Analysis of Enterovirus evolution in Canada over a 23-year period
Bibliographic record
Abstract
The non-polio Enteroviruses (NPEV) cause a glut of severe diseases which are especially burdensome in the pediatric population. This study uses a novel approach to evaluate the relationship between recombination amongst non-polio enteroviruses and circulation. The National Centre for Enterovirus (NCEV) surveillance system showed that from 1991-2013 there were 2628 Enterovirus positive samples surveyed including 2167 (83.9%) Enterovirus B strains, 326 (12.6%) Enterovirus A strains, 85 (3.3%) Enterovirus D strains and 5 (0.2%) Enterovirus C strains. Echovirus 30 (Enterovirus B) was the most prevalent serotype followed by Coxsackievirus A16 (Enterovirus A) followed by several other Enterovirus B serotypes. To evaluate the genetics of these species 269 strains from 17 Enterovirus B serotypes, 2 Enterovirus A serotypes and 1 Enterovirus D serotype were chosen for full genome sequencing. These serotypes were representative of 93.4% of Enterovirus B strains, 91.1% of Enterovirus A strains, and 100% of Enterovirus D circulating. Phylogenetic analysis was used to genotype strains and used to identify hundreds of recombination events between serotypes. Comparisons between VP1 average pairwise identities between serotypes and recombination events did not show a definitive association between the two. However, a significant association between temporal co-circulation and recombination events was identified, as well as an association between geographic co-circulation and recombination events. Enterovirus B genotypes were evaluated chronologically by serotype and compared to surveillance data to test the hypothesis that outbreaks were associated with recombination events. However, outbreaks strains were identified in years preceding the outbreaks and identified recombination events were not associated with any outbreaks. Recombination events between Canadian strains within the Enterovirus A species or the Enterovirus D species were not found. This study presents new information about the dynamics of NPEV circulation and recombination. It also highlights complexities of genetics analyses through genotyping and tracking genotypes through the surveillance period. Finally, this study sets the stage for future pairings of full genomic analyses with surveillance and stresses the importance of continued surveillance.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.003 | 0.008 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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 source (direct Gemma or distilled Codex), 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".