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2. Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Author

Kotwa, Jonathon D., Lobb, Briallen, Massé, Ariane, Gagnier, Marianne, Aftanas, Patryk, Banerjee, Arinjay, Banete, Andra, Blais-Savoie, Juliette, Bowman, Jeff, Buchanan, Tore, Chee, Hsien-Yao, Kruczkiewicz, Peter, Nirmalarajah, Kuganya, Soos, Catherine, Vernygora, Oksana, Yip, Lily, Lindsay, L. Robbin, McGeer, Allison J., Maguire, Finlay, Lung, Oliver, Doxey, Andrew C., Pickering, Bradley, and Mubareka, Samira

Published
2023
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4. Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

Author

Pickering, Bradley, Lung, Oliver, Maguire, Finlay, Kruczkiewicz, Peter, Kotwa, Jonathon D., Buchanan, Tore, Gagnier, Marianne, Guthrie, Jennifer L., Jardine, Claire M., Marchand-Austin, Alex, Massé, Ariane, McClinchey, Heather, Nirmalarajah, Kuganya, Aftanas, Patryk, Blais-Savoie, Juliette, Chee, Hsien-Yao, Chien, Emily, Yim, Winfield, Banete, Andra, Griffin, Bryan D., Yip, Lily, Goolia, Melissa, Suderman, Matthew, Pinette, Mathieu, Smith, Greg, Sullivan, Daniel, Rudar, Josip, Vernygora, Oksana, Adey, Elizabeth, Nebroski, Michelle, Goyette, Guillaume, Finzi, Andrés, Laroche, Geneviève, Ariana, Ardeshir, Vahkal, Brett, Côté, Marceline, McGeer, Allison J., Nituch, Larissa, Mubareka, Samira, and Bowman, Jeff

Published
2022
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6. Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study.

Author

Nirmalarajah, Kuganya, Aftanas, Patryk, Barati, Shiva, Chien, Emily, Crowl, Gloria, Faheem, Amna, Farooqi, Lubna, Jamal, Alainna J., Khan, Saman, Kotwa, Jonathon D., Li, Angel X., Mozafarihashjin, Mohammad, Nasir, Jalees A., Shigayeva, Altynay, Yim, Winfield, Yip, Lily, Zhong, Xi Zoe, Katz, Kevin, Kozak, Robert, and McArthur, Andrew G.

Subjects
SUPERVISED learning, COVID-19, AMINO acid sequence, PATIENTS' attitudes, CORONAVIRUSES
Abstract

Background: Drivers of COVID-19 severity are multifactorial and include multidimensional and potentially interacting factors encompassing viral determinants and host-related factors (i.e., demographics, pre-existing conditions and/or genetics), thus complicating the prediction of clinical outcomes for different severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants. Although millions of SARS-CoV-2 genomes have been publicly shared in global databases, linkages with detailed clinical data are scarce. Therefore, we aimed to establish a COVID-19 patient dataset with linked clinical and viral genomic data to then examine associations between SARS-CoV-2 genomic signatures and clinical disease phenotypes. Methods: A cohort of adult patients with laboratory confirmed SARS-CoV-2 from 11 participating healthcare institutions in the Greater Toronto Area (GTA) were recruited from March 2020 to April 2022. Supervised machine learning (ML) models were developed to predict hospitalization using SARS-CoV-2 lineage-specific genomic signatures, patient demographics, symptoms, and pre-existing comorbidities. The relative importance of these features was then evaluated. Results: Complete clinical data and viral whole genome level information were obtained from 617 patients, 50.4% of whom were hospitalized. Notably, inpatients were older with a mean age of 66.67 years (SD ± 17.64 years), whereas outpatients had a mean age of 44.89 years (SD ± 16.00 years). SHapley Additive exPlanations (SHAP) analyses revealed that underlying vascular disease, underlying pulmonary disease, and fever were the most significant clinical features associated with hospitalization. In models built on the amino acid sequences of functional regions including spike, nucleocapsid, ORF3a, and ORF8 proteins, variants preceding the emergence of variants of concern (VOCs) or pre-VOC variants, were associated with hospitalization. Conclusions: Viral genomic features have limited utility in predicting hospitalization across SARS-CoV-2 diversity. Combining clinical and viral genomic datasets provides perspective on patient specific and virus-related factors that impact COVID-19 disease severity. Overall, clinical features had greater discriminatory power than viral genomic features in predicting hospitalization. [ABSTRACT FROM AUTHOR]

Published
2025
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10. Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses

