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

Document Type : Original Article

Authors

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

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

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

4 Clinical 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.

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