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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.
Cancer immunotherapies using monoclonal antibodies to block inhibitory checkpoints are showing durable remissions in many types of cancer patients, although the majority of breast cancer patients acquire little benefit. Human melanoma and lung cancer patient studies suggest that immune checkpoint inhibitors are often potent in patients that already have intratumoral T cell infiltrate; although it remains unknown what types of interventions can result in an intratumoral T cell infiltrate in breast cancer. Using non-T cell-inflamed mammary tumors, we assessed what biological processes and downstream inflammation can overcome the barriers to spontaneous T cell priming. Here we show a specific type of combination therapy, consisting of oncolytic virus and chemotherapy, activates necroptosis and limits tumor growth in autochthonous tumors. Combination therapy activates proinflammatory cytokines; intratumoral influx of myeloid cells and cytotoxic T cell infiltrate in locally treated and distant autochthonous tumors to render them susceptible to immune checkpoint inhibitors.
Samuel T. Workenhe; Andrew Nguyen; David Bakhshinyan; Jiarun Wei; David N. Hare; Kelly L. MacNeill; Yonghong Wan; Andrew Oberst; Jonathan L. Bramson; Jalees A. Nasir; Alyssa Vito; Nader El-Sayes; Sheila K. Singh; Andrew G. McArthur; Karen L. Mossman. De novo necroptosis creates an inflammatory environment mediating tumor susceptibility to immune checkpoint inhibitors. Communications Biology 2020, 3, 645 .
AMA StyleSamuel T. Workenhe, Andrew Nguyen, David Bakhshinyan, Jiarun Wei, David N. Hare, Kelly L. MacNeill, Yonghong Wan, Andrew Oberst, Jonathan L. Bramson, Jalees A. Nasir, Alyssa Vito, Nader El-Sayes, Sheila K. Singh, Andrew G. McArthur, Karen L. Mossman. De novo necroptosis creates an inflammatory environment mediating tumor susceptibility to immune checkpoint inhibitors. Communications Biology. 2020; 3 (1):645.
Chicago/Turabian StyleSamuel T. Workenhe; Andrew Nguyen; David Bakhshinyan; Jiarun Wei; David N. Hare; Kelly L. MacNeill; Yonghong Wan; Andrew Oberst; Jonathan L. Bramson; Jalees A. Nasir; Alyssa Vito; Nader El-Sayes; Sheila K. Singh; Andrew G. McArthur; Karen L. Mossman. 2020. "De novo necroptosis creates an inflammatory environment mediating tumor susceptibility to immune checkpoint inhibitors." Communications Biology 3, no. 1: 645.
Since its emergence in Wuhan, China, in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected ≈6 million persons worldwide. As SARS-CoV-2 spreads across the planet, we explored the range of human cells that can be infected by this virus. We isolated SARS-CoV-2 from 2 infected patients in Toronto, Canada; determined the genomic sequences; and identified single-nucleotide changes in representative populations of our virus stocks. We also tested a wide range of human immune cells for productive infection with SARS-CoV-2. We confirm that human primary peripheral blood mononuclear cells are not permissive for SARS-CoV-2. As SARS-CoV-2 continues to spread globally, it is essential to monitor single-nucleotide polymorphisms in the virus and to continue to isolate circulating viruses to determine viral genotype and phenotype by using in vitro and in vivo infection models.
Arinjay Banerjee; Jalees 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 Ostrowski; Robert A. Kozak; Andrew G. McArthur; Karen Mossman; Samira Mubareka. Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2. Emerging Infectious Diseases 2020, 26, 2054 -2063.
AMA StyleArinjay Banerjee, Jalees 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 Ostrowski, Robert A. Kozak, Andrew G. McArthur, Karen Mossman, Samira Mubareka. Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2. Emerging Infectious Diseases. 2020; 26 (9):2054-2063.
Chicago/Turabian StyleArinjay Banerjee; Jalees 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 Ostrowski; Robert A. Kozak; Andrew G. McArthur; Karen Mossman; Samira Mubareka. 2020. "Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2." Emerging Infectious Diseases 26, no. 9: 2054-2063.
