Surveillance for SARS-CoV-2 Variants of Concern and Initial Detection of Omicron using RT-PCR in the Kurdistan region of Iraq

Abstract

. Abstract Background: Omicron (B.1.1.529), a novel SARS-CoV-2 variant (VOC), is a highly diverse variant with many mutations. Immune evasion is possible, as is increased transmissibility within the populations. The RT-qPCR method may be effectively utilised for variant surveillance. This is to rule in or rule out significant variants quickly. Objectives: As a result, the goal of this study was to track the prevalence of the SARS-CoV-2 Omicron variant in the local community using the SGTF test in conjunction with the SARS-CoV-2 S-gene mutations RT-PCR assays. Patients and methods: The study included 255 SARS-CoV-2 positive specimens collected in Erbil central public health laboratory between January 1 to February 6, 2022, for routine testing purposes. The SARS-CoV-2 variant profiling was performed on extracted RNA using PowerChek SARS-CoV-2 S-gene Mutation Detection Kit Ver.3.0 plus S-gene Target Failure (SGTF) of the TaqPath™ COVID -19 CE-IVD RT-PCR Kit . Results: The samples were surveyed, resulting in a positivity rate of (86.6%) for Omicron BA.1, (3.1%) Omicron BA.2, (1.7%) Delta variant (B.1.617.2), and (8.6%) were inconclusive variants. Among Omicron COVID-19 cases, 89 (38.5%) were fully vaccinated, and 4 (1.7%) received full vaccination plus a booster dose. Nevertheless, 16 (7%) of the confirmed Omicron COVID-19 cases had a documented previous SARS-CoV-2 infection. Conclusion: The SARS-CoV-2 S-gene mutations RT-PCR assay is a cost-effective and fast method for the surveillance of SARS-CoV-2 variants of concern. Currently, Omicron BA1 is the predominant SARS-CoV-2 variant in the Kurdistan region/Iraq, and the emergence of the Omicron BA2 variant is of high concern.