Author

Banerjee, Arinjay, El-Sayes, Nader, Budylowski, Patrick, Jacob, Rajesh Abraham, Richard, Daniel, Maan, Hassaan, Aguiar, Jennifer A., Demian, Wael L., Baid, Kaushal, D'Agostino, Michael R., Ang, Jann Catherine, Murdza, Tetyana, Tremblay, Benjamin J.-M., Afkhami, Sam, Karimzadeh, Mehran, Irving, Aaron T., Yip, Lily, Ostrowski, Mario, Hirota, Jeremy A., Kozak, Robert, Capellini, Terence D., Miller, Matthew S., Wang, Bo, Mubareka, Samira, McGeer, Allison J., McArthur, Andrew G., Doxey, Andrew C., and Mossman, Karen

Published
2021
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13. Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

Author

Pickering, Bradley, Lung, Oliver, Maguire, Finlay, Kruczkiewicz, Peter, Kotwa, Jonathon D., Buchanan, Tore, Gagnier, Marianne, Guthrie, Jennifer L., Jardine, Claire M., Marchand-Austin, Alex, Massé, Ariane, McClinchey, Heather, Nirmalarajah, Kuganya, Aftanas, Patryk, Blais-Savoie, Juliette, Chee, Hsien-Yao, Chien, Emily, Yim, Winfield, Banete, Andra, Griffin, Bryan D., Yip, Lily, Goolia, Melissa, Suderman, Matthew, Pinette, Mathieu, Smith, Greg, Sullivan, Daniel, Rudar, Josip, Vernygora, Oksana, Adey, Elizabeth, Nebroski, Michelle, Goyette, Guillaume, Finzi, Andrés, Laroche, Geneviève, Ariana, Ardeshir, Vahkal, Brett, Côté, Marceline, McGeer, Allison J., Nituch, Larissa, Mubareka, Samira, and Bowman, Jeff

Published
2023
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14. Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2

Author

Banerjee, Arinjay, Nasir, Jalees A., Budylowski, Patrick, Yip, Lily, Aftanas, Patryk, Christie, Natasha, Ghalami, Ayoob, Baid, Kaushal, Raphenya, Amogelang R., Hirota, Jeremy A., Miller, Matthew S., McGeer, Allison J., Ostrowski, Mario, Kozak, Robert A., McArthur, Andrew G., Mossman, Karen, and Mubareka, Samira

Subjects
Health aspects, Severe acute respiratory syndrome -- Health aspects, Coronaviruses -- Health aspects, Cells (Biology) -- Health aspects, Genetic polymorphisms -- Health aspects, COVID-19 -- Health aspects
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 in Wuhan, China (1). SARS-CoV-2 has since spread to [approximately equal to]185 countries and infected [approximately equal to]6 million [...]

Published
2020
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16. A homogeneous split-luciferase assay for rapid and sensitive detection of anti-SARS CoV-2 antibodies

Author

Yao, Zhong, Drecun, Luka, Aboualizadeh, Farzaneh, Kim, Sun Jin, Li, Zhijie, Wood, Heidi, Valcourt, Emelissa J., Manguiat, Kathy, Plenderleith, Simon, Yip, Lily, Li, Xinliu, Zhong, Zoe, Yue, Feng Yun, Closas, Tatiana, Snider, Jamie, Tomic, Jelena, Drews, Steven J., Drebot, Michael A., McGeer, Allison, Ostrowski, Mario, Mubareka, Samira, Rini, James M., Owen, Shawn, and Stagljar, Igor

Published
2021
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17. Burden of noninfluenza respiratory viral infections in adults admitted to hospital: analysis of a multiyear Canadian surveillance cohort from 2 centres

Author

Lee, Nelson, Smith, Stephanie, Zelyas, Nathan, Klarenbach, Scott, Zapernick, Lori, Bekking, Christian, So, Helen, Yip, Lily, Tipples, Graham, Taylor, Geoff, and Mubareka, Samira

Subjects
Statistics, Care and treatment, Patient outcomes, Hospital patients -- Statistics, Virus diseases -- Statistics -- Care and treatment -- Patient outcomes
Abstract