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.
Hassaan Maan; Hamza Mbareche; Amogelang R Raphenya; Arinjay Banerjee; Jalees A Nasir; Robert A Kozak; Natalie Knox; Samira Mubareka; Andrew G McArthur; Bo Wang. Genotyping SARS-CoV-2 through an interactive web application. The Lancet Digital Health 2020, 2, e340 -e341.
AMA StyleHassaan Maan, Hamza Mbareche, Amogelang R Raphenya, Arinjay Banerjee, Jalees A Nasir, Robert A Kozak, Natalie Knox, Samira Mubareka, Andrew G McArthur, Bo Wang. Genotyping SARS-CoV-2 through an interactive web application. The Lancet Digital Health. 2020; 2 (7):e340-e341.
Chicago/Turabian StyleHassaan Maan; Hamza Mbareche; Amogelang R Raphenya; Arinjay Banerjee; Jalees A Nasir; Robert A Kozak; Natalie Knox; Samira Mubareka; Andrew G McArthur; Bo Wang. 2020. "Genotyping SARS-CoV-2 through an interactive web application." The Lancet Digital Health 2, no. 7: e340-e341.
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.
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.
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
Brian P Alcock; Amogelang R Raphenya; Tammy T Y Lau; Kara K Tsang; Mégane Bouchard; Arman Edalatmand; William Huynh; Anna-Lisa V Nguyen; Annie A Cheng; Sihan Liu; Sally Y Min; Anatoly Miroshnichenko; Hiu-Ki Tran; Rafik E Werfalli; Jalees A Nasir; Martins Oloni; David J Speicher; Alexandra Florescu; Bhavya Singh; Mateusz Faltyn; Anastasia Hernandez-Koutoucheva; Arjun N Sharma; Emily Bordeleau; Andrew C Pawlowski; Haley L Zubyk; Damion Dooley; Emma Griffiths; Finlay Maguire; Geoff L Winsor; Robert G Beiko; Fiona S L Brinkman; William W L Hsiao; Gary V Domselaar; Andrew G McArthur. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research 2019, 48, D517 -D525.
AMA StyleBrian P Alcock, Amogelang R Raphenya, Tammy T Y Lau, Kara K Tsang, Mégane Bouchard, Arman Edalatmand, William Huynh, Anna-Lisa V Nguyen, Annie A Cheng, Sihan Liu, Sally Y Min, Anatoly Miroshnichenko, Hiu-Ki Tran, Rafik E Werfalli, Jalees A Nasir, Martins Oloni, David J Speicher, Alexandra Florescu, Bhavya Singh, Mateusz Faltyn, Anastasia Hernandez-Koutoucheva, Arjun N Sharma, Emily Bordeleau, Andrew C Pawlowski, Haley L Zubyk, Damion Dooley, Emma Griffiths, Finlay Maguire, Geoff L Winsor, Robert G Beiko, Fiona S L Brinkman, William W L Hsiao, Gary V Domselaar, Andrew G McArthur. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research. 2019; 48 ():D517-D525.
Chicago/Turabian StyleBrian P Alcock; Amogelang R Raphenya; Tammy T Y Lau; Kara K Tsang; Mégane Bouchard; Arman Edalatmand; William Huynh; Anna-Lisa V Nguyen; Annie A Cheng; Sihan Liu; Sally Y Min; Anatoly Miroshnichenko; Hiu-Ki Tran; Rafik E Werfalli; Jalees A Nasir; Martins Oloni; David J Speicher; Alexandra Florescu; Bhavya Singh; Mateusz Faltyn; Anastasia Hernandez-Koutoucheva; Arjun N Sharma; Emily Bordeleau; Andrew C Pawlowski; Haley L Zubyk; Damion Dooley; Emma Griffiths; Finlay Maguire; Geoff L Winsor; Robert G Beiko; Fiona S L Brinkman; William W L Hsiao; Gary V Domselaar; Andrew G McArthur. 2019. "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database." Nucleic Acids Research 48, no. : D517-D525.