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Dr. Mohammed Rohaim
Post Doctoral Researcher

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0 Genetics
0 Innate Immunity
0 Molecular Virology
0 Virology
0 Diagnostic

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Short Biography

Mohammed A. Rohaim received a PhD degree in Virology and innate Immunity jointly from the Department of Virology, Cairo University, Egypt; The Pirbright Institute, Surrey, UK, and The Lancaster University, Lancaster, the UK in 2018. He is currently a Postdoc Researcher at Lancaster University, UK. His research interests are to understand viral and cellular factors that regulate the pathobiology of emerging viruses and defining the functional role of evolutionary changes on virus anti-genicity, virulence, improving vaccines, and developing assays for rapid detection and differentiation of viruses of veterinary and medical importance.

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Journal article
Published: 26 August 2021 in Electronics
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An artificial intelligence-assisted low-cost portable device for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presented here. This standalone temperature-controlled device houses tubes designed for conducting reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays. Moreover, the device utilises tubes illuminated by LEDs, an in-built camera, and a small onboard computer with automated image acquisition and processing algorithms. This intelligent device significantly reduces the normal assay run time and removes the subjectivity associated with operator interpretation of colourimetric RT-LAMP results. To further improve this device’s usability, a mobile app has been integrated into the system to control the LAMP assay environment and to visually display the assay results by connecting the device to a smartphone via Bluetooth. This study was undertaken using ~5000 images produced from the ~200 LAMP amplification assays using the prototype device. Synthetic RNA and a small panel of positive and negative SARS-CoV-2 patient samples were assayed for this study. State-of-the-art image processing and artificial intelligence algorithms were applied to these images to analyse them and to select the most efficient algorithm. The template matching algorithm for image extraction and MobileNet CNN architecture for classification results provided 98.0% accuracy with an average run time of 20 min to confirm the endpoint result. Two working points were chosen based on the best compromise between sensitivity and specificity. The high sensitivity point has a sensitivity value of 99.12% and specificity value of 70.8%, while at the high specificity point, the sensitivity is 96.05% and specificity 93.59%. Furthermore, this device provides an efficient and cost-effective platform for non-health professionals to detect not only SARS-CoV-2 but also other pathogens in resource-limited laboratories, factories, airports, schools, universities, and homes.

ACS Style

Mukunthan Tharmakulasingam; Nouman S. Chaudhry; Anil Fernando; Manoharanehru Branavan; Wamadeva Balachandran; Aurore C. Poirier; Mohammed A. Rohaim; Muhammad Munir; Roberto M. La Ragione. An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2. Electronics 2021, 10, 2065 .

AMA Style

Mukunthan Tharmakulasingam, Nouman S. Chaudhry, Anil Fernando, Manoharanehru Branavan, Wamadeva Balachandran, Aurore C. Poirier, Mohammed A. Rohaim, Muhammad Munir, Roberto M. La Ragione. An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2. Electronics. 2021; 10 (17):2065.

Chicago/Turabian Style

Mukunthan Tharmakulasingam; Nouman S. Chaudhry; Anil Fernando; Manoharanehru Branavan; Wamadeva Balachandran; Aurore C. Poirier; Mohammed A. Rohaim; Muhammad Munir; Roberto M. La Ragione. 2021. "An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2." Electronics 10, no. 17: 2065.

Journal article
Published: 06 August 2021 in International Journal of Molecular Sciences
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Mammalian cells utilize a wide spectrum of pathways to antagonize the viral replication. These pathways are typically regulated by antiviral proteins and can be constitutively expressed but also exacerbated by interferon induction. A myriad of interferon-stimulated genes (ISGs) have been identified in mounting broad-spectrum antiviral responses. Members of the interferon-induced transmembrane (IFITM) family of proteins are unique among these ISGs due to their ability to prevent virus entry through the lipid bilayer into the cell. In the current study, we generated transgenic chickens that constitutively and stably expressed chicken IFITM1 (chIFITM1) using the avian sarcoma-leukosis virus (RCAS)-based gene transfer system. The challenged transgenic chicks with clinical dose 104 egg infective dose 50 (EID50) of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 (clade 2.2.1.2) showed 100% protection and significant infection tolerance. Although challenged transgenic chicks displayed 60% protection against challenge with the sub-lethal dose (EID50 105), the transgenic chicks showed delayed clinical symptoms, reduced virus shedding, and reduced histopathologic alterations compared to non-transgenic challenged control chickens. These finding indicate that the sterile defense against H5N1 HPAIV offered by the stable expression of chIFITM1 is inadequate; however, the clinical outcome can be substantially ameliorated. In conclusion, chIFITM proteins can inhibit influenza virus replication that can infect various host species and could be a crucial barrier against zoonotic infections.

ACS Style

Mohammed Rohaim; Mohammad Al-Natour; Mohammed Abdelsabour; Rania El Naggar; Yahia Madbouly; Kawkab Ahmed; Muhammad Munir. Transgenic Chicks Expressing Interferon-Inducible Transmembrane Protein 1 (IFITM1) Restrict Highly Pathogenic H5N1 Influenza Viruses. International Journal of Molecular Sciences 2021, 22, 8456 .