The global burden of lower respiratory tract infections is substantial, leading to many hospital admissions and deaths, especially among young children and older adults. (1) Respiratory viruses are responsible for [...], BACKGROUND: Data on the outcomes of noninfluenza respiratory virus (NIRV) infections among hospitalized adults are lacking. We aimed to study the burden, severity and outcomes of NIRV infections in this population. METHODS: We analyzed pooled patient data from 2 hospital-based respiratory virus surveillance cohorts in 2 regions of Canada during 3 consecutive seasons (2015/16, 2016/17, 2017/18; n = 2119). We included patients aged [greater than or equal to] 18 years who developed influenza-like illness or pneumonia and were hospitalized for management. We included patients confirmed positive for [greater than or equal to] 1 virus by multiplex polymerase chain reaction assays (respiratory syncytial virus [RSV], human rhinovirus/ enterovirus (hRV), human coronavirus (hCoV), metapneumovirus, parainfluenza virus, adenovirus, influenza viruses). We compared patient characteristics, clinical severity conventional outcomes (e.g., hospital length-of stay, 30-day mortality) and ordinal outcomes (5 levels: discharged, receiving convalescent care, acute ward or intensive care unit [ICU] care and death) for patients with NIRV infections and those with influenza. RESULTS: Among 2119 adults who were admitted to hospital, 1156 patients (54.6%) had NIRV infections (hRV 14.9%, RSV 12.9%, hCoV 8.2%) and 963 patients (45.4%) had influenza (n = 963). Patients with NIRVs were younger (mean 66.4 [standard deviation 20.4] yr), and more commonly had immunocompromising conditions (30.3%) and delay in diagnosis (median 4.0 [interquartile range (IQR) 2.0-7.0] days). Overall, 14.6% (12.4%-19.5%) of NIRV infections were acquired in hospital. Admission to ICU (18.2%, median 6.0 [IQR 3.0-13.0] d), hospital length-of-stay (median 5.0 [IQR 2.0-10.0] d) and 30-day mortality (8.4%; RSV 9.5%, hRV 6.6%, hCoV 9.2%) and the ordinal outcomes were similar for patients with NIRV infection and those with influenza. Age > 60 years, immuno-compromised state and hospital-acquired viral infection were associated with worse outcomes. The estimated median cost per acute care admission was $6000 (IQR $2000-$16 000). INTERPRETATION: The burden of NIRV infection is substantial in adults admitted to hospital and associated outcomes may be as severe as for influenza, suggesting a need to prioritize therapeutics and vaccines for at-risk people.

Published
2021
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19. Surveillance for SARS-CoV-2 in Norway Rats (Rattus norvegicus) from Southern Ontario

Author

Robinson, Sarah J., primary, Kotwa, Jonathon D., additional, Jeeves, Simon P., additional, Himsworth, Chelsea G., additional, Pearl, David L., additional, Weese, J. Scott, additional, Lindsay, L. Robbin, additional, Dibernardo, Antonia, additional, Toledo, Nikki P. L., additional, Pickering, Bradley S., additional, Goolia, Melissa, additional, Chee, Hsien-Yao, additional, Blais-Savoie, Juliette, additional, Chien, Emily, additional, Yim, Winfield, additional, Yip, Lily, additional, Mubareka, Samira, additional, and Jardine, Claire M., additional

Published
2023
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23. Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

Author

Pickering, Bradley, primary, Lung, Oliver, additional, Maguire, Finlay, additional, Kruczkiewicz, Peter, additional, Kotwa, Jonathon D., additional, Buchanan, Tore, additional, Gagnier, Marianne, additional, Guthrie, Jennifer L., additional, Jardine, Claire M., additional, Marchand-Austin, Alex, additional, Massé, Ariane, additional, McClinchey, Heather, additional, Nirmalarajah, Kuganya, additional, Aftanas, Patryk, additional, Blais-Savoie, Juliette, additional, Chee, Hsien-Yao, additional, Chien, Emily, additional, Yim, Winfield, additional, Banete, Andra, additional, Griffin, Bryan D., additional, Yip, Lily, additional, Goolia, Melissa, additional, Suderman, Matthew, additional, Pinette, Mathieu, additional, Smith, Greg, additional, Sullivan, Daniel, additional, Rudar, Josip, additional, Vernygora, Oksana, additional, Adey, Elizabeth, additional, Nebroski, Michelle, additional, Goyette, Guillaume, additional, Finzi, Andrés, additional, Laroche, Geneviève, additional, Ariana, Ardeshir, additional, Vahkal, Brett, additional, Côté, Marceline, additional, McGeer, Allison J., additional, Nituch, Larissa, additional, Mubareka, Samira, additional, and Bowman, Jeff, additional

Published
2022
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25. Surveillance for SARS-CoV-2 in Norway rats ( Rattus norvegicus ) from southern Ontario

