Novel SARS-CoV-2 Omicron variants in İstanbul; Rapid Preponderance of BA.2 and BA.5

Abstract

Objective: In Turkey, the fourth wave of SARS-CoV-2 started in December 2021 and peaked in mid-January 2022. Afterward, peaks were seen in the number of COVID-19 cases because of Omicron BA.2 and BA.5 variants. Our study aimed to observe the prevalence and viral load-related transmissibility rates of the Omicron BA.2 and BA.5 variant infections in our region between January 21 and July 01, 2022, using an easy and cost-effective PCR screening method. Methods:The frequency of BA.2 and BA.5 were determined by the two-stage allele-specific and drop-out RT-PCR method targeting NSP6 105-107del, spike 69-70del, and spike L452R mutation-specific primers. Transmissibility of the Omicron variants was assessed using cycle threshold (Ct) values (a proxy for SARS-CoV-2 viral load and infectivity). Also, using the next generation sequencing (NGS) method, existing mutations were analyzed by generating full-length sequences of the representative, randomly selected samples from the Omicron variants determined by PCR screening test. Results:We defined the first case of BA.2 on January 19, 2022, in İstanbul University-Cerrahpaşa School of Medicine COVID-19 Molecular Diagnosis Laboratory. Following this, it was observed that BA.1 lost its dominance due to the increased transmissibility of BA.2. On May 5, we defined the first case of BA.5, and as of July this Omicron variant rapidly became preponderant, with a frequency of more than 85%. Compared with BA.1, BA.2 and BA.5 were associated with 2.82 (95% CI: 2.33-4.12) and 2.49 (95% CI: 2.16-3.55) fewer cycles, respectively, meaning higher transmissibility. As confirmed by the NGS results, it was concluded that screening with NSP6 105-107del, spike 69-70del and spike L452R mutation targeted PCR method, which is used uniquely in our hospital in Turkey, can be an easy and cost-effective method in the follow-up of Omicron variants. Conclusion:The higher viral load detection in infections with BA.2 and BA.5 reflects a prolonged disease period, and increased transmissibility, so rapid expansion of these Omicron variants in Turkey is inevitable. Even though the prevalence of the Omicron variants in the population can be monitored in near real-time by the PCR screening method, more sequencing studies are needed for the early identification of new mutations that will emerge.

Immunogenicity, safety and clinical outcomes of the SARS-CoV-2 BNT162b2 vaccine in adolescents with type 1 diabetes

“…However, as more transmissible novel strain, omicron variant became prevalent worldwide since the start of 2022, the vaccine effectiveness was found to be decreased remarkably ( 46 – 48 ). In this research, the 6-month post-vaccination follow-up period through which the cases with breakthrough infections were diagnosed coincided with the time span when the omicron variant displaced the previously dominant delta variant in Turkey ( 49 , 50 ). At the end of the follow-up, no significant difference was found in the rate of symptomatic breakthrough infections between adolescents with T1D and healthy controls.…”

Prof. Kenan Midilli, MD: Great Virologist, Brilliant Scientist, and Passionate Intellectual (1963-2022)

“…Because of his high potential for critical appraisal, he had a significant role as a member of the editorial board of the Infectious Diseases and Clinical Microbiology Journal (IDCM), which was launched in 2019, just before the COVID-19 pandemic. He contributed significantly to the journal with his comments on the emerging variants of SARS-CoV-2 (17)(18)(19).…”