Sequence evidence that the D614G clade of SARS-CoV-2 was already circulating in northern Italy in the fall of 2019
Bibliographic record
Abstract
Elucidating ancestor-descendant relationships of viral lineages is crucial for addressing the question of when and where a virulent viral strain originated. The D614G clade, with an Aspartate-614 to Glycine (D614G) mutation, includes all recent variants of SARS-CoV-2 and tend to be more infectious than the viral strains isolated in Wuhan. The D614G clade is characterized by TTTG at four nucleotide sites (sites 241, 3037, 14408 and 23403 following the reference genome NC_045512), in contrast to CCCA shared among early SARS-CoV-2 genomes sampled in China and those that can be traced to China. It was believed that the TTTG lineage descended from the early viral CCCA lineages. A set of SARS-CoV-2 sequences collected from Sept. 12 to Dec. 18, 2019, in Lombardy, Milan and Turin in Italy provided, for the first time, strong evidence that the D614G/TTTG lineage has already been circulating in Italy in 2019. I discussed extensively the controversies arising from this set of early SARS-CoV-2 sequences.
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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 | 0.000 | 0.001 |
| 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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".