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Mr. Mahmoud Bayoumi
Lancaster University, Lancaster, UK

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0 Genetics
0 Molecular Biology
0 Viral evolution
0 epigenetic regulation
0 viral diseases

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Original article
Published: 04 March 2021 in Comparative Clinical Pathology
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The aim of this study was to explore the diagnostic value of matrix metalloproteinase (MMP)-2 and -9, and cyclooxygenase-2 (COX-2) enzymes in the synovial fluid of horses with different forms of arthritis. Thirty-two horses were involved in this study and based on the clinical, radiographic, and synovial fluid examinations, the horses were divided into three groups: control (group I; n = 12), septic arthritis (group II; n = 5), and aseptic arthritis (group III; n = 15). After routine analysis, synovial fluid was used for assessment of MMP-2 and MMP–9 activities by gelatin zymography, and COX-2 relative gene expression by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Synovial fluid gelatin zymography showed significant gelatinolytic activity for MMP-9 in group II. COX-2 exhibited a 50-fold expression in group II and a 4.5-fold expression in group III compared to group I. In conclusion, the results confirm that MMP-9 and COX-2 detection offers an important diagnostic potential for septic and aseptic arthritis in horses.

ACS Style

Salma W. Abdelhaleem; Mostafa M. Bashandy; Shaymaa I. Salem; Faisal A. Torad; Huda O. AbuBakr; Mahmoud M. Bayoumi. Synovial fluid analysis of MMP-2, MMP-9, and COX-2 as diagnostic markers for naturally occurring septic and aseptic arthritis in horses. Comparative Clinical Pathology 2021, 1 -7.

AMA Style

Salma W. Abdelhaleem, Mostafa M. Bashandy, Shaymaa I. Salem, Faisal A. Torad, Huda O. AbuBakr, Mahmoud M. Bayoumi. Synovial fluid analysis of MMP-2, MMP-9, and COX-2 as diagnostic markers for naturally occurring septic and aseptic arthritis in horses. Comparative Clinical Pathology. 2021; ():1-7.

Chicago/Turabian Style

Salma W. Abdelhaleem; Mostafa M. Bashandy; Shaymaa I. Salem; Faisal A. Torad; Huda O. AbuBakr; Mahmoud M. Bayoumi. 2021. "Synovial fluid analysis of MMP-2, MMP-9, and COX-2 as diagnostic markers for naturally occurring septic and aseptic arthritis in horses." Comparative Clinical Pathology , no. : 1-7.

Journal article
Published: 01 September 2020 in Viruses
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Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.

ACS Style

Mohammed Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar Khalifa; Mohammad Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Jayde Whittingham-Dowd; Elisabeth Shaw; Matt Hodges; Lisa Butler; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2. Viruses 2020, 12, 972 .

AMA Style

Mohammed Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar Khalifa, Mohammad Al-Natour, Mahmoud Bayoumi, Aurore Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman Chaudhry, Ravinder Sodi, Amy Brown, Peter Burkhart, Wendy Hacking, Judy Botham, Joe Boyce, Hayley Wilkinson, Craig Williams, Jayde Whittingham-Dowd, Elisabeth Shaw, Matt Hodges, Lisa Butler, Michelle Bates, Roberto La Ragione, Wamadeva Balachandran, Anil Fernando, Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2. Viruses. 2020; 12 (9):972.

Chicago/Turabian Style

Mohammed Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar Khalifa; Mohammad Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Jayde Whittingham-Dowd; Elisabeth Shaw; Matt Hodges; Lisa Butler; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. 2020. "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2." Viruses 12, no. 9: 972.

