Results 11 to 20 of about 2,036 (163)

Viral phylodynamics.

PLoS Computational Biology, 2013
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viralphylogenies.
Erik M Volz, Katia Koelle, Trevor Bedford   +2 more
doaj   +4 more sources

What We Talk About When We Talk About Microbial Species. [PDF]

Mol Ecol
ABSTRACT Genome annotation, alignment and phylogenetics are at the centre of most studies in evolutionary genomics. These techniques function best when rooted in prior work. Genes are mined from new genomes using evidence from old gene models. These genomes are aligned to well‐worn references to create matrices for tree reconstruction.
Narechania A, Gopalakrishnan S, Gilbert MTP.   +2 more
europepmc   +2 more sources

Variational Phylodynamic Inference Using Pandemic-scale Data [PDF]

Molecular Biology and Evolution, 2022
Abstract The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for improved surveillance and ...
Caleb Ki, Jonathan Terhorst
openaire   +2 more sources

Phylodynamics of Infectious Disease Epidemics [PDF]

Genetics, 2009
AbstractWe present a formalism for unifying the inference of population size from genetic sequences and mathematical models of infectious disease in populations. Virus phylogenies have been used in many recent studies to infer properties of epidemics. These approaches rely on coalescent models that may not be appropriate for infectious diseases.
Volz, Erik M., Pond, Sergei L. Kosakovsky, Ward, M. J., Leigh Brown, Andrew J., Frost, Simon D. W.   +4 more
openaire   +3 more sources

Phylodynamic Inference across Epidemic Scales [PDF]

Molecular Biology and Evolution, 2017
Within-host genetic diversity and large transmission bottlenecks confound phylodynamic inference of epidemiological dynamics. Conventional phylodynamic approaches assume that nodes in a time-scaled pathogen phylogeny correspond closely to the time of transmission between hosts that are ancestral to the sample.
Volz, E, Romero-Severson, E, Leitner, TK
openaire   +4 more sources

TreeTime: maximum likelihood phylodynamic analysis [PDF]

Virus Evolution, 2017
Mutations that accumulate in the genome of replicating biological organisms can be used to infer their evolutionary history. In the case of measurably evolving organisms genomes often reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens.
Sagulenko, Pavel, Puller, Vadim, Neher, Richard A.   +2 more
openaire   +5 more sources

Phylodynamics of Alagoas vesiculovirus in Brazil

Brazilian Journal of Microbiology, 2022
The vesicular stomatitis virus belongs to the Rhabdoviridae family, genus Vesiculovirus. Four species (New Jersey, Indiana, Cocal, and Alagoas) are responsible for disease outbreaks in Western Hemisphere countries. In Brazil, the Alagoas virus is responsible for the main outbreaks of the disease, mainly in the states of the Northeast, Midwest, and ...
Antônio Augusto, Fonseca Júnior, Mateus, Laguardia-Nascimento, Aline Aparecida Silva, Barbosa, Valdenia Lopes, da Silva Gonçalves, Anapolino Macedo, de Oliveira, Anselmo Vasconcelos, Rivetti Júnior, Marcelo Fernandes, Camargos   +6 more
openaire   +2 more sources

Decoding the fundamental drivers of phylodynamic inference

Molecular Biology and Evolution, 2022
AbstractDespite its increasing role in the understanding of infectious disease transmission at the applied and theoretical levels, phylodynamics lacks a well-defined notion of ideal data and optimal sampling. We introduce a formal method to visualise and quantify the relative impact of pathogen genome sequence and sampling times—two fundamental sources
Leo A. Featherstone, Sebastian Duchene, Timothy G. Vaughan   +2 more
openaire   +4 more sources

Phylodynamics on local sexual contact networks [PDF]

PLOS Computational Biology, 2016
AbstractPhylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks.
Rasmussen, David A, Kouyos, Roger, Günthard, Huldrych F, Stadler, Tanja   +3 more
openaire   +6 more sources

Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta

Microbiology Spectrum, 2023
Genomic surveillance and epidemiology have shed light on the viral diversity driving coronavirus disease 2019 (COVID-19) outbreaks and are important during waves of highly transmissible and immune-escaping variants of interest or of concern (VOCs).
Nidia S. Trovao, Vincent Pan, Chirag Goel, Pilar Gallego-García, Yunxi Liu, Christopher Barbara, Rebecca Borg, Mark Briffa, Chanelle Cilia, Laura Grech, Mario Vassallo, Todd J. Treangen, David Posada, Afshin Beheshti, Joseph Borg, Graziella Zahra   +15 more
doaj   +1 more source