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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 +6 more
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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. +4 more
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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 +2 more
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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 +7 more
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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 +15 more
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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.
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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 +2 more
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Early phylodynamics analysis of the COVID-19 epidemic in France [PDF]
, 2021 International audienceFrance was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis.
Thibault, Vincent +19 more
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Life, 2021 Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome
Maria Bousali +15 more
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cinthylorein/Colombia-COVID-19-phylodynamics: Zenodo
, 2023 making this repository citeable via ...
cinthylorein
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