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Point-of-care tests (POCT) are promising tools to detect SARS-CoV-2 in specific settings. Initial reports suggest the ID NOW™ COVID-19 assay (Abbott Diagnostics Inc, USA) is less sensitive than standard real-time reverse transcription polymerase chain reaction (rRT-PCR) assays. This has raised concern over false negatives in SARS-CoV-2 POCT. We compared the performance of the ID NOW™ COVID-19 assay to our in-house rRT-PCR assay to assess whether dry swabs used in ID NOW™ testing could be stored in transport media and be re-tested by rRT-PCR for redundancy and to provide material for further investigation. Paired respiratory swabs collected from patients at three acute care hospitals were used. One swab in transport media (McMaster Molecular Media (MMM)) was tested for SARS-CoV-2 by a laboratory-developed two-target rRT-PCR assay. The second was stored dry in a sterile container and tested by the ID NOW™ COVID-19 assay. Following ID NOW™ testing, dry swabs were stored in MMM for up to 48 h and re-tested by rRT-PCR. Serially diluted SARS-CoV-2 particles were used to assess the impact of heat inactivation and storage time. Respiratory swabs (n = 343) from 179 individuals were included. Using rRT-PCR results as the comparator, the ID NOW™ COVID-19 assay had positive (PPA) and negative (NPA) percent agreements of 87.0% (95% CI:0.74–0.94) and 99.7% (95% CI:0.98–0.99). Re-tested swabs placed in MMM following ID NOW testing had PPA and NPA of 88.8% (95% CI:0.76–0.95) and 99.7% (95% CI:0.98–0.99), respectively. Storing spent dry swabs in transport media for redundancy rRT-PCR testing is a potential approach to address possible false negatives with the ID NOW™ COVID-19 assay.
Laura E Burnes; Shawn T Clark; Elena Sheldrake; Amna Faheem; Betty P Poon; Natasha Christie-Holmes; Laura Finlay; Christopher Kandel; Michael Phan; Caylin Frankland; Trevor Lau; Jonathan B Gubbay; Antoine Corbeil; Kevin Katz; Robert A. Kozak. One swab, two tests: validation of dual SARS-CoV-2 testing on the Abbott ID NOW™. Journal of Clinical Virology 2021, 141, 104896 .
AMA StyleLaura E Burnes, Shawn T Clark, Elena Sheldrake, Amna Faheem, Betty P Poon, Natasha Christie-Holmes, Laura Finlay, Christopher Kandel, Michael Phan, Caylin Frankland, Trevor Lau, Jonathan B Gubbay, Antoine Corbeil, Kevin Katz, Robert A. Kozak. One swab, two tests: validation of dual SARS-CoV-2 testing on the Abbott ID NOW™. Journal of Clinical Virology. 2021; 141 ():104896.
Chicago/Turabian StyleLaura E Burnes; Shawn T Clark; Elena Sheldrake; Amna Faheem; Betty P Poon; Natasha Christie-Holmes; Laura Finlay; Christopher Kandel; Michael Phan; Caylin Frankland; Trevor Lau; Jonathan B Gubbay; Antoine Corbeil; Kevin Katz; Robert A. Kozak. 2021. "One swab, two tests: validation of dual SARS-CoV-2 testing on the Abbott ID NOW™." Journal of Clinical Virology 141, no. : 104896.
Background The aim of this prospective cohort study was to determine the burden of SARS-CoV-2 in air and on surfaces in rooms of patients hospitalized with COVID-19, and to identify patient characteristics associated with SARS-CoV-2 environmental contamination. Methods Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at six acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 viral RNA and cultured to determine potential infectivity. Whole viral genomes were sequenced from nasopharyngeal and surface samples. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated using a mixed-effects logistic regression model. Findings SARS-CoV-2 RNA was detected from surfaces (125/474 samples; 42/78 patients) and air (3/146 samples; 3/45 patients) in COVID-19 patient rooms; 14% (6/42) of surface samples from three patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, a PCR-positive nasopharyngeal swab with a cycle threshold of ≤30 on or after surface sampling date, higher Charlson co-morbidity score, and shorter time from onset of illness to sample date were significantly associated with detection of SARS-CoV-2 RNA in surface samples. Interpretation The infrequent recovery of infectious SARS-CoV-2 virus from the environment suggests that the risk to healthcare workers from air and near-patient surfaces in acute care hospital wards is likely limited. Surface contamination was greater when patients were earlier in their course of illness and in those with hypoxia, multiple co-morbidities, and higher SARS-CoV-2 RNA concentration in NP swabs. Our results suggest that, while early detection and isolation of COVID-19 patients is important, air and surfaces may pose limited risk a few days after admission to acute care hospitals.
