Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619
Bibliographic record
Abstract
Since late 2020, the emergence of variants of concern (VOCs) of SARS-CoV-2 has been of concern to public health, researchers and policymakers. Mutations in the SARS-CoV-2 genome-for which clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity-illustrate the importance of genomic surveillance and monitoring the evolution and geographic spread of novel lineages. Lineage B.1.619 was first detected in Switzerland in January 2021, in international travellers returning from Cameroon. This lineage was subsequently also detected in Rwanda, Belgium, Cameroon, France, and many other countries and is characterised by spike protein amino acid mutations N440K and E484K in the receptor binding domain, which are associated with immune escape and higher infectiousness. In this study, we perform a phylogeographic analysis to track the geographic origin and subsequent dispersal of SARS-CoV-2 lineage B.1.619. We employ a recently developed travel history-aware phylogeographic model, enabling us to incorporate genomic sequences with associated travel information. We estimate that B.1.619 most likely originated in Cameroon, in November 2020. We estimate the influence of the number of air-traffic passengers on the dispersal of B.1.619 but find no significant effect, illustrative of the complex dispersal patterns of SARS-CoV-2 lineages. Finally, we examine the metadata associated with infected Belgian patients and report a wide range of symptoms and medical interventions.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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) | 0.002 | 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 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".