Sequence relationship of FL-RhCMV with NHP CMVs.
Bibliographic record
Abstract
<p>A phylogenetic tree for FL-RhCMV and rodent and primate CMVs was constructed based on full genome alignments using the Geneious Prime Tree Builder application. Sequences previously published include RhCMV 180.92 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref037" target="_blank">37</a>] as well as the RhCMV isolates 19262, 19936 and 24514 and the Cynomolgus CMV isolates 31906, 31907, 31908 and 31909 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref041" target="_blank">41</a>]. We also included the published sequences for the CyCMV strains Ottawa [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref046" target="_blank">46</a>] and Mauritius [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref047" target="_blank">47</a>], the simian (African green monkey) CMV isolates Colburn [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref094" target="_blank">94</a>], GR2715 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref045" target="_blank">45</a>] and stealth virus 1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref095" target="_blank">95</a>] as well as the BaCMV strains OCOM4-37 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref096" target="_blank">96</a>] and OCOM4-52 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref097" target="_blank">97</a>] and the DrCMV strain OCOM6-2 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref097" target="_blank">97</a>]. For comparison we included the HCMV TR3 strain [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref034" target="_blank">34</a>], the chimpanzee CMV strain Heberling [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref098" target="_blank">98</a>] and the only two complete genome sequences of new world NHP CMVs, Aotine betaherpesvirus 1 (AoHV-1) strain S34E [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref099" target="_blank">99</a>] and Saimiriine betaherpesvirus 4 (SaHV-4) strain SqSHV [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref100" target="_blank">100</a>]. New genome sequences included in this alignment are as follows: the two RhCMV isolates 34844 and KF03, the CyCMV isolate 31709, the Japanese macaque CMV JaCMV 24655 and the two baboon CMVs BaCMV 31282 and 34826. These CMVs were isolated from fibroblast co-cultures of urine samples obtained from NHP housed either at the Oregon National Primate Research Center (ONPRC) or the Tulane National Primate Research Center (TNPRC). Also included in the alignment are the genomic sequences of the previously published RhCMV isolates UCD52 and UCD59 that originated at the UC Davis National Primate Research Center [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref029" target="_blank">29</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref030" target="_blank">30</a>]. The rodent CMVs include the rat CMV (RCMV) isolates Maastricht [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref101" target="_blank">101</a>], England [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref102" target="_blank">102</a>] and Berlin [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref103" target="_blank">103</a>], the guinea pig CMV (GPCMV) isolate 22122 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref104" target="_blank">104</a>] and the murine CMV (MCMV) strain Smith [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1008666#ppat.1008666.ref105" target="_blank">105</a>], which was used as an outgroup.</p>
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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 | 0.000 | 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) | 0.060 | 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".