Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Egypt

Kandeil, Ahmed; Mostafa, Ahmed; El-Shesheny, Rabeh; Shehata, Mahmoud; Roshdy, Wael H.; Showky, Shymaa; Gomaa, Mokhtar R.; Taweel, Ahmed El; Kayed, Ahmed S.; Mahmoud, Sara H.; Moatasim, Yassmin; Kutkat, Omnia; Kamel, Mina Nabil; Mahrous, Noura; Sayes, Mohamed El; Guindy, Nancy M. El; Naguib, Amal; Ali, Mohammed Farid

doi:10.1128/mra.00489-20

Cited by 54 publications

(46 citation statements)

References 3 publications

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“…Still, the results of the present work offer interesting insights into how the virus got into Morocco and primary lessons as to understanding the dynamics of the initial introductions and local transmission of SARS-CoV-2 in Morocco. This being a global pandemic, the conclusions of this study, taken together with those of recent similar studies such as those done in Egypt 16 , South Africa 17 and Brazil 12 , might be applicable to other developing countries. The results of the methodology of genomic surveillance that we developed, and the methodology itself would be helpful in the case of resurgence or the emergence of any new pandemic-causing pathogen.…”

Section: Discussionsupporting

confidence: 67%

Genomic evidence of multiple SARS-CoV-2 introductions into Morocco

et al. 2020

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Background: The recent emergence of a novel coronavirus (SARS-CoV-2) has caused serious public health concerns due to its rapid dissemination worldwide. A total of 8,931 positive cases had been reported in Morocco by the 16th of June 2020. Methods: To better understand the SARS-CoV-2 pandemic in this North African country, we analyzed the complete genome sequences of the virus related to Morocco by constructing a phylogenetic tree and creating a variant network using the available Moroccan and other sequences in dedicated databases. Results: Phylogenetic and variant network analyses of SARS-CoV-2 strains from early patients with COVID-19 in Morocco showed multiple spatiotemporal introductions from Italy (ten), France (seven), Spain (one) and Portugal (one). This is consistent with the assumption that the early infections in Morocco were imported, mainly from Europe. The 17 virus strains form two independent phylogenetic clusters and provide evidence for early community-based transmission following the initial introductions of the virus. We then catalogued 13 novel mutations in the SARS-CoV-2 isolates from Moroccan patients. Interestingly, the recurrent missense variant A>G at position 23,403 in the spike gene, known to be associated with virus severity, has been identified in all Moroccan isolates. Conclusions: These primary findings testify of the importance of the genomic surveillance strategies as a means of understanding the virus spread dynamics, counteracting the pandemic outbreak, and drawing useful lessons for dealing with any future emerging infectious pathogens.

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Section: Discussionsupporting

confidence: 67%

Genomic evidence of multiple SARS-CoV-2 introductions into Morocco

et al. 2020

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“…It is noteworthy mentioning that there are a few reports from UAE (49 isolates), Egypt (2 isolates), and Iran (7 isolates). However, in addition to the small number of samples used, these studies are based on the phylogenetic analysis only and no association with epidemiological surveillance was performed ( Tabibzadeh et al, 2020 , Tayoun et al, 2020 , Kandeil et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country

Al-Mahruqi

Wahaibi

Khan

et al. 2021

International Journal of Infectious Diseases

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Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. Methods: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The wholegenome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. Findings: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Interpretation: Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.

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“…Indeed, the increasing diversification of SARS-CoV-2 strains has already been underlined—the complete genome sequencing of SARS-CoV-2 strains isolated in Asia, Europe, North, and South America identified 3 different genetic clades [ 35 ]. In Indian and Egyptian genetic studies, several mutations were recorded but the isolated SARS-CoV-2 strains were at least 99.7% identical to 2019-nCoV-WHU01 strain [ 36 , 37 ]. Thus, the real implication in the pathogenicity remains to be confirmed.…”

Section: Discussionmentioning

confidence: 99%

Characteristics, onset, and evolution of neurological symptoms in patients with COVID-19

et al. 2020

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Background A wide range of neurological manifestations has been described in COVID-19. Methods In this nationwide retrospective observational study, patients in Tunisia diagnosed with COVID-19 between the 2nd of March and the 16th of May 2020 were contacted by telephone. We collected demographic and clinical data and specified characteristics and evolution of main neurological symptoms. Results Of 1034 confirmed COVID-19 patients, 646 were included (mean age 42.17 years old) and 466 (72.1%) had neurological symptoms. Neurological symptoms were isolated 22.7% ( n = 106). Headache was the most frequent neurological symptom ( n = 279, 41.1%): mainly frontotemporal ( n = 143, 51.1%) and mild or moderate ( n = 165, 59.1%). When associated with fever ( n = 143, 51.3%), headache was more likely to be severe and present at onset. Recovery was reported in 83.2%. Smell and taste impairment were found in 37.9% ( n = 245) and 36.8% ( n = 238) respectively. Among them, 65.3% (156/239) were anosmic and 63.2% (146/231) were ageusic. A complete improvement was found in 72.1% (174/240) of smell impairment and in 76.8% (179/233) of taste impairment. Myalgia ( n = 241, 37.3%) and sleep disturbances ( n = 241, 37.3%) were also frequent. Imported cases had more neurological symptoms ( p = 0.001). In 14.5%, neurological symptoms preceded the respiratory signs (RS). RS were associated with more frequent ( p = 0.006) and numerous ( p < 0.001) neurological symptoms. Conclusions Neurological symptoms in COVID-19 are frequent, can be isolated and present at onset. A total recovery is the most recorded outcome. RS are predictive of neurological symptoms. Studies in to virus and host genetics should be considered to understand the different phenotypes.

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Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Egypt

Cited by 54 publications

References 3 publications

Genomic evidence of multiple SARS-CoV-2 introductions into Morocco

Genomic evidence of multiple SARS-CoV-2 introductions into Morocco

Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country

Characteristics, onset, and evolution of neurological symptoms in patients with COVID-19

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