Global genetic diversity of Infectious Salmon Anemia Virus (ISAV) a scoping review protocol
Bibliographic record
Abstract
BACKGROUND: Infectious salmon anemia virus is one of the most important pathogens responsible for causing infectious salmon anemia in Atlantic salmon (Salmo salar). Following its first emergence in 1980s in Norway, it has been reported in several salmon producing countries worldwide, with new variants frequently reported. These variants mostly exhibit differences in segments 5 and 6 of the genome, which contribute to the genetic diversity and variability in virulence. Despite the considerable economic losses associated with ISA, there remains a critical gap in available information on genetic diversity and classification. This study aims to provide a comprehensive and up-to-date synopsis of all known ISAV variants worldwide. METHODS: The Population, Concept, Context approach was used to formulate the research primary question. The primary research question of this review is "What variants of ISAV with respect to segment 5 and 6 has been identified globally in Atlantic salmon?" To address this question, four databases: PubMed, CAB Abstracts via (EBSCO host), Scopus, and the Earth, Atmospheric & Aquatic Science Collection via ProQuest will be used for primary literature search with no language and geographical area restrictions. Studies will be screened using predefined inclusion and exclusion criteria and will be imported in COVIDENCE. Two co-authors will independently screen, extract data, and assess the selected studies. Any discrepancies between the authors will be resolved with the assistance of two other co-authors in each stage of the protocol. DISCUSSION: To the best of our knowledge, this protocol outlines the first scoping review which will provide insights into the genetic diversity of ISAV, offering a comprehensive overview of the reported variants and their distribution globally. These findings could enhance our understanding of the genetic diversity of the virus, help customize mitigation strategies based on variants involved and provide foundation to develop a universally accepted nomenclature system.
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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 | 0.099 | 0.122 |
| Meta-epidemiology (narrow) | 0.003 | 0.004 |
| Meta-epidemiology (broad) | 0.007 | 0.009 |
| Bibliometrics | 0.026 | 0.015 |
| Science and technology studies | 0.005 | 0.004 |
| Scholarly communication | 0.008 | 0.008 |
| Open science | 0.006 | 0.009 |
| Research integrity | 0.007 | 0.004 |
| Insufficient payload (model declined to judge) | 0.112 | 0.016 |
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".