Philippe Lemey

The paper analyzes the spread of H5N1 B3.13 in U.S. dairy cattle using genomic data and movement networks, finding that cattle movement, not birds, drives the outbreak.

This study shows bovine H5N1 influenza viruses have adapted to efficiently use NeuGc receptors in cattle, enhancing replication without significantly altering zoonotic risk.

This study uses phylogeographic and phylodynamic methods to analyze DENV genome data, revealing asymmetric global spread patterns and the role of travel over climate in DENV transmission.

The paper presents tools to harmonize viral genomic data across repositories and mask lab-specific artifacts, improving phylogenetic analysis accuracy.

This study uses a Bayesian mixed-effects molecular clock model to analyze HBV genomic data, revealing declining evolutionary rates and linking viral spread to human migration patterns.

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

The paper introduces a pipeline for automated viral genome reconstruction and variant analysis from metagenomic data, validated on simulated and real datasets.

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

The paper reports the emergence of mpox in Guinea, identifying both clade IIa and IIb strains, with clade IIb associated with sustained human-to-human transmission.

This study identifies ancient RNA virus genomes in Adelie penguin mummies, revealing viral sequences from specimens up to 2000 years old.

This study uses whole-genome sequencing and phylodynamic methods to analyze the evolutionary history and ecological dynamics of Jamestown Canyon virus, revealing its slow evolution and transmission patterns.

This study investigates the co-phylogenetic history of Leishmania parasites and Leishmaniavirus, finding strong phylogenetic congruence at the subgenus and species level, with weaker signals in some cases due to intraspecific host switching.

The paper introduces HIPSTR, a new consensus tree method that outperforms MCC in capturing high-support clades, and presents an updated TreeAnnotator X with faster computational routines.

This study traces the historical and phylogeographical spread of Rice yellow mottle virus (RYMV) in East Africa, linking its dispersal to rice cultivation, trade, and human activities.

This study develops and compares three novel landscape phylogeographic methods to assess environmental impacts on viral spread, providing guidelines for their use and open-source tools for viral epidemiology research.

This study evaluates dispersal metrics for viruses using simulation and compares their spread in animal populations, finding robustness to sampling effort and human-mediated dispersal signatures.

The paper analyzes the genomic diversity of Leishmania (Viannia) braziliensis across the Neotropical Realm, identifying two major parasite groups associated with different biomes and highlighting ecological and epidemiological differences.

This paper introduces PIV models to estimate dispersal velocity of evolving lineages and shows improved accuracy in predicting pathogen spread using West Nile virus data.

The paper reports a massive H5N1 outbreak in elephant seals and documents evidence for mammal-to-mammal transmission and spillover to birds.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

The paper investigates gene flow between mainland and island vampire bat populations in Trinidad, finding genetic distinctness and male-biased gene flow, with implications for rabies virus spread.

The paper analyzes B. pertussis genotype dynamics post-vaccine policy changes, showing fitness shifts and regional diversity patterns.

This paper introduces BETS, a Bayesian method to evaluate temporal signal in sequence data, showing it accurately classifies datasets with or without temporal signal across various empirical examples.

January 2020 cases in Germany and Washington State were contained, while separate later introductions from China seeded the first sustained SARS-CoV-2 transmission networks in Italy and Washington State.