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Interferons are an essential component of the innate arm of the immune system and are arguably one of the most important lines of defence against viruses. The human IFN system and its functionality has already been largely characterized and studied in detail. However, the IFN systems of bats have only been marginally examined to date up until the recent developments of the Bat1k project which have now opened new opportunities in research by identifying six new bat genomes to possess novel genes that are likely associated with viral tolerance exhibited in bats. Interestingly, bats have been hypothesized to possess the ability to establish a host-virus relationship where despite being infected, they exhibit limited signs of disease and still retain the ability to transmit the disease into other susceptible hosts. Bats are one of the most abundant and widespread vertebrates on the planet and host many zoonotic viruses that are highly pathogenic to humans. Several genomics, immunological, and biological features are thought to underlie novel antiviral mechanisms of bats. This review aims to explore the bat IFN system and developments in its diverse IFN features, focusing mainly on the model species, the Australian black flying fox (Pteropus alecto), while also highlighting bat innate immunity as an exciting and fruitful area of research to understand their ability to control viral-mediated pathogenesis.
Emily Clayton; Muhammad Munir. Fundamental Characteristics of Bat Interferon Systems. Frontiers in Cellular and Infection Microbiology 2020, 10, 527921 .
AMA StyleEmily Clayton, Muhammad Munir. Fundamental Characteristics of Bat Interferon Systems. Frontiers in Cellular and Infection Microbiology. 2020; 10 ():527921.
Chicago/Turabian StyleEmily Clayton; Muhammad Munir. 2020. "Fundamental Characteristics of Bat Interferon Systems." Frontiers in Cellular and Infection Microbiology 10, no. : 527921.
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.
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 StyleMohammed 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 StyleMohammed 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.
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.
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 StyleMohammed 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 StyleMohammed 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.
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.
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 StyleMohammed 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 StyleMohammed 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.