The ongoing COVID-19 pandemic is the greatest health-care challenge of this generation. Early viral genome sequencing studies of small cohorts have indicated the possibility of distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genotypes.1 If these subtypes result in an altered virus tropism or pathogenesis in infected hosts, this could have immediate implications for vaccine design, drug development, and efforts to control the pandemic. Therefore, the genomic surveillance and characterisation of circulating viral strains is a high priority for research and development. To facilitate the epidemiological tracking of SARS-CoV-2, researchers worldwide have created various web-portals and tools, such as the Johns Hopkins University COVID-19 dashboard. An unprecedented effort to make COVID-19-related data accessible in near real-time has resulted in more than 25 000 publicly available genome sequences of SARS-CoV-2 on Global Initiative on Sharing All Influenza Data (GISAID). Although platforms to survey epidemiological data are prevalent, tools that summarise publicly available viral genome data are scarce and those that are available do not offer users the ability to analyse in-house sequencing data. To address this gap, we have developed an accessible application, the COVID-19 Genotyping Tool (CGT).
Full paper at The Lancet Digital Health.
Featured on CBC’s The National: Scientists develop an app that tracks how COVID-19 mutates person-to-person
Thanks to hard work by Jalees Nasir, Amos Raphenya, Dr. Kendrick Smith (Perimeter Institute), and Dr. Finlay Maguire (Dalhousie) with help from our Ontario Coronavirus Genomics Coalition (ONCoV) colleagues, particularly Dr. Jared Simpson (OICR), Dr. Hamza Mbareche (Sunnybrook Health Sciences Centre), Dr. Hassaan Mann (Vector Institute), and Dr. Natalie Knox (Public Health Agency of Canada), the McArthur lab is proud to release the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) bioinformatics workflow for SARS-CoV-2 genome analysis based on Illumina sequencing data, available here: https://github.com/jaleezyy/covid-19-signal
RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA library construction. Here, we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance.
The McArthur lab is honoured to collaborate with our clinical colleagues across Ontario in sequencing of SARS-CoV-2 clinical isolates, to better understand the epidemiology of the pandemic. Our colleague Dr. Samira Mubareka explains it best:
The McArthur lab welcomes back summer students Rachel Tran & Arman Edalatmand plus first timers Marcel Jansen & Emily Panousis! These four will be covering a lot of ground this summer, including AMR transmission dynamics, machine learning for automated bio curation, prediction of antibiotic production in Streptomycetes, algorithm development, and data harmonization.
Welcome Ashraf Bazan, who has joined the lab and the McMaster Biochemistry & Biomedical Sciences graduate program! A familiar face in the IIDR as he started if the Coombes lab, Ashraf joins us to lead an antimicrobial resistance (AMR) metagenomics investigation of azithromycin treatment of childhood diarrheal disease in Botswana, in collaboration with Dr. Jeffrey Pernica. Welcome Ashraf!
Banerjee, A., J.A. Nasir, P. Budylowski, L. Yip, P. Aftanas, N. Christie, A. Ghalami, K. Baid, A.R. Raphenya, J.A. Hirota, M.S. Miller, A.J. McGeer, M.A. Ostrowski, R.A. Kozak, A.G. McArthur, K. Mossman, & S. Mubareka
SARS-CoV-2 emerged in December 2019 in Wuhan, China and has since infected over 1.5 million people, of which over 100,000 have died. As SARS-CoV-2 spreads across the planet, speculations remain about the evolution of the virus and the range of human cells that can be infected by SARS-CoV-2. In this study, we report the isolation of SARS-CoV-2 from two COVID-19 patients in Toronto, Canada. We determined the genomic sequences of the two isolates and identified single nucleotide changes in representative populations of our virus stocks. More importantly, we have tested a wide range of human immune cells for infectivity with SARS-CoV-2. We confirm from our studies that human primary peripheral blood mononuclear cells (PBMCs) are not permissive to SARS-CoV-2. As SARS-CoV-2 continues to spread globally, it is essential to monitor any small nucleotide polymorphisms in the virus and to continue to isolate circulating strains of the virus to determine cell susceptibility and pathogenicity using in vitro and in vivo infection models.
Hear Arinjay & Andrew talk about their SARS-CoV-2 work: https://www.youtube.com/watch?v=SVzDHESnssg
Rachel Tran | Biochem 4T15 – Exploring the diversity of clinical multidrug resistance in Hamilton, Canada
Arman Edalatmand | Biochem 4T15 – Improving upon CARD*Shark and contextualizing antimicrobial resistance genes
Marcel Jansen | Biochem 4T15 – Translating the Comprehensive Antimicrobial Resistance Database to act as a stopgap for MEGARes
William Huynh | Biochem 4T15 – Expansion of Resistance Gene Identifier allows the identification of putative and novel frameshift mutations
Sohaib Syed | BiomedDC 4A15 – Expanding the scope of antimicrobial resistance surveillance of Mycobacterium tuberculosis in the Comprehensive Antibiotic Resistance Database
Thanks also goes to our 3rd year students Corie Niu (Biochem 3R06), Hamna Imtiaz (Biochem 3R06), Anna-Lisa Nguyen (HthSci 4D03), Sarah Yaqoob (Science 3RP3), & Hafsa Omer (LifeSci 3RP3)!