Jonathon D. Kotwa; Alainna J. Jamal; Hamza Mbareche; Lily Yip; Patryk Aftanas; Shiva Barati; Natalie G. Bell; Elizabeth Bryce; Eric D Coomes; Gloria Crowl; Caroline Duchaine; Amna Faheem; Lubna Farooqi; Ryan Hiebert; Kevin Katz; Saman Khan; Robert Kozak; Angel X. Li; Henna P. Mistry; Mohammad Mozafarihashjin; Jalees A. Nasir; Kuganya Nirmalarajah; Emily M. Panousis; Aimee Paterson; Simon Plenderleith; Jeff Powis; Karren Prost; Renee Schryer; Maureen Taylor; Marc Veillette; Titus Wong; Xi Zoe Zhong; Andrew G. McArthur; Allison J. McGeer; Samira Mubareka. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada. 2021, 1 .
AMA StyleJonathon D. Kotwa, Alainna J. Jamal, Hamza Mbareche, Lily Yip, Patryk Aftanas, Shiva Barati, Natalie G. Bell, Elizabeth Bryce, Eric D Coomes, Gloria Crowl, Caroline Duchaine, Amna Faheem, Lubna Farooqi, Ryan Hiebert, Kevin Katz, Saman Khan, Robert Kozak, Angel X. Li, Henna P. Mistry, Mohammad Mozafarihashjin, Jalees A. Nasir, Kuganya Nirmalarajah, Emily M. Panousis, Aimee Paterson, Simon Plenderleith, Jeff Powis, Karren Prost, Renee Schryer, Maureen Taylor, Marc Veillette, Titus Wong, Xi Zoe Zhong, Andrew G. McArthur, Allison J. McGeer, Samira Mubareka. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada. . 2021; ():1.
Chicago/Turabian StyleJonathon D. Kotwa; Alainna J. Jamal; Hamza Mbareche; Lily Yip; Patryk Aftanas; Shiva Barati; Natalie G. Bell; Elizabeth Bryce; Eric D Coomes; Gloria Crowl; Caroline Duchaine; Amna Faheem; Lubna Farooqi; Ryan Hiebert; Kevin Katz; Saman Khan; Robert Kozak; Angel X. Li; Henna P. Mistry; Mohammad Mozafarihashjin; Jalees A. Nasir; Kuganya Nirmalarajah; Emily M. Panousis; Aimee Paterson; Simon Plenderleith; Jeff Powis; Karren Prost; Renee Schryer; Maureen Taylor; Marc Veillette; Titus Wong; Xi Zoe Zhong; Andrew G. McArthur; Allison J. McGeer; Samira Mubareka. 2021. "Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada." , no. : 1.
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), calls for prompt and accurate diagnosis and rapid turnaround time for test results to limit transmission. Here, we evaluated two independent molecular assays, the Biomeme SARS-CoV-2 test, and the Precision Biomonitoring TripleLock SARS-CoV-2 test on a field-deployable point-of-care real-time PCR instrument, Franklin three9, in combination with Biomeme M1 Sample Prep Cartridge Kit for RNA 2.0 (M1) manual extraction system for rapid, specific, and sensitive detection of SARS-COV-2 in cell culture, human, and animal clinical samples. The Biomeme SARS-CoV-2 assay, which simultaneously detects two viral targets, the orf1ab and S genes, and the Precision Biomonitoring TripleLock SARS-CoV-2 assay that targets the 5′ untranslated region (5′ UTR) and the envelope (E) gene of SARS-CoV-2 were highly sensitive and detected as low as 15 SARS-CoV-2 genome copies per reaction. In addition, the two assays were specific and showed no cross-reactivity with Middle Eastern respiratory syndrome coronavirus (MERS-CoV), infectious bronchitis virus (IBV), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis (TGE) virus, and other common human respiratory viruses and bacterial pathogens. Also, both assays were highly reproducible across different operators and instruments. When used to test animal samples, both assays equally detected SARS-CoV-2 genetic materials in the swabs from SARS-CoV-2-infected hamsters. The M1 lysis buffer completely inactivated SARS-CoV-2 within 10 min at room temperature enabling safe handling of clinical samples. Collectively, these results show that the Biomeme and Precision Biomonitoring TripleLock SARS-CoV-2 mobile testing platforms could reliably and promptly detect SARS-CoV-2 in both human and animal clinical samples in approximately an hour and can be used in remote areas or health care settings not traditionally serviced by a microbiology laboratory.
