Human virome in health and respiratory disease: A scoping review
Bibliographic record
Abstract
The human virome comprises viruses that infect cells in the body, which include eukaryotic viruses and prokaryotic viruses (bacteriophages), and it is influenced by individual variation, diet, and disease status. Human virome can cause acute, persistent, or latent infection, whereas in other cases, the viruses coexist with the host as symbionts. In the past, bacteria genomes have received more attention than other microorganisms, while many viral genome studies have not been fully developed. Additionally, in virome studies, most have focused on the gut virome and have not fully investigated the role of virome in other body sites of human disease, such as the respiratory tract, particularly in childhood respiratory diseases. The lungs are the second largest barrier site and are affected by various diseases, of which the microbiome is a key factor. Defining the respiratory virome can be significantly challenging due to several factors, including difficulties in acquiring samples from the lower airways, variations in the respiratory virome across different regions of the lung, and the lack of appropriate approaches to identify viruses. In addition, there are few studies on the similarities and differences between adult and pediatric viromes. The primary objective of this scoping review was to comprehensively map the evidence and uncover research gaps for human virome in health and respiratory disease. We further focused on the composition and differences of respiratory viromes between adults and children, the role of virome in the development of respiratory diseases, and how commensal viruses shape and influence the immune system. Furthermore, we will review how studies of the human virome differ before and after the COVID-19 pandemic.
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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 | 0.017 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.004 |
| Bibliometrics | 0.011 | 0.011 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.006 | 0.001 |
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".