Genetic variability of SARS-CoV-2 virus in the inter-peak period

Abstract

The aim of the study – to determine the variants of SARS-CoV-2 virus in the inter-peak period (before the beginning of the new wave) in patients of Kharkiv and Kharkiv region with confirmed SARS-CoV-2 infection. Materials and methods. The smears (40 nasopharyngeal samples) from patients with symptoms of ARVI or suspected COVID-19, who were hospitalized to MNE KRC "Regional clinical infectious diseases hospital" in June 2021 and who were identified as positive for SARS-CoV-2 were used study for research conducting. Cross-sectional study of the detection of variants of SARS-CoV-2 circulating in the Kharkiv region in June 2021 was conducted. According to the method of systematic probabilistic sampling for the study of genetic variability of SARS-COV-2, 40 patients with COVID-19 were selected. Among the studied patients, females predominated – 25 people against 15, respectively. The average age of patients was 60.4 years (minimum - 25 years, maximum - 91 years). All patients were hospitalized in the presence of respiratory failure, but community-acquired pneumonia was visualized instrumentally (computed tomography, radiography, ultrasound) in 38 patients. Clinical group III was established in 21 patients, clinical group IV – in 17. Mortality among the studied group was 15%. Research results. The predominant circulation of variant 201/501Y.V1 (alpha) was detected during PCR studies on variants of SARS-CoV-2 virus circulating in Kharkiv and the Kharkiv region in the inter-peak period (before the beginning of the third wave). Alpha variant was detected in 35 patients (87.5%) with typical for this virus mutation – N501Y, but the presence of additional mutations was identified in 1 patient. The original SARS-CoV-2 virus was detected in 5 patients (12.5%), but in 1 of them with the presence of the N501Y mutation. Circulation of only variant 201/501Y.V1 was detected in all residents of the region. Circulation of SARS-CoV-2 variants 20H/501Y.V2 (beta), 20J/501Y.V3 (gamma), 20C/S.452R (previously epsilon) was not detected in Kharkiv and the region, and the E484K mutation was not found in any patient.

Conclusions. The dominant variant circulating in Kharkiv and the region in the inter-peak period is the alpha variant, which prevails over the original virus due to the increased level of contagiousness and more rapid spread.

Key words: COVID-19, SARS-COV-2, genetic variability.

DOI: 10.5281/zenodo.6350409