AMA Style

Mohammed Rohaim, Mohammad Al-Natour, Mohammed Abdelsabour, Rania El Naggar, Yahia Madbouly, Kawkab Ahmed, Muhammad Munir. Transgenic Chicks Expressing Interferon-Inducible Transmembrane Protein 1 (IFITM1) Restrict Highly Pathogenic H5N1 Influenza Viruses. International Journal of Molecular Sciences. 2021; 22 (16):8456.

Chicago/Turabian Style

Mohammed Rohaim; Mohammad Al-Natour; Mohammed Abdelsabour; Rania El Naggar; Yahia Madbouly; Kawkab Ahmed; Muhammad Munir. 2021. "Transgenic Chicks Expressing Interferon-Inducible Transmembrane Protein 1 (IFITM1) Restrict Highly Pathogenic H5N1 Influenza Viruses." International Journal of Molecular Sciences 22, no. 16: 8456.

Journal article
Published: 01 August 2021 in iScience
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Global deployment of an effective and safe vaccine is necessary to curtail the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we evaluated a Newcastle disease virus (NDV)-based vectored-vaccine in mice and hamsters for its immunogenicity, safety and protective efficacy against SARS-CoV-2. Intranasal administration of recombinant (r)NDV-S vaccine expressing spike (S) protein of SARS-CoV-2 to mice induced high levels of SARS-CoV-2-specific neutralizing immunoglobulin A (IgA) and IgG2a antibodies and T cell-mediated immunity. Hamsters immunised with two doses of vaccine showed complete protection from lung infection, inflammation, and pathological lesions following SARS-CoV-2 challenge. Importantly, administration of two doses of intranasal rNDV-S vaccine significantly reduced the SARS-CoV-2 shedding in nasal turbinate and lungs in hamsters. Collectively, intranasal vaccination has the potential to control infection at the site of inoculation, which should prevent both clinical disease and virus transmission to halt the spread of the COVID-19 pandemic.

ACS Style

Jun-Guy Park; Fatai S. Oladunni; Mohammed A. Rohaim; Jayde Whittingham-Dowd; James Tollitt; Matthew D.J. Hodges; Nadin Fathallah; Muhsref Bakri Assas; Wafaa Alhazmi; Abdullah Almilaibary; Munir Iqbal; Pengxiang Chang; Renee Escalona; Vinay Shivanna; Jordi B. Torrelles; John J. Worthington; Lucy H. Jackson-Jones; Luis Martinez-Sobrido; Muhammad Munir. Immunogenicity and Protective Efficacy of an Intranasal Live-attenuated Vaccine Against SARS-CoV-2. iScience 2021, 1 .

AMA Style

Jun-Guy Park, Fatai S. Oladunni, Mohammed A. Rohaim, Jayde Whittingham-Dowd, James Tollitt, Matthew D.J. Hodges, Nadin Fathallah, Muhsref Bakri Assas, Wafaa Alhazmi, Abdullah Almilaibary, Munir Iqbal, Pengxiang Chang, Renee Escalona, Vinay Shivanna, Jordi B. Torrelles, John J. Worthington, Lucy H. Jackson-Jones, Luis Martinez-Sobrido, Muhammad Munir. Immunogenicity and Protective Efficacy of an Intranasal Live-attenuated Vaccine Against SARS-CoV-2. iScience. 2021; ():1.

Chicago/Turabian Style

Jun-Guy Park; Fatai S. Oladunni; Mohammed A. Rohaim; Jayde Whittingham-Dowd; James Tollitt; Matthew D.J. Hodges; Nadin Fathallah; Muhsref Bakri Assas; Wafaa Alhazmi; Abdullah Almilaibary; Munir Iqbal; Pengxiang Chang; Renee Escalona; Vinay Shivanna; Jordi B. Torrelles; John J. Worthington; Lucy H. Jackson-Jones; Luis Martinez-Sobrido; Muhammad Munir. 2021. "Immunogenicity and Protective Efficacy of an Intranasal Live-attenuated Vaccine Against SARS-CoV-2." iScience , no. : 1.

Original article
Published: 05 February 2021 in Transboundary and Emerging Diseases
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Duckling short beak and dwarfism syndrome virus (SBDSV), an emerging goose parvovirus, has caused short beak and dwarfism syndrome (SBDS) in Chinese duck flocks since 2015. Presently, there is no commercial vaccine against SBDS. In the present study, a virus‐like particle (VLP)‐based candidate vaccine was developed against this disease. A baculovirus expression system was used to express the SBDSV VP2 protein in Sf9 cells. Immunofluorescence assay, sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS‐PAGE) and Western blotting were used to confirm protein expression. Furthermore, transmission electron microscopy was used to observe the formation of VLPs. VLPs were formulated into an oil‐adjuvanted maternal vaccine to evaluate humoral responses in breeding ducks via latex particle agglutination inhibition assay (LPAI) and microneutralization assay. The offspring were challenged with SBDSV to test the protective efficacy. A single dose of SBDSV was able to induce the high level of LPAI antibodies in ducks, with LPAI and neutralization peak titres of 4.9 ± 1.20 log2 and 7.1 ± 1.20 log2, respectively, at 4 weeks post‐vaccination (wpv). The average LPAI titre of yolk antibodies in duck eggs receiving 2 doses (first and boost doses) of the vaccine was 5.3 ± 1.09 log2 at 4 weeks post‐boost. The protective efficacy of the maternal vaccine was 87.5%–100%. These results indicate that SBDSV VLPs can be a promising vaccine candidate for controlling SBDS.

