Overview of infectious salmon anaemia virus (<scp>ISAV</scp>) in Atlantic Canada and first report of an <scp>ISAV</scp> North American‐<scp>HPR</scp>0 subtype
Bibliographic record
Abstract
The infectious salmon anaemia virus (ISAV) is an important viral disease of farmed Atlantic salmon that has caused considerable financial losses for salmon farmers around the world, including Atlantic Canada. It is listed as a notifiable disease by the World Organization for Animal Health, and to this day, culling of infected cages or farms remains the current practice in many countries to mitigate the spread of the virus. In Atlantic Canada, ISAV was first detected in 1996 and continues to be detected. While some outbreaks seemed to have arisen from isolated infections of unknown source, others were local clusters resulting from horizontal spread of infection. This study provides a description of the detected ISAV isolates in Atlantic Canada between 2012 and 2016, and explores the phylogenetic relatedness between these ISAV isolates. A key finding is the detection for the first time of a North American-HPR0 ISAV subtype, which was predicted to exist for many years. Through phylogenetic analysis, a scenario emerges with at least three separate incursions of ISAV in Atlantic Canada. An initial ISAV introduction follows a genotypic separation between North America and Europe which resulted in the NA and EU genotypes known today; this separation predates the salmon aquaculture industry. The second incursion of ISAV from Europe to North America led to a sublineage in Atlantic Canada consisting of EU-HPR∆ isolates detected in Nova Scotia and New Brunswick, and the predominant form of ISAV-HPR0 (EU). Finally, we observed what could be the third and most recent incursion of ISAV in Newfoundland, in the form of an isolate highly similar to ISAV EU-HPR0 isolates found in the Faroe Islands and the one isolate from Norway.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.006 | 0.005 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".