The spread of SARS-CoV-2 Omicron (B. 1.1.529) variant and its subtypes in Latvia in 2021/2022

ABSTRACT

Objectives. Due to the rapid spread of the SARS-CoV-2 Omicron variant (B. 1.1.529) in Latvia at the end of 2021 and the beginning of 2022, it has become essential to determine the rate of its epidemiological spread and the rate of its dominance over the SARS-CoV-2 Delta variant (B.1. 617.2). The aim of the study was to determine the rate of Omicron variant prevalence in Latvia and, at the same time, differentiate Omicron subtypes BA.1 (variant B.1.1.529.1) and BA.2 (variant B.1.1.529.2). METHODS. The presence of the SARS-CoV-2 virus in nasopharyngeal and oropharyngeal swab samples was determined by RNA extraction and reverse transcription polymerase chain reaction. Altogether 36,719 samples were tested for mutations E484A, N501Y and deletion 69/70del. The RNA was extracted by fully automated nucleic acid extraction device Seegene NIMBUS and using STARMag 96 X 4 Universal Cartridge Kit (Seegene Inc.) reagents. For the RT-PCR reaction, the NovaplexTM SARS-CoV-2 Variants VII Assay (Seegene Inc.) reagent kit was used. The RT-PCR test kit can determine SARS-CoV-2 Omicron variant specific mutations (E484A and N501Y) as well as deletion 69/70del, with which it is possible to determine the sample affiliation to the Omicron subtypes BA.1 (with the deletion) or BA.2 (without the deletion). RESULTS. SARS-CoV-2 Omicron variant (B.1.1.529) became a dominant SARS-CoV-2 virus variant within 10 weeks in the territory of Latvia. Its presence in the population in the 48th week of 2021 was determined as 2% and in the 5th week of 2022 hit the rate of 98%. The highest increase took place in the first and second week of 2022 with an overall increase rate of 17%. The change of SARS-CoV-2 Omicron (B.1.1.529) subvariant BA.1 to BA.2 was found to happen within 6 weeks. The spread of the BA.2 subtype in the population in the 52nd week of 2021 was at the rate of 12%, however, in the 5th week of 2022, it hit almost 100%. The BA.2 subtype became a dominant subvariant in the 2nd week of 2022. CONCLUSIONS. The SARS-CoV-2 Omicron variant (B.1.1.529) became a dominant variant of the virus in the population of Latvia at the end of 2021 and the beginning of 2022. The rapid spread of the Omicron variant can be associated with its high infectivity.