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Rapid Research Response Team - COVID-19

Following a call by President Tony Chan for KAUST PIs to contribute through their research capabilities to alleviate the COVID-19 pandemic, efforts coordinated by Donal Bradley, KAUST vice president for research, and Pierre Magistretti, KAUST dean of the Biological and Environmental Science and Engineering division, mobilized a group of faculty to form the Rapid Research Response Team (R3T). The focus of R3T is to collaborate with and strongly support the Kingdom's healthcare stakeholders to help combat the spread of COVID-19.  
Efforts are focusing on the development of rapid diagnostic platforms, genomic analysis of the virus and bioinformatic tools to help track the spread and evolution of the disease. These efforts are based on research projects and competencies established over the years at KAUST. They are also part of the Smart Health Initiative recently established at KAUST to implement joint research projects with medical centers in the Kingdom.
R3T's group of faculty has been in close contact with the Saudi Centers for Disease Control (CDC) and the Ministry of Health (MoH) to coordinate efforts that will synergize to ensure fast and reliable diagnostic tests, as the demand in the Kingdom and internationally for the tests will increase. Initial efforts are aimed at optimizing existing tests to decrease the amount of reagents used without compromising reliability. 
The group is also monitoring developments in other academic and biotechnology laboratories. In particular, R3T initiated a collaboration with the University of Oxford to implement a novel test that would greatly simplify the virus detection process.

Inexpensive transistors for rapid SARS-CoV-2 detection

Bioengineering, Material Science

Rapid Coronavirus RNA detection using reverse transcription loop-mediated isothermal amplification (RT-LAMP)

Bioscience, Computer Science

Defining signatures of COVID-19 susceptibility through DNA methylation patterns

Bioscience

CT-based detection, segmentation and classification system for COVID-19

Bioengineering, Computer Science

Utilization of computational tools and big data for COVID-19 drug development and viral surveillance

Bioscience

Production of recombinant enzymes for use in biomedical applications

Bioscience

Immunodiagnostics to detect the COVID-19 virus

Bioengineering

Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences

Bioscience, Computer Science

Detection of the SARS-CoV-2 virus in wastewater for early outbreak detection

Bioscience

Point-of-care diagnostics and monitoring of COVID-19

Bioscience

Rapid and Sensitive Detection of SARS-CoV-2 with a nanobody-transistor sensor

Bioengineering, Bioscience

Rapid colorimetric assay for detection of COVID-19

Bioengineering

Using naturally occurring bacterial gas vesicles to develop a novel vaccination approach to the SARS-CoV-2 virus

Bioscience

Testing novel generation antisense oligonucleotides for potential therapeutic use in COVID-19 infections.

Bioscience

Unraveling the global genetic signatures of the SARS-CoV-2 virus

Bioscience

Statistical and rule-based mesoscale modeling of the SARS-CoV-2 virus

Bioengineering, Computer Science
Latest publications

Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing

Chongwei Bi, Gerardo Ramos-Mandujano, Yeteng Tian, Sara Mfarrej, Andri Rachmadi, Sharif Hala, Jinna Xu, Fadwa S Alofi, Asim Khogeer, Anwar M Hashem, Naif AM Almontashiri, Concepcion Rodriguez Esteban, Estrella Nuñez Delicado, Juan Carlos Izpisua Belmonte, Arnab Pain, Mo Li


https://www.cell.com/med/fulltext/S2666-6340(21)00117-3

A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples. Gerardo

Ramos-Mandujano, Rahul Salunke, Sara Mfarrej, Andri Rachmadi, Sharif Hala, Jinna Xu, Fadwa S Alofi, Asim Khogeer, Anwar M Hashem, Naif AM Almontashiri, Afrah Alsomali, Samir Hamdan, Peiying Hong, Arnab Pain, Mo Li


https://onlinelibrary.wiley.com/doi/10.1002/gch2.202000068

No Evidence for Temperature-Dependence of the COVID-19 Epidemic. Front. Public Health 8:436. doi: 10.3389/fpubh.2020.00436

Jamil T, Alam I, Gojobori T and Duarte CM (2020)


View this publication

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics.