Author

Robinson, Sarah J., primary, Kotwa, Jonathon D., additional, Jeeves, Simon, additional, Himsworth, Chelsey, additional, Pearl, David, additional, Weese, J. Scott, additional, Lindsay, Robbin, additional, Dibernardo, Antonia, additional, Toledo, Nikki P.L., additional, Pickering, Bradley, additional, Goolia, Melissa, additional, Chee, Hsien-Yao, additional, Blais-Savoie, Juliette, additional, Chien, Emily, additional, Yim, Winfield, additional, Yip, Lily, additional, Mubareka, Samira, additional, and Jardine, Claire, additional

Published
2022
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26. Similar duration of viral shedding of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) delta variant between vaccinated and incompletely vaccinated individuals

Author

Kandel, Christopher E., primary, Banete, Andra, additional, Taylor, Maureen, additional, Llanes, Andrea, additional, McCready, Janine, additional, Crowl, Gloria, additional, Young, Matthew, additional, Li, Angel X., additional, Chien, Emily, additional, Yim, Winfield, additional, Yip, Lily, additional, Kozak, Robert, additional, McGeer, Allison J., additional, Mubareka, Samira, additional, and Powis, Jeff E., additional

Published
2022
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29. Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission

Author

Pickering, Bradley, primary, Lung, Oliver, additional, Maguire, Finlay, additional, Kruczkiewicz, Peter, additional, Kotwa, Jonathon D., additional, Buchanan, Tore, additional, Gagnier, Marianne, additional, Guthrie, Jennifer L., additional, Jardine, Claire M., additional, Marchand-Austin, Alex, additional, Massé, Ariane, additional, McClinchey, Heather, additional, Nirmalarajah, Kuganya, additional, Aftanas, Patryk, additional, Blais-Savoie, Juliette, additional, Chee, Hsien-Yao, additional, Chien, Emily, additional, Yim, Winfield, additional, Banete, Andra, additional, Griffin, Bryan D., additional, Yip, Lily, additional, Goolia, Melissa, additional, Suderman, Matthew, additional, Pinette, Mathieu, additional, Smith, Greg, additional, Sullivan, Daniel, additional, Rudar, Josip, additional, Adey, Elizabeth, additional, Nebroski, Michelle, additional, Goyette, Guillaume, additional, Finzi, Andrés, additional, Laroche, Geneviève, additional, Ariana, Ardeshir, additional, Vahkal, Brett, additional, Côté, Marceline, additional, McGeer, Allison J., additional, Nituch, Larissa, additional, Mubareka, Samira, additional, and Bowman, Jeff, additional

Published
2022
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30. First detection of SARS-CoV-2 infection in Canadian wildlife identified in free-ranging white-tailed deer (Odocoileus virginianus) from southern Québec, Canada

Author

Kotwa, Jonathon D., primary, Massé, Ariane, additional, Gagnier, Marianne, additional, Aftanas, Patryk, additional, Blais-Savoie, Juliette, additional, Bowman, Jeff, additional, Buchanan, Tore, additional, Chee, Hsien-Yao, additional, Dibernardo, Antonia, additional, Kruczkiewicz, Peter, additional, Nirmalarajah, Kuganya, additional, Soos, Catherine, additional, Yip, Lily, additional, Lindsay, L. Robbin, additional, Lung, Oliver, additional, Pickering, Bradley, additional, and Mubareka, Samira, additional

Published
2022
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31. Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B

Author

Liu, Jun, primary, Budylowski, Patrick, additional, Samson, Reuben, additional, Griffin, Bryan D., additional, Babuadze, Giorgi, additional, Rathod, Bhavisha, additional, Colwill, Karen, additional, Abioye, Jumai A., additional, Schwartz, Jordan A., additional, Law, Ryan, additional, Yip, Lily, additional, Ahn, Sang Kyun, additional, Chau, Serena, additional, Naghibosadat, Maedeh, additional, Arita, Yuko, additional, Hu, Queenie, additional, Yue, Feng Yun, additional, Banerjee, Arinjay, additional, Hardy, W. Rod, additional, Mossman, Karen, additional, Mubareka, Samira, additional, Kozak, Robert A., additional, Pollanen, Michael S., additional, Martin Orozco, Natalia, additional, Gingras, Anne-Claude, additional, Marcusson, Eric G., additional, and Ostrowski, Mario A., additional

Published
2022
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32. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada, March-May 2020

