- Overview
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My primary research interest is in the diagnosis and epidemiology of viral infections. My research involves application of molecular methods to improve detection and help understand the epidemiology and genetic heterogeneity of viruses, with a focus on respiratory viruses and emerging viral pathogens. I am also focusing on the use of newer molecular technologies in the hospital microbiology laboratory setting to support outbreak management and pathogen detection.
- Publications
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Effectiveness of Influenza Vaccination During Pregnancy Against Laboratory-Confirmed Seasonal Influenza Among Infants Under 6 Months of Age in Ontario, Canada
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiad539
2024Targeted amplification-based whole genome sequencing of Monkeypox virus in clinical specimens
Microbiology Spectrum
DOI: 10.1128/spectrum.02979-23
2024Population immunity to varicella in Canada: A Canadian Immunization Research Network (CIRN) study
PLoS ONE
DOI: 10.1371/journal.pone.0309154
2024Investigation of suspected false positive norovirus results on a syndromic gastrointestinal multiplex molecular panel
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2024.105732
2024Effectiveness of mRNA COVID-19 Monovalent and Bivalent Vaccine Booster Doses Against Omicron Severe Outcomes Among Adults Aged =50 Years in Ontario, Canada: A Canadian Immunization Research Network Study
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiad419
2024Effectiveness of modified vaccinia Ankara-Bavarian Nordic vaccine against mpox infection: emulation of a target trial
BMJ
DOI: 10.1136/bmj-2023-078243
2024Inferring Enterovirus D68 Transmission Dynamics from the Genomic Data of Two 2022 North American outbreaks
Research Square
DOI: 10.21203/rs.3.rs-4362075/v1
2024Measuring waning protection from seasonal influenza vaccination during nine influenza seasons, Ontario, Canada, 2010/11 to 2018/19
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2024.29.8.2300239
2024Disproportionate Rates of COVID-19 Among Black Canadian Communities: Lessons from a Cross-Sectional Study in the First Year of the Pandemic
Journal of Racial and Ethnic Health Disparities
DOI: 10.1007/s40615-023-01903-z
2024Practice recommendations regarding parental presence in NICUs during pandemics caused by respiratory pathogens like COVID-19
Frontiers in Pediatrics
DOI: 10.3389/fped.2024.1390209
2024Effectiveness of one dose of MVA-BN vaccine against mpox infection in males in Ontario, Canada: A target trial emulation
medRxiv
DOI: 10.1101/2023.10.04.23296566
2023Maternal varicella antibodies in children aged less than one year: Assessment of antibody decay
PLoS ONE
DOI: 10.1371/journal.pone.0287765
2023Maternal mRNA covid-19 vaccination during pregnancy and delta or omicron infection or hospital admission in infants: test negative design study
BMJ
DOI: 10.1136/bmj-2022-074035
2023Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels
Analytical Chemistry
DOI: 10.1021/acs.analchem.2c04630
2023Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes
Nature Communications
DOI: 10.1038/s41467-023-36566-1
2023Effectiveness of mRNA COVID-19 monovalent and bivalent vaccine booster doses against Omicron severe outcomes among adults aged =50 years in Ontario, Canada
medRxiv
DOI: 10.1101/2023.04.11.23288403
2023Protection conferred by COVID-19 vaccination, prior SARS-CoV-2 infection, or hybrid immunity against Omicron-associated severe outcomes among community-dwelling adults
medRxiv
DOI: 10.1101/2023.08.24.23294503
2023Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves
Infectious Disease Modelling
DOI: 10.1016/j.idm.2023.02.003
2023Burden of Severe Illness Associated With Laboratory-Confirmed Influenza in Adults Aged 50-64 Years, 2010-2011 to 2016-2017
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofac664
2023Evaluating the Impact of Statin Use on Influenza Vaccine Effectiveness and Influenza Infection in Older Adults
Clinical Infectious Diseases
DOI: 10.1093/cid/ciad148
2023Environmental Testing of Surfaces in the Room of a Patient With Mpox
Clinical Infectious Diseases
DOI: 10.1093/cid/ciac654
2023Association Between Cycle Threshold Value and Vaccination Status Among Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Cases in Ontario, Canada, in December 2021
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofad282
2023COVID-19 Vaccine Effectiveness Against Omicron Infection and Hospitalization
Pediatrics
DOI: 10.1542/peds.2022-059513
2023Author Correction: Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes (Nature Communications, (2023), 14, 1, (1273), 10.1038/s41467-023-36566-1)
Nature Communications
DOI: 10.1038/s41467-023-37906-x
2023Vaccine effectiveness estimates from an early-season influenza A(H3N2) epidemic, including unique genetic diversity with reassortment, Canada, 2022/23
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2023.28.5.2300043
2023Environmental Surface Contamination with Monkeypox Virus in the Ambulatory Setting in Toronto, Canada
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofac648
2023Detection of Large Genomic RNA via DNAzyme-Mediated RNA Cleavage and Rolling Circle Amplification: SARS-CoV-2 as a Model
