Ana T Duggan, Jennifer Klunk, Ashleigh F Porter, Anna N Dhody, Robert Hicks, Geoffrey L Smith, Margaret Humphreys, Andrea M McCollum, Whitni B Davidson, Kimberly Wilkins, Yu Li, Amanda Burke, Hanna Polasky, Lowell Flanders, Debi Poinar, Amogelang R Raphenya, Tammy T Y Lau, Brian Alcock, Andrew G McArthur, G Brian Golding, Edward C Holmes, Hendrik N Poinar

Genome Biol. 2020 Jul 20;21(1):175.

Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.

Image: CDC/Dr. Fred Murphy; Sylvia Whitfield, CC BY

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Congratulations to Kara Tsang and Arman Edalatmand for being awarded Ontario Graduate Scholarships! Spoiler Alert: Arman is joining us for his Biochemistry & Biomedical Sciences MSc in September!

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Arinjay Banerjee, Patrick Budylowski, Daniel Richard, Hassaan Maan, Jennifer A. Aguiar, Nader El-Sayes, Michael R. D’Agostino, Benjamin J.-M. Tremblay, Sam Afkhami, Mehran Karimzadeh, Lily Yip, Mario Ostrowski, Jeremy A. Hirota, Robert Kozak, Terence D. Capellini, Matthew S. Miller, Andrew G. McArthur, Bo Wang, Andrew C. Doxey, Samira Mubareka, & Karen Mossman

bioRxiv doi:10.1101/2020.06.18.158154

Two highly pathogenic human coronaviruses that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) have evolved proteins that can inhibit host antiviral responses, likely contributing to disease progression and high case-fatality rates. SARS-CoV-2 emerged in December 2019 resulting in a global pandemic. Recent studies have shown that SARS-CoV-2 is unable to induce a robust type I interferon (IFN) response in human cells, leading to speculation about the ability of SARS-CoV-2 to inhibit innate antiviral responses. However, innate antiviral responses are dynamic in nature and gene expression levels rapidly change within minutes to hours. In this study, we have performed a time series RNA-seq and selective immunoblot analysis of SARS-CoV-2 infected lung (Calu-3) cells to characterize early virus-host processes. SARS-CoV-2 infection upregulated transcripts for type I IFNs and interferon stimulated genes (ISGs) after 12 hours. Furthermore, we analyzed the ability of SARS-CoV-2 to inhibit type I IFN production and downstream antiviral signaling in human cells. Using exogenous stimuli, we discovered that SARS-CoV-2 is unable to modulate IFNβ production and downstream expression of ISGs, such as IRF7 and IFIT1. Thus, data from our study indicate that SARS-CoV-2 may have evolved additional mechanisms, such as masking of viral nucleic acid sensing by host cells to mount a dampened innate antiviral response. Further studies are required to fully identify the range of immune-modulatory strategies of SARS-CoV-2.


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Maan, H., H. Mbareche, A.R. Raphenya, A. Banerjee, J.A. Nasir, R.A. Kozak, N. Knox, S. Mubareka, A.G. McArthur, & B. Wang.

The Lancet Digital Health, in press.

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

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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:


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The McArthur lab welcomes Ahmed Draia for an internship placement as part of McMaster’s Masters of Biomedical Discovery & Commercialization (MBDC) program. Reflective of his joint training in business and biomedical discovery, Ahmed will be spending 4 months with us as Project Manager for our Ontario Coronavirus Genomics Coalition (ONCoV) work.

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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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