Bibliographic record
Abstract
Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient’s nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada.Methods: Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases. Data Dictionary: Unit_of_Transmission: Hospital Unit where a infection prevention and control epidemiologist identified a possible transmission event. Unit_Acquisition: Hospital Unit where a infection prevention and control epidemiologist identified a possible acquisition event. Collection Date (yyyy-mm-dd, UTC): date at which a nasopharyngeal specimen was collected from a symptomatic case for SARS-CoV-2 molecular diagnostic testing using qRT-PCR. log_GE: Logarithmic base ten genome-equivalents per millilitre of SARS-CoV-2 detected by envelope gene target using qRT-PCR. Fold.Change.ace3: Relative gene expression data of ACE2 expression (full-length/ transmembrane transcript variant). Linearge: SARS-CoV-2 viral lineage as classified by the PANGOLIN tool (Version 1.15.1), viral genome alignments are available on GISAID.
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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 | 0.001 | 0.008 |
| Meta-epidemiology (narrow) | 0.003 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.005 | 0.007 |
| Science and technology studies | 0.004 | 0.001 |
| Scholarly communication | 0.007 | 0.004 |
| Open science | 0.004 | 0.005 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.650 | 0.568 |
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".