Results 11 to 20 of about 2,107 (180)

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

Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A

Frontiers in Microbiology, 2022
Senecavirus A (SVA) is a member of the genus Senecavirus in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss
Han Gao, Han Gao, Han Gao, Han Gao, Yong-jie Chen, Yong-jie Chen, Yong-jie Chen, Yong-jie Chen, Xiu-qiong Xu, Zhi-ying Xu, Zhi-ying Xu, Zhi-ying Xu, Zhi-ying Xu, Si-jia Xu, Si-jia Xu, Si-jia Xu, Si-jia Xu, Jia-bao Xing, Jia-bao Xing, Jia-bao Xing, Jia-bao Xing, Jing Liu, Jing Liu, Jing Liu, Jing Liu, Yun-feng Zha, Yan-kuo Sun, Yan-kuo Sun, Yan-kuo Sun, Yan-kuo Sun, Gui-hong Zhang, Gui-hong Zhang, Gui-hong Zhang, Gui-hong Zhang   +33 more
doaj   +3 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

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   +2 more sources

Decoding the fundamental drivers of phylodynamic inference

Molecular Biology and Evolution, 2022
Abstract Despite 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 ...
Leo A. Featherstone, Sebastian Duchene, Timothy G. Vaughan   +2 more
openaire   +4 more sources

Recent advances in computational phylodynamics [PDF]

Current Opinion in Virology, 2018
Time-stamped, trait-annotated phylogenetic trees built from virus genome data are increasingly used for outbreak investigation and monitoring ongoing epidemics. This routinely involves reconstructing the spatial and demographic processes from large data sets to help unveil the patterns and drivers of virus spread.
Baele, Guy, Dellicour, Simon, Suchard, Marc A, Lemey, Philippe, Vrancken, Bram   +4 more
openaire   +3 more sources

Evolutionary dynamics of Usutu virus: Worldwide dispersal patterns and transmission dynamics in Europe

Frontiers in Microbiology, 2023
BackgroundUsutu virus (USUV) is an emerging mosquito-borne Flavivirus, with birds as the main zoonotic reservoir. Humans are accidental hosts and mostly develop mild or even asymptomatic infections, although severe complications such as encephalitis can ...
Marina Siljic, Rastko Sehovic, Marko Jankovic, Gorana Stamenkovic, Ana Loncar, Marija Todorovic, Maja Stanojevic, Valentina Cirkovic   +7 more
doaj   +1 more source

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

Adaptive preferential sampling in phylodynamics

ArXiv, 2020
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that represents the sample ancestral relationships.
Cappello, Lorenzo, Palacios, Julia A.
openaire   +3 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