SMDP: SARS-CoV-2 Mutation Distribution Profiler for rapid estimation of mutational histories of unusual lineages
Bibliographic record
Abstract
SARS-CoV-2 usually evolves at a relatively constant rate over time. Occasionally, however, lineages arise with higher-than-expected numbers of mutations given the date of sampling. Such lineages can arise for a variety of reasons, including selection pressures imposed by evolution during a chronic infection or exposure to mutation-inducing drugs like molnupiravir. We have developed an open-source web-based application (SMDP: SARS-CoV-2 Mutation Distribution Profiler; https://eringill.shinyapps.io/covid_mutation_distributions) that compares a list of user-submitted lineage-defining mutations or a FASTA file containing a single genome (from which lineage-defining mutations are calculated) with established mutation distributions including those observed during (1) the first nine months of the pandemic, (2) during the global transmission of Omicron, (3) during the chronic infection of immunocompromised patients, and (4) during zoonotic spillover from humans to deer. The application calculates the most likely distribution for the user's mutation list and displays log likelihoods for all distributions. In addition, the transition:transversion ratio of the user's list is calculated to determine whether there is evidence of exposure to a mutation-inducing drug such as molnupiravir and indicates whether the list contains mutations in the proofreading domain of nsp14 which could lead to a higher-than-expected mutation rate in the lineage. This tool will be useful for public health and researchers seeking to rapidly infer evolutionary histories of SARS-CoV-2 variants, which can aid risk assessment and public health responses.
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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 | 0.002 | 0.006 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.016 | 0.009 |
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".