Related Experiment Video
Updated: Jul 19, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
Phylogenies increase power to detect highly transmissible viral genome variants
Michael R May1, Bruce Rannala1
1Department of Evolution and Ecology, University of California Davis, Davis, CA USA.
Abstract:
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.
Related Concept Videos
Viral Mutations
Evolutionary Relationships through Genome Comparisons
Viruses with RNA Genomes
Viral Recombination
Modern Molecular Taxonomy
Gene Evolution - Fast or Slow?
In contrast, regions which code...