ACS Style

Shifeng Xiao; Shao Wang; Dandan Jiang; Xiaoxia Cheng; Xiaoli Zhu; Fengqiang Lin; Bo Yu; Hui Dong; Xiuzhen Wang; Muhammad Munir; Mohammed A. Rohaim; Shilong Chen; Shaoying Chen. VP2 virus‐like particles elicit protective immunity against duckling short beak and dwarfism syndrome in ducks. Transboundary and Emerging Diseases 2021, 1 .

AMA Style

Shifeng Xiao, Shao Wang, Dandan Jiang, Xiaoxia Cheng, Xiaoli Zhu, Fengqiang Lin, Bo Yu, Hui Dong, Xiuzhen Wang, Muhammad Munir, Mohammed A. Rohaim, Shilong Chen, Shaoying Chen. VP2 virus‐like particles elicit protective immunity against duckling short beak and dwarfism syndrome in ducks. Transboundary and Emerging Diseases. 2021; ():1.

Chicago/Turabian Style

Shifeng Xiao; Shao Wang; Dandan Jiang; Xiaoxia Cheng; Xiaoli Zhu; Fengqiang Lin; Bo Yu; Hui Dong; Xiuzhen Wang; Muhammad Munir; Mohammed A. Rohaim; Shilong Chen; Shaoying Chen. 2021. "VP2 virus‐like particles elicit protective immunity against duckling short beak and dwarfism syndrome in ducks." Transboundary and Emerging Diseases , no. : 1.

Review article
Published: 23 November 2020 in Microbial Pathogenesis
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Coronaviruses (CoVs) are causing a number of human and animal diseases because of their zoonotic nature such as Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19). These viruses can infect respiratory, gastrointestinal, hepatic and central nervous systems of human, livestock, birds, bat, mouse, and many wild animals. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerging respiratory virus and is causing CoVID-19 with high morbidity and considerable mortality. All CoVs belong to the order Nidovirales, family Coronaviridae, are enveloped positive-sense RNA viruses, characterised by club-like spikes on their surfaces and large RNA genome with a distinctive replication strategy. Coronavirus have the largest RNA genomes (∼26–32 kilobases) and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. Non-structural proteins (nsp) 7–16 are cleaved from two large replicase polyproteins and guide the replication and processing of coronavirus RNA. Coronavirus replicase has more or less universal activities, such as RNA polymerase (nsp 12) and helicase (nsp 13), as well as a variety of unusual or even special mRNA capping (nsp 14, nsp 16) and fidelity regulation (nsp 14) domains. Besides that, several smaller subunits (nsp 7– nsp 10) serve as essential cofactors for these enzymes and contribute to the emerging “nsp interactome.” In spite of the significant progress in studying coronaviruses structural and functional properties, there is an urgent need to understand the coronaviruses evolutionary success that will be helpful to develop enhanced control strategies. Therefore, it is crucial to understand the structure, function, and interactions of coronaviruses RNA synthesizing machinery and their replication strategies.

ACS Style

Mohammed A. Rohaim; Rania F. El Naggar; Emily Clayton; Muhammad Munir. Structural and functional insights into non-structural proteins of coronaviruses. Microbial Pathogenesis 2020, 150, 104641 -104641.

AMA Style

Mohammed A. Rohaim, Rania F. El Naggar, Emily Clayton, Muhammad Munir. Structural and functional insights into non-structural proteins of coronaviruses. Microbial Pathogenesis. 2020; 150 ():104641-104641.

Chicago/Turabian Style

Mohammed A. Rohaim; Rania F. El Naggar; Emily Clayton; Muhammad Munir. 2020. "Structural and functional insights into non-structural proteins of coronaviruses." Microbial Pathogenesis 150, no. : 104641-104641.

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.

