Entire genome sequences of two new HCV subtypes, 6r and 6s, and characterization of unique HVR1 variation patterns within genotype 6
Bibliographic record
Abstract
Hepatitis C virus genotype 6 currently contains 21 recognized subtypes, 6a-6u, for which 6r and 6s lack complete genome sequences. In this study, we entirely sequenced variants QC245 and QC66 from Cambodian immigrants in Canada representing subtypes 6r and 6s, respectively. The two genomes shared 75.3% nucleotide similarities to each other and 72.0-82.9% to 21 reference sequences representing subtypes 6a-6q, 6t-6u and variants km41 and gz52557. QC66 and QC245 displayed genome lengths of 9473 and 9450 nt and each contained a single open reading frame of 9051 nt. In 10 protein encoding regions QC245 and QC66 shared common sizes with TV249/6t and 537796/6l isolates, respectively. Phylogenetic analyses demonstrated that QC245 was more closely related to subtype 6f, but both QC66 and QC245 were subtypically different from all other genotype 6 subtypes. Our full-length sequence data confirmed the status of subtype 6r and 6s within genotype 6. Analysis of partial sequences revealed seven 6t and two 6s isolates that were all isolated from Cambodian immigrants. Analysis of the hypervariable region 1 sequences of 81 genotype 6 variants revealed two unique patterns of variation. First, most variants showed an amino acid deletion at the 4th position and second, many contained a basic residue at the 7th position. Possible roles of these two variation patterns are further discussed.
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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 | 0.000 | 0.001 |
| 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".