Chemistry - A European Journal
DOI: 10.1002/chem.202300075
2023Geographic clustering of travel-acquired infections in Ontario, Canada, 2008-2020
PLOS Global Public Health
DOI: 10.1371/journal.pgph.0001608
2023Estimating the Incidence of First RSV Hospitalization in Children Born in Ontario, Canada
Journal of the Pediatric Infectious Diseases Society
DOI: 10.1093/jpids/piad045
2023Impact of coronavirus disease 2019 (COVID-19) pre-test probability on positive predictive value of high cycle threshold severe acute respiratory coronavirus virus 2 (SARS-CoV-2) real-time reverse transcription polymerase chain reaction (RT-PCR) test results
Infection Control & Hospital Epidemiology
Jonathan B. Gubbay and Heather Rilkoff and Heather L. Kristjanson and Jessica D. Forbes and Michelle Murti and AliReza Eshaghi and George Broukhanski and Antoine Corbeil and Nahuel Fittipaldi and Jessica P. Hopkins and Erik Kristjanson and Julianne V. Kus and Liane Macdonald and Anna Majury and Gustavo V Mallo and Tony Mazzulli and Roberto G. Melano and Romy Olsha and Stephen J. Perusini and Vanessa Tran and Vanessa G. Allen and Samir N. Patel
DOI: 10.1017/ice.2021.369
09/2022Effect of maternal vitamin D supplementation on nasal pneumococcal acquisition, carriage dynamics and carriage density in infants in Dhaka, Bangladesh
BMC Infectious Diseases
DOI: 10.1186/s12879-022-07032-y
2022Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada
Scientific Reports
DOI: 10.1038/s41598-022-13995-4
2022Effectiveness of COVID-19 vaccines against Omicron or Delta symptomatic infection and severe outcomes
medRxiv
DOI: 10.1101/2021.12.30.21268565
2022Effectiveness of COVID-19 Vaccines Over Time Prior to Omicron Emergence in Ontario, Canada: Test-Negative Design Study
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofac449
2022Author Correction: Emergence of a mutation in the nucleocapsid gene of SARS-CoV-2 interferes with PCR detection in Canada (Scientific Reports, (2022), 12, 1, (10867), 10.1038/s41598-022-13995-4)
Scientific Reports
DOI: 10.1038/s41598-022-17590-5
2022Adverse Outcomes Associated with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant B.1.351 Infection in Vaccinated Residents of a Long-Term Care Home, Ontario, Canada
Clinical Infectious Diseases
DOI: 10.1093/cid/ciab523
2022Estimated Effectiveness of COVID-19 Vaccines Against Omicron or Delta Symptomatic Infection and Severe Outcomes
JAMA Network Open
DOI: 10.1001/jamanetworkopen.2022.32760
2022Population immunity to measles in Canada using Canadian Health Measures survey data – A Canadian Immunization Research Network (CIRN) study
Vaccine
DOI: 10.1016/j.vaccine.2022.04.011
2022Influenza Vaccine Effectiveness by A(H3N2) Phylogenetic Subcluster and Prior Vaccination History: 2016-2017 and 2017-2018 Epidemics in Canada
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiaa138
2022A Prolonged Outbreak of Human Adenovirus A31 (HAdV-A31) Infection on a Pediatric Hematopoietic Stem Cell Transplantation Ward with Whole Genome Sequencing Evidence of International Linkages
Journal of Clinical Microbiology
DOI: 10.1128/jcm.00665-22
2022Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern
Microbiology Spectrum
DOI: 10.1128/spectrum.00681-21
2022Effectiveness of COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe outcomes with variants of concern in Ontario
Nature Microbiology
DOI: 10.1038/s41564-021-01053-0
2022Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer
Journal of the American Chemical Society
DOI: 10.1021/jacs.2c09870
2022Monkeypox Virus Detection in Different Clinical Specimen Types
Emerging Infectious Diseases
DOI: 10.3201/eid2812.221160
2022Influenza vaccine effectiveness against A(H3N2) during the delayed 2021/22 epidemic in Canada
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2022.27.38.2200720
2022Impact of COVID-19 pre-test probability on positive predictive value of high cycle threshold SARS-CoV-2 real-time reverse transcription PCR test results
Jonathan B. Gubbay and Heather Rilkoff and Heather L. Kristjanson and Jessica D. Forbes and Michelle Murti and AliReza Eshaghi and George Broukhanski and Antoine Corbeil and Nahuel Fittipaldi and Jessica P. Hopkins and Erik Kristjanson and Julianne V. Kus and Liane Macdonald and Anna Majury and Gustavo V Mallo and Tony Mazzulli and Roberto G. Melano and Romy Olsha and Stephen J. Perusini and Vanessa Tran and Vanessa G Allen and Samir N Patel
DOI: 10.1101/2021.03.02.21252768
03/2021Prevalence of Co-Infections with Respiratory Viruses in Individuals Investigated for SARS-CoV-2 in Ontario, Canada
Viruses
Adriana Peci and Vanessa Tran and Jennifer L. Guthrie and Ye Li and Paul Nelson and Kevin L. Schwartz and AliReza Eshaghi and Sarah A. Buchan and Jonathan Gubbay
DOI: 10.3390/v13010130
01/2021Real-time RT-PCR allelic discrimination assay for detection of N501Y mutation in the spike protein of SARS-CoV-2 associated with variants of concern
medRxiv
DOI: 10.1101/2021.06.23.21258782
2021Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic
CMAJ
DOI: 10.1503/cmaj.202485
2021Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: Test negative design study
The BMJ
DOI: 10.1136/bmj.n1943
