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Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations
Viruses, 2022 The multi-type birth–death model with sampling is a phylodynamic model which enables the quantification of past population dynamics in structured populations based on phylogenetic trees.
Jérémie Scire +4 more
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Eight challenges in phylodynamic inference
Epidemics, 2015 Epidemics ...
Frost, Simon D.W. +5 more
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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
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Viruses, 2021 The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed
D. Collins Owuor +13 more
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Diverse Large HIV-1 Non-subtype B Clusters Are Spreading Among Men Who Have Sex With Men in Spain
Frontiers in Microbiology, 2019 In Western Europe, the HIV-1 epidemic among men who have sex with men (MSM) is dominated by subtype B. However, recently, other genetic forms have been reported to circulate in this population, as evidenced by their grouping in clusters predominantly ...
Elena Delgado +91 more
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Phylodynamic Inference for Structured Epidemiological Models
PLoS Computational Biology, 2014 Coalescent theory is routinely used to estimate past population dynamics and demographic parameters from genealogies. While early work in coalescent theory only considered simple demographic models, advances in theory have allowed for increasingly complex demographic scenarios to be considered.
David A. Rasmussen +2 more
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Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus [PDF]
PLoS Pathogens, 2010 Understanding the role of humans in the dispersal of predominantly animal pathogens is essential for their control. We used newly developed Bayesian phylogeographic methods to unravel the dynamics and determinants of the spread of dog rabies virus (RABV) in North Africa. Each of the countries studied exhibited largely disconnected spatial dynamics with
Talbi, Chiraz +14 more
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Emerging Concepts of Data Integration in Pathogen Phylodynamics [PDF]
Systematic Biology, 2016 Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics ...
Baele, Guy +3 more
openaire +7 more sources
Viruses, 2023 Dengue fever is among the most significant public health concerns in Brazil. To date, the highest number of Dengue notifications in the Americas has been reported in Brazil, with cases accounting for a total number of 3,418,796 reported cases as of mid ...
Hegger Fritsch +20 more
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Viruses, 2020 Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology.
Giovanni Franzo +7 more
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