Chukwunonso Onyilagha; Henna Mistry; Peter Marszal; Mathieu Pinette; Darwyn Kobasa; Nikesh Tailor; Yohannes Berhane; Charles Nfon; Bradley Pickering; Samira Mubareka; David Bulir; Sylvia Chong; Robert Kozak; Aruna Ambagala. Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2. Scientific Reports 2021, 11, 1 -12.
AMA StyleChukwunonso Onyilagha, Henna Mistry, Peter Marszal, Mathieu Pinette, Darwyn Kobasa, Nikesh Tailor, Yohannes Berhane, Charles Nfon, Bradley Pickering, Samira Mubareka, David Bulir, Sylvia Chong, Robert Kozak, Aruna Ambagala. Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2. Scientific Reports. 2021; 11 (1):1-12.
Chicago/Turabian StyleChukwunonso Onyilagha; Henna Mistry; Peter Marszal; Mathieu Pinette; Darwyn Kobasa; Nikesh Tailor; Yohannes Berhane; Charles Nfon; Bradley Pickering; Samira Mubareka; David Bulir; Sylvia Chong; Robert Kozak; Aruna Ambagala. 2021. "Evaluation of mobile real-time polymerase chain reaction tests for the detection of severe acute respiratory syndrome coronavirus 2." Scientific Reports 11, no. 1: 1-12.
Ebola virus (EBOV) is a virulent pathogen, notorious for inducing life-threatening hemorrhagic fever, that has been responsible for several outbreaks in Africa and remains a public health threat. Yet, its pathogenesis is still not completely understood. Although there have been numerous studies on host transcriptional response to EBOV, with an emphasis on the clinical features, the impact of EBOV infection on post-transcriptional regulatory elements, such as microRNAs (miRNAs), remains largely unexplored. MiRNAs are involved in inflammation and immunity and are believed to be important modulators of the host response to viral infection. Here, we have used small RNA sequencing (sRNA-Seq), qPCR and functional analyses to obtain the first comparative miRNA transcriptome (miRNome) of a human liver cell line (Huh7) infected with one of the following three EBOV strains: Mayinga (responsible for the first Zaire outbreak in 1976), Makona (responsible for the West Africa outbreak in 2013–2016) and the epizootic Reston (presumably innocuous to humans). Our results highlight specific miRNA-based immunity pathways and substantial differences between the strains beyond their clinical manifestation and pathogenicity. These analyses shed new light into the molecular signature of liver cells upon EBOV infection and reveal new insights into miRNA-based virus attack and host defense strategy.
Idrissa Diallo; Jeffrey Ho; Benoit Laffont; Jonathan Laugier; Abderrahim Benmoussa; Marine Lambert; Zeinab Husseini; Geoff Soule; Robert Kozak; Gary Kobinger; Patrick Provost. Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. International Journal of Molecular Sciences 2021, 22, 3792 .
AMA StyleIdrissa Diallo, Jeffrey Ho, Benoit Laffont, Jonathan Laugier, Abderrahim Benmoussa, Marine Lambert, Zeinab Husseini, Geoff Soule, Robert Kozak, Gary Kobinger, Patrick Provost. Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. International Journal of Molecular Sciences. 2021; 22 (7):3792.
Chicago/Turabian StyleIdrissa Diallo; Jeffrey Ho; Benoit Laffont; Jonathan Laugier; Abderrahim Benmoussa; Marine Lambert; Zeinab Husseini; Geoff Soule; Robert Kozak; Gary Kobinger; Patrick Provost. 2021. "Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus." International Journal of Molecular Sciences 22, no. 7: 3792.