2021Duration of SARS-CoV-2 shedding: A population-based, Canadian study
PLoS ONE
DOI: 10.1371/journal.pone.0252217
2021Characteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic
PLoS ONE
DOI: 10.1371/journal.pone.0253941
2021The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada: A population-based study
The Lancet Regional Health - Americas
DOI: 10.1016/j.lana.2021.100015
2021Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device
Nano Letters
DOI: 10.1021/acs.nanolett.1c01280
2021Influenza Vaccine Effectiveness against All-Cause Mortality following Laboratory-Confirmed Influenza in Older Adults, 2010-2011 to 2015-2016 Seasons in Ontario, Canada
Clinical Infectious Diseases
DOI: 10.1093/cid/ciaa1862
2021The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada
medRxiv
DOI: 10.1101/2021.04.15.21255591
2021Effects of Maternal Vitamin D Supplementation during Pregnancy and Lactation on Infant Acute Respiratory Infections: Follow-up of a Randomized Trial in Bangladesh
Journal of the Pediatric Infectious Diseases Society
DOI: 10.1093/jpids/piab032
2021Effectiveness of mRNA and ChAdOx1 COVID-19 vaccines against symptomatic SARSCoV-2 infection and severe outcomes with variants of concern in Ontario
medRxiv
DOI: 10.1101/2021.06.28.21259420
2021Effectiveness of BNT162b2 and mRNA-1273 COVID-19 Vaccines against Symptomatic SARS-CoV-2 Infection and Severe COVID-19 Outcomes in Ontario, Canada
SSRN
DOI: 10.2139/ssrn.3845993
2021One swab, two tests: Validation of dual SARS-CoV-2 testing on the Abbott ID NOW™
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2021.104896
2021Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic,Enquête sur une éclosion importante de SRAS-CoV-2 dans un établissement de soins de longue durée au début de la pandémie
CMAJ
DOI: 10.1128/JB.00358-19
2021Evaluation of commercial SARS-CoV-2 serological assays in Canadian public health laboratories
Diagnostic Microbiology and Infectious Disease
DOI: 10.1016/j.diagmicrobio.2021.115412
2021Effectiveness of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes in Ontario, Canada: A test-negative design study
medRxiv
DOI: 10.1101/2021.05.24.21257744
2021Surveillance for Common Arboviruses in Whole Blood of Malaria-Free Ill Returned Canadian Travelers to the Americas
Current Infectious Disease Reports
DOI: 10.1007/s11908-021-00762-1
2021S-Gene Target Failure as a Marker of Variant B.1.1.7 among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021
JAMA - Journal of the American Medical Association
DOI: 10.1001/jama.2021.5607
2021Validation of a Laboratory-Developed Triplex Molecular Assay for Simultaneous Detection of Gastrointestinal Adenovirus and Rotavirus in Stool Specimens
Pathogens
Rachel R. Higgins and Adriana Peci and Mark Cardona and Jonathan B. Gubbay
DOI: 10.3390/pathogens9050326
04/2020Influenza vaccine does not increase the risk of coronavirus or other noninfluenza respiratory viruses: Retrospective analysis from Canada, 2010-2011 to 2016-2017
Clinical Infectious Diseases
DOI: 10.1093/cid/ciaa626
2020Diagnostic Sensitivity of Nasopharyngeal RT-PCR in a Long-Term Care Home Outbreak
Journal of the American Medical Directors Association
DOI: 10.1016/j.jamda.2020.08.018
2020Diagnosing COVID-19: The Disease and Tools for Detection
ACS nano
DOI: 10.1021/acsnano.0c02624
2020Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2020.104433
2020Paediatric critical illness associated with respiratory infection: A single-centre, retrospective cohort study
BMJ Paediatrics Open
DOI: 10.1136/bmjpo-2020-000640
2020Interim estimates of 2019/20 vaccine effectiveness during early-season co-circulation of influenza A and B viruses, Canada, February 2020
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2020.25.7.2000103
2020The impact of repeated vaccination using 10-year vaccination history on protection against influenza in older adults: A test-negative design study across the 2010/11 to 2015/16 influenza seasons in Ontario, Canada
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2020.25.1.1900245
2020Diagnosis and Management of First Case of COVID-19 in Canada: Lessons Applied from SARS-CoV-1
Clinical Infectious Diseases
DOI: 10.1093/cid/ciaa227
2020Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide
bioRxiv
DOI: 10.1101/2020.06.08.140459
2020Presence of flavivirus antibodies does not lead to a greater number of symptoms in a small cohort of canadian travelers infected with zika virus
Viruses
DOI: 10.3390/v12020140
2020Influenza Vaccine Effectiveness in Preventing Hospitalizations in Older Patients With Chronic Obstructive Pulmonary Disease
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiz419
2020Haemophilus parainfluenza bacteremia post-ERCP and cholecystectomy in a pediatric patient: A case report
Official Journal of the Association of Medical Microbiology and Infectious Disease Canada
Jelena Popov and Arend Strikwerda and Jonathan Gubbay and Nikhil Pai
DOI: 10.3138/jammi.2018-0027
10/2019Genetic characterization of human metapneumovirus identified through community and facility-based surveillance of infants in Dhaka, Bangladesh
Journal of Medical Virology
DOI: 10.1002/jmv.25351
2019Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada: Possible cohort effect following the 2009 influenza pandemic
