SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis

Abstract

COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt.

Identification, propagation and molecular characterization of SARS-CoV-2 delta variant isolated from Egyptian COVID-19 patients

“…Our findings regarding the whole genome sequencing of SARS-CoV-2 recovered in 2020 showed that all strains belong to the 20A clade and were mutated and carried D614G, V5F, Q57H and G823S mutations. In agreement with this finding, several studies conducted to track the distribution of viral clades in Egypt reported the higher prevalence of all clades with D614G mutation in 2020 ( Hamed et al, 2021 ; Alotaibi et al, 2022 ; Zekri et al, 2021 ; Kandeil et al, 2020 ). Two isolates were recovered from COVID-19 patients, in September 2021, (accession codes: EPI_ISL_4748272 and EPI_ISL_4748283) were AY.119.2 and AY.44 Pango Lineage, respectively.…”

“…In 2020, 144 Egyptian SARS-CoV-2 isolates were found to have at least 99% identity to the reference strain Wuhan-Hu-1 and exhibited a distinct mutation pattern (D614G/Q57H/V5F/G823S) ( Seadawy et al, 2022 ). During the second wave of the pandemic, the genomic sequences of SARS-CoV-2 were dramatically changed, resulting in several variants that were assigned as variants of concern (VOC) according to the WHO ( Alotaibi et al, 2022 ).…”

The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021

“…We found that fever, fatigue, and cough were the predominant symptoms, while sore throat, loss of taste, anosmia, and GIT symptoms were reported but with less frequency. These observations are in line with the findings of previous investigations (Doghish et al, 2021;Ibrahim et al, 2021;Alotaibi et al, 2022b;Cascella et al, 2022).…”

“…We observed that males (75.6%) were more susceptible to COVID-19 infection than females (24.4%), with an approximate mean age of 37. This was in accordance with previous research conducted in Egypt during the first and second waves of COVID-19, which reported that those aged 40 to 60 were the most frequently infected ( AboKresha et al, 2021 ; Alotaibi et al, 2022b ). Furthermore, we recorded each patient’s clinical manifestations in order to contribute to the development of a more clear and comprehensive clinical presentation of COVID-19, which is still unclear due to the SARS-CoV-2 high mutational rate.…”

A comparison of COVID-19 between Egypt and the United Kingdom

“…Egypt had an endemic level of about 150-200 cases per day until November 2020, with death around 15-25 per day until December, when locally sourced SARS-CoV-2 mutations exhibited at least 99% identity with the Wuhan strain (12). Following this, the number of cases and deaths increased, with a subsequent biphasic trend.…”