Publication date: Jun 04, 2025
Several years ago, I published a paper that described the discrepancy between outgroup and date-based methods for rooting the SARS-CoV-2 phylogenetic tree, and proposed the discrepancy could arise from biases among the available early viral sequences. Here, I explain why the root remains uncertain, including via an interactive narrative at https://nextstrain. org/groups/jbloomlab/narratives/SARS2-rooting/early-SARS2-trees-v1 that enables the reader to examine the underlying data and understand discrepancies that lead different methods to reach different inferences about the root. I also demonstrate clear evidence of bias among the earliest available sequences, and explain why the root of the SARS-CoV-2 tree cannot be conclusively resolved with the current data.
Open Access PDF
Semantics
| Type | Source | Name |
|---|---|---|
| disease | MESH | COVID 19 |
| pathway | REACTOME | Reproduction |
| drug | DRUGBANK | Esomeprazole |
| disease | IDO | symptom |
| drug | DRUGBANK | Coenzyme M |
| disease | MESH | mutation rate |
| disease | MESH | pneumonia |
| disease | IDO | cell |
| disease | IDO | pathogen |
| drug | DRUGBANK | Troleandomycin |
| disease | MESH | uncertainty |
| drug | DRUGBANK | Serine |
| drug | DRUGBANK | (S)-Des-Me-Ampa |
| disease | IDO | host |