Identifying SARS-CoV-2 lineage and spike protein mutations: A single center cross-sectional study | ||
| Microbes and Infectious Diseases | ||
| Articles in Press, Accepted Manuscript, Available Online from 17 September 2024 | ||
| Document Type: Original Article | ||
| DOI: 10.21608/mid.2024.304807.2084 | ||
| Authors | ||
| Ali N.M, Gubran1; Dalia Elsayed Metwally2; Ezz Eldein Anwar Saleh2; Reham Abo-Elwafa3; Rasha Emad4; Iman Salah Naga* 2 | ||
| 1Diagnostic and molecular microbiology, Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Science and Technology, Aden, Yemen | ||
| 2Department of Microbiology, Medical Research Institute, University of Alexandria, Alexandria, Egypt | ||
| 3Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt | ||
| 4Clinical pharmacy, Alexandria Main University Hospital, Alexandria, Egypt | ||
| 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. | ||
| Keywords | ||
| COVID-19; D614G mutation; Pango lineage; SARS-CoV-2; Spike protein | ||
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