Journal article
Published: 24 August 2020 in Vaccines
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The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) caused an ongoing unprecedented global public health crises of coronavirus disease in 2019 (CoVID-19). The precipitously increased death rates, its impact on livelihood and trembling economies warrant the urgent development of a SARS-CoV-2 vaccine which would be safe, efficacious and scalable. Owing to unavailability of the vaccine, we propose a de novo synthesized avian orthoavulavirus 1 (AOaV-1)-based topical respiratory vaccine candidate against CoVID-19. Avirulent strain of AOaV-1 was engineered to express full length spike (S) glycoprotein which is highly neutralizing and a major protective antigen of the SARS-CoV-2. Broad-scale in vitro characterization of a recombinant vaccine candidate demonstrated efficient co-expression of the hemagglutinin-neuraminidase (HN) of AOaV-1 and S protein of SARS-CoV-2, and comparable replication kinetics were observed in a cell culture model. The recombinant vaccine candidate virus actively replicated and spread within cells independently of exogenous trypsin. Interestingly, incorporation of S protein of SARS-CoV-2 into the recombinant AOaV-1 particles attributed the sensitivity to anti-SARS-CoV-2 antiserum and more prominently to anti-AOaV-1 antiserum. Finally, our results demonstrated that the recombinant vaccine vector stably expressed S protein after multiple propagations in chicken embryonated eggs, and this expression did not significantly impact the in vitro growth characteristics of the recombinant. Taken together, the presented respiratory vaccine candidate is highly attenuated in primates per se, safe and lacking pre-existing immunity in human, and carries the potential for accelerated vaccine development against CoVID-19 for clinical studies.

ACS Style

Mohammed Rohaim; Muhammad Munir. A Scalable Topical Vectored Vaccine Candidate against SARS-CoV-2. Vaccines 2020, 8, 472 .

AMA Style

Mohammed Rohaim, Muhammad Munir. A Scalable Topical Vectored Vaccine Candidate against SARS-CoV-2. Vaccines. 2020; 8 (3):472.

Chicago/Turabian Style

Mohammed Rohaim; Muhammad Munir. 2020. "A Scalable Topical Vectored Vaccine Candidate against SARS-CoV-2." Vaccines 8, no. 3: 472.

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.

Journal article
Published: 29 May 2020 in Genes
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In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.

ACS Style

Mohammed A. Rohaim; Rania F. El El Naggar; Mohammed A. Abdelsabour; Mahmoud H. A. Mohamed; Ibrahim M. El-Sabagh; Muhammad Munir. Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events. Genes 2020, 11, 1 .

AMA Style

Mohammed A. Rohaim, Rania F. El El Naggar, Mohammed A. Abdelsabour, Mahmoud H. A. Mohamed, Ibrahim M. El-Sabagh, Muhammad Munir. Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events. Genes. 2020; 11 (6):1.

Chicago/Turabian Style

Mohammed A. Rohaim; Rania F. El El Naggar; Mohammed A. Abdelsabour; Mahmoud H. A. Mohamed; Ibrahim M. El-Sabagh; Muhammad Munir. 2020. "Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events." Genes 11, no. 6: 1.

Journal article
Published: 05 December 2019 in Vaccines
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Infectious laryngotracheitis virus (ILTV) is a promising vaccine vector due to its heterologous gene accommodation capabilities, low pathogenicity, and potential to induce cellular and humoral arms of immunity. Owing to these characteristics, different gene-deletion versions of ILTVs have been successfully deployed as a vector platform for the development of recombinant vaccines against multiple avian viruses using conventional recombination methods, which are tedious, time-demanding, and error-prone. Here, we applied a versatile, and customisable clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 accompanied with Cre–Lox system to simultaneously delete virulence factors and to insert foreign genes in the ILTV genome. Using this pipeline, we successfully deleted thymidine kinase (TK) and unique short 4 (US4) genes and inserted fusion (F) gene of the Newcastle disease virus without adversely affecting ILTV replication and expression of the F protein. Taken together, the proposed approach offers novel tools to attenuate (by deletion of virulence factor) and to generate multivalent (by insertion of heterologous genes) vaccine vectors to protect chickens against pathogens of poultry and public health importance.

ACS Style

Mustafa Ozan Atasoy; Mohammed A. Rohaim; Muhammad Munir. Simultaneous Deletion of Virulence Factors and Insertion of Antigens into the Infectious Laryngotracheitis Virus Using NHEJ-CRISPR/Cas9 and Cre–Lox System for Construction of a Stable Vaccine Vector. Vaccines 2019, 7, 207 .

AMA Style

Mustafa Ozan Atasoy, Mohammed A. Rohaim, Muhammad Munir. Simultaneous Deletion of Virulence Factors and Insertion of Antigens into the Infectious Laryngotracheitis Virus Using NHEJ-CRISPR/Cas9 and Cre–Lox System for Construction of a Stable Vaccine Vector. Vaccines. 2019; 7 (4):207.

Chicago/Turabian Style

Mustafa Ozan Atasoy; Mohammed A. Rohaim; Muhammad Munir. 2019. "Simultaneous Deletion of Virulence Factors and Insertion of Antigens into the Infectious Laryngotracheitis Virus Using NHEJ-CRISPR/Cas9 and Cre–Lox System for Construction of a Stable Vaccine Vector." Vaccines 7, no. 4: 207.