Author

Kotwa, Jonathon D, Jamal, Alainna J, Mbareche, Hamza, Yip, Lily, Aftanas, Patryk, Barati, Shiva, Bell, Natalie G, Bryce, Elizabeth, Coomes, Eric, Crowl, Gloria, Duchaine, Caroline, Faheem, Amna, Farooqi, Lubna, Hiebert, Ryan, Katz, Kevin, Khan, Saman, Kozak, Robert, Li, Angel X, Mistry, Henna P, Mozafarihashjin, Mohammad, Nasir, Jalees A, Nirmalarajah, Kuganya, Panousis, Emily M, Paterson, Aimee, Plenderleith, Simon, Powis, Jeff, Prost, Karren, Schryer, Renée, Taylor, Maureen, Veillette, Marc, Wong, Titus, Zhong, Xi Zoe, Mc Arthur, Andrew G, Mc Geer, Allison J, and Mubareka, Samira

Subjects
Adult, Canada, Inpatients, SARS-CoV-2, aerosol, viruses, Health Personnel, Air Microbiology, COVID-19, Respiratory Aerosols and Droplets, Environmental Exposure, Middle Aged, AcademicSubjects/MED00290, contamination, COVID-19 Nucleic Acid Testing, Nasopharynx, Major Article, surface, Humans, Pandemics, Aged
Abstract

We determined the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in air and on surfaces in rooms of patients hospitalized with coronavirus disease 2019 (COVID-19) and investigated patient characteristics associated with SARS-CoV-2 environmental contamination.Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at 6 acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 ribonucleic acid (RNA), cultured to determine potential infectivity, and whole viral genomes were sequenced. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated.Severe acute respiratory syndrome coronavirus 2 RNA was detected from surfaces (125 of 474 samples; 42 of 78 patients) and air (3 of 146 samples; 3 of 45 patients); 17% (6 of 36) of surface samples from 3 patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, polymerase chain reaction-positive nasopharyngeal swab (cycle threshold of ≤30) on or after surface sampling date, higher Charlson comorbidity score, and shorter time from onset of illness to sampling date were significantly associated with detection of SARS-CoV-2 RNA in surface samples.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.

Published
2021

34. SARS-CoV-2 wildlife surveillance in Ontario and Québec, Canada

Author

Greenhorn, Janet E., primary, Kotwa, Jonathon D., additional, Bowman, Jeff, additional, Bruce, Laura, additional, Buchanan, Tore, additional, Buck, Peter A., additional, Dibernardo, Antonia, additional, Flockhart, Logan, additional, Gagnier, Marianne, additional, Hou, Aaron, additional, Jardine, Claire M., additional, Lair, Stephane, additional, Lindsay, L. Robbin, additional, Masse, Ariane, additional, Muchaal, Pia K., additional, Nituch, Larissa A., additional, Sotto, Angelo, additional, Stevens, Brian, additional, Yip, Lily, additional, and Mubareka, Samira, additional

Published
2021
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35. Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March–May 2020

Author

Kotwa, Jonathon D, primary, Jamal, Alainna J, additional, Mbareche, Hamza, additional, Yip, Lily, additional, Aftanas, Patryk, additional, Barati, Shiva, additional, Bell, Natalie G, additional, Bryce, Elizabeth, additional, Coomes, Eric, additional, Crowl, Gloria, additional, Duchaine, Caroline, additional, Faheem, Amna, additional, Farooqi, Lubna, additional, Hiebert, Ryan, additional, Katz, Kevin, additional, Khan, Saman, additional, Kozak, Robert, additional, Li, Angel X, additional, Mistry, Henna P, additional, Mozafarihashjin, Mohammad, additional, Nasir, Jalees A, additional, Nirmalarajah, Kuganya, additional, Panousis, Emily M, additional, Paterson, Aimee, additional, Plenderleith, Simon, additional, Powis, Jeff, additional, Prost, Karren, additional, Schryer, Renée, additional, Taylor, Maureen, additional, Veillette, Marc, additional, Wong, Titus, additional, Zoe Zhong, Xi, additional, McArthur, Andrew G, additional, McGeer, Allison J, additional, and Mubareka, Samira, additional

Published
2021
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37. Pathogenesis and transmission of SARS-CoV-2 D614G, Alpha, Gamma, Delta, and Omicron variants in golden hamsters

Author

Banete, Andra, Griffin, Bryan D., Corredor, Juan C., Chien, Emily, Yip, Lily, Gunawardena, Tarini N. A., Nirmalarajah, Kuganya, Liang, Jady, Lee, Yaejin, Leacy, Alexander, Pagliarani, Sara, de Borja, Richard, Yim, Winfield, Lee, Hunsang, Onodera, Yu, Aftanas, Patryk, Budylowski, Patrick, Ahn, Sang Kyun, Pei, Yanlong, Ouyang, Hong, Kent, Laura, Li, Xinliu Angel, Ostrowski, Mario A., Kozak, Robert A., Wootton, Sarah K., Christie-Holmes, Natasha, Gray-Owen, Scott D., Taipale, Mikko, Simpson, Jared T., Maguire, Finlay, McGeer, Allison J., Zhang, Haibo, Susta, Leonardo, Moraes, Theo J., and Mubareka, Samira