We describe the case of a 33-year-old woman with recurrent granulomatous mastitis associated with Corynebacterium kroppenstedtii. This organism has been increasingly associated with granulomatous mastitis, specifically the cystic neutrophilic histopathologic variant, although currently there is a paucity both of reported cases and genomic sequence data. We highlight the challenges in the diagnosis and treatment of this entity, in particular focusing on the various methods of microbiologic identification, including MALDI-TOF, 16 s rRNA PCR and whole-genome sequencing.
Charlie Tan; Fang-I Lu; Patryk Aftanas; Kara K. Tsang; Samira Mubareka; Adrienne Chan; Robert Kozak. Whole genome sequence of Corynebacterium kroppenstedtii isolated from a case of recurrent granulomatous mastitis. IDCases 2020, 23, e01034 .
AMA StyleCharlie Tan, Fang-I Lu, Patryk Aftanas, Kara K. Tsang, Samira Mubareka, Adrienne Chan, Robert Kozak. Whole genome sequence of Corynebacterium kroppenstedtii isolated from a case of recurrent granulomatous mastitis. IDCases. 2020; 23 ():e01034.
Chicago/Turabian StyleCharlie Tan; Fang-I Lu; Patryk Aftanas; Kara K. Tsang; Samira Mubareka; Adrienne Chan; Robert Kozak. 2020. "Whole genome sequence of Corynebacterium kroppenstedtii isolated from a case of recurrent granulomatous mastitis." IDCases 23, no. : e01034.
Widely available and easily accessible testing for COVID-19 is a cornerstone of pandemic containment strategies. Nasopharyngeal swabs (NPS) are the currently accepted standard for sample collection but are limited by their need for collection devices and sampling by trained healthcare professionals. The aim of this study was to compare the performance of saliva to NPS in an outpatient setting. This was a prospective study conducted at three centers, which compared the performance of saliva and NPS samples collected at the time of assessment center visit. Samples were tested by real-time reverse transcription polymerase chain reaction and sensitivity and overall agreement determined between saliva and NPS. Clinical data was abstracted by chart review for select study participants. Of the 432 paired samples, 46 were positive for SARS-CoV-2, with seven discordant observed between the two sample types (four individuals testing positive only by NPS and three by saliva only). The observed agreement was 98.4% (kappa coefficient 0.91) and a composite reference standard demonstrated sensitivity of 0.91 and 0.93 for saliva and NPS samples, respectively. On average, the Ct values obtained from saliva as compared to NPS were higher by 2.76. This study demonstrates that saliva performs comparably to NPS for the detection of SARS-CoV-2. Saliva was simple to collect, did not require transport media, and could be tested with equipment readily available at most laboratories. The use of saliva as an acceptable alternative to NPS could support the use of widespread surveillance testing for SARS-CoV-2.
Christopher Kandel; Jennifer Zheng; Janine McCready; Mihaela Anca Serbanescu; Hilary Racher; Melissa Desaulnier; Jeff E Powis; Kyle Vojdani; Laura Finlay; Elena Sheldrake; Christie Vermeiren; Kevin Katz; Allison McGeer; Robert Kozak; Lee W Goneau. Detection of SARS-CoV-2 from Saliva as Compared to Nasopharyngeal Swabs in Outpatients. Viruses 2020, 12, 1314 .
AMA StyleChristopher Kandel, Jennifer Zheng, Janine McCready, Mihaela Anca Serbanescu, Hilary Racher, Melissa Desaulnier, Jeff E Powis, Kyle Vojdani, Laura Finlay, Elena Sheldrake, Christie Vermeiren, Kevin Katz, Allison McGeer, Robert Kozak, Lee W Goneau. Detection of SARS-CoV-2 from Saliva as Compared to Nasopharyngeal Swabs in Outpatients. Viruses. 2020; 12 (11):1314.
Chicago/Turabian StyleChristopher Kandel; Jennifer Zheng; Janine McCready; Mihaela Anca Serbanescu; Hilary Racher; Melissa Desaulnier; Jeff E Powis; Kyle Vojdani; Laura Finlay; Elena Sheldrake; Christie Vermeiren; Kevin Katz; Allison McGeer; Robert Kozak; Lee W Goneau. 2020. "Detection of SARS-CoV-2 from Saliva as Compared to Nasopharyngeal Swabs in Outpatients." Viruses 12, no. 11: 1314.