Journal article
Published: 25 October 2019 in Vaccines
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Interferons (IFNs) play central roles in establishing innate immunity and mediating adaptive immunity against multiple pathogens. Three known types of IFNs identify their cognate receptors, initiate cascades of signalling events and eventually result in the induction of a myriad of IFN-stimulated genes (ISGs). These ISGs perform a multitude of functions and cumulatively corroborate a bespoke antiviral state to safeguard hosts against invading viruses. Owing to the unique nature of a chicken’s immune system and the lack of foundational profiling information on the nature and dynamic expression of IFN-specific ISGs at the genome scale, we performed a systematic and extensive analysis of type I, II and III IFN-induced genes in chicken. Employing pan-IFN responsive chicken fibroblasts coupled with transcriptomics, we observed an over-representation of up-regulated ISGs compared to down-regulated ISGs by all types of IFNs. Intriguingly, prediction of IFN-stimulated response element (ISRE) and gamma-IFN activation sequence (GAS) revealed a substantial number of GAS motifs in selective and significantly induced ISGs in chicken. Extensive comparative, genome-wide and differential expression analysis of ISGs under equivalent signalling input catalogue a set of genes that were either IFN-specific or independent of types of IFNs used to prime fibroblasts. These comprehensive datasets, first of their kinds in chicken, will establish foundations to elucidate the mechanisms of actions and breadth of antiviral action of ISGs, which may propose alternative avenues for targeted antiviral therapy against viruses of poultry of public health importance.

ACS Style

Diwakar Santhakumar; Mohammed Abdelmohsen Shahaat Rohaim; Muhammad Munir. Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts. Vaccines 2019, 7, 160 .

AMA Style

Diwakar Santhakumar, Mohammed Abdelmohsen Shahaat Rohaim, Muhammad Munir. Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts. Vaccines. 2019; 7 (4):160.

Chicago/Turabian Style

Diwakar Santhakumar; Mohammed Abdelmohsen Shahaat Rohaim; Muhammad Munir. 2019. "Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts." Vaccines 7, no. 4: 160.

Preprint
Published: 04 October 2019
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Interferons (IFNs) play central roles in establishing innate immunity and mediating adaptive immunity against multiple pathogens. Three known types of IFNs identify their cognate receptors, initiate cascades of signalling events and eventually result in the induction of myriad of IFN-stimulated genes (ISGs). These ISGs perform multitude of functions and cumulatively corroborate a bespoke antiviral state to safeguard hosts against invading viruses. Owing to unique nature of chicken’s immune system and lack of foundational profiling information on the nature and dynamic expression of IFN-specific ISGs at the genome scale, we performed a systematic and extensive analysis of type I, II and III IFN-induced genes in chicken. Employing pan-IFN responsive chicken fibroblasts coupled with transcriptomics we observed an overwhelming over-representation of up-regulated ISGs by all types of IFNs. Intriguingly, prediction of IFN-stimulated response element (ISRE) and gamma-IFN activation sequence (GAS) revealed a substantial number of GAS motifs in selective significantly induced ISGs in chicken. Extensive comparative, genome-wide and differential expression analysis of ISGs under equivalent signalling input catalogue a set of genes that were either IFN-specific or independent of types of IFNs used to prime fibroblasts. These comprehensive datasets, first of their kinds in chicken, will establish foundations to elucidate the mechanisms of actions and breadth of antiviral action of ISGs which may propose alternative avenues for the targeted antiviral therapy against viruses of poultry and public health importance.

ACS Style

Diwakar Santhakumar; Mohammed A. Rohaim; Muhammad Munir. Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts. 2019, 793448 .

AMA Style

Diwakar Santhakumar, Mohammed A. Rohaim, Muhammad Munir. Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts. . 2019; ():793448.

Chicago/Turabian Style

Diwakar Santhakumar; Mohammed A. Rohaim; Muhammad Munir. 2019. "Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts." , no. : 793448.

Journal article
Published: 12 August 2019 in Avian Pathology
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Newcastle disease (ND), caused by virulent Avian avulavirus 1 (AAvV 1), affects a wide range of avian species worldwide. Recently, several AAvVs of diverse genotypes have emerged with varying genomic and residue substitutions, and subsequent clinical impact on susceptible avian species. We assessed the clinico-pathological influence of two different AAvV 1 pathotypes [wild bird originated-velogenic strain (sub-genotype VIIi, MF437287) and feral pigeon originated-mesogenic strain (sub-genotype VIm, KU885949)] in commercial broiler chickens and pigeons. The velogenic strain caused 100% mortality in both avian species while the mesogenic strain caused 0% and 30% mortality in chickens and pigeons, respectively. Both strains showed tissue tropism for multiple tissues including visceral organs; however, minor variances were observed according to host and pathotype. The observed gross and microscopic lesions were typical of AAvV 1 infection. Utilizing oropharyngeal and cloacal swabs, a comparable pattern of viral shedding was observed for both strains from each of the infected individuals of both avian species. The study concludes a varying susceptibility of chickens and pigeons to different wild bird-originated AAvV 1 pathotypes and, therefore, suggests continuous monitoring and surveillance of currently prevailing strains for effective control of the disease worldwide, particularly in disease-endemic countries.

