Nasir, J.A et al. 2020. SIGNALing the Need for Surveillance: A Comparison of Whole Genome Sequencing Methods for SARS-CoV-2.
Edalatmand, A. & A.G. McArthur. 2020. Contextualizing antimicrobial resistance elements through biomedical literature information extraction.
Omer, H. & A.G. McArthur. 2020. Biocuration of fluoroquinolone-resistant Salmonella enterica and the challenges of AMR knowledge acquisition.
Panousis, E. et al. 2020. Analysis and Dissemination of RISC-CoV genome sequences using the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL).
Imtiaz, H. et al. 2020. Biocuration and bioinformatics for antimicrobial resistance (AMR) profiling in N. gonorrhoeae.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been reported in the Kingdom of Saudi Arabia, where Middle East respiratory syndrome coronavirus (MERS-CoV) causes seasonal outbreaks with a case fatality rate of ~37 %. Here we show that there exists a theoretical possibility of future recombination events between SARS-CoV-2 and MERS-CoV RNA. Through computational analyses, we have identified homologous genomic regions within the ORF1ab and S genes that could facilitate recombination, and have analysed co-expression patterns of the cellular receptors for SARS-CoV-2 and MERS-CoV, ACE2 and DPP4, respectively, to identify human anatomical sites that could facilitate co-infection. Furthermore, we have investigated the likely susceptibility of various animal species to MERS-CoV and SARS-CoV-2 infection by comparing known virus spike protein-receptor interacting residues. In conclusion, we suggest that a recombination between SARS-CoV-2 and MERS-CoV RNA is possible and urge public health laboratories in high-risk areas to develop diagnostic capability for the detection of recombined coronaviruses in patient samples.
Jalees A. Nasir, Robert A. Kozak, Patryk Aftanas, Amogelang R. Raphenya, Kendrick M. Smith, Finlay Maguire, Hassaan Maan, Muhannad Alruwaili, Arinjay Banerjee, Hamza Mbareche, Brian P. Alcock, Natalie C. Knox, Karen Mossman, Bo Wang, Julian A. Hiscox, Andrew G. McArthur, & Samira Mubareka
Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts.
Emma J. Griffiths, Ruth E. Timme, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Catarina Inês Mendes, Simon H. Tausch, Allison Black, Thomas R. Connor, Gregory H. Tyson, David M. Aanensen, Brian Alcock, Josefina Campos, Alan Christoffels, Anders Gonçalves da Silva, Emma Hodcroft, William W.L. Hsiao, Lee S. Katz, Samuel M. Nicholls, Paul E. Oluniyi, Idowu B. Olawoye, Amogelang R. Raphenya, Ana Tereza R. Vasconcelos, Adam A. Witney, & Duncan R. MacCannell
The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.
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
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
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
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.
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
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.