tetano
Editor, Senior Moderator
Sci Adv
. 2024 Aug 16;10(33):eadk7623.
doi: 10.1126/sciadv.adk7623. Epub 2024 Aug 14. Early detection of highly transmissible viral variants using phylogenomics
Michael R May[SUP] 1 [/SUP], Bruce Rannala[SUP] 1 [/SUP]
Affiliations
As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a serious threat to global health. Statistical models of genome sequence evolution may provide a critical tool for early detection of these strains. Using a novel stochastic model that links transmission rates to the entire viral genome sequence, we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count-based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations. We find that phylogenies in particular can detect novel transmission-enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance.
. 2024 Aug 16;10(33):eadk7623.
doi: 10.1126/sciadv.adk7623. Epub 2024 Aug 14. Early detection of highly transmissible viral variants using phylogenomics
Michael R May[SUP] 1 [/SUP], Bruce Rannala[SUP] 1 [/SUP]
Affiliations
- PMID: 39141727
- DOI: 10.1126/sciadv.adk7623
As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a serious threat to global health. Statistical models of genome sequence evolution may provide a critical tool for early detection of these strains. Using a novel stochastic model that links transmission rates to the entire viral genome sequence, we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count-based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations. We find that phylogenies in particular can detect novel transmission-enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance.