Validation of oral-nasal specimen collection for influenza and respiratory syncytial virus detection
Bibliographic record
Abstract
Objective: Respiratory virus testing is routinely performed and ways to obtain specimens aside from a nasopharyngeal swab are needed for pandemic preparedness. The main objective is to validate a self-collected oral-nasal swab for the detection of Influenza and respiratory syncytial virus (RSV). Design: Diagnostic test validation of a self-collected oral nasal swab as compared to a provider-collected nasopharyngeal swab. Setting: Emergency Department at Michael Garron Hospital. Participants: Consecutive individuals who presented to the Emergency Department with a suspected viral upper respiratory tract infection were included if they self-collected an oral-nasal swab. Individuals testing positive for Influenza or RSV along with randomly selected participants who tested negative were eligible for inclusion. Interventions: All participants had the paired oral-nasal swab tested using a multiplex respiratory virus polymerase chain reaction for the three respiratory pathogens and compared to the nasopharyngeal swab. Results: 48 individuals tested positive for Influenza, severe acute respiratory coronavirus virus 2 (SARS-CoV-2) or RSV along with 80 who tested negative. 110 were symptomatic with the median time from symptom onset to testing of 1 day (interquartile range 2-5 days). Using the clinical nasopharyngeal swab as the reference standard, the sensitivity was 0.75 (95% CI, 0.43-0.95) and specificity was 0.99 (95% CI, 0.93-1.00) for RSV, sensitivity is 0.67 (95% CI, 0.49-0.81) and specificity is 0.96 (95% CI, 0.89-0.99) for Influenza. Conclusions: Multiplex testing with a self-collected oral-nasal swab for Influenza and RSV is not an acceptable substitute for a healthcare provider collected nasopharyngeal swab primarily due to suboptimal Influenza test characteristics.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.004 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 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) | 0.000 | 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 teacher head, 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".