Genomic characterization of SARS-CoV-2 in Egypt

Zekri, Abdel Rahman N.; Amer, Khaled; Hafez, Mohammed M.; Hassan, Zeinab K.; Ahmed, Ola; Soliman, Hany; Bahnasy, Abeer; Hamid, Wael Abdel; Gad, Ahmad; Ali, Mahmoud Mohammed Ahmed; Hassan, Waël; Madboly, Mahmoud Samir; Raouf, Ahmad A.; Khattab, Ayman A.; Hamdy, Mona S; Soliman, May Sherif; Sissy, Maha Hamdi El; Khateeb, Sara M. El; Ezzelarab, Moushira Hosny; Fathalla, Lamiaa A.; Abouelhoda, Mohamed

doi:10.1016/j.jare.2020.11.012

Cited by 15 publications

(13 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, the spike proteins (SP) of all Egyptian tested strains (n = 144) are completely identical in that they have a G to D substitution at site 614 compared with the reference strain (NC_045512). All clades with D614G mutation are characterized by higher transmission, however, clades GH and GR showed higher virulence and significantly showed higher incidence among death or severe cases [ 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 ].…”

Section: Discussionmentioning

confidence: 99%

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

Alotaibi

El‐Masry

Seadawy

et al. 2022

Heliyon

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

Alotaibi

El‐Masry

Seadawy

et al. 2022

Heliyon

View full text Add to dashboard Cite

show abstract

“…In addition, they found that Asp 614 Gly was the most frequent mutation appearing in all their samples. Interestingly Asp 614 Gly also appeared in 83% of our samples ( Zekri et al, 2021 ).…”

Section: Discussionmentioning

confidence: 59%

Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study

Agwa

Elghazaly

Meteini

et al. 2022

Front. Mol. Biosci.

View full text Add to dashboard Cite

The SARS-CoV-2 pandemic has led to over 4.9 million deaths as of October 2021. One of the main challenges of creating vaccines, treatment, or diagnostic tools for the virus is its mutations and emerging variants. A couple of variants were declared as more virulent and infectious than others. Some approaches were used as nomenclature for SARS-CoV-2 variants and lineages. One of the most used is the Pangolin nomenclature. In our study, we enrolled 35 confirmed SARS-CoV-2 patients and sequenced the viral RNA in their samples. We also aimed to highlight the hallmark mutations in the most frequent lineage. We identified a seven-mutation signature for the SARS-CoV-2 C36 lineage, detected in 56 countries and an emerging lineage in Egypt. In addition, we identified one mutation which was highly negatively correlated with the lineage. On the other hand, we found no significant correlation between our clinical outcomes and the C36 lineage. In conclusion, the C36 lineage is an emerging SARS-CoV-2 variant that needs more investigation regarding its clinical outcomes compared to other strains. Our study paves the way for easier diagnosis of variants of concern using mutation signatures.

show abstract

“…Other obstacles could have been global supply chain issues for reagents and consumables. In contrast, several developing countries exhibited wills as well as capacities to sequence SARS-CoV-2 genomes and scaled up next-sequencing technologies [30][31][32]. This is another example that the SARS-CoV-2 pandemic is reshuffling the cards globally.…”

Section: Discussionmentioning

confidence: 99%

Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales

Colson

Raoult

2021

Viruses

View full text Add to dashboard Cite

It has now been over a year since SARS-CoV-2 first emerged in China, in December 2019, and it has spread rapidly around the world. Some variants are currently considered of great concern. We aimed to analyze the numbers of SARS-CoV-2 genome sequences obtained in different countries worldwide until January 2021. On 28 January 2021, we downloaded the deposited genome sequence origin from the GISAID database, and from the “Our world in data” website we downloaded numbers of SARS-CoV-2-diagnosed cases, numbers of SARS-CoV-2-associated deaths, population size, life expectancy, gross domestic product (GDP) per capita, and human development index per country. Files were merged and data were analyzed using Microsoft Excel software. A total of 450,968 SARS-CoV-2 genomes originating from 135 countries on the 5 continents were available. When considering the 19 countries for which the number of genomes per 100 deaths was >100, six were in Europe, while eight were in Asia, three were in Oceania and two were in Africa. Six (30%) of these countries are beyond rank 75, regarding the human development index and four (20%) are beyond rank 80 regarding GDP per capita. Moreover, the comparisons of the number of genomes sequenced per 100 deaths to the human development index by country show that some Western European countries have released similar or lower numbers of genomes than many African or Asian countries with a lower human development index. Previous data highlight great discrepancies between the numbers of available SARS-CoV-2 genomes per 100 cases and deaths and the ranking of countries regarding wealth and development.

show abstract

Genomic characterization of SARS-CoV-2 in Egypt

Cited by 15 publications

References 35 publications

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

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

Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study

Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales

Contact Info

Product

Resources

About