ACS Style

Aziz- Ul- Rahman; Mohammed Abdelmohsen Shahaat Rohaim; Rania F. El Naggar; Ghulam Mustafa; Umer Chaudhry; Muhammad Zubair Shabbir. Comparative clinico-pathological assessment of velogenic (sub-genotype VIIi) and mesogenic (sub-genotype VIm) Avian avulavirus 1 in chickens and pigeons. Avian Pathology 2019, 48, 610 -621.

AMA Style

Aziz- Ul- Rahman, Mohammed Abdelmohsen Shahaat Rohaim, Rania F. El Naggar, Ghulam Mustafa, Umer Chaudhry, Muhammad Zubair Shabbir. Comparative clinico-pathological assessment of velogenic (sub-genotype VIIi) and mesogenic (sub-genotype VIm) Avian avulavirus 1 in chickens and pigeons. Avian Pathology. 2019; 48 (6):610-621.

Chicago/Turabian Style

Aziz- Ul- Rahman; Mohammed Abdelmohsen Shahaat Rohaim; Rania F. El Naggar; Ghulam Mustafa; Umer Chaudhry; Muhammad Zubair Shabbir. 2019. "Comparative clinico-pathological assessment of velogenic (sub-genotype VIIi) and mesogenic (sub-genotype VIm) Avian avulavirus 1 in chickens and pigeons." Avian Pathology 48, no. 6: 610-621.

Short report
Published: 01 August 2019 in Virus Genes
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Infectious bronchitis virus (IBV) affects both vaccinated and unvaccinated flocks worldwide, with a significant impact on the poultry industry. The aim of the present study is to characterize an emerging variant pathogenic IBV originating from field outbreaks in vaccinated Egyptian layer flock. Samples were collected from disease-suspected flock with a history of administration of live and inactivated IBV vaccines (Ma5 type). Virus propagation in embryonated chicken eggs (ECEs), after three successive passages, revealed typical IBV lesions such as curling and dwarfism. The reported isolate was identified by a real-time reverse transcriptase PCR assay targeting nucleocapsid (N) gene and, further characterized by full-length spike (S1) gene sequencing. Phylogenetic analysis revealed clustering of the isolated virus within 4/91 genotype of GI-13 lineage. Deduced amino acid sequences identity revealed 75–76% and 88–90% similarity with the currently used classic (H120, Ma5, and M41) and variant vaccine strains (4/91 and CR88) in Egypt, respectively. Recombination analysis gave an evidence for distinct patterns of origin for the studied isolate providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-13 lineage in the Egyptian field. The studied isolate (IBV/CK/EG/Fadllah-10/2019) emerged as a result of recombination between the variant group (Egy/var I genotype, GI-23 lineage) as a major parent and the CR88 variant vaccine strain (4/91 genotype, GI-13 lineage) as minor parent. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants which ascertain the importance of disease monitoring in vaccinated flocks as well as re-appropriation for the current vaccine strategies.

ACS Style

Mohammed A. Rohaim; Rania F. El Naggar; Mohamed M. Hamoud; Abdel-Hamid I. Bazid; Abdulrhman M. Gamal; Samah E. Laban; Mohammed A. Abdel-Sabour; Shimaa A. E. Nasr; Manal M. Zaki; Muhammad Z. Shabbir; Osama K. Zahran; Muhammad Munir. Emergence and genetic analysis of variant pathogenic 4/91 (serotype 793/B) infectious bronchitis virus in Egypt during 2019. Virus Genes 2019, 55, 720 -725.

AMA Style

Mohammed A. Rohaim, Rania F. El Naggar, Mohamed M. Hamoud, Abdel-Hamid I. Bazid, Abdulrhman M. Gamal, Samah E. Laban, Mohammed A. Abdel-Sabour, Shimaa A. E. Nasr, Manal M. Zaki, Muhammad Z. Shabbir, Osama K. Zahran, Muhammad Munir. Emergence and genetic analysis of variant pathogenic 4/91 (serotype 793/B) infectious bronchitis virus in Egypt during 2019. Virus Genes. 2019; 55 (5):720-725.

Chicago/Turabian Style

Mohammed A. Rohaim; Rania F. El Naggar; Mohamed M. Hamoud; Abdel-Hamid I. Bazid; Abdulrhman M. Gamal; Samah E. Laban; Mohammed A. Abdel-Sabour; Shimaa A. E. Nasr; Manal M. Zaki; Muhammad Z. Shabbir; Osama K. Zahran; Muhammad Munir. 2019. "Emergence and genetic analysis of variant pathogenic 4/91 (serotype 793/B) infectious bronchitis virus in Egypt during 2019." Virus Genes 55, no. 5: 720-725.

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.