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.
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. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses 2020, 12, 895 .
AMA StyleJalees 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. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses. 2020; 12 (8):895.
Chicago/Turabian StyleJalees 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. 2020. "A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture." Viruses 12, no. 8: 895.
SUMMARY Type I interferons (IFNs) are our first line of defence against a virus. Protein over-expression studies have suggested the ability of SARS-CoV-2 proteins to block IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wildtype SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are lacking. Here we demonstrate that SARS-CoV-2 infection induces a mild type I IFN response in vitro and in moderate cases of COVID-19. In vitro stimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Our data demonstrate that SARS-CoV-2 is not adept in blocking type I IFN responses and provide support for ongoing IFN clinical trials.
Arinjay Banerjee; Nader El-Sayes; Patrick Budylowski; Daniel Richard; Hassaan Maan; Jennifer A. Aguiar; Kaushal Baid; Michael R. D’Agostino; Jann Catherine Ang; Benjamin J.-M. Tremblay; Sam Afkhami; Mehran Karimzadeh; Aaron T. Irving; Lily Yip; Mario A Ostrowski; Jeremy A. Hirota; Robert Kozak; Terence D. Capellini; Matthew S. Miller; Bo Wang; Samira Mubareka; Allison J. McGeer; Andrew G. McArthur; Andrew C. Doxey; Karen Mossman. Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses. 2020, 1 .
AMA StyleArinjay Banerjee, Nader El-Sayes, Patrick Budylowski, Daniel Richard, Hassaan Maan, Jennifer A. Aguiar, Kaushal Baid, Michael R. D’Agostino, Jann Catherine Ang, Benjamin J.-M. Tremblay, Sam Afkhami, Mehran Karimzadeh, Aaron T. Irving, Lily Yip, Mario A Ostrowski, Jeremy A. Hirota, Robert Kozak, Terence D. Capellini, Matthew S. Miller, Bo Wang, Samira Mubareka, Allison J. McGeer, Andrew G. McArthur, Andrew C. Doxey, Karen Mossman. Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses. . 2020; ():1.
Chicago/Turabian StyleArinjay Banerjee; Nader El-Sayes; Patrick Budylowski; Daniel Richard; Hassaan Maan; Jennifer A. Aguiar; Kaushal Baid; Michael R. D’Agostino; Jann Catherine Ang; Benjamin J.-M. Tremblay; Sam Afkhami; Mehran Karimzadeh; Aaron T. Irving; Lily Yip; Mario A Ostrowski; Jeremy A. Hirota; Robert Kozak; Terence D. Capellini; Matthew S. Miller; Bo Wang; Samira Mubareka; Allison J. McGeer; Andrew G. McArthur; Andrew C. Doxey; Karen Mossman. 2020. "Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses." , no. : 1.
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.
Arinjay Banerjee; Jalees A. Nasir; Patrick Budylowski; Lily Yip; Patryk Aftanas; Natasha Christie; Ayoob Ghalami; Kaushal Baid; Amogelang R. Raphenya; Jeremy A Hirota; Matthew S. Miller; Allison J McGeer; Mario A Ostrowski; Robert A. Kozak; Andrew G McArthur; Karen Mossman; Samira Mubareka. Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2. 2020, 1 .
AMA StyleArinjay Banerjee, Jalees A. Nasir, Patrick Budylowski, Lily Yip, Patryk Aftanas, Natasha Christie, Ayoob Ghalami, Kaushal Baid, Amogelang R. Raphenya, Jeremy A Hirota, Matthew S. Miller, Allison J McGeer, Mario A Ostrowski, Robert A. Kozak, Andrew G McArthur, Karen Mossman, Samira Mubareka. Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2. . 2020; ():1.