Sateesh Maddirevula, Hiroyuki Kuwahara, Nour Ewida, Hanan E. Shamseldin, Nisha Patel, Fatema Alzahrani, Tarfa AlSheddi, Eman AlObeid, Mona Alenazi, Hessa S. Alsaif, Maha Alqahtani, Maha AlAli, Hatoon Al Ali, Rana Helaby, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Nadine Hanna, Dorota Monies, Nada Derar, Afaf Alsagheir, Amal Alhashem, Badr Alsaleem, Hamoud Alhebbi, Sami Wali, Ramzan Umarov, Xin Gao & Fowzan S. Alkuraya.


https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02053-9

COVID-19 lockdown allows researchers to quantify the effects of human activity on wildlife.

Rutz, C., M.-C. Loretto, A. Bates, S. C. Davidson, C. M. Duarte, W. Jetz, M. Johnson, A. Kato, R. Kays, T. Mueller, R. B. Primack, Y. Ropert-Coudert, M. Tucker, M. Wikelski and F. Cagnacci.


https://doi.org/10.1038/s41559-020-1237-z

Modeling quantitative traits for COVID-19 case reports.

Nuria Queralt-Rosinach, Susan Bello, Robert Hoehndorf, Claus Weiland, Philippe Rocca-Serra, Paul N Schofield


https://www.medrxiv.org/content/10.1101/2020.06.18.20135103v1

Multiplex Isothermal Amplification Coupled with Nanopore Sequencing for Rapid Detection and Mutation Surveillance of SARS-CoV-2.

Chongwei Bi, Gerardo Ramos-Mandujano, Sharif Hala, Jinna Xu, Sara Mfarrej, Fadwa S Alofi, Asim Khogeer, Anwar M Hashem, Naif A.M. Almontashiri, Arnab Pain, Mo Li


https://www.medrxiv.org/content/10.1101/2020.06.12.20129247v1

A Rapid, Accurate and Machine-agnostic Segmentation and Quantification Method for CT-based COVID-19 Diagnosis.

Longxi Zhou ; Zhongxiao Li ; Juexiao Zhou ; Haoyang Li ; Yupeng Chen ; Yuxin Huang ; Dexuan Xie ; Lintao Zhao ; Ming Fan ; Shahrukh Hashmi ; Faisal AbdelKareem ; Riham Eiada ; Xigang Xiao ; Lihua Li ; Zhaowen Qiu ; Xin Gao


https://ieeexplore.ieee.org/document/9115057

Estimating and forecasting COVID-19 attack rates and mortality.

David I. Ketcheson, Hernando C. Ombao, Paula Moraga, Tarig Ballal, Carlos M. Duarte.


https://www.medrxiv.org/content/10.1101/2020.05.11.20097972v1

Assessing the age- and gender-dependence of the severity and case fatality rates of COVID-19 disease in Spain. -

Paula Moraga, David I. Ketcheson, Hernando C. Ombao, Carlos M. Duarte


https://wellcomeopenresearch.org/articles/5-117/v1

Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences -

Wang Liu-Wei, Şenay Kafkas, Jun Chen, Jesper Tegnér and Robert Hoehndorf


https://www.biorxiv.org/content/10.1101/2020.04.22.055095v1

No Evidence for Temperature-Dependence of the COVID-19 Epidemic -

Tahira Jamil, Intikhab Syed Alam, Takashi Gojobori, Carlos Duarte


www.medrxiv.org/content/10.1101/2020.03.29.20046706v1

Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019 -

Intikhab alam, Allan Kamau, Maxat Kulmanov, Stefan T. Arold, Arnab Pain, Takashi Gojobori, Carlos M. Duarte


https://www.frontiersin.org/articles/10.3389/fcimb.2020.00405/abstract

Computational Drug Repositioning and Elucidation of Mechanism of Action of Compounds against SARS-CoV-2 -

Francesco Napolitano, Gennaro Gambardella, Diego Carrella, Xin Gao, Diego di Bernardo


https://arxiv.org/ftp/arxiv/papers/2004/2004.07697.pdf