Original research article
Published: 14 September 2018 in Frontiers in Immunology
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Innate antiviral immunity establishes first line of defense against invading pathogens through sensing their molecular structures such as viral RNA. This antiviral potential of innate immunity is mainly attributed to a myriad of IFN-stimulated genes (ISGs). Amongst well-characterized ISGs, we have previously shown that antiviral potential of chicken IFN-induced proteins with tetratricopeptides repeats 5 (chIFIT5) is determined by its interaction potential with 5′ppp containing viral RNA. Here, we generated transgenic chickens using avian sarcoma-leukosis virus (RCAS)-based gene transfer system that constitutively and stably express chIFIT5. The transgenic chickens infected with clinical dose (EID50 104 for HPAIV and 105 EID50 for vNDV) of high pathogenicity avian influenza virus (HPAIV; H5N1) or velogenic strain of Newcastle disease virus (vNDV; Genotype VII) showed marked resistance against infections. While transgenic chickens failed to sustain a lethal dose of these viruses (EID50 105 for HPAIV and 106 EID50 for vNDV), a delayed and lower level of clinical disease and mortality, reduced virus shedding and tissue damage was observed compared to non-transgenic control chickens. These observations suggest that stable expression of chIFIT5 alone is potentially insufficient in providing sterile protection against these highly virulent viruses; however, it is sufficient to ameliorate the clinical outcome of these RNA viruses. These findings propose the potential of innate immune genes in conferring genetic resistance in chickens against highly pathogenic and zoonotic viral pathogens causing sever disease in both animals and humans.

ACS Style

Mohammed A. Rohaim; Diwakar Santhakumar; Rania F. El Naggar; Munir Iqbal; Hussein A. Hussein; Muhammad Munir. Chickens Expressing IFIT5 Ameliorate Clinical Outcome and Pathology of Highly Pathogenic Avian Influenza and Velogenic Newcastle Disease Viruses. Frontiers in Immunology 2018, 9, 1 .

AMA Style

Mohammed A. Rohaim, Diwakar Santhakumar, Rania F. El Naggar, Munir Iqbal, Hussein A. Hussein, Muhammad Munir. Chickens Expressing IFIT5 Ameliorate Clinical Outcome and Pathology of Highly Pathogenic Avian Influenza and Velogenic Newcastle Disease Viruses. Frontiers in Immunology. 2018; 9 ():1.

Chicago/Turabian Style

Mohammed A. Rohaim; Diwakar Santhakumar; Rania F. El Naggar; Munir Iqbal; Hussein A. Hussein; Muhammad Munir. 2018. "Chickens Expressing IFIT5 Ameliorate Clinical Outcome and Pathology of Highly Pathogenic Avian Influenza and Velogenic Newcastle Disease Viruses." Frontiers in Immunology 9, no. : 1.

Original article
Published: 02 July 2018 in Archives of Virology
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Despite extensive vaccination campaigns, Newcastle disease virus (NDV) remains endemic in many countries worldwide, and factors that contribute to this failure include mismatched vaccines, partial immunization, and poor husbandry practices. In order to overcome the problem of genetic divergence between circulating field strains and vaccine strains, we saponin-adjuvanted an Egyptian field strain and assessed its safety and immunogenicity in chickens. Immunization of chickens with the vaccine followed by challenge with a velogenic reference strain revealed the potential of the saponin-adjuvanted vaccine to induce a strong immune response that resulted in complete protection of chickens. Importantly, in vaccinated chickens, virus shedding was abolished, providing an added advantage over the currently available commercial live-attenuated and inactivated vaccines, which are unable to prevent shedding. A histopathological investigation demonstrated that the vaccinated chickens had less-severe lesions than challenged unvaccinated and mock-vaccinated chickens. We propose using this formulation as an alternative and improved NDV vaccine platform that can be exploited to control disease not only in Egypt but also in other disease-endemic countries.

ACS Style

Wahid H. El-Dabae; Hussein Aly Hussein; Mohammed Abdelmohsen Shahaat Rohaim; Munir M. El-Safty; Nagwa S. Ata; Ismail M. Reda. Saponin-adjuvanted vaccine protects chickens against velogenic Newcastle disease virus. Archives of Virology 2018, 163, 2423 -2432.

AMA Style

Wahid H. El-Dabae, Hussein Aly Hussein, Mohammed Abdelmohsen Shahaat Rohaim, Munir M. El-Safty, Nagwa S. Ata, Ismail M. Reda. Saponin-adjuvanted vaccine protects chickens against velogenic Newcastle disease virus. Archives of Virology. 2018; 163 (9):2423-2432.

Chicago/Turabian Style

Wahid H. El-Dabae; Hussein Aly Hussein; Mohammed Abdelmohsen Shahaat Rohaim; Munir M. El-Safty; Nagwa S. Ata; Ismail M. Reda. 2018. "Saponin-adjuvanted vaccine protects chickens against velogenic Newcastle disease virus." Archives of Virology 163, no. 9: 2423-2432.

