Genetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico
Bibliographic record
Abstract
ABSTRACT The recent global outbreak of Monkeypox, caused by the Monkeypox virus (MPVX) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. Here, we analyze 880 MPXV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPXV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPXV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than SNPs variations, which do not contribute significantly to genome diversity. Although the genome presents multiple SNP sites in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is the amino acid site 63 of the protein encoded by the Cop-A4L gene, intricately related to viral maturity, for which we picked up a strong signal of positive selection. Ancestral state reconstruction deduced that the ancestral state at site 63 corresponds to the amino acid valine, present only in isolates of clade I. However, the isolates of the current outbreak evolved for threonine at site 63. Finally, our findings contribute to the knowledge of the evolutionary processes of the Monkeypox virus.
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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 | 0.000 |
| 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) | 0.001 | 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".