Forecasting framework for dominant SARS-CoV-2 strains before clade replacement using phylogeny-informed genetic distances
Our framework demonstrated high predictability for identifying the next clade root before replacement in both training and test datasets (area under the receiver operating characteristic curve [AUROC] > 0.90) by incorporating differential weighting of non-synonymous and synonymous genetic distances. Additionally, the framework solely using spike gene data demonstrated similar accuracy to those using the complete genome. Overall, our approach establishes quantifiable molecular criteria for identifying potential updates to the SARS-CoV-2 vaccine, contributing to proactive pandemic preparedness.
Authors
- Kyuyoung Lee (ORCID: https://orcid.org/0000-0002-2299-7839)
- Jeong‐Sun Yang (ORCID: https://orcid.org/0000-0001-5005-9738)
- Soyoung Lee (ORCID: https://orcid.org/0000-0002-4614-2931)
- Philippe Lemey (ORCID: https://orcid.org/0000-0003-2826-5353)
- Hyunbeen Kim
- Atanas V. Demirev (ORCID: https://orcid.org/0000-0003-1624-4977)
- Man‐Seong Park (ORCID: https://orcid.org/0000-0002-7427-486X)
- Sangyi Lee (ORCID: https://orcid.org/0000-0003-3312-1901)
- Woo‐Jin Shin (ORCID: https://orcid.org/0000-0002-2386-2717)
- Kyung-Chang Kim
- Jin Il Kim (ORCID: https://orcid.org/0000-0001-8833-2138)
- Jooyeon Lee (ORCID: https://orcid.org/0000-0001-5220-0950)
- Jun‐Hyung Cho (ORCID: https://orcid.org/0000-0003-2075-2333)
- Sejik Park (ORCID: https://orcid.org/0000-0002-1664-5423)
- Seunghye Cho
Institutions
- Korea University (KR)
- Rega Institute for Medical Research (BE)
- Korea National Institute of Health (KR)
- KU Leuven (BE)
Publication Details
- Journal
- Frontiers in Microbiology
- Published
- 2025-06-20
- DOI
- https://doi.org/10.3389/fmicb.2025.1619546
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00