Results 21 to 30 of about 2,869 (209)

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

Resistome phylodynamics of multidrug-resistant <i>Shigella</i> isolated from diarrheal patients. [PDF]

Microbiol Spectr
Multi-drug resistance (MDR) in Shigella continues to pose a significant public health challenge, particularly in developing countries. Recent advances in genomics strengthen the surveillance of MDR-pathogens and antimicrobial resistance (AMR) mediators ...
Asad A, Nayeem MAJ, Mostafa MG, Begum R, Faruque SN, Nusrin S, Jahan I, Hayat S, Islam Z.   +8 more
europepmc   +2 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

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave

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, Aristea Dimadi, Evangelia-Georgia Kostaki, Sotirios Tsiodras, Georgios K. Nikolopoulos, Dionyssios N. Sgouras, Gkikas Magiorkinis, George Papatheodoridis, Vasiliki Pogka, Giota Lourida, Aikaterini Argyraki, Emmanouil Angelakis, George Sourvinos, Apostolos Beloukas, Dimitrios Paraskevis, Timokratis Karamitros   +15 more
doaj   +1 more source

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

Phylogeography and Biological Characterizations of H12 Influenza A Viruses

Viruses, 2022
Influenza A virus (IAV) is widespread in wild bird reservoirs. Sixteen hemagglutinin subtypes are associated with wild waterfowl hosts; some subtypes are isolated infrequently, one of which