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Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS-CoV-2 to Gain Resistance Deschenes, Natalie M.; Perez-Vargas, Jimena; Zhong, Zoe; Thomas, Merrilee; Kenward, Calem; Mosimann, Wesley A.; Worrall, Liam J.; Waglechner, Nicholas; Li, Angel XinLiu; Maguire, Finlay; Aftanas, Patryk; Smith, Jason R.; Lim, Jared; Young, Robert N.; Cherkasov, Artem; Farooqi, Lubna; Moinuddin, Adnan; Siddiqi, Lina; Malik, Imaan; Lefebvre, Maxime; Paetzel, Mark; Strynadka, Natalie C. J.; Jean, Francois; McGeer, Allison; Kozak, Robert A. Share Save
Comparison of pharyngeal and invasive isolates of Streptococcus pyogenes by whole-genome sequencing in Toronto, Canada Zeppa, Joseph J.; Avery, Ellen G.; Aftanas, Patryk; Choi, Erin; Uleckas, Simone; Patel, Prachi; Waglechner, Nicholas; Jimenez, Hubert; Vermeiren, Christie; Katz, Kevin; Li, Xena X.; Maguire, Finlay; Kozak, Robert Share Save
Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study 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; Mcarthur, Andrew G.; Daneman, Nick; Maguire, Finlay; Mcgeer, Allison J.; Duvvuri, Venkata R.; Mubareka, Samira Share Save
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes Nasir, Jalees A.; Maguire, Finlay; Smith, Kendrick M.; Panousis, Emily M.; Baker, Sheridan J. C.; Aftanas, Patryk; Raphenya, Amogelang R.; Alcock, Brian P.; Maan, Hassaan; Knox, Natalie C.; Banerjee, Arinjay; Mossman, Karen; Wang, Bo; Simpson, Jared T.; Kozak, Robert A.; Mubareka, Samira; Mcarthur, Andrew G. Share Save
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Use of whole genome sequencing to identify low-frequency mutations in SARS-CoV-2 patients treated with remdesivir Nirmalarajah, Kuganya; Yim, Winfield; Aftanas, Patryk; Li, Angel X.; Shigayeva, Altynay; Yip, Lily; Zhong, Zoe; Mcgeer, Allison J.; Maguire, Finlay; Mubareka, Samira; Kozak, Robert Share Save
Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants Banerjee, Arinjay; Lew, Jocelyne; Kroeker, Andrea; Baid, Kaushal; Aftanas, Patryk; Nirmalarajah, Kuganya; Maguire, Finlay; Kozak, Robert; McDonald, Ryan; Lang, Amanda; Gerdts, Volker; Straus, Sharon E.; Gilbert, Lois; Li, Angel Xinliu; Mozafarihashjin, Mohammad; Walmsley, Sharon; Gingras, Anne-Claude; Wrana, Jeffrey L.; Mazzulli, Tony; Colwill, Karen; McGeer, Allison J.; Mubareka, Samira; Falzarano, Darryl Share Save
Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020 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, Renee; Taylor, Maureen; Veillette, Marc; Wong, Titus; Zhong, Xi Zoe; McArthur, Andrew G.; McGeer, Allison J.; Mubareka, Samira Share Save
Isolation, Sequence, Infectivity and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 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; Mubareka, Samira Share Save
A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture Nasir, Jalees A.; Kozak, Robert A.; Aftanas, Patryk; Raphenya, Amogelang R.; Smith, Kendrick M.; Maguire, Finlay; Maan, Hassaan; Alruwaili, Muhannad; Banerjee, Arinjay; Mbareche, Hamza; Alcock, Brian P.; Knox, Natalie C.; Mossman, Karen; Wang, Bo; Hiscox, Julian A.; McArthur, Andrew G.; Mubareka, Samira Share Save
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