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Abstract
Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68’s infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic’s origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.
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1 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354); York University, Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, Toronto, Canada (GRID:grid.21100.32) (ISNI:0000 0004 1936 9430)
2 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354)
3 University of Pennsylvania, Department of Pathobiology, School of Veterinary Medicine, Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972)
4 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354); University of Toronto, Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0001 2157 2938)
5 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354); Centre de recherche du CHU de Québec-Université Laval, Axe Maladies infectieuses et immunitaires, Québec, Canada (GRID:grid.23856.3a) (ISNI:0000 0004 1936 8390)
6 ETH Zürich, Department of Biosystems Science and Engineering, Basel, Switzerland (GRID:grid.5801.c) (ISNI:0000 0001 2156 2780); Swiss Institute of Bioinformatics, Lausanne, Switzerland (GRID:grid.419765.8) (ISNI:0000 0001 2223 3006)
7 Public Health Agency of Canada, National Microbiology Laboratory, Montreal, Canada (GRID:grid.415368.d) (ISNI:0000 0001 0805 4386)
8 Simon Fraser University, Department of Mathematics, Burnaby, Canada (GRID:grid.61971.38) (ISNI:0000 0004 1936 7494)
9 University of Toronto, Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0001 2157 2938); Sunnybrook Research Institute, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0004 0469 1398)
10 University of Georgia, Center for the Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Athens, USA (GRID:grid.213876.9) (ISNI:0000 0004 1936 738X)
11 Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Baltimore, USA (GRID:grid.21107.35) (ISNI:0000 0001 2171 9311)
12 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354); University of British Columbia, Department of Pathology and Laboratory Medicine, Faculty of Medicine, Vancouver, Canada (GRID:grid.17091.3e) (ISNI:0000 0001 2288 9830)
13 York University, Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, Toronto, Canada (GRID:grid.21100.32) (ISNI:0000 0004 1936 9430)
14 Public Health Ontario, Toronto, Canada (GRID:grid.415400.4) (ISNI:0000 0001 1505 2354); York University, Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, Toronto, Canada (GRID:grid.21100.32) (ISNI:0000 0004 1936 9430); University of Toronto, Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0001 2157 2938)