Published
2025
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38. Sensitivity of Nasopharyngeal Swabs and Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2

Author

Jamal, Alainna J, Mozafarihashjin, Mohammad, Coomes, Eric, Powis, Jeff, Li, Angel X, Paterson, Aimee, Anceva-Sami, Sofia, Barati, Shiva, Crowl, Gloria, Faheem, Amna, Farooqi, Lubna, Khan, Saman, Prost, Karren, Poutanen, Susan, Taylor, Maureen, Yip, Lily, Zhong, Xi Zoe, McGeer, Allison J, Mubareka, Samira, Coleman, Brenda L, Chen, Danny, Farshait, Nataly, Gold, Wayne, Kandel, Christopher E, Katz, Kevin, Kozak, Robert, Mazzulli, Tony, Muller, Matthew, Opavsky, Anne, Ostrowski, Mario, Plevneshi, Agron, Rau, Neil, Ricciuto, Daniel, Richardson, David, Rose, David, Sales, Valerie, and Walmsley, Sharon

Subjects
0301 basic medicine, Microbiology (medical), medicine.medical_specialty, Saliva, Canada, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Saliva sample, medicine.disease_cause, Real-Time Polymerase Chain Reaction, Gastroenterology, law.invention, 03 medical and health sciences, 0302 clinical medicine, stomatognathic system, law, Internal medicine, Nasopharynx, medicine, Humans, 030212 general & internal medicine, Polymerase chain reaction, Coronavirus, saliva, business.industry, SARS-CoV-2, Brief Report, COVID-19, nasopharyngeal swab, Reverse transcriptase, 3. Good health, Real-time polymerase chain reaction, Infectious Diseases, AcademicSubjects/MED00290, business
Abstract

We enrolled 91 consecutive inpatients with COVID-19 at 6 hospitals in Toronto, Canada, and tested 1 nasopharyngeal swab/saliva sample pair from each patient using real-time RT-PCR for severe acute respiratory syndrome coronavirus 2. Sensitivity was 89% for nasopharyngeal swabs and 72% for saliva (P = .02). Difference in sensitivity was greatest for sample pairs collected later in illness.

Published
2020

39. Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device

Author

Zhang, Yuwei, primary, Malekjahani, Ayden, additional, Udugama, Buddhisha N., additional, Kadhiresan, Pranav, additional, Chen, Hongmin, additional, Osborne, Matthew, additional, Franz, Max, additional, Kucera, Mike, additional, Plenderleith, Simon, additional, Yip, Lily, additional, Bader, Gary D., additional, Tran, Vanessa, additional, Gubbay, Jonathan B., additional, McGeer, Allison, additional, Mubareka, Samira, additional, and Chan, Warren C. W., additional

Published
2021
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40. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada

Author

Kotwa, Jonathon D., primary, Jamal, Alainna J., additional, Mbareche, Hamza, additional, Yip, Lily, additional, Aftanas, Patryk, additional, Barati, Shiva, additional, Bell, Natalie G., additional, Bryce, Elizabeth, additional, Coomes, Eric, additional, Crowl, Gloria, additional, Duchaine, Caroline, additional, Faheem, Amna, additional, Farooqi, Lubna, additional, Hiebert, Ryan, additional, Katz, Kevin, additional, Khan, Saman, additional, Kozak, Robert, additional, Li, Angel X., additional, Mistry, Henna P., additional, Mozafarihashjin, Mohammad, additional, Nasir, Jalees A., additional, Nirmalarajah, Kuganya, additional, Panousis, Emily M., additional, Paterson, Aimee, additional, Plenderleith, Simon, additional, Powis, Jeff, additional, Prost, Karren, additional, Schryer, Renée, additional, Taylor, Maureen, additional, Veillette, Marc, additional, Wong, Titus, additional, Zhong, Xi Zoe, additional, McArthur, Andrew G., additional, McGeer, Allison J., additional, and Mubareka, Samira, additional

Published
2021
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41. Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B

