• Publications
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Testing macro–evolutionary models using incomplete molecular phylogenies
  • O. Pybus, P. Harvey
  • Biology, Medicine
  • Proceedings of the Royal Society of London…
  • 22 November 2000
New statistical methods are developed and used to infer past patterns of speciation and extinction from molecular phylogenies that suggest that, in some cases, speciation rates have decreased through time. Expand
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
It is shown that the new swine-origin influenza A (H1N1) virus emerged in Mexico and the United States was derived from several viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the outbreak. Expand
Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings
Transmissibility is substantially higher than that of seasonal flu, and comparable with lower estimates of R0 obtained from previous influenza pandemics, by analyzing the outbreak in Mexico, early data on international spread, and viral genetic diversity, which makes an early assessment of transmissibility and severity. Expand
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
The cross-platform software tool, TempEst (formerly known as Path-O-Gen), is introduced, for the visualization and analysis of temporally sampled sequence data and can be used to assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and identify sequences whose genetic divergence and sampling date are incongruent. Expand
Global Distribution and Prevalence of Hepatitis C Virus Genotypes
It is calculated that HCV genotype 1 is the most prevalent worldwide, comprising 83.4 million cases (46.2% of all HCV cases), approximately one‐third of which are in East Asia. Expand
Zika virus in the Americas: Early epidemiological and genetic findings
Results of phylogenetic and molecular clock analyses show a single introduction of ZikV into the Americas, which is estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. Expand
The effect of human mobility and control measures on the COVID-19 epidemic in China
Real-time mobility data from Wuhan and detailed case data including travel history are used to elucidate the role of case importation in transmission in cities across China and to ascertain the impact of control measures. Expand
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
A rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread and is designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. Expand
The genomic and epidemiological dynamics of human influenza A virus
It is shown that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps, suggesting a sink–source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir to sink populations in temperate regions. Expand
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis
A comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Expand