S. Lequime

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data

This study shows that endogenous viral elements can mimic exogenous viruses in transcriptomic data, leading to false positives and biased virus discovery.

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.

Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster

This study shows that innate immune pathways in Drosophila constrain RNA virus evolution by reducing genetic diversity and virulence when disrupted.

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.

High transmissibility and fetal pathogenicity of recent Zika virus strains from the African lineage

This study compares transmissibility and pathogenicity of recent African and Asian Zika virus strains, finding African strains more transmissible, lethal, and capable of causing fetal death.

Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection

This study adapts DENV-1 to Ae. albopictus mosquitoes through in vivo selection, identifying adaptive mutations that enhance infectivity but show limited individual transmission efficiency.

Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries

The paper shows that a non-retroviral EVE in Aedes aegypti limits replication of its cognate virus, CFAV, through piRNA-mediated antiviral activity in ovaries.

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.

European and tropical Aedes albopictus mosquito populations have similar systemic Zika virus infection dynamics

This study shows that European and tropical Aedes albopictus populations have similar systemic Zika virus infection dynamics, suggesting potential for autochthonous transmission.