Prevalence of SARS-CoV-2 Variants in COVID-19 Positive Patients

Abstract

Objective: Of the existing variants, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2), and omicron (B.1.1.529) were defined as variants of concern (VOCs) by World Health Organization. We aimed to retrospectively assess the distribution of VOCs in patients with positive COVID-19 real-time polymerase chain reaction (RT-PCR) test. Methods: Between April 2021 and December 31, 2021, 4260 patients whose clinical samples were sent with a COVID-19 PCR test request were included in the study. Of the patients whose samples were evaluated, 2173 (51%) were male, and 2087 (49%) were female. Viral nucleic acid isolation was performed by treating nasopharyngeal swabs, bronchoalveolar lavage, and tracheal aspirate samples with viral nucleic acid buffer (vNAT). SARS-CoV-2 variants were detected by Bio-Speedy® SARS-CoV-2 Variant Plus kit (Bioeksen AR-GE Technologies, Turkey), which targets variant-specific genome regions only found in B.1.1.7, B.1.351, and P.1 as well as ORF1ab and N gene regions. We used Bio-Speedy® SARS-CoV-2 Emerging Plus kit and CFX96 DX real-time PCR system to detect SARS-Cov-2 variants; N D3L mutation was targeted to detect the alpha variant, SL452R mutation to detect the delta variant, and S E484K mutation, which is widespread, to detect the gamma and the mu variants. Results: SARS-CoV-2 RT-PCR was positive in 773 (18.14%) of 4260 samples, and different SARS-CoV-2 variants were detected in 316 (40.88%) of positive samples. 407 (52.65%) of the patients with real-time polymerase chain reaction (RT-PCR) positive test were women, and the mean age was 41.7 years. While no variant type was detected in 457 (59.12%) of the patients, the alpha variant was detected in 156 (20.18%) and the delta variants in 137 (17.72%) patients. Conclusion: In our study, we found that the alpha variant was the dominant type in April, May, and June, and the delta variant became dominant as of July until the end of the year. Decreased rates of delta variants towards the end of 2021 and an increase in the other variants suggest the omicron variant, widely spread globally. Therefore, we believe that the omicron variant has been our country’s dominant type since November 2021. In conclusion, molecular surveillance studies that are planned in the light of epidemiological data and assessment of the frequency and genomic analyzes of regional and global variants are required.