Recent Submissions

  • iSCAN: A Point-of-Care SARS-CoV-2 Diagnostic Test

    Mahas, Ahmed; Marsic, Tin; Ali, Zahir; Aman, Rashid; Gundra, Sivakrishna Rao; Ghouniemy, Ahmed; Hassan, Norhan; Mahfouz, Magdy M. (2021-11-22) [Poster]
    Type VI CRISPR-Cas systems have been repurposed for various applications such as gene knock-down, viral interference, and molecular diagnostics. However, the identification and characterization of thermophilic orthologues will expand and unlock the potential of diverse biotechnological applications. In this work, we identified and characterized a novel, thermostable orthologue of the Cas13a family, from the thermophilic organism Thermoclostridium caenicola (TccCas13a). We show that TccCas13a has a close phylogenetic relation to HheCas13a and shares several properties such as thermostability and inability .
  • Quick and Easy Assembly of a One-step qRT-PCR Kit for COVID-19 Diagnostics Using In-House Enzymes

    Takahashi, Masateru; Tehseen, Muhammad; Salunke, Rahul; Takahashi, Etsuko; Mfarrej, Sara; Sobhy, Mohamed A.; Alhamlan, Fatimah S.; Hala, Sharif; Mandujano, Gerardo R.; Al-Qahtani, Ahmed A.; Alofi, Fadwa S.; Alsomali, Afrah; Hashem, Anwar M.; Khogeer, Asim; Almontashiri, Naif A. M.; Lee, Jae Man; Mon, Hiroaki; Sakashita, Kosuke; Li, Mo; Kusakabe, Takahiro; Pain, Arnab; Hamdan, Samir (2021-11-22) [Poster]
    One-step qRT-PCR is the most widely applied method for COVID-19 diagnostics. Notwithstanding the facts that one-step qRT-PCR is well-suited for the diagnosis of COVID-19 and that there are many commercially available one-step qRT- PCR kits in the market, their high cost and unavailability due to airport closures and shipment restriction became a major bottleneck that had driven the desire to produce the key components of such kits locally. Here, we provide a simple, economical, and powerful one-step qRT-PCR kit based on patent-free, specifically-tailored versions of Moloney Murine Leukemia Virus Reverse Transcriptase and Thermus aquaticus DNA polymerase and termed the R3T (Rapid Research Response Team) One-step qRT-PCR. We also demonstrate the robustness of our enzyme production strategies and provide the optimal reaction conditions for their efficient augmentation in a one-step approach. Our kit was routinely able to reliably detect as low as 10 copies of the synthetic RNAs of the SARS-CoV-2. More importantly, our kit successfully detected COVID-19 in clinical samples of broad viral titers with similar reliability and selectivity as that of the Invitrogen SuperScript III Platinum One-step qRT-PCR and TaqPath 1-Step RT-qPCR kits. Overall, our kit has shown robust performance in both laboratory settings and the Saudi Ministry of Health-approved testing facility.
  • Saudi Arabian SARS-CoV-2 genome analysis reveals the functional impact of N protein mutations on differential host-virus interactions

    Shuaib, Muhammad (2021-11-22) [Poster]
    Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.
  • Host-Directed editing of SARS-CoV-2 genome: From perspective of host APOBEC and ZAP

    Sadykov, Mukhtar; Mourier, Tobias; Guan, Qingtian; Pain, Arnab (2021-11-22) [Poster]
    RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanism is still largely unknown. To address this, we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in CpG loss over just a few months. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.
  • MesoCraft – 3D Modeling Software for Creating Mesoscale Atomistic Models

    Strnad, Ondrej (2021-11-22) [Poster]
    MesoCraft is a new 3D modeling tool implementing visual programming approach. It provides the user with the capabilities of loading, rendering and manipulating several modalities (protein data, volumetric data, meshes) and overlaying them inside one rendering view. The modeling algorithm is based on statistical and rule based modeling approaches that are rapid to author, fast to construct, and easy to revise. Biological information can be incorporated by interactively defining the rules that spatially characterize the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual programming feedback loop.
  • Tracking COVID-19 through mutation fingerprints, worldwide.

    Alam, Intikhab; Uludağ, Mahmut; Radovanovic, Aleksandar; Incitti, Roberto; Kamau, Allan A.; Alarawi, Mohammed; Gojobori, Takashi (2021-11-22) [Poster]
    The SARS-CoV-2 virus causing the COVID-19 pandemic, has been sequenced in patients over 4.5 million times with over 2 million genomes belong to Delta while 1 million genomes belong to Alpha variant. This increase in the sequencing efforts is due to WHO call on stepping up sequencing to actively track the rise of mutations or variants of concern related to increased infectivity and evasion of antibodies. Here, we present a daily updated geographic sequencing effort and genomic 'mutation fingerprints' based COVID-19 virus mutation tracking system (CovMT) that processes publicly available genome data from GISAID. The CovMT interactive resource is available online for scientists, general public and public health authorities at