Monitoring and assessment of SARS-CoV-2 evolution

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.

Keywords

• covid-19
• sars-cov-2
• genetic variability