Original research article
Published: 15 July 2020 in Frontiers in Cell and Developmental Biology
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The addition of a methyl group to the N6 position of adenosine (m6A) is the most common posttranscriptional RNA modification, and it regulates most steps of RNA metabolism including splicing, stability, translation, nuclear-export, and RNA structures. Besides cellular RNA, m6A modifications have also been detected on viral RNA. A range of recent studies have demonstrated the crucial roles of m6A in the virus–host interactions; however, m6A cellular machineries are only characterized in limited mammalian species. Herein, we aim to present comprehensive evolutionary insights into major m6A writers, erasers, and readers and draw a comparative structural analysis between avian and mammalian m6A-associated machineries. The comparative collinearity on the chromosomal scale revealed that the majority of m6A-related genes were found less syntenic even among avian species. Genetic analysis of avian m6A erasers revealed a distinct phylogenetic clustering compared to mammalian orthologs and shared a weak percent (55%) identity with mammalian species with low identity percentage (55%). The overall comparative three-dimensional (3D) structure analyses among different mammalian species were maintained through synonymous structural mutations. Unlike erasers, the putative 3D structures in the active sites as for the aromatic cage in YTH-domain of YTHDC1 and two pivotal loops in MTD-domains in METTL3 exhibited structural alterations in chicken. In conjunction with in silico investigations, influenza viruses significantly downregulated gene the transcription of m6A writers and erasers, whereas m6A readers were moderately regulated in chicken fibroblasts. In light of these findings, future detailed biochemical and crystallographic studies are warranted to define the roles of m6A machinery in regulating both viral and cellular RNA metabolism in avian species.

ACS Style

Mahmoud Bayoumi; Mohammed Abdelmohsen Shahaat Rohaim; Muhammad Munir. Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery. Frontiers in Cell and Developmental Biology 2020, 8, 543 .

AMA Style

Mahmoud Bayoumi, Mohammed Abdelmohsen Shahaat Rohaim, Muhammad Munir. Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery. Frontiers in Cell and Developmental Biology. 2020; 8 ():543.

Chicago/Turabian Style

Mahmoud Bayoumi; Mohammed Abdelmohsen Shahaat Rohaim; Muhammad Munir. 2020. "Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery." Frontiers in Cell and Developmental Biology 8, no. : 543.

Other
Published: 10 July 2020
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Until vaccines and effective therapeutics become available, the practical way to transit safely out of the current lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms, and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ∼200 coronavirus disease (CoVID-19)-suspected patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. The system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.

ACS Style

Mohammed A Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar E Khalifa; Mohammed Q Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman S Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2. 2020, 1 .

AMA Style

Mohammed A Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar E Khalifa, Mohammed Q Al-Natour, Mahmoud Bayoumi, Aurore Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman S Chaudhry, Ravinder Sodi, Amy Brown, Peter Burkhart, Wendy Hacking, Judy Botham, Joe Boyce, Hayley Wilkinson, Craig Williams, Michelle Bates, Roberto La Ragione, Wamadeva Balachandran, Anil Fernando, Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2. . 2020; ():1.

Chicago/Turabian Style

Mohammed A Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar E Khalifa; Mohammed Q Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman S Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. 2020. "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2." , no. : 1.

Erratum
Published: 24 June 2020 in Molecular and Cellular Probes
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ACS Style

Basem M. Ahmed; Haitham M. Amer; Jonas Kissenkoetter; Ahmed Abd El Wahed; Mahmoud Bayoumi; SusanE Böhlken-Fascher; Mahmoud A. Elgamal; Nahed Yehia; Ausama A. Yousif; Mohamed A. Shalaby. Corrigendum to “Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay”. [Mol. Cell. Probes 50 (2020) 101511]. Molecular and Cellular Probes 2020, 53, 101616 .

AMA Style

Basem M. Ahmed, Haitham M. Amer, Jonas Kissenkoetter, Ahmed Abd El Wahed, Mahmoud Bayoumi, SusanE Böhlken-Fascher, Mahmoud A. Elgamal, Nahed Yehia, Ausama A. Yousif, Mohamed A. Shalaby. Corrigendum to “Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay”. [Mol. Cell. Probes 50 (2020) 101511]. Molecular and Cellular Probes. 2020; 53 ():101616.

Chicago/Turabian Style

Basem M. Ahmed; Haitham M. Amer; Jonas Kissenkoetter; Ahmed Abd El Wahed; Mahmoud Bayoumi; SusanE Böhlken-Fascher; Mahmoud A. Elgamal; Nahed Yehia; Ausama A. Yousif; Mohamed A. Shalaby. 2020. "Corrigendum to “Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay”. [Mol. Cell. Probes 50 (2020) 101511]." Molecular and Cellular Probes 53, no. : 101616.