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2019.24.15.1900104
2019Vaccine Effectiveness against Lineage-matched and -mismatched Influenza B Viruses across 8 Seasons in Canada, 2010-2011 to 2017-2018
Clinical Infectious Diseases
DOI: 10.1093/cid/ciy876
2019Equity and impact: Ontario's infant rotavirus immunization program five years following implementation. A population-based cohort study
Vaccine
DOI: 10.1016/j.vaccine.2019.01.061
2019Measles antibody levels in young infants
Pediatrics
DOI: 10.1542/peds.2019-0630
2019Interim estimates of 2018/19 vaccine effectiveness against influenza A(H1N1)pdm09, Canada, January 2019
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2019.24.4.1900055
2019Cost-effectiveness of measles control during elimination in Ontario, Canada, 2015
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2019.24.11.1800370
2019Influenza virus RNA recovered from droplets and droplet nuclei emitted by adults in an acute care setting
Journal of Occupational and Environmental Hygiene
DOI: 10.1080/15459624.2019.1591626
2019Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada
Scientific Reports
DOI: 10.1038/s41598-019-47740-1
2019Effects of absolute humidity, relative humidity, temperature, and wind speed on influenza activity in Toronto, Ontario, Canada
Applied and Environmental Microbiology
DOI: 10.1128/AEM.02426-18
2019Characteristics and Outcomes of Young Children Hospitalized with Laboratory-confirmed Influenza or Respiratory Syncytial Virus in Ontario, Canada, 2009-2014
Pediatric Infectious Disease Journal
DOI: 10.1097/INF.0000000000002164
2019Can routinely collected laboratory and health administrative data be used to assess influenza vaccine effectiveness? Assessing the validity of the Flu and Other Respiratory Viruses Research (FOREVER) Cohort
Vaccine
DOI: 10.1016/j.vaccine.2019.06.011
2019The direct healthcare costs attributable to West Nile virus illness in Ontario, Canada: A population-based cohort study using laboratory and health administrative data
BMC Infectious Diseases
DOI: 10.1186/s12879-019-4596-9
2019Assessment of population immunity to measles in Ontario, Canada: a Canadian Immunization Research Network (CIRN) study
Human Vaccines and Immunotherapeutics
DOI: 10.1080/21645515.2019.1619402
2019Influenza vaccine effectiveness among patients with cancer: A population-based study using health administrative and laboratory testing data from Ontario, Canada
Journal of Clinical Oncology
DOI: 10.1200/JCO.19.00354
2019Paradoxical clade- And age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: Potential imprint-regulated effect of vaccine (I-REV)
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2019.24.46.1900585
2019Enterovirus d68 in a community hospital: A test-negative case-control study
JAMMI
DOI: 10.3138/jammi.3.1.03
2018Zika virus infection in a pregnant Canadian traveler with congenital fetal malformations noted by ultrasonography at 14-weeks gestation
Tropical Diseases, Travel Medicine and Vaccines
DOI: 10.1186/s40794-018-0062-8
2018Canada-Wide Epidemic of emm74 Group A Streptococcus Invasive Disease
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofy085
2018Limitations of administrative data to identify measles cases in Ontario, Canada: a cautionary tale
Canadian Journal of Public Health
DOI: 10.17269/s41997-018-0021-1
2018Early season co-circulation of influenza a(H3N2) and b(yamagata): Interim estimates of 2017/18 vaccine effectiveness, Canada, january 2018
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2018.23.5.18-00035
2018Laboratory testing and phylogenetic analysis during a mumps outbreak in Ontario, Canada
Virology Journal
DOI: 10.1186/s12985-018-0996-5
2018Rotavirus genotypes circulating in Ontario, Canada, before and after implementation of the rotavirus immunization program
Vaccine
DOI: 10.1016/j.vaccine.2018.02.064
2018Molecular characterization of predominant Streptococcus pneumoniae serotypes causing invasive infections in Canada: The SAVE study, 2011-15
Journal of Antimicrobial Chemotherapy
DOI: 10.1093/jac/dky157
2018Use of genome sequencing to define institutional influenza outbreaks, Toronto, Ontario, Canada, 2014-15
Emerging Infectious Diseases
DOI: 10.3201/eid2403.171499
2018Targeting intracellular ion homeostasis for the control of respiratory syncytial virus
American Journal of Respiratory Cell and Molecular Biology
DOI: 10.1165/rcmb.2017-0345OC
2018Serotype distribution of invasive Streptococcus pneumoniae in adults 65¿years of age and over after the introduction of childhood 13-valent pneumococcal conjugate vaccination programs in Canada, 2010–2016
Vaccine
DOI: 10.1016/j.vaccine.2018.06.018
2018Acute myocardial infarction after laboratory-confirmed influenza infection
New England Journal of Medicine
DOI: 10.1056/NEJMoa1702090
2018Zoonotic Influenza and Human Health—Part 2: Clinical Features, Diagnosis, Treatment, and Prevention Strategies
Current Infectious Disease Reports
DOI: 10.1007/s11908-018-0643-8
2018Zoonotic Influenza and Human Health—Part 1: Virology and Epidemiology of Zoonotic Influenzas
Current Infectious Disease Reports
DOI: 10.1007/s11908-018-0642-9
2018Should sex be considered an effect modifier in the evaluation of influenza vaccine effectiveness?
