S. Dellicour

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 impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

This study examines how Quaternary river rearrangements in western Amazonia influenced the evolutionary history and population structure of uakari monkeys.

Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations

This study evaluates how sampling bias affects viral spread inference using phylogeographic models and proposes strategies to mitigate its impact through simulation and empirical datasets.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

The paper analyzes the evolutionary dynamics of five dominant SARS-CoV-2 lineages in Mexico, showing lineage replacement patterns and regional spread.

Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization

This study shows that the Omicron variant of SARS-CoV-2 is resistant to most monoclonal antibodies and vaccine-induced antibodies, with reduced neutralization compared to Delta.

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.

KoT: an automatic implementation of the K/θ method for species delimitation

KoT automates the K/θ species delimitation method, enabling analysis of large datasets and testing different threshold ratios.

Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution

This study uses phylodynamic methods to show that the B.1.1.7 SARS-CoV-2 variant likely originated once and spread globally rather than evolving convergently from multiple sources.

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.

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

This paper introduces a phylodynamic workflow to analyze SARS-CoV-2 lineage dispersal, showing external introductions were key in Belgium and lockdowns had limited impact on transmission.

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.