Screening for SARS-CoV-2 variants in Egypt using multiplex PCR
Ismail, G., Omar, N., Rashad, S., Abdelghaffar, H., Mostafa, M., Mohamed, S., Elshafei, A., Ibraheem, Y. (2024). Screening for SARS-CoV-2 variants in Egypt using multiplex PCR. EKB Journal Management System, 5(1), 20-28. doi: 10.21608/mid.2023.242453.1636
Ghada Ismail; Nashwa Naguib Omar; Samar Saad Rashad; Hossam Abdelghaffar; Marwa Salah Mostafa; Shereen Saeed Mohamed; Ahmed Elshafei; Yasmeen Mohammad Mahmood Ali Ibraheem. "Screening for SARS-CoV-2 variants in Egypt using multiplex PCR". EKB Journal Management System, 5, 1, 2024, 20-28. doi: 10.21608/mid.2023.242453.1636
Ismail, G., Omar, N., Rashad, S., Abdelghaffar, H., Mostafa, M., Mohamed, S., Elshafei, A., Ibraheem, Y. (2024). 'Screening for SARS-CoV-2 variants in Egypt using multiplex PCR', EKB Journal Management System, 5(1), pp. 20-28. doi: 10.21608/mid.2023.242453.1636
Ismail, G., Omar, N., Rashad, S., Abdelghaffar, H., Mostafa, M., Mohamed, S., Elshafei, A., Ibraheem, Y. Screening for SARS-CoV-2 variants in Egypt using multiplex PCR. EKB Journal Management System, 2024; 5(1): 20-28. doi: 10.21608/mid.2023.242453.1636

Screening for SARS-CoV-2 variants in Egypt using multiplex PCR

Microbes and Infectious Diseases
Article 4, Volume 5, Issue 1, February 2024, Page 20-28  XML PDF (871.25 K)
Document Type: Original Article
DOI: 10.21608/mid.2023.242453.1636
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Authors
Ghada Ismailorcid 1, 2; Nashwa Naguib Omarorcid 1; Samar Saad Rashad1; Hossam Abdelghaffar3, 4; Marwa Salah Mostafaorcid 5; Shereen Saeed Mohamedorcid 2; Ahmed Elshafeiorcid 6; Yasmeen Mohammad Mahmood Ali Ibraheem email orcid 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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