Open Forum Infectious Diseases
DOI: 10.1093/ofid/ofy211
2018Age-Related Differences in Influenza B Infection by Lineage in a Community-Based Sentinel System, 2010-2011 to 2015-2016, Canada
Journal of Infectious Diseases
DOI: 10.1093/infdis/jix393
2017Seasonal Influenza Forecasting in Real Time Using the Incidence Decay With Exponential Adjustment Model
Open Forum Infectious Diseases
DOI: 10.1093/OFID/OFX166
2017Pre-and post-pandemic trends in antiviral use in hospitalized patients with laboratory-confirmed influenza: 2004/05–2013/14, Toronto, Canada
Antiviral Research
DOI: 10.1016/j.antiviral.2017.01.025
2017Measuring influenza RNA quantity after prolonged storage or multiple freeze/thaw cycles
Journal of Virological Methods
DOI: 10.1016/j.jviromet.2017.05.018
2017The utility of measles and rubella IgM serology in an elimination setting, Ontario, Canada, 2009–2014
PLoS ONE
DOI: 10.1371/journal.pone.0181172
2017Global distribution and evolutionary history of enterovirus D68, with emphasis on the 2014 outbreak in Ontario, Canada
Frontiers in Microbiology
DOI: 10.3389/fmicb.2017.00257
2017Vaccine effectiveness against laboratory-confirmed influenza hospitalizations among young children during the 2010-11 to 2013-14 influenza seasons in Ontario, Canada
PLoS ONE
DOI: 10.1371/journal.pone.0187834
2017Serial vaccination and the antigenic distance hypothesis: Effects on influenza vaccine effectiveness during A(H3N2) epidemics in Canada, 2010-2011 to 2014-2015
Journal of Infectious Diseases
DOI: 10.1093/infdis/jix074
2017Influenza and rhinovirus viral load and disease severity in upper respiratory tract infections
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2016.11.008
2017Detecting and quantifying influenza virus with self- versus investigator-collected mid-turbinate nasal swabs
Journal of Medical Virology
DOI: 10.1002/jmv.24753
2017Beyond Antigenic Match: Possible Agent-Host and Immuno-epidemiological Influences on Influenza Vaccine Effectiveness during the 2015-2016 Season in Canada
Journal of Infectious Diseases
DOI: 10.1093/infdis/jix526
2017Measles outbreak with unique virus genotyping, Ontario, Canada, 2015
Emerging Infectious Diseases
DOI: 10.3201/eid2307.161145
2017Interim estimates of 2016/17 vaccine effectiveness against influenza A(H3N2), Canada, January 2017
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2017.22.6.30460
2017Evaluation of euroimmun anti-zika virus igm and igg enzyme-linked immunosorbent assays for zika virus serologic testing
Journal of Clinical Microbiology
DOI: 10.1128/JCM.00442-17
2017Challenges in interpretation of diagnostic test results in a mumps outbreak in a highly vaccinated population
Clinical and Vaccine Immunology
DOI: 10.1128/CVI.00542-16
2017Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing
PLoS ONE
DOI: 10.1371/journal.pone.0178040
2017Lineage-specific epitope profiles for HPAI H5 pre-pandemic vaccine selection and evaluation
Influenza and other Respiratory Viruses
DOI: 10.1111/irv.12466
2017Evaluation of altona diagnostics RealStar zika virus reverse transcription-PCR test kit for Zika virus PCR testing
Journal of Clinical Microbiology
DOI: 10.1128/JCM.02153-16
2017Evaluation and Comparison of Multiple Test Methods, Including Real-time PCR, for Legionella Detection in Clinical Specimens
Frontiers in Public Health
DOI: 10.3389/fpubh.2016.00175
2016Whole-genome sequencing for surveillance of invasive pneumococcal diseases in Ontario, Canada: Rapid prediction of genotype, antibiotic resistance and characterization of emerging serotype 22F
Frontiers in Microbiology
DOI: 10.3389/fmicb.2016.02099
2016Spectrum of viral pathogens in blood of malaria-free Ill travelers returning to Canada
Emerging Infectious Diseases
DOI: 10.3201/eid2205.151875
2016Interim estimates of 2015/16 vaccine effectiveness against influenza a(H1N1)pdm09, Canada, February 2016
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2016.21.11.30168
2016High incidence of invasive group a streptococcus disease caused by strains of uncommon emm types in Thunder Bay, Ontario, Canada
Journal of Clinical Microbiology
DOI: 10.1128/JCM.02201-15
2016Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada
Infection, Genetics and Evolution
DOI: 10.1016/j.meegid.2016.04.007
2016Much left to learn about Zika
The Canadian nurse
2016A perfect storm: Impact of genomic variation and serial vaccination on low influenza vaccine effectiveness during the 2014-2015 season
Clinical Infectious Diseases
DOI: 10.1093/cid/ciw176
2016Mutations acquired during cell culture isolation may affect antigenic characterisation of influenza A(H3N2) clade 3C.2a viruses
Eurosurveillance
DOI: 10.2807/1560-7917.ES.2016.21.3.30112
2016Epidemiology of Zika virus, 1947-2007
