Associate Professor

Jonathan B. Gubbay

Department of Laboratory Medicine & Pathobiology - Medical Microbiology


Ontario Agency for Health Protection & Promotion
661 University Ave., Suite 1701, Toronto, Ontario Canada M5G 1M1
Research Interests
Genetics Genomics & Proteomics, Infectious Diseases & Immunopathology
Appointment Status

Dr Jonathan Gubbay is a Medical Microbiologist with Public Health Ontario and oversees the virus detection, arboviruses and respiratory bacteriology laboratories. 

He is an assistant professor in the Department of Laboratory Medicine and Pathobiology as well as in Pediatrics at the University of Toronto. 

He is also a part-time staff physician in the Division of Infectious Diseases at The Hospital for Sick Children.

Dr Gubbay completed his medical degree and training in paediatric infectious diseases in Sydney, Australia followed by medical microbiology training in Canada at the University of Toronto. 

He holds a Master of Medical Science degree in Clinical Epidemiology. 

He has a research interest in the molecular epidemiology and diagnosis of respiratory viral and emergence of antiviral resistance. 

His research work involves application of molecular methods to help understand the epidemiology and genetic heterogeneity of respiratory viruses. He is currently exploring the clinical utility of viral load measurements of respiratory viruses.


Research Synopsis


My research interests include the study of respiratory viruses and emerging viral pathogens, with a focus on laboratory detecion, molecular epidemiology, antiviral resistance and clinical significance of viral loads.

Molecular Investigation of Respiratory Viruses

My main research focus is respiratory viral pathogens, with emphasis on molecular typing of viruses, and applying molecular methods to understanding the molecular epidemiology and genetic heterogeneity of respiratory viruses. I am also exploring the clinical utility of viral load measurements of respiratory viruses.

This work will assist with better understanding interplay of viral genetics with clinical presentation and severity of respiratory viral infections. Research on viral load measurement will help understand if such quantitation of respiratory viruses can be used to predict infectivity and guide infection control approaches, in particular periods of isolation. In addition, correlation between viral load and clincal severity/prognosis are being evaluated.

Antiviral Resistance in Influenza

I am conducting research surveillance on neuraminidase inhibitor resistance in influenza viruses. Future goals include evaluating novel drugs for antiviral effects on influenza and other respiratory viruses.

This work has led to publications on the prevalence of neuraminidase inhibitor resistance in influenza viruses in  Ontario and provides useful surveillance infromation, in addition to the detection of rarely described novel forms of resistance. 


Recent Publications


Duvvuri VR, Deng X, Teatero S, Memari N, Athey T, Fittipaldi N and Gubbay JB. Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada. Infect Genet Evol. 2016 Apr 9. 2016 Apr 9. pii: S1567-1348(16)30133-2. doi: 10.1016/j.meegid.2016.04.007.

Duvvuri VR, Granados A, Rosenfeld P, Bahl J, Eshaghi A, Gubbay JB. Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics. Sci Rep. 2015 Sep 30;5:14268.

Peci A, Winter AL, Warshawsky B, Booth TF, Eshaghi A, Li A, Perusini S, Olsha R, Marchand-Austin A, Kristjanson E, Gubbay JB. Epidemiology of Enterovirus D68 in Ontario. PLoS One. 2015 Nov 23;10(11):e0142841. Manuscript in preparation

Deng X, Arya G, Memari N, Mackenzie R, MacMullin G, Low DE, Pillai DR and Gubbay JB. Genetic analysis of invasive pneumococcal isolates from children in ontario, Canada, 2007-2012. Pediatr Infect Dis J. 2015 Jun. 2015 Jun;34(6):594-8. doi: 10.1097/INF.0000000000000697

Neemuchwala A, Duvvuri VR, Marchand-Austin A, Li A, Gubbay JB. Human metapneumovirus prevalence and molecular epidemiology in respiratory outbreaks in Ontario, Canada. J Med Virol. 2015 Feb 1;87(2):269-74. 2015 Feb;87(2):269-74. doi: 10.1002/jmv.24024. Epub 2014 Aug 5.