Journal article
Published: 15 January 2020 in Molecular and Cellular Probes
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Highly pathogenic avian influenza H5N1 virus causes heavy losses in poultry farms worldwide. Molecular diagnostic techniques like RT-PCR and real-time RT-PCR are considered the gold standard for identification of H5 influenza viruses in clinical samples. These techniques are hampered by the need of well-equipped laboratories, large space requirement, and relatively long time-to-result. Recombinase polymerase amplification (RPA) assay represents an excellent alternative to PCR since it is more simple, rapid, economic, and portable. Reverse transcription RPA (RT-RPA) assay was recently developed for sensitive and specific detection of H5N1 virus in 6–10 min. To ensure the accuracy of the developed assay, two approaches for using a positive control were evaluated in this study. These approaches included: 1) all-in-one (internal positive control; IPC), 2) two-tubes-per-one-sample (external positive control; EPC). Sigma virus (SIGV) RNA and turkey mitochondrial DNA were tested as positive controls in both approaches. For all-in-one approach, both targets (H5 and IPC) were strongly inhibited. In contrast, very good amplification signals were obtained for the two types of EPC with no effect on the analytical sensitivity and specificity of H5 RT-RPA assay in two-tubes-per-one-sample approach. The performance of EPC-based H5 RT-RPA was further validated using 13 tracheal swabs. The results were compared to real-time RT-PCR and proved superior specificity in detecting H5N1 but not H5N8 viruses. Inclusion of EPC did not affect the aptitude of both assays in terms of sensitivity, specificity and reproducibility. In conclusion, the two-tubes-per-one-sample approach was more reliable to control the false negative results in H5 RT-RPA assay.

ACS Style

Basem M. Ahmed; Haitham A. Amer; Jonas Kissenkoetter; Ahmed Abd El Wahed; Mahmoud M. Bayoumi; SusanE. Böhlken-Fascher; Mahmoud A. Elgamal; Nahed Yehia; Ausama Yousif; Mohamed A. Shalaby. Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay. Molecular and Cellular Probes 2020, 50, 101511 .

AMA Style

Basem M. Ahmed, Haitham A. Amer, Jonas Kissenkoetter, Ahmed Abd El Wahed, Mahmoud M. Bayoumi, SusanE. Böhlken-Fascher, Mahmoud A. Elgamal, Nahed Yehia, Ausama Yousif, Mohamed A. Shalaby. Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay. Molecular and Cellular Probes. 2020; 50 ():101511.

Chicago/Turabian Style

Basem M. Ahmed; Haitham A. Amer; Jonas Kissenkoetter; Ahmed Abd El Wahed; Mahmoud M. Bayoumi; SusanE. Böhlken-Fascher; Mahmoud A. Elgamal; Nahed Yehia; Ausama Yousif; Mohamed A. Shalaby. 2020. "Evaluating two approaches for using positive control in standardizing the avian influenza H5 reverse transcription recombinase polymerase amplification assay." Molecular and Cellular Probes 50, no. : 101511.

Original article
Published: 14 January 2020 in Archives of Virology
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Infectious laryngotracheitis (ILT) is a respiratory disease that causes significant economic losses in the poultry industry worldwide. In this study, ILT outbreaks were reported on 30 farms located in eight Egyptian governorates between January 2018 and May 2019. Gross examination of diseased chickens revealed congestion and hemorrhage of laryngeal and tracheal mucosa with fibrinohemorrhagic casts and/or caseous material in the lumens. Histopathological examination showed epithelial sloughing, syncytium formation, heterophilic exudation, and development of eosinophilic intranuclear inclusion bodies. Infectious laryngotracheitis virus (ILTV) antigen was detected in the tracheal epithelium, infiltrated inflammatory cells, and syncytial cells, using immunohistochemistry. PCR targeting a portion of the thymidine kinase gene was further utilized to confirm the presence of ILTV DNA. The complete coding sequences of three envelope glycoprotein genes, gG, gD, and gJ, and a partial sequence of the infected cell polypeptide 4 (ICP4) gene from samples representing all of the farms and disease outbreaks were determined. Five prototype strains with unique sequences were chosen for detailed molecular characterization. Sequence comparisons and phylogenetic analysis of the partial ICP4 gene revealed that two strains were chicken embryo origin (CEO)-vaccine-like strains, and three were tissue culture origin (TCO)-vaccine-like strains. Analysis of the gJ gene sequence indicated that all of the strains were CEO vaccine-like strains. It was predicted that the latter three strains were recombinants of CEO- and TCO-vaccine-like strains. In conclusion, immunohistochemistry coupled with multi-genomic PCR sequencing proved to be efficient for identification and typing of ILTV strains during disease outbreaks. Both CEO-vaccine-like and recombinant virus strains were circulating in Egypt during the 2018 and 2019 outbreaks.

