Co-detections versus coinfections in the context of SARS-CoV-2 diagnostics
Bibliographic record
Abstract
As the northern hemisphere enters the winter season, and as uptake of SARS-CoV-2 vaccination is being followed by a general relaxation of stringent pandemic control measures, it is expected that other typical seasonal respiratory viruses will rebound in their prevalence. The study of Chekuri et al.1 and many similar articles raise the spectre of having coexisting respiratory virus epidemics simultaneous with the lingering COVID-19 pandemic and thus potentially complicating morbidity, diagnostics and prevention. In the context of this complicated winter season, the semantics of ‘coinfection’ and the implications of diagnostic testing are critical to review. The majority of diagnostic assays, which are of a multiplex fashion, depend on RNA or DNA amplification. Pointed thresholds of positivity or negativity can be fallible. There are often no secondary diagnostic assays and the testing readout is generally accepted for the result so given. The mere positive determinations, however, do not prove infection. That is, ‘co-detection’ does not necessarily imply ‘coinfection’.2,3 Diagnostic RNA or DNA amplification targets may be single or multiple, and amplification thresholds are not uniform between commercial and in-house assays. Measures of prolonged detection may occur in the absence of viable microbe and thus the timing of co-detection may simply coincide with the presence of inactive and non-diagnostic RNA or DNA. For previously common endemic respiratory coronaviruses, the co-detection concept raises several concerns for determining true coinfection.2 This is especially suggested by the positive determinations that are not uncommonly seen among respiratory samples from asymptomatic control groups.4–6 Among co-detections, respiratory syncytial virus and influenza virus are more often associated with active infection and thus the exclusion of samples with these detections may skew the perceptions of coinfection comorbidity if it should occur.3–5 In this light, future studies of coinfection will benefit from confirmatory diagnostic methods that are applicable to the determination of timeliness for associated disease and the veritable coincident laboratory test positivity. None to declare.
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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 | 0.029 |
| Meta-epidemiology (narrow) | 0.000 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.003 | 0.002 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.036 | 0.020 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
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".