Rediscovering “Baculovirus-A” (Johnson, 1976): The complete genome of ‘Callinectes sapidus nudivirus’
Bibliographic record
Abstract
Callinectes sapidus, or the 'blue crab', supports an extensive east-coast USA fishery and was one of the first crustacean species in which viruses were observed. Pioneering research by Dr Phyllis Johnson led to these initial discoveries, one of which included the discovery of a virus termed "Baculovirus-A". This virus was considered a potential member of the Baculoviridae, Nimaviridae, or Nudiviridae, in which all viral members are rod-shaped dsDNA viruses found in the nucleus of their host cell. With the availability of genomic and bioinformatic tools, such as Illumina HiSeq and assembly programs, it is now possible to assemble the genomes of viruses and gain additional genomic insight, which can shed light on viral taxonomy. Using these tools, alongside electron micrographs and histology slides, we reveal that the hepatopancreas-infecting 'Baculovirus-A' from Callinectes sapidus is a member of the Nudiviridae, resembling genetic and protein similarity to other crab and lobster infecting nudiviruses from the Gammanudivirus genus. Histologically, the virus causes nuclear hypertrophy as observed for other gammanuriviruses. The genome of the virus is circular, 122,436 bp in length, and encodes a predicted 98 protein coding genes, including all of the nudivirus core genes. The prevalence of virus from across Florida, USA, is provided alongside a genomic comparison of the new viral genome against other Gammanudivirus species, revealing the average prevalence to be 2.2% and that Callinectes sapidus nudivirus is distantly similar to the recently described Carcinus maenas nudivirus from Canada.
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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 | 0.001 | 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".