BMJ Global Health
DOI: 10.1136/bmjgh-2016-000087
2016Association of serotype with respiratory presentations of pneumococcal infection, Ontario, Canada, 2003-2011
Vaccine
DOI: 10.1016/j.vaccine.2015.11.021
2016Maternal vitamin D supplementation during pregnancy and lactation to prevent acute respiratory infections in infancy in Dhaka, Bangladesh (MDARI trial): Protocol for a prospective cohort study nested within a randomized controlled trial
BMC Pregnancy and Childbirth
DOI: 10.1186/s12884-016-1103-9
2016Epidemiology of enterovirus D68 in Ontario
PLoS ONE
DOI: 10.1371/journal.pone.0142841
2015Interim estimates of 2014/15 vaccine effectiveness against influenza A(H3N2) from Canada’s sentinel physician surveillance network, January 2015
Eurosurveillance
DOI: 10.2807/1560-7917.ES2015.20.4.21022
2015Genetic Analysis of Invasive Pneumococcal Isolates from Children in Ontario, Canada, 2007-2012
Pediatric Infectious Disease Journal
DOI: 10.1097/INF.0000000000000697
2015Detection of enterovirus D68 in Canadian laboratories
Journal of Clinical Microbiology
DOI: 10.1128/JCM.03686-14
2015Acute respiratory infections in travelers returning from MERS-CoV–Affected areas
Emerging Infectious Diseases
DOI: 10.3201/eid2109.150472
2015Strengths and limitations of assessing influenza vaccine effectiveness using routinely collected, passive surveillance data in Ontario, Canada, 2007 to 2012: Balancing efficiency versus quality
Eurosurveillance
DOI: 10.2807/1560-7917.ES2015.20.16.21100
2015Randomized evaluation of live attenuated vs. inactivated influenza vaccines in schools (RELATIVES) cluster randomized trial: Pilot results from a household surveillance study to assess direct and indirect protection from influenza vaccination
Vaccine
DOI: 10.1016/j.vaccine.2015.07.044
2015Influenza virus emitted by naturally-infected hosts in a healthcare setting
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2015.11.002
2015Randomized evaluation of live attenuated vs. inactivated influenza vaccines in schools (RELATIVES) pilot study: A cluster randomized trial
Vaccine
DOI: 10.1016/j.vaccine.2014.11.044
2015Integrated sentinel surveillance linking genetic, antigenic, andepidemiologic monitoring of influenza vaccine-virus relatedness and effectiveness during the 2013-2014 influenza season
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiv177
2015Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: Global and local transmission dynamics
Scientific Reports
DOI: 10.1038/srep14268
2015Human metapneumovirus prevalence and molecular epidemiology in respiratory outbreaks in Ontario, Canada
Journal of Medical Virology
DOI: 10.1002/jmv.24024
2015Interim estimates of 2013/14 vaccine effectiveness against influenza A(H1N1)PDM09 from Canada's sentinel surveillance network, January 2014
Eurosurveillance
DOI: 10.2807/1560-7917.ES2014.19.5.20690
2014Multiple influenza a (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient
Antimicrobial Agents and Chemotherapy
DOI: 10.1128/AAC.03667-14
2014Genetic characterization of seasonal influenza A (H3N2) viruses in Ontario during 2010-2011 influenza season: High prevalence of mutations at antigenic sites
Influenza and other Respiratory Viruses
DOI: 10.1111/irv.12219
2014Previous antibiotic exposure and antimicrobial resistance in invasive pneumococcal disease: Results from prospective surveillance
Clinical Infectious Diseases
DOI: 10.1093/cid/ciu497
2014Preexisting CD4+ T-cell immunity in human population to avian influenza H7N9 virus: Whole proteome-wide immunoinformatics analyses
PLoS ONE
DOI: 10.1371/journal.pone.0091273
2014Coxsackieviruses in Ontario, January 2005 to December 2011
International Journal of Infectious Diseases
DOI: 10.1016/j.ijid.2014.04.013
2014Influenza A/subtype and B/lineage effectiveness estimates for the 2011-2012 trivalent vaccine: Cross-season and cross-lineage protection with unchanged vaccine
Journal of Infectious Diseases
DOI: 10.1093/infdis/jiu048
2014Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses
PLoS ONE
DOI: 10.1371/journal.pone.0092153
2014Performance of rapid influenza diagnostic testing in outbreak settings
Journal of Clinical Microbiology
DOI: 10.1128/JCM.02024-14
2014Optimal number of samples to test for institutional respiratory infection outbreaks in Ontario
Epidemiology and Infection
DOI: 10.1017/S0950268812002531
2013Variant influenza A (H1N1) virus infection in Canada
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2013.03.011
2013T cell memory to evolutionarily conserved and shared hemagglutinin epitopes of H1N1 viruses: A pilot scale study
BMC Infectious Diseases
DOI: 10.1186/1471-2334-13-204
2013RISK FACTORS FOR INFLUENZA AMONG HEALTH CARE WORKERS DURING 2009 PANDEMIC, TORONTO, ONTARIO, CANADA
