSEGISandData/COVID-19

Graham, R. L., Sparks, J. S., Eckerle, L. D., Sims, A. C., & Denison, M. R. (2008). SARS coronavirus replicase proteins in pathogenesis. Virus Research, 133(1), 88-100. https://doi.org/10.1016/j.virusres.2007.02.017

Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., Duan, Y., Zhang, H., Wang, Y., Qian, Z., Cui, J., & Lu, J. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7(6), 1012-1023. https://doi.org/10.1093/nsr/nwaa036

Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet, 395(10224), 565-574. https://doi.org/10.1016/S0140-6736(20)30251-8

Forster, P., Forster, L., Renfrew, C., & Forster, M. (2020). Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9241-9243. https://doi.org/10.1073/pnas.2004999117

Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450-452. https://doi.org/10.1038/s41591-020-0820-9

Biswas, N. K., & Majumder, P. P. (2020). Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Indian Journal of Medical Research, 151(5), 450-458. https://doi.org/10.4103/ijmr.IJMR_1125_20

Kumar, R., Verma, H., Singhvi, N., Sood, U., Gupta, V., Singh, M., Kumari, R., Hira, P., Nagar, S., Talwar, C., Nayyar, N., Anand, S., Rawat, C. D., Verma, M., Negi, R. K., Singh, Y., & Lal, R. (2020). Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. mSystems, 5(4), Article e00505-20. https://doi.org/10.1128/mSystems.00505-20

Maitra, A., Sarkar, M. C., Raheja, H., Biswas, N. K., Chakraborti, S., Singh, A. K., Ghosh, S., Sarkar, S., Patra, S., Mondal, R. K., Ghosh, T., Chatterjee, A., Banu, H., Majumdar, A., Chinnaswamy, S., Srinivasan, N., Dutta, S., & DAS, S. (2020). Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Journal of Biosciences, 45(1), Article 76. https://doi.org/10.1007/s12038-020-00046-1

Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, 181(2), 281-292.e6. https://doi.org/10.1016/j.cell.2020.02.058

Zeng, R., Yang, R. F., Shi, M. D., Jiang, M. R., Xie, Y. H., Ruan, H. Q., Jiang, X. S., Shi, L., Zhou, H., Zhang, L., Wu, X. D., Lin, Y., Ji, Y. Y., Xiong, L., Jin, Y., Dai, E. H., Wang, X. Y., Si, B. Y., Wang, J., Wang, H. X., … Wu, J. R. (2004). Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients. Journal of Molecular Biology, 341(1), 271-279. https://doi.org/10.1016/j.jmb.2004.06.016

Mercatelli, D., & Giorgi, F. M. (2020). Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Frontiers in Microbiology, 11, Article 1800. https://doi.org/10.3389/fmicb.2020.01800

Seyran, M., Pizzol, D., Adadi, P., El-Aziz, T., Hassan, S. S., Soares, A., Kandimalla, R., Lundstrom, K., Tambuwala, M., Aljabali, A., Lal, A., Azad, G. K., Choudhury, P. P., Uversky, V. N., Sherchan, S. P., Uhal, B. D., Rezaei, N., & Brufsky, A. M. (2021). Questions concerning the proximal origin of SARS-CoV-2. Journal of Medical Virology, 93(3), 1204-1206. https://doi.org/10.1002/jmv.26478

Becker, M., Dulovic, A., Junker, D., Ruetalo, N., Kaiser, P. D., Pinilla, Y. T., Heinzel, C., Haering, J., Traenkle, B., Wagner, T. R., Layer, M., Mehrlaender, M., Mirakaj, V., Held, J., Planatscher, H., Schenke-Layland, K., Krause, G., Strengert, M., Bakchoul, T., Althaus, K., … Schneiderhan-Marra, N. (2021). Immune response to SARS-CoV-2 variants of concern in vaccinated individuals. Nature Communications, 12(1), Article 3109. https://doi.org/10.1038/s41467-021-23473-6

Nyberg, T., Twohig, K. A., Harris, R. J., Seaman, S. R., Flannagan, J., Allen, H., Charlett, A., De Angelis, D., Dabrera, G., & Presanis, A. M. (2021). Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis. BMJ, 373, Article n1412. https://doi.org/10.1136/bmj.n1412

Ramesh, S., Govindarajulu, M., Parise, R. S., Neel, L., Shankar, T., Patel, S., Lowery, P., Smith, F., Dhanasekaran, M., & Moore, T. (2021). Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy. Vaccines, 9(10), Article 1195. https://doi.org/10.3390/vaccines9101195

Moreira, F., D'arc, M., Mariani, D., Herlinger, A. L., Schiffler, F. B., Rossi, Á. D., Leitão, I. C., Miranda, T., Cosentino, M., Tôrres, M., da Costa, R., Gonçalves, C., Faffe, D. S., Galliez, R. M., Junior, O., Aguiar, R. S., Dos Santos, A., Voloch, C. M., Castiñeiras, T., & Tanuri, A. (2021). Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil. Virus Evolution, 7(2), Article veab087. https://doi.org/10.1093/ve/veab087

Sanyaolu, A., Okorie, C., Marinkovic, A., Haider, N., Abbasi, A. F., Jaferi, U., Prakash, S., & Balendra, V. (2021). The emerging SARS-CoV-2 variants of concern. Therapeutic Advances in Infectious Disease, 8, Article 20499361211024372. https://doi.org/10.1177/20499361211024372

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O'Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., … Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), 266-269. https://doi.org/10.1038/s41586-021-03470-x

Zeiser, F. A., Donida, B., da Costa, C. A., Ramos, G. O., Scherer, J. N., Barcellos, N. T., Alegretti, A. P., Ikeda, M., Müller, A., Bohn, H. C., Santos, I., Boni, L., Antunes, R. S., Righi, R., & Rigo, S. J. (2022). First and second COVID-19 waves in Brazil: A cross-sectional study of patients' characteristics related to hospitalization and in-hospital mortality. Lancet Regional Health. Americas, 6, Article 100107. https://doi.org/10.1016/j.lana.2021.100107

National Center for Immunization and Respiratory Diseases (NCIRD), & Division of Viral Diseases. (2020, February 11). Coronavirus Disease 2019 (COVID-19). Centers for Disease Control and Prevention. CDC. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html#print

Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., Reddy, N. P., Sanchez San Martin, C., Federman, S., Cheng, J., Balcerek, J., Taylor, J., Streithorst, J. A., Miller, S., Kumar, G. R., Sreekumar, B., … Chiu, C. Y. (2021). Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. medRxiv, Article 2021.03.07.21252647. https://doi.org/10.1101/2021.03.07.21252647

Madewell, Z. J., Yang, Y., Longini, I. M., Jr, Halloran, M. E., & Dean, N. E. (2020). Household Transmission of SARS-CoV-2: A Systematic Review and Meta-analysis. JAMA Network Open, 3(12), Article e2031756. https://doi.org/10.1001/jamanetworkopen.2020.31756

Published

2022-01-26

How to Cite

1.
Miasoiedov VV, Nartov PV, Yurko KV, Lesovoy VM, Kapustnyk VA, Bondarenko AV, Cherniak MY, Yakushchenko VA, Kucheriavchenko VV, Maslova VS, Bondarenko OV. Monitoring and assessment of SARS-CoV-2 evolution. Zaporozhye Medical Journal [Internet]. 2022Jan.26 [cited 2024Nov.13];24(1):109-14. Available from: http://zmj.zsmu.edu.ua/article/view/241658

Issue

Section

Review