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380328

Identifying SARS-CoV-2 lineage and spike protein mutations: A single center cross-sectional study

Article

Last updated: 04 May 2025

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Subjects

-

Tags

Clinical microbiology

Abstract

Background: Since the onset of SARS-CoV-2 pandemic, it has become a hot spot for research. Aim: This study aimed to detect variations in the spike protein of SARS-CoV-2 isolated from Egyptian patients and correlate them with laboratory data. Methods: Fifty patients with positive nasopharyngeal swabs by PCR were enrolled in this cross-sectional study. Partial spike protein was successfully amplified and sequenced for 23 isolates. This study determined the clade, variant and lineage. Phylogenetic analysis was performed to detect heterogeneity among our isolates. Results: The partial spike protein belonged to 3 clades and 3 Pango lineages. The most common lineage was C.36.3 (56.5%), followed by B.1.1.7 (39%) then B.1.1 (4.5%). D614G mutation was present in 100% of isolates, while the second most frequent mutation was Q677H (60.9%) followed by L452R (52.2%).  B.1.1.7 lineage was associated with higher WBC and lymphocytes compared to other lineages (p= 0.02, p=0.012, respectively). Conclusion: Level of WBC may significantly differ according to the infecting lineage. This finding may impact progression of SARS-CoV-2 infection.

DOI

10.21608/mid.2024.304807.2084

Keywords

COVID-19, D614G mutation, Pango lineage, SARS-CoV-2, Spike protein

Authors

First Name

Ali

Last Name

Gubran

MiddleName

N.M,

Affiliation

Diagnostic and molecular microbiology, Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Science and Technology, Aden, Yemen

Email

a.alyafei@aden.ust.edu

City

-

Orcid

-

First Name

Dalia

Last Name

Metwally

MiddleName

Elsayed

Affiliation

Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt

Email

dr.dalia.ragab@hotmail.com

City

-

Orcid

-

First Name

Ezz Eldein

Last Name

Saleh

MiddleName

Anwar

Affiliation

Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt

Email

saleh5558@yahoo.com

City

-

Orcid

-

First Name

Reham

Last Name

Abo-Elwafa

MiddleName

-

Affiliation

Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt

Email

reham.abdelhalem@alexmed.edu.eg

City

-

Orcid

-

First Name

Rasha

Last Name

Emad

MiddleName

-

Affiliation

Clinical pharmacy, Alexandria Main University Hospital, Alexandria, Egypt

Email

rosharoshaemad@gmail.com

City

-

Orcid

-

First Name

Iman

Last Name

Naga

MiddleName

Salah

Affiliation

Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt

Email

iman.naga@alexu.edu.eg

City

-

Orcid

-

Volume

6

Article Issue

2

Related Issue

55370

Issue Date

2025-05-01

Receive Date

2024-07-16

Publish Date

2025-05-01

Page Start

414

Page End

428

Print ISSN

2682-4132

Online ISSN

2682-4140

Article File

MID_Volume 6_Issue 2_Pages 414-428.pdf

PDF . 1.1MB

Link

https://mid.journals.ekb.eg/article_380328.html

Detail API

http://journals.ekb.eg?_action=service&article_code=380328

Order

1

Type

Original Article

Type Code

1,157

Publication Type

Journal

Publication Title

Microbes and Infectious Diseases

Publication Link

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

MainTitle

Identifying SARS-CoV-2 lineage and spike protein mutations: A single center cross-sectional study

Details

Type

Article

Created At

04 May 2025