Romanian Journal of Infectious Diseases
DOI: 10.3201/eid1904.111812
2013Low seroconversion after one dose of AS03-adjuvanted H1N1 pandemic influenza vaccine in solid-organ transplant recipients
Canadian Journal of Infectious Diseases and Medical Microbiology
DOI: 10.1155/2013/256756
2013Macrolide-resistant mycoplasma pneumoniae in humans, Ontario, Canada, 2010-2011
Emerging Infectious Diseases
DOI: 10.3201/eid1909.121466
2013Evaluation of 2009 pandemic H1N1 influenza vaccination in adults with lymphoid malignancies receiving chemotherapy or following autologous stem cell transplant
Leukemia and Lymphoma
DOI: 10.3109/10428194.2012.742524
2013Vaccine effectiveness against laboratory-confirmed influenza hospitalizations among elderly adults during the 2010-2011 season
Clinical Infectious Diseases
DOI: 10.1093/cid/cit404
2013Local public health response to vaccine-associated measles: Case report
BMC Public Health
DOI: 10.1186/1471-2458-13-269
2013Pneumococcal vaccination programs and the burden of invasive pneumococcal disease in Ontario, Canada, 1995-2011
Vaccine
DOI: 10.1016/j.vaccine.2013.09.049
2013Laboratory-confirmed influenza B infection in immunized long-term care facility residents receiving oseltamivir prophylaxis in Ontario
Infection Control and Hospital Epidemiology
DOI: 10.1086/673455
2013Temporal changes in respiratory adenovirus serotypes circulating in the greater Toronto area, Ontario, during December 2008 to April 2010
Virology Journal
DOI: 10.1186/1743-422X-10-15
2013Interim estimates of influenza vaccine effectiveness in 2012/13 from Canada's sentinel surveillance network, January 2013
Eurosurveillance
DOI: 10.2807/ese.18.05.20394-en
2013Have changing pneumococcal vaccination programmes impacted disease in Ontario?
Vaccine
DOI: 10.1016/j.vaccine.2013.04.007
2013Expression of recombinant HA1 protein for specific detection of influenza A/H1N1/2009 antibodies in human serum
Microbiology and Immunology
DOI: 10.1111/j.1348-0421.2012.00517.x
2013Community-acquired respiratory viruses and co-infection among patients of Ontario sentinel practices, April 2009 to February 2010
Influenza and other Respiratory Viruses
DOI: 10.1111/j.1750-2659.2012.00418.x
2013A sentinel platform to evaluate influenza vaccine effectiveness and new variant circulation, Canada 2010-2011 season
Clinical Infectious Diseases
DOI: 10.1093/cid/cis431
2012Serotype distribution of invasive Streptococcus pneumoniae in Canada during the introduction of the 13-valent pneumococcal conjugate vaccine, 2010
Canadian Journal of Microbiology
DOI: 10.1139/W2012-073
2012Genetic variability of human respiratory syncytial virus a strains circulating in Ontario: A novel genotype with a 72 nucleotide G gene duplication
PLoS ONE
DOI: 10.1371/journal.pone.0032807
2012Potential T cell epitopes within swine-origin triple reassortant influenza A (H3N2) variant virus which emerged in 2011: An immunoinformatics study
Vaccine
DOI: 10.1016/j.vaccine.2012.07.054
2012The role of torovirus in nosocomial viral gastroenteritis at a large tertiary pediatric centre
Canadian Journal of Infectious Diseases and Medical Microbiology
DOI: 10.1155/2012/134961
2012Respiratory viral infections in institutions from late stage of the first and second waves of pandemic influenza A (H1N1) 2009, Ontario, Canada
Influenza and other Respiratory Viruses
DOI: 10.1111/j.1750-2659.2012.00336.x
2012Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient
Journal of Clinical Microbiology
DOI: 10.1128/JCM.00682-12
2012Poor seroprotection but allosensitization after adjuvanted pandemic influenza H1N1 vaccine in kidney transplant recipients
Transplant Infectious Disease
DOI: 10.1111/tid.12006
2012Pandemic H1N1 influenza infection and vaccination in humans induces cross-protective antibodies that target the hemagglutinin stem
Frontiers in Immunology
DOI: 10.3389/fimmu.2012.00087
2012Immunogenicity of a half-dose of adjuvanted 2009 pandemic H1N1 influenza vaccine in adults: A prospective cohort study
European Journal of Clinical Microbiology and Infectious Diseases
DOI: 10.1007/s10096-011-1352-5
2012Detection of an influenza B virus strain with reduced susceptibility to neuraminidase inhibitor drugs
Journal of Clinical Microbiology
DOI: 10.1128/JCM.05069-11
2011Humoral and cell-mediated immunity to pandemic H1N1 influenza in a Canadian cohort one year post-pandemic: Implications for vaccination
PLoS ONE
DOI: 10.1371/journal.pone.0028063
2011Analytical performance of norovirus real-time RT-PCR detection protocols in Canadian laboratories
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2010.10.008
2011An assessment of mumps vaccine effectiveness by dose during an outbreak in Canada
CMAJ. Canadian Medical Association Journal
