Mapping of putative virulence motifs on infectious salmon anemia virus surface glycoprotein genes
Bibliographic record
Abstract
Infectious salmon anemia virus (ISAV) is classified in the genus Isavirus of the family Orthomyxoviridae. Although virulence variation of ISAV can be demonstrated experimentally in fish, virus strain identification is ambiguous because the correlates of pathogenicity and/or antigenicity of ISAV are not well defined. Thirteen ISAV isolates characterized for their ability to kill fish were used to search for markers of virulence on the virus surface glycoprotein genes; haemagglutinin-esterase (HE) and fusion (F) protein genes. A single amino acid change N164D in the putative globular head of the HE protein, and a deletion/insertion of ≤13 aa with the presence of a specific motif 352FNT354 in the highly polymorphic region spanning residues 337V to M372 in the HE protein stalk, in combination with a specific motif 265YP266 very close to the trypsin-cleavage site 267RA/G268 of the precursor F0 protein were correlated with reduced cytopathogenicity and reduced virulence for Atlantic salmon. Phylogenetic analysis suggests that the original ancestral ISAV was virulent. The virulence of the North American genotype has not changed much, whereas the European genotype evolved into two genogroups, the real-European genogroup that is still virulent and the European-in-North America genogroup, which is of lower virulence. A novel phylogenetic software program, backtrack, estimated that the North American and European genotypes diverged between 1879 and 1891, whereas the European-in-North America genogroup diverged from the real-European genogroup between 1976 and 1988. This direction of evolution supports insertion of specific motifs in the HE protein, resulting in ISAV attenuation.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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) | 0.001 | 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".