Peci A, Winter AL, King EC, Blair J and Gubbay JB. Performance of rapid influenza diagnostic testing in outbreak settings. J Clin Microbiol. 2014 Dec. 2014 Dec;52(12):4309-17. doi: 10.1128/JCM.02024-14. Epub 2014 Oct 15

Eshaghi A, Shalhoub S, Rosenfeld P, Li A, Higgins RR, Stogios PJ, Savchenko A, Bastien N, Li Y, Rotstein C, Gubbay JB. Multiple influenza A (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient. Antimicrob Agents Chemother. 2014 Dec 1;58(12):7188-97. 2014 Dec;58(12):7188-97. doi: 10.1128/AAC.03667-14. Epub 2014 Sep 22.

Duvvuri VR, Duvvuri B, Alice C, Wu GE, Gubbay JB and Wu J. Preexisting CD4+ T-Cell Immunity in Human Population to Avian Influenza H7N9 Virus: Whole Proteome-Wide Immunoinformatics Analyses. PLoS One. 2014. 2014 Mar 7;9(3):e91273. doi: 10.1371/journal.pone.0091273. eCollection 2014. 

Winter AL, Peci A, Eshaghi A, Baird M, Memari N, Kristjanson E, Balogun E, Higgins RR, Li A, Farrell DJ and Gubbay JB. Laboratory-confirmed influenza B infection in immunized long-term care facility residents receiving oseltamivir prophylaxis in ontario. Infect Control Hosp Epidemiol. 2013 Nov. 2013 Nov;34(11):1225-8. doi: 10.1086/673455. Epub 2013 Sep 25.

Peci A, Marchand-Austin A, Winter AL, Gubbay JB. Optimal number of samples to test for institutional respiratory infection outbreaks in Ontario. Epidemiol Infect. 2013 Aug 1;141(8):1781-5. doi: 10.1017/S0950268812002531. Epub 2012 Nov 12. Erratum in: Epidemiol Infect. 2013 Aug;141(8):1786. Winter, A-J [corrected to Winter, A-L]. PMID: 23146341.

Duvvuri VR, Duvvuri B, Jamnik V, Gubbay JB, Wu J and Wu GE. T cell memory to evolutionarily conserved and shared hemagglutinin epitopes of H1N1 viruses: a pilot scale study. BMC Infect Dis. 2013. 2013 May 4;13:204. doi: 10.1186/1471-2334-13-204

Winter AL, Eshaghi A, Farrell DJ, King A, Li A, Li Y and Gubbay JB. Variant influenza A (H1N1) virus infection in Canada. J Clin Virol. 2013 Jul. 2013 Jul;57(3):279-81. doi: 10.1016/j.jcv.2013.03.011. Epub 2013 Apr 15.

Abbas KZ, Lombos E, Duvvuri VR, Olsha R, Higgins RR and Gubbay JB. Temporal changes in respiratory adenovirus serotypes circulating in the greater Toronto area, Ontario, during December 2008 to April 2010. Virol J. 2013 Jan 7;10:15. doi: 10.1186/1743-422X-10-15.

Eshaghi A, Duvvuri VR, Lai R, Nadarajah JT, Li A, SN Patel1, DE Low, JB Gubbay. Genetic Variability of Human Respiratory Syncytial Virus A Strains Circulating in Ontario: A Novel Genotype with a 72 Nucleotide G Gene Duplication. PLoS ONE. (2012), 7(3): e32807.

Duvvuri VR, Marchand-Austin A, Eshaghi A, Patel SN, Low DE and Gubbay JB. Potential T cell epitopes within swine-origin triple reassortant influenza A (H3N2) variant virus which emerged in 2011: an immunoinformatics study. Vaccine. 2012 Sep 14;30(42):6054-63. doi: 10.1016/j.vaccine.2012.07.054. Epub 2012 Aug 8.