Screening for SARS-CoV-2 variants in Egypt using multiplex PCR | ||
| Microbes and Infectious Diseases | ||
| Article 4, Volume 5, Issue 1, February 2024, Pages 20-28 PDF (871.25 K) | ||
| Document Type: Original Article | ||
| DOI: 10.21608/mid.2023.242453.1636 | ||
| Authors | ||
| Ghada Ismail1, 2; Nashwa Naguib Omar1; Samar Saad Rashad1; Hossam Abdelghaffar3, 4; Marwa Salah Mostafa5; Shereen Saeed Mohamed2; Ahmed Elshafei6; Yasmeen Mohammad Mahmood Ali Ibraheem* 7 | ||
| 1Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt. | ||
| 2Reference Laboratory of the Egyptian University Hospitals (RLEUH), Egypt. | ||
| 3Department of ENT, Faculty of Medicine, Helwan University, Egypt | ||
| 4Supreme Council for University Hospitals, Egypt. | ||
| 5Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt. | ||
| 6Theodor Bilharz Research Institute, Cairo, Egypt. | ||
| 7Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt. | ||
| Abstract | ||
| Background: Since the beginning of SARS-CoV-2 pandemic, numerous variants have emerged as a result of mutations occurring in earlier strains. A number of these variants have been linked with waves of widespread infections. The importance of the Variants of Concern (VOCs) lies in increased transmissibility, morbidity, and mortality, as well as escaping detection by conventional methods and resistance to treatment and vaccines. Aim of this study: Our aim is to screen for the presence of six SARS-CoV-2 variants in Egypt, for better understanding of its epidemiology during the epidemic. Methods: In this study, 2650 SARS-Cov-2 RNA positive nasopharyngeal specimens were collected at the Reference Laboratory of Egyptian University Hospitals (RLEUH) during the period from December 2020 through October 2021. All the samples were subjected to AllPlex SARS-CoV-2 Master assay, Variant I, II and Novaplex Variant IV Assays. Six VOCs could be detected by this method, which are alpha, beta, gamma, delta, delta plus and epsilon. Results: According to our data, the most detected variant was delta variant comprising 1308 (49%) of the cases. This was followed by alpha variant 121 (5%), delta plus 57 (2%) and gamma 8 (0.3%). 1156 (44%) of the cases were designated as other variants. Beta and epsilon variants were not detected in our study. Conclusions: Our data show that multiplex PCR assays are helpful in the characterization of the genomic epidemiology of SARS-COV-2. Although the new generation sequencing remains the gold standard for surveillance of variants, AllPlexTM Assays can provide a rapid and affordable option. | ||
| Keywords | ||
| SARS-COV-2; Variants of Concern; Multiplex PCR; Epidemiology | ||
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