Molecular study of the SARS-CoV-2 new variants in Iran

Introduction Various strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified worldwide such as lineages B.1.1.7 in the United Kingdom in December 2020, B.1.351, B.1.1.54, B.1.1.56 and C.1 in South Africa in 2020, and P 1 in Brazil during November 2020. We developed a multiplex real-time PCR assay for the molecular diagnosis of the SARS-CoV-2 new variants in Iran. Materials and methods In this cross-sectional study, 210 RNA samples were extracted from nasopharyngeal swabs using the GenePure Plus fully automatic Nucleic Acid Purification System model NPA-32+ (Hangzhou Bioer Technology Co., Ltd. (BIOER)) by magnetic beads method. The multiplexed real-time PCR assay was conducted to detect new strains of SARS-CoV-2. Results Among 210 patients diagnosed with SARS-CoV-2, 48 individuals were selected for the assessment of the presence or absence of the B.1.1.7 (United Kingdom), B.1.351 (South Africa), P. 1 (Brazil), B.1.526 (New York State) and B.1.375 (United States) variants. The B.1.1.7 variant was detected in 58.34% of the samples analysed. However, the B.1.351 (South Africa), P.1 (Brazil), B.1.526 (New York State) and B.1.375 (United States) variants were not identified in our study. Conclusion SARS-CoV-2 B.1.1.7 UK Variant was the predominant strain from February 2020 to May 2021. In the case of other lineages, it is necessary to carry out the Sanger sequencing for clarification.