Reconstruction of SARS-CoV-2 transmissibility within households in the UK Virus Watch Study
Bibliographic record
Abstract
Households provide ideal settings to study SARS-CoV-2 transmission due to close proximity and extended exposure among members. Understanding transmission patterns is crucial for implementing effective control measures. We analysed whole genome sequences from 237 subjects across 162 households within the Virus Watch Prospective Community Cohort Study (372 total participants). We incorporated minority variants as indicators of within-host genomic diversity into phylogenetic models to reconstruct viral relationships more accurately than using consensus sequences alone. In 73/162 households with multiple infections, phylogeny identified eight secondary cases resulting from separate introduction events rather than within-household transmission. For the remaining 65 households, including minority variants resolved transmission chains that were otherwise uncertain. Our approach demonstrates that integrating within-host genetic diversity into phylogenetic models alongside epidemiological data provides a robust method to accurately identify household transmission events, assess infection risk factors, and improve secondary attack rate estimation, essential for understanding viral spread dynamics.
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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 | 0.003 | 0.001 |
| 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 | 0.001 |
| 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".