Chicago/Turabian StyleArinjay Banerjee; Jalees A. Nasir; Patrick Budylowski; Lily Yip; Patryk Aftanas; Natasha Christie; Ayoob Ghalami; Kaushal Baid; Amogelang R. Raphenya; Jeremy A Hirota; Matthew S. Miller; Allison J McGeer; Mario A Ostrowski; Robert A. Kozak; Andrew G McArthur; Karen Mossman; Samira Mubareka. 2020. "Isolation, sequence, infectivity and replication kinetics of SARS-CoV-2." , no. : 1.
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause a hemorrhagic fever in humans, with a case fatality rate of up to 40%. Cases of CCHFV have been reported in Africa, Asia, and southern Europe; and recently, due to the expanding range of its vector, autochthonous cases have been reported in Spain. Although it was discovered over 70 years ago, our understanding of the pathogenesis of this virus remains limited.
Robert A. Kozak; Russell S. Fraser; Mia J. Biondi; Anna Majer; Sarah J. Medina; Bryan D. Griffin; Darwyn Kobasa; Patrick J. Stapleton; Chantel Urfano; Giorgi Babuadze; Kym Antonation; Lisa Fernando; Stephanie Booth; Brandon N. Lillie; Gary P. Kobinger. Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus. PLOS Neglected Tropical Diseases 2020, 14, e0008105 .
AMA StyleRobert A. Kozak, Russell S. Fraser, Mia J. Biondi, Anna Majer, Sarah J. Medina, Bryan D. Griffin, Darwyn Kobasa, Patrick J. Stapleton, Chantel Urfano, Giorgi Babuadze, Kym Antonation, Lisa Fernando, Stephanie Booth, Brandon N. Lillie, Gary P. Kobinger. Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus. PLOS Neglected Tropical Diseases. 2020; 14 (4):e0008105.
Chicago/Turabian StyleRobert A. Kozak; Russell S. Fraser; Mia J. Biondi; Anna Majer; Sarah J. Medina; Bryan D. Griffin; Darwyn Kobasa; Patrick J. Stapleton; Chantel Urfano; Giorgi Babuadze; Kym Antonation; Lisa Fernando; Stephanie Booth; Brandon N. Lillie; Gary P. Kobinger. 2020. "Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus." PLOS Neglected Tropical Diseases 14, no. 4: e0008105.
The World Health Organization has highlighted the need for improved surveillance and understanding of the health burden imposed by non-influenza RNA respiratory viruses. Human coronaviruses (CoVs) are a major cause of respiratory and gastrointestinal tract infections with associated morbidity and mortality. The objective of our study was to characterize the epidemiology of CoVs in our tertiary care centre, and identify clinical correlates of disease severity. A cross-sectional study was performed of 226 patients admitted with confirmed CoV respiratory tract infection between 2010 and 2016. Variables consistent with a severe disease burden were evaluated including symptoms, length of stay, intensive care unit (ICU) admission and mortality. CoVs represented 11.3% of all positive respiratory virus samples and OC43 was the most commonly identified CoV. The majority of infections were community-associated while 21.6% were considered nosocomial. The average length of stay was 11.8 days with 17.3% of patients requiring ICU admission and an all-cause mortality of 7%. In a multivariate model, female gender and smoking were associated with increased likelihood of admission to ICU or death. This study highlights the significant burden of CoVs and justifies the need for surveillance in the acute care setting.
Robert Kozak; Karren Prost; Lily Yip; Victoria Williams; Jerome A. Leis; Samira Mubareka. Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario. Journal of Clinical Virology 2020, 126, 104338 -104338.
AMA StyleRobert Kozak, Karren Prost, Lily Yip, Victoria Williams, Jerome A. Leis, Samira Mubareka. Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario. Journal of Clinical Virology. 2020; 126 ():104338-104338.
Chicago/Turabian StyleRobert Kozak; Karren Prost; Lily Yip; Victoria Williams; Jerome A. Leis; Samira Mubareka. 2020. "Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario." Journal of Clinical Virology 126, no. : 104338-104338.
