The nasopharyngeal virome in adults with acute respiratory infection
Bibliographic record
Abstract
Abstract Background Respiratory infections are a leading cause of morbidity and mortality worldwide, with a significant proportion thought to have a viral aetiology. Traditional diagnostic approaches often rely on targeted assays for “common” respiratory pathogens, leaving a substantial fraction of infections unidentified. Here, we used metagenomic next generation sequencing (mNGS) to characterize the nasopharyngeal virome associated with acute respiratory infection (ARI), with and without a positive PCR test result for a panel of common respiratory viruses. Methods Nasopharyngeal swabs from symptomatic outpatients (n=49), of whom 32 tested positive by a multiplex viral PCR, and asymptomatic controls (n=4) were characterized by mNGS. The virome taxa were stratified into human, non-human eukaryotic host, and bacteriophage sub-groups. We used a phage host classification as a proxy to establish bacterial taxa present in the nasopharynx. We then compared the virome biodiversity and presence of pathogens with known respiratory effects across the participant sub-groups. Results The nasopharyngeal virome exhibited similar diversity across the PCR-positive and - negative subsets. Among the top ARI-associated human viruses were enterovirus (16.3%, human rhinovirus, HRV-A), roseolovirus (14.3%, human betaherpesvirus 7, HBV-7) and lymphocryptovirus (8.16%, Epstein-Barr virus, EBV). The top three ARI-associated phage hosts were Streptococcus spp (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). The virome of both asymptomatic and symptomatic subjects was also abundant in the Staphylococcus (60.4%) and Propionibacterium (Cutibacterium) acnes bacteriophages (90.6%). The PCR and mNGS results were relatively concordant for human rhinovirus (HRV), but not for other PCR panel targets, including human parainfluenza (HPIV), adenovirus (HAdV), bocavirus (BoV) and seasonal coronavirus (HCoV). Conclusions mNGS revealed a high diversity of pathogens that could be cause to respiratory symptomatology, either as a single infection or a co-infection between viral and bacterial species. The clinical significance of the mNGS versus multiplex PCR findings warrants further investigation.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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".