Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks
Bibliographic record
Abstract
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 (R t ) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The R t 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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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".