Author

Liu, Jun, primary, Budylowski, Patrick, additional, Samson, Reuben, additional, Griffin, Bryan D., additional, Babuadze, Giorgi, additional, Rathod, Bhavisha, additional, Colwill, Karen, additional, Abioye, Jumai A., additional, Schwartz, Jordan A, additional, Law, Ryan, additional, Yip, Lily, additional, Ahn, Sang Kyun, additional, Chau, Serena, additional, Naghibosadat, Maedeh, additional, Arita, Yuko, additional, Hu, Queenie, additional, Yue, Feng Yun, additional, Banerjee, Arinjay, additional, Mossman, Karen, additional, Mubareka, Samira, additional, Kozak, Robert A., additional, Pollanen, Michael S., additional, Orozco, Natalia Martin, additional, Gingras, Anne-Claude, additional, Marcusson, Eric G., additional, and Ostrowski, Mario A., additional

Published
2021
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42. Detection of SARS-CoV-2 Viral Particles Using Direct, Reagent-Free Electrochemical Sensing

Author

Yousefi, Hanie, primary, Mahmud, Alam, additional, Chang, Dingran, additional, Das, Jagotamoy, additional, Gomis, Surath, additional, Chen, Jenise B., additional, Wang, Hansen, additional, Been, Terek, additional, Yip, Lily, additional, Coomes, Eric, additional, Li, Zhijie, additional, Mubareka, Samira, additional, McGeer, Allison, additional, Christie, Natasha, additional, Gray-Owen, Scott, additional, Cochrane, Alan, additional, Rini, James M., additional, Sargent, Edward H., additional, and Kelley, Shana O., additional

Published
2021
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43. A Homogeneous Split-Luciferase Assay for Rapid and Sensitive Detection of Anti-SARS CoV-2 Antibodies

Author

Stagljar, Igor, primary, Owen, Shawn, additional, Yao, Zhong, additional, Drecun, Luka, additional, Aboualizadeh, Farzaneh, additional, Kim, Sun Jin, additional, Li, Zhijie, additional, Valcourt, Emelissa J, additional, Manguiat, Kathy, additional, Wood, Heidi, additional, Plenderleith, Simon, additional, Yip, Lily, additional, Li, Xinliu, additional, Zhong, Zoe, additional, Yue, Feng Yun, additional, Snider, Jamie, additional, Tomic, Jelena, additional, Drebot, Michael A., additional, McGeer, Allison, additional, Ostrowski, Mario, additional, Mubareka, Samira, additional, and Rini, James, additional

Published
2020
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44. Detection of SARS-CoV-2 Viral Particles Using Direct, Reagent-Free Electrochemical Sensing

Author

Yousefi, Hanie, primary, mahmud, alam, additional, Chang, Dingran, additional, Das, Jagotamoy, additional, Gomis, Surath, additional, Chen, Jenise B., additional, Wang, Hansen, additional, Been, Terek, additional, Yip, Lily, additional, Coomes, Eric, additional, Li, Zhijie, additional, Mubareka, Samira, additional, McGeer, Allison, additional, Christie, Natasha, additional, Gray-Owen, Scott, additional, Cochrane, Alan, additional, Rini, James M., additional, Sargent, Edward H., additional, and Kelley, Shana O., additional

Published
2020
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45. Experimental and natural evidence of SARS-CoV-2 infection-induced activation of type I interferon responses

Author

Banerjee, Arinjay, primary, El-Sayes, Nader, additional, Budylowski, Patrick, additional, Richard, Daniel, additional, Maan, Hassaan, additional, Aguiar, Jennifer A., additional, Baid, Kaushal, additional, D’Agostino, Michael R., additional, Ang, Jann Catherine, additional, Tremblay, Benjamin J.-M., additional, Afkhami, Sam, additional, Karimzadeh, Mehran, additional, Irving, Aaron T., additional, Yip, Lily, additional, Ostrowski, Mario, additional, Hirota, Jeremy A., additional, Kozak, Robert, additional, Capellini, Terence D., additional, Miller, Matthew S., additional, Wang, Bo, additional, Mubareka, Samira, additional, McGeer, Allison J., additional, McArthur, Andrew G., additional, Doxey, Andrew C., additional, and Mossman, Karen, additional

Published
2020
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46. Sequence, infectivity and replication kinetics of SARS-CoV-2 isolated from COVID-19 patients in Canada

Author

Banerjee, Arinjay, primary, Nasir, Jalees A., additional, Budylowski, Patrick, additional, Yip, Lily, additional, Aftanas, Patryk, additional, Christie, Natasha, additional, Ghalami, Ayoob, additional, Baid, Kaushal, additional, Raphenya, Amogelang R., additional, Hirota, Jeremy A., additional, Miller, Matthew S., additional, Ostrowski, Mario, additional, Kozak, Robert A., additional, McArthur, Andrew G., additional, Mossman, Karen, additional, and Mubareka, Samira, additional

Published
2020
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47. SARS-CoV-2 wildlife surveillance in Ontario and Québec.