DOI: 10.1503/cmaj.101371
2011Neuraminidase-inhibitor resistance testing for pandemic influenza A (H1N1) 2009 in Ontario, Canada
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2010.12.007
2011Multidrug-resistant pandemic (H1N1) 2009 infection in immunocompetent child
Emerging Infectious Diseases
DOI: 10.3201/eid1708.102004
2011Early post-transplant vaccination with pandemic influenza A/H1N1 vaccine in pediatric heart transplant recipients
Pediatric Transplantation
DOI: 10.1111/j.1399-3046.2010.01433.x
2011Seroprevalence of pandemic influenza H1N1 in Ontario from January 2009-May 2010
PLoS ONE
DOI: 10.1371/journal.pone.0026427
2011Long term immune responses to pandemic influenza A/H1N1 infection in solid organ transplant recipients
PLoS ONE
DOI: 10.1371/journal.pone.0028627
2011Evaluation of pandemic H1N1 (2009) influenza vaccine in adults with solid tumor and hematological malignancies on active systemic treatment
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2010.11.013
2011Evaluation and verification of the seeplex diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens
Journal of Clinical Microbiology
DOI: 10.1128/JCM.00599-11
2011When should a diagnosis of influenza be considered in adults requiring intensive care unit admission? Results of population-based active surveillance in Toronto
Critical Care
DOI: 10.1186/cc10331
2011Effectiveness of AS03 adjuvanted pandemic H1N1 vaccine: case-control evaluation based on sentinel surveillance system in Canada, autumn 2009.
BMJ (Clinical research ed.)
DOI: 10.1136/bmj.c7297
2011Severe human rhinovirus outbreak associated with fatalities in a long-term care facility in Ontario, Canada
Journal of the American Geriatrics Society
DOI: 10.1111/j.1532-5415.2010.03091.x
2010Rhinovirus outbreaks in long-term care facilities, Ontario, Canada
Emerging Infectious Diseases
DOI: 10.3201/eid1609.100476
2010High prevalence of asymptomatic bocavirus in daycare: Is otitis media a confounder?
Journal of Infectious Diseases
DOI: 10.1086/656786
2010Transmission of influenza A pandemic (H1N1) 2009 virus in a long-term care facility in Ontario, Canada
Infection Control and Hospital Epidemiology
DOI: 10.1086/657337
2010Respiratory infection in institutions during early stages of pandemic (H1N1) 2009, Canada
Emerging Infectious Diseases
DOI: 10.3201/eid1512.091022
2009Older age and a reduced likelihood of 2009 H1N1 virus infection
New England Journal of Medicine
DOI: 10.1056/NEJMc0907256
2009Multiplex PCR tests sentinel the appearance of pandemic influenza viruses including H1N1 swine influenza
Journal of Clinical Virology
DOI: 10.1016/j.jcv.2009.05.031
2009Clinical features, epidemiology, antimicrobial resistance, and exotoxin genes (including that of Panton-Valentine leukocidin) of gentamicin-susceptible methicillin-resistant Staphylococcus aureus (GS-MRSA) isolated at a paediatric teaching hospital in New South Wales, Australia
Pathology
DOI: 10.1080/00313020701716276
2008Cellulitis in childhood invasive pneumococcal disease: A population-based study
Journal of Paediatrics and Child Health
DOI: 10.1111/j.1440-1754.2006.00872.x
2006 - Research
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Establishment of a pilot clinical database and specimen biorepository for further microbiology investigations (e.g. next-generation sequencing) in children who are test-negative with routine investigations
GrantsCo-Investigator. COVID-19 Vaccine Responses among African Canadian Children with and without Sickle Cell Disease. Funding Source: Canadian Institute for Health Research
Co-Investigator: COVID-19 Vaccine Responses among African Canadians: Sustainability of Immune Responses and Safety Profiles. Funding Source: Canadian Institute for Health Research
Co-Investigator: A quantum dot portable diagnostic device for COVID-19. Funding Source: Toronto COVID-19 Action Fund
Co-Investigator: Just-in-time pathogenomics for SARS-CoV-2, data for immediate action. Funding Source: Toronto COVID-19 Action Fund
Co-Investigator: Sero-epidemiology network – population immunity to mumps in Canada. Funding Source: CIHR/Public Health Agency of Canada (PHAC) Canadian Immunization Research Network
Co-Investigator: A data linkage-enabled sample bank at PHO – proof of concept study. Funding Source: Public Health Ontario Project Initiation Fund
Pneumonia and malaria: Innovations tackle leading threats to children under five
Globally, pneumonia and malaria are among the leading causes of death for children under five, due in part to health-care resource gaps in low- and middle-income countries. New BCCHR investigator and pediatric infectious diseases expert Dr. Michael T. Hawkes is developing diagnostic and treatment tools to address these shortages.
