Bibliographic record
Abstract
Origin and Evolution of Hepatitis VirusesViral infection with hepatitis A, B, C, D, or E viruses (HAV, HBV, HCV, HDV, HEV) results in the syndrome of hepatitis, characterized by inflammation of the liver.Each virus is classified within a different virus family, yet all have hepatocyte-specific tropism and similar clinical manifestations.Full permissive infection with human hepatitis viruses is limited to higher primates, except for HEV, yet hepatitis-like viruses are known to infect invertebrates and all manner of vertebrates, including animals of the Laurasiatheria clade, such as bats and other insectivorous small mammals, suggesting an ancient origin and complex evolutionary history for hepatitis viruses.The definitive origin of these viruses remains largely unknown.This Special Research Topic includes papers on HBV, HCV, HDV, and HEV, and includes studies investigating the consequences of virus evolution, such as geographic distribution and clinical outcomes.Other papers investigate intra-patient evolution, including super-infection and recombination, but also evolution over extensive timescales, thus providing a glimpse into hepatitis virus origins.Several papers within the Topic presented important perspectives on the origins of HBV and HDV.The paper by Locarnini et al. elucidates the origin of primate HBV in the context of host evolution and migration.The authors posit that the evolutionary impetus giving rise to contemporary human and Old World non-human primate (NHP) HBV involved early human migration out of Africa during the upper Paleolithic era and the Neolithic agricultural expansion.The authors conclude that HBV evolution has occurred over many thousands of years with lineages disappearing over time and extant genotypes arising from specific population movements, such as slave trading.Most importantly, their investigation suggests that co-evolution among human and NHP HBV is not supported.The study by Netter et al. also investigated possible co-evolution of HDV and HDV-like agents with their hosts.In this important study, the authors advance the idea that HDV, a satellite virus most similar to plant viroids, likely originated within a cellular transcriptome as a circular RNA with ribozyme activity.Although delta-like agents have been detected in a multitude of different animals, including birds, fish, and insects, the helper virus, if indeed one is required, is not known.The paper suggests that host shifting, not co-divergence, is the suggested mode of HDV evolution based on HDV/host phylogeny.Viral genomic recombination, as a mechanism of evolution involving viral superinfection, was the focus of several papers within the Research Topic.Jose-Abrego et al. observed that a high percentage (56%) of HIV-HBV co-infected patients were infected with multiple heterologous HBV genotypes (gt), including gtH, providing opportunity for genomic recombination.The paper from Giersch et al. presents an elegant study of HDV superinfection amongst gts1 and 3 using a human chimeric liver mouse model, observing that recombination is not a significant evolutionary process for HDV.Productive infection with multiple HDV strains, regardless of genotype, was not observed
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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 | 0.004 | 0.015 |
| Meta-epidemiology (narrow) | 0.004 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.006 | 0.005 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.009 | 0.015 |
| Insufficient payload (model declined to judge) | 0.012 | 0.012 |
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".