SARS-CoV-2 is a novel betacoronavirus and the aetiological agent of the current COVID-19 outbreak that originated in Hubei Province, China. While polymerase chain reaction is the front-line tool for SARS-CoV-2 surveillance, application of amplification-free and culture-free methods for isolation of SARS-CoV-2 RNA, partnered with next-generation sequencing, would provide a useful tool for both surveillance and research of SARS-CoV-2. We here release into the public domain a set of bait capture hybridization probe sequences for enrichment of SARS-CoV-2 RNA from complex biological samples. These probe sequences have been designed using rigorous bioinformatics methods to provide sensitivity, accuracy, and minimal off-target hybridization. Probe design was based on existing, validated approaches for detecting antimicrobial resistance genes in complex samples and it is our hope that this SARS-CoV-2 bait capture platform, once validated by those with samples in hand, will be of aid in combating the current outbreak.
Jalees A. Nasir; David J. Speicher; Robert A. Kozak; Hendrik N. Poinar; Matthew S. Miller; Andrew G. McArthur. Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2. 2020, 1 .
AMA StyleJalees A. Nasir, David J. Speicher, Robert A. Kozak, Hendrik N. Poinar, Matthew S. Miller, Andrew G. McArthur. Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2. . 2020; ():1.
Chicago/Turabian StyleJalees A. Nasir; David J. Speicher; Robert A. Kozak; Hendrik N. Poinar; Matthew S. Miller; Andrew G. McArthur. 2020. "Rapid Design of a Bait Capture Platform for Culture- and Amplification-Free Next-Generation Sequencing of SARS-CoV-2." , no. : 1.
In order to expand hepatitis C virus (HCV) screening, a change in the diagnostic paradigm is warranted to improve accessibility and decrease costs, such as utilizing dried blood spot (DBS) collection. In our study, blood from 68 patients with chronic HCV infection was spotted onto DBS cards and stored at the following temperatures for one week: −80 °C, 4 °C, 21 °C, 37 °C, and alternating 37 °C and 4 °C; to assess whether temperature change during transportation would affect sensitivity. Sample was eluted from the DBS cards and tested for HCV antibodies (HCV-Ab) and HCV core antigen (core-Ag). HCV-Abs were detected from 68/68 DBS samples at −80 °C, 4 °C, 21 °C, and 67/68 at 37 °C and alternating 37 °C and 4 °C. Sensitivity of core-Ag was as follows: 94% (−80 °C), 94% (4 °C), 91% (21 °C), 93% (37 °C), and 93% (37 °C/4 °C). Not only did temperature not greatly affect sensitivity, but sensitivities are higher than previously reported, and support the use of this assay as an alternative to HCV RNA. We then completed a head-to-head comparison (n = 49) of venous versus capillary samples, and one versus two DBS. No difference in core-Ag sensitivity was observed by sample type, but there was an improvement when using two spots. We conclude that HCV-Abs and core-Ag testing from DBS cards has high diagnostic accuracy and could be considered as an alternative to HCV RNA in certain settings.
Mia J. Biondi; Marjolein Van Tilborg; David Smookler; Gregory Heymann; Analiza Aquino; Stephen Perusini; Erin Mandel; Robert A. Kozak; Vera Cherepanov; Matthew Kowgier; Bettina Hansen; Lee W. Goneau; Harry L.A. Janssen; Tony Mazzulli; Gavin Cloherty; Robert J. De Knegt; Jordan J. Feld. Hepatitis C Core-Antigen Testing from Dried Blood Spots. Viruses 2019, 11, 830 .
AMA StyleMia J. Biondi, Marjolein Van Tilborg, David Smookler, Gregory Heymann, Analiza Aquino, Stephen Perusini, Erin Mandel, Robert A. Kozak, Vera Cherepanov, Matthew Kowgier, Bettina Hansen, Lee W. Goneau, Harry L.A. Janssen, Tony Mazzulli, Gavin Cloherty, Robert J. De Knegt, Jordan J. Feld. Hepatitis C Core-Antigen Testing from Dried Blood Spots. Viruses. 2019; 11 (9):830.
Chicago/Turabian StyleMia J. Biondi; Marjolein Van Tilborg; David Smookler; Gregory Heymann; Analiza Aquino; Stephen Perusini; Erin Mandel; Robert A. Kozak; Vera Cherepanov; Matthew Kowgier; Bettina Hansen; Lee W. Goneau; Harry L.A. Janssen; Tony Mazzulli; Gavin Cloherty; Robert J. De Knegt; Jordan J. Feld. 2019. "Hepatitis C Core-Antigen Testing from Dried Blood Spots." Viruses 11, no. 9: 830.