Progress and challenges in virus genomic epidemiology
Genomic epidemiology, which links pathogen genomes with associated metadata to
understand disease transmission, has become a key component of outbreak response …
understand disease transmission, has become a key component of outbreak response …
Human outbreaks of a novel reassortant Oropouche virus in the Brazilian Amazon region
FG Naveca, TAP de Almeida, V Souza, V Nascimento… - Nature Medicine, 2024 - nature.com
Abstract The Brazilian western Amazon is experiencing its largest laboratory-confirmed
Oropouche virus (OROV) outbreak, with more than 6,300 reported cases between 2022 and …
Oropouche virus (OROV) outbreak, with more than 6,300 reported cases between 2022 and …
Relax, keep walking—a practical guide to continuous phylogeographic inference with BEAST
Spatially explicit phylogeographic analyses can be performed with an inference framework
that employs relaxed random walks to reconstruct phylogenetic dispersal histories in …
that employs relaxed random walks to reconstruct phylogenetic dispersal histories in …
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B. 1.1. 7 emergence
Understanding the causes and consequences of the emergence of severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet …
syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet …
Temporal signal and the phylodynamic threshold of SARS-CoV-2
S Duchene, L Featherstone… - Virus …, 2020 - academic.oup.com
The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome
sequence data have been generated and made publicly available in near real time. Early …
sequence data have been generated and made publicly available in near real time. Early …
The episodic resurgence of highly pathogenic avian influenza H5 virus
Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021,
increasingly causing mass mortality in wild birds and poultry and incidental infections in …
increasingly causing mass mortality in wild birds and poultry and incidental infections in …
Context-specific emergence and growth of the SARS-CoV-2 Delta variant
Abstract The SARS-CoV-2 Delta (Pango lineage B. 1.617. 2) variant of concern spread
globally, causing resurgences of COVID-19 worldwide,. The emergence of the Delta variant …
globally, causing resurgences of COVID-19 worldwide,. The emergence of the Delta variant …
Phylogeographic analysis of the Bantu language expansion supports a rainforest route
The Bantu expansion transformed the linguistic, economic, and cultural composition of sub-
Saharan Africa. However, the exact dates and routes taken by the ancestors of the speakers …
Saharan Africa. However, the exact dates and routes taken by the ancestors of the speakers …
A unified genealogy of modern and ancient genomes
The sequencing of modern and ancient genomes from around the world has revolutionized
our understanding of human history and evolution. However, the problem of how best to …
our understanding of human history and evolution. However, the problem of how best to …
The recovery, interpretation and use of ancient pathogen genomes
The ability to sequence genomes from ancient biological material has provided a rich source
of information for evolutionary biology and engaged considerable public interest. Although …
of information for evolutionary biology and engaged considerable public interest. Although …