الفهرس 
INTRODUCTIONOnly 14 pages are availabe for public view
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Abstract
19 is a life-threatening respiratory pandemic with significant effects on humankind affecting more than 771 million and killing more than 6 million cases by the end
of 2023. Since its discovery, SARS-CoV-2 has adapted many variants through different
types of viral proteins mutations. Outside S protein mutations that many studies have addressed, mutations in the N protein affect virus virulence, disease severity, and immunityescaping behavior, leading to challenges in diagnosis, management, and vaccine development.
The aim of this study was firstly to investigate mutations, if any, in the N protein of SARS-CoV-2 isolated from Egyptian patients and secondly to compare them with the
reference sequence virus from china and their correlation with disease severity.
This cross-sectional study included 80 hospitalized SARS-CoV-2-positive patients selected over a 4-months period from April to July 2022. Nasopharyngeal swabs and blood samples were collected, and viral Ct, D-dimer, ferritin, LDH, CRP, and TLC levels were tested. In addition, clinical severity data were collected from patient’s records, including; demographic data, risk factors, and clinical symptoms. Out of 80 SARS-CoV-2-positive patients, 40 PCR products were successfully sequenced by one-direction Sanger sequencing method, and mutations were determined through alignment against the Wuhan reference genome (Accession NC-045512.2) using Bioedit software version 7.2.5. All sequences were submitted to the GISAD and NCBI databases. Clades, lineages, and variants were identified
using GISAID Audacity Instant tool and phylogenetic analysis was made using MEGA X
version 11 and iTOL version 5 softwares.
Patients were classified into 3 groups according to clinical severity: 27.5% were mild, 31.25% were moderate, and 41.25% were severe COVID-19 patients. Older age 50 years or more, presence of comorbidities, long duration of hospital stay, and abnormal laboratory results were statistically significant associated with severe infection. Regarding
clinical symptoms, fatigue was the most common symptoms in 71% followed by abdominal pain in 48%. All severe patients were statistically significant associated with all clinical symptoms except abdominal pain.
Among the 40 N protein sequences, 10 pango-lineages, 6 clades, and 3 variants were identified. Omicron was the most common variant (60%) that fell into the GRA clade and harbored five Pango-lineages, and the most frequent lineage was BA.2.12.1 in (35%) of the sequenced samples. In addition, 24 point mutations in the N protein were detected, and the most frequent mutations were R203K/M followed by G204R mutations, with frequencies of 97.5% and 95%, respectively. However, there was no significant difference in clinical
severity between the detected lineages or clades among sequenced cases.