Original article
Published: 19 June 2018 in Archives of Virology
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Newcastle disease virus (NDV), the type member of the species Avian avulavirus 1 (formerly known as avian paramyxovirus serotype 1), causes a highly contagious and economically important disease in a myriad of avian species around the globe. While extensive vaccination programs have been implemented in ND-endemic countries, the disease is continuously spreading in commercial, backyard, and wild captive poultry. In order to investigate the evolution of the virus and assess the efficiency of the vaccine regimens that are currently being applied in commercial poultry, four wild-bird-origin NDV strains were characterized biologically, based on mean death time and intracerebral pathogenicity index, and genetically, based on the cleavage motif (112RRQKRF117) in the fusion (F) protein. Based on these features, all of the isolates were characterized as velogenic strains of NDV. Phylogenetic analysis based on the complete genome sequence revealed clustering of these isolates within class II, genotype VII. This class of NDV remains the predominant genotype in the Egyptian poultry industry, as well as in those of many Asian and African countries. To investigate the potential of these wild-bird-origin NDV isolates to cause infection in domesticated poultry and to assess the efficacy of currently available vaccines for protection of commercial poultry, an extensive animal challenge experiment was performed. Cumulative clinicopathological and immunological investigations of virus-challenged chickens indicate that these isolates can potentially be transmitted between chicken and cause systemic infections, and the currently applied vaccines are unable to prevent clinical disease and virus shedding. Taken together, the data represent a comprehensive evaluation of the ability of Egyptian wild-bird-origin NDV strains to cause infection in commercial poultry and highlights the need for a continuous and large-scale surveillance as well as revised vaccine approaches. These integrated and multifaceted strategies would be crucial in any efforts to control and eradicate the disease globally.

ACS Style

Rania F. El Naggar; Mohammed A. Rohaim; Abdel-Hamid Bazid; Hussein Ahmed; Hussein A. Hussein; Muhammad Munir. Biological characterization of wild-bird-origin avian avulavirus 1 and efficacy of currently applied vaccines against potential infection in commercial poultry. Archives of Virology 2018, 163, 2743 -2755.

AMA Style

Rania F. El Naggar, Mohammed A. Rohaim, Abdel-Hamid Bazid, Hussein Ahmed, Hussein A. Hussein, Muhammad Munir. Biological characterization of wild-bird-origin avian avulavirus 1 and efficacy of currently applied vaccines against potential infection in commercial poultry. Archives of Virology. 2018; 163 (10):2743-2755.

Chicago/Turabian Style

Rania F. El Naggar; Mohammed A. Rohaim; Abdel-Hamid Bazid; Hussein Ahmed; Hussein A. Hussein; Muhammad Munir. 2018. "Biological characterization of wild-bird-origin avian avulavirus 1 and efficacy of currently applied vaccines against potential infection in commercial poultry." Archives of Virology 163, no. 10: 2743-2755.

Journal article
Published: 01 May 2018 in Scientific Reports
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The intracellular actions of interferon (IFN)-regulated proteins, including IFN-induced proteins with tetratricopeptide repeats (IFITs), attribute a major component of the protective antiviral host defense. Here we applied genomics approaches to annotate the chicken IFIT locus and currently identified a single IFIT (chIFIT5) gene. The profound transcriptional level of this effector of innate immunity was mapped within its unique cis-acting elements. This highly virus- and IFN-responsive chIFIT5 protein interacted with negative sense viral RNA structures that carried a triphosphate group on its 5′ terminus (ppp-RNA). This interaction reduced the replication of RNA viruses in lentivirus-mediated IFIT5-stable chicken fibroblasts whereas CRISPR/Cas9-edited chIFIT5 gene knockout fibroblasts supported the replication of RNA viruses. Finally, we generated mosaic transgenic chicken embryos stably expressing chIFIT5 protein or knocked-down for endogenous chIFIT5 gene. Replication kinetics of RNA viruses in these transgenic chicken embryos demonstrated the antiviral potential of chIFIT5 in ovo. Taken together, these findings propose that IFIT5 specifically antagonize RNA viruses by sequestering viral nucleic acids in chickens, which are unique in innate immune sensing and responses to viruses of both poultry and human health significance.

ACS Style

Diwakar Santhakumar; Mohammed Abdelmohsen Shahaat Rohaim; Hussein A. Hussein; Pippa Hawes; Helena Lage Ferreira; Shahriar Behboudi; Munir Iqbal; Venugopal Nair; Clarice W. Arns; Muhammad Munir. Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses. Scientific Reports 2018, 8, 1 -20.

AMA Style

Diwakar Santhakumar, Mohammed Abdelmohsen Shahaat Rohaim, Hussein A. Hussein, Pippa Hawes, Helena Lage Ferreira, Shahriar Behboudi, Munir Iqbal, Venugopal Nair, Clarice W. Arns, Muhammad Munir. Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses. Scientific Reports. 2018; 8 (1):1-20.

Chicago/Turabian Style

Diwakar Santhakumar; Mohammed Abdelmohsen Shahaat Rohaim; Hussein A. Hussein; Pippa Hawes; Helena Lage Ferreira; Shahriar Behboudi; Munir Iqbal; Venugopal Nair; Clarice W. Arns; Muhammad Munir. 2018. "Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses." Scientific Reports 8, no. 1: 1-20.