Polymorphism of human papillomavirus type 31 isolates infecting the genital tract of HIV‐seropositive and HIV‐seronegative women at risk for HIV infection
Bibliographic record
Abstract
The genomic polymorphism of high-risk human papillomavirus (HPV) for types other than 16 has not been extensively described. We describe here the genomic polymorphism of high-risk HPV type 31 in 79 women (62 HIV-seropositive, 17 HIV-seronegative) by PCR-sequencing of the long control region (LCR), E6 and E7. LCR polymorphism was generated by 25 (6.4%) single-nucleotide variations over 391 bases. Each variant compared to the prototype contained from 2 to 13 variations (mean of 9.4 +/- 3.3, median of 10). Considering the number of variation sites in each region of HPV genome, the LCR was more variable than E6 (13 over 496 nucleotide (nt), P=0.03) and E7 (9 over 296 nt, P=0.03). Non-synonymous nucleotide variations were found in 31 (75.6%) of 41 isolates and were observed at six positions in E6. Each of the 8 HPV-31 E7 variants contained from 2 to 5 mutations (mean of 4.29 +/- 1.11, median of 5) compared to the prototype. Three non-synonymous E6 and E7 variations were within cysteine arrays. The LCR prototype was significantly over-represented in Caucasian women (14 (25%) of 56) compared to women of African descent (0 (0%) of 15 women, P=0.03). Four (23.5%) of 17 women with persistent versus 6 (25.0%) of 24 women with transient infections were infected by the prototype (P=1.00). HPV-31 LCR was more polymorphic than oncogenes and was associated with ethnicity.
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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 | 0.002 |
| 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".