P. Lemey

How fast are viruses spreading in the wild?

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.

Population genetics, phylogeography and gene flow of mainland and island vampire bat (Desmodus rotundus) populations: an investigation into mainland-island bat movement

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.

Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus

This study examines how poultry vaccination affects H5 avian influenza virus transmission and evolution, finding increased nonsynonymous divergence in vaccinated poultry lineages.

Revisiting the origins of the Sobemovirus genus: a case for ancient origins of plant viruses

This study applies a mechanistic model to correct for time-dependent rate phenomena in plant viruses, revealing an ancient origin for sobemoviruses over four million years ago.

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.

The evolutionary history of hepaciviruses

This study identifies novel rodent hosts of hepaciviruses, documents their diversity, and estimates the origin of the genus to be about 22 million years ago.

Synchrony of Bird Migration with Avian Influenza Global Spread; Implications for Vulnerable Bird Orders

The paper uses phylodynamic analyses to link bird migration patterns with the global spread of HPAIV H5 clade 2.3.4.4, identifying vulnerable bird orders and highlighting Suliformes and Ciconiiformes as important in virus dispersal.

Parasite hybridization promotes spreading of endosymbiotic viruses

This study shows that parasite hybridization in cutaneous leishmaniasis increases the spread of endosymbiotic viruses, contributing to disease severity.

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016.

The paper analyzes MPXV genomes to show evidence of APOBEC3 deaminase editing, suggesting sustained human transmission since 2016.

Evolution of influenza A virus hemagglutinin H1 and H3 across host species

This study compares the evolutionary rates of influenza A virus hemagglutinin H1 and H3 across different host species, finding higher nonsynonymous mutation rates in mammals and specific glycosylation site accumulation in humans and swine.

Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history

The paper identifies Flaviviridae-derived endogenous viral elements in shrew genomes, revealing an ancient origin of pestiviruses and their potential role as natural reservoirs.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

Updated vaccine protects from infection with SARS-CoV-2 variants, prevents transmission and is immunogenic against Omicron in hamsters

This study shows an updated vaccine candidate provides full protection against multiple SARS-CoV-2 variants, prevents transmission, and induces neutralizing antibodies against Omicron in hamsters.

Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens

The paper characterizes the virome of 1725 game animals in China, identifying 71 mammalian viruses, 45 novel, and highlighting potential zoonotic risks.

Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

The paper predicts that Lassa virus endemic areas will expand beyond West Africa due to environmental changes, increasing the population at risk from 100 million to 700 million by 2070.

Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic

Unravelling the evolutionary relationships of hepaciviruses within and across rodent hosts

This study identifies novel hepacivirus genomes in rodents from sub-Saharan Africa, revealing co-infections and expanding the known diversity of hepaciviruses in rodent hosts.

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

This study uses phylogeographic and phylodynamic methods to test hypotheses about West Nile virus dispersal and genetic diversity, finding temperature influences on spread and no strong evidence for migratory bird flyway restriction.

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.

This paper integrates travel history data into Bayesian phylogeographic analysis of SARS-CoV-2 to improve virus spread reconstructions and address sampling bias.

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

The paper shows SARS-CoV-2's ability to infect humans stems from its evolutionary history in bats, not human adaptation, with evidence of positive selection in bat viruses and weak purifying selection in SARS-CoV-2.

Temporal signal and the phylodynamic threshold of SARS-CoV-2

This study assesses the phylodynamic threshold of SARS-CoV-2 by analyzing genome sequences over time to determine when reliable evolutionary rate and outbreak timing estimates became possible.

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

This paper estimates the divergence date of SARS-CoV-2 from its bat reservoir to be between 1948 and 1982, identifies non-recombinant regions for phylogenetic analysis, and highlights the role of horseshoe bats in viral emergence.

nosoi: a stochastic agent-based transmission chain simulation framework in R

nosoi simulates transmission chains for infectious diseases using an agent-based framework, enabling validation of reconstruction methods and exploration of epidemic dynamics.

The history of measles: from a 1912 genome to an antique origin

The paper sequences a 1912 measles virus genome and uses molecular clock modeling to estimate measles virus divergence from rinderpest virus as early as the 4th century BCE.

A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

The paper recovers a near-full-length HIV-1 genome from 1966, validating molecular clock estimates and providing direct genomic evidence for HIV-1 evolution in the 1960s.