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

 

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Krishna A Srinivasan, Suman K Virdee, Andrew G McArthur

Brief Funct Genomics 2020 May 16 [Epub ahead of print]

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.

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The McArthur lab welcomes new Curator-Developer William Huynh to the Comprehensive Antibiotic Resistance Database staff. Looking forward to pushing CARD forward with William’s help!

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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:

Dr. Samira Mubareka Infectious Diseases Physician & Virologist – Sunnybrook Health Sciences Centre & Research Institute and the University of Toronto

COVID-19 Research: Genomics, Rapid Execution & Funding

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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.

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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!

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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

bioRxiv doi:10.1101/2020.04.11.037382

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

See also: McMaster researcher plays key role in isolating COVID-19 virus for use in urgent research

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COVID19 kept us from celebrating together, but we are very proud of the work you have accomplished!

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)!

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Quick update on the status of the McArthur Lab and the Comprehensive Antibiotic Resistance Database. While our home institution McMaster University is closed to on-site research and undergraduate/graduate teaching, all McArthur Lab members and CARD staff are working from home. However, like many genomics labs in Canada we are directly helping our clinical colleagues in analysis of SARS-CoV-2 sequences, lending processing power, staff time, and expertise. Response time for CARD might be a bit slow as we are stretched a bit thin. But on May 1st, 2020 we will be joined by William Huynh as Junior CARD Curator & Help Desk manager. We are excited to have William join us and expect to come back strong supporting the AMR research community in May.

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