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326268

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

Article

Last updated: 04 Jan 2025

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Subjects

-

Tags

Medical virology

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.

DOI

10.21608/mid.2023.242453.1636

Keywords

SARS-CoV-2, Variants of concern, Multiplex PCR, Epidemiology

Authors

First Name

Ghada

Last Name

Ismail

MiddleName

-

Affiliation

Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt., Reference Laboratory of the Egyptian University Hospitals (RLEUH), Egypt.

Email

ghada.ismail@yahoo.com

City

Cairo

Orcid

0000-0001-5368-0837

First Name

Nashwa

Last Name

Omar

MiddleName

Naguib

Affiliation

Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.

Email

nousha_22@hotmail.com

City

-

Orcid

0000-0002-2607-2518

First Name

Samar

Last Name

Rashad

MiddleName

Saad

Affiliation

Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.

Email

samarsaadrashad@gmail.com

City

Cairo

Orcid

-

First Name

Hossam

Last Name

Abdelghaffar

MiddleName

-

Affiliation

Department of ENT, Faculty of Medicine, Helwan University, Egypt, Supreme Council for University Hospitals, Egypt.

Email

uhd@scu.eg

City

Cairo

Orcid

-

First Name

Marwa

Last Name

Mostafa

MiddleName

Salah

Affiliation

Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt.

Email

marwa75_jan@cu.edu.eg

City

Cairo

Orcid

0000-0002-8906-8938

First Name

Shereen

Last Name

Mohamed

MiddleName

Saeed

Affiliation

Reference Laboratory of the Egyptian University Hospitals (RLEUH), Egypt.

Email

sherinsaeed84@gmail.com

City

Cairo

Orcid

0000-0002-5286-0235

First Name

Ahmed

Last Name

Elshafei

MiddleName

-

Affiliation

Theodor Bilharz Research Institute, Cairo, Egypt.

Email

drshefo@hotmail.com

City

Cairo

Orcid

0000-0001-6140-6379

First Name

Yasmeen

Last Name

Ibraheem

MiddleName

Mohammad Mahmood Ali

Affiliation

Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.

Email

yasmeen.ibraheem@gmail.com

City

-

Orcid

0000-0002-5286-0235

Volume

5

Article Issue

1

Related Issue

45807

Issue Date

2024-02-01

Receive Date

2023-10-14

Publish Date

2024-02-01

Page Start

20

Page End

28

Print ISSN

2682-4132

Online ISSN

2682-4140

Article File

MID_Volume 5_Issue 1_Pages 20-28.pdf

PDF . 892.2kB

Link

https://mid.journals.ekb.eg/article_326268.html

Detail API

https://mid.journals.ekb.eg/service?article_code=326268

Order

4

Type

Original Article

Type Code

1,157

Publication Type

Journal

Publication Title

Microbes and Infectious Diseases

Publication Link

https://mid.journals.ekb.eg/

MainTitle

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

Details

Type

Article

Created At

25 Dec 2024