ACS Style

Mahmoud Bayoumi; Mohamed El-Saied; Haitham Amer; Mostafa Bastami; Ezz Eldein Sakr; Magdy El-Mahdy. Molecular characterization and genetic diversity of the infectious laryngotracheitis virus strains circulating in Egypt during the outbreaks of 2018 and 2019. Archives of Virology 2020, 165, 661 -670.

AMA Style

Mahmoud Bayoumi, Mohamed El-Saied, Haitham Amer, Mostafa Bastami, Ezz Eldein Sakr, Magdy El-Mahdy. Molecular characterization and genetic diversity of the infectious laryngotracheitis virus strains circulating in Egypt during the outbreaks of 2018 and 2019. Archives of Virology. 2020; 165 (3):661-670.

Chicago/Turabian Style

Mahmoud Bayoumi; Mohamed El-Saied; Haitham Amer; Mostafa Bastami; Ezz Eldein Sakr; Magdy El-Mahdy. 2020. "Molecular characterization and genetic diversity of the infectious laryngotracheitis virus strains circulating in Egypt during the outbreaks of 2018 and 2019." Archives of Virology 165, no. 3: 661-670.

Journal article
Published: 14 January 2019 in Viruses
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Avian coronaviruses (ACoVs) are continuously evolving and causing serious economic consequences in the poultry industry and around the globe. Owing to their extensive genetic diversity and high mutation rates, controlling ACoVs has become a challenge. In this context, the potential contribution of wild birds in the disease dynamics, especially in domesticated birds, remains largely unknown. In the present study, five hundred fifty-seven (n = 557) cloacal/fecal swabs were collected from four different wild bird species from eight Egyptian governorates during 2016 and a total of fourteen positive isolates were used for phylodynamics and evolutionary analysis. Genetic relatedness based on spike (S1) gene demonstrated the clustering of majority of these isolates where nine isolates grouped within Egy/variant 2 (IS/885 genotype) and five isolates clustered within Egy/variant 1 (IS/1494/06 genotype). Interestingly, these isolates showed noticeable genetic diversity and were clustered distal to the previously characterized Egy/variant 1 and Egy/variant 2 in Egyptian commercial poultry. The S1 gene based comparison of nucleotide identity percentages revealed that all fourteen isolates reported in this study were genetically related to the variant GI-23 lineage with 92–100% identity. Taken together, our results demonstrate that ACoVs are circulating in Egyptian wild birds and highlight their possible contributions in the disease dynamics. The study also proposes that regular monitoring of the ACoVs in wild birds is required to effectively assess the role of wild birds in disease spread, and the emergence of ACoVs strains in the country.

ACS Style

Mohammed A. Rohaim; Rania F. El Naggar; Ahmed M. Helal; Mahmoud Bayoumi; Mohamed A. El-Saied; Kawkab A. Ahmed; Muhammad Z. Shabbir; Muhammad Munir. Genetic Diversity and Phylodynamics of Avian Coronaviruses in Egyptian Wild Birds. Viruses 2019, 11, 57 .

AMA Style

Mohammed A. Rohaim, Rania F. El Naggar, Ahmed M. Helal, Mahmoud Bayoumi, Mohamed A. El-Saied, Kawkab A. Ahmed, Muhammad Z. Shabbir, Muhammad Munir. Genetic Diversity and Phylodynamics of Avian Coronaviruses in Egyptian Wild Birds. Viruses. 2019; 11 (1):57.

Chicago/Turabian Style

Mohammed A. Rohaim; Rania F. El Naggar; Ahmed M. Helal; Mahmoud Bayoumi; Mohamed A. El-Saied; Kawkab A. Ahmed; Muhammad Z. Shabbir; Muhammad Munir. 2019. "Genetic Diversity and Phylodynamics of Avian Coronaviruses in Egyptian Wild Birds." Viruses 11, no. 1: 57.