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Phylogenies increase power to detect highly transmissible viral genome variants

As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a significant threat to global health. Viral genome sequences, combined with statistical models of sequence evolution, may provide a critical tool for early detection of these str...

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Detalles Bibliográficos
Autores principales: May, Michael R, Rannala, Bruce
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418580/
https://www.ncbi.nlm.nih.gov/pubmed/37577556
http://dx.doi.org/10.1101/2023.07.28.23293332
Descripción
Sumario:As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a significant threat to global health. Viral genome sequences, combined with statistical models of sequence evolution, may provide a critical tool for early detection of these strains. Using a novel statistical model that links transmission rates to the entire viral genome sequence, we study the power of phylogenetic methods—using a phylogenetic tree relating viral samples—and count-based methods—using case-counts of variants over time—to detect increased transmission rates, and to identify causative mutations. We find that phylogenies in particular can detect novel variants very soon after their origin, and may facilitate the development of early detection systems for outbreak surveillance.