Author

Greenhorn, Janet E., Kotwa, Jonathon D., Bowman, Jeff, Bruce, Laura, Buchanan, Tore, Buck, Peter A., Davy, Christina M., Dibernardo, Antonia, Flockhart, Logan, Gagnier, Marianne, Hou, Aaron, Jardine, Claire M., Lair, Stephane, Lindsay, L. Robbin, Massé, Ariane, Muchaal, Pia K., Nituch, Larissa A., Sotto, Angelo, Stevens, Brian, and Yip, Lily

Subjects
SARS-CoV-2, COVID-19 pandemic, RACCOON, RABIES virus
Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 pandemic, is capable of infecting a variety of wildlife species. Wildlife living in close contact with humans are at an increased risk of SARSCoV- 2 exposure and, if infected, have the potential to become a reservoir for the pathogen, making control and management more difficult. The objective of this study is to conduct SARSCoV- 2 surveillance in urban wildlife from Ontario and Québec, increasing our knowledge of the epidemiology of the virus and our chances of detecting spillover from humans into wildlife. Methods: Using a One Health approach, we leveraged activities of existing research, surveillance and rehabilitation programs among multiple agencies to collect samples from 776 animals from 17 different wildlife species between June 2020 and May 2021. Samples from all animals were tested for the presence of SARS-CoV-2 viral ribonucleic acid, and a subset of samples from 219 animals across three species (raccoons, Procyon lotor; striped skunks, Mephitis mephitis; and mink, Neovison vison) were also tested for the presence of neutralizing antibodies. Results: No evidence of SARS-CoV-2 viral ribonucleic acid or neutralizing antibodies was detected in any of the tested samples. Conclusion: Although we were unable to identify positive SARS-CoV-2 cases in wildlife, continued research and surveillance activities are critical to better understand the rapidly changing landscape of susceptible animal species. Collaboration between academic, public and animal health sectors should include experts from relevant fields to build coordinated surveillance and response capacity. [ABSTRACT FROM AUTHOR]

Published
2022

49. Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020.

Author

Kotwa, Jonathon D, Jamal, Alainna J, Mbareche, Hamza, Yip, Lily, Aftanas, Patryk, Barati, Shiva, Bell, Natalie G, Bryce, Elizabeth, Coomes, Eric, Crowl, Gloria, Duchaine, Caroline, Faheem, Amna, Farooqi, Lubna, Hiebert, Ryan, Katz, Kevin, Khan, Saman, Kozak, Robert, Li, Angel X, Mistry, Henna P, and Mozafarihashjin, Mohammad

Subjects
SARS-CoV-2, CORONAVIRUS diseases, COVID-19, SURFACE contamination
Abstract

Background: We determined the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in air and on surfaces in rooms of patients hospitalized with coronavirus disease 2019 (COVID-19) and investigated 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 6 acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 ribonucleic acid (RNA), cultured to determine potential infectivity, and whole viral genomes were sequenced. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated.Results: Severe acute respiratory syndrome coronavirus 2 RNA was detected from surfaces (125 of 474 samples; 42 of 78 patients) and air (3 of 146 samples; 3 of 45 patients); 17% (6 of 36) of surface samples from 3 patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, polymerase chain reaction-positive nasopharyngeal swab (cycle threshold of ≤30) on or after surface sampling date, higher Charlson comorbidity score, and shorter time from onset of illness to sampling date were significantly associated with detection of SARS-CoV-2 RNA in surface samples.Conclusions: 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. [ABSTRACT FROM AUTHOR]

Published
2022
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50. Similar duration of viral shedding of the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) delta variant between vaccinated and incompletely vaccinated individuals

Author

Kandel, Christopher E., Banete, Andra, Taylor, Maureen, Llanes, Andrea, McCready, Janine, Crowl, Gloria, Young, Matthew, Li, Angel X., Chien, Emily, Yim, Winfield, Yip, Lily, Kozak, Robert, McGeer, Allison J., Mubareka, Samira, and Powis, Jeff E.

Abstract

AbstractAmong outpatients with coronavirus disease 2019 (COVID-19) due to the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) δ (delta) variant who did and did not receive 2 vaccine doses at 7 days after symptom onset, there was no difference in viral shedding (cycle threshold difference 0.59, 95% CI, −4.68 to 3.50; P= .77) with SARS-CoV-2 cultured from 2 (7%) of 28 and 1 (4%) of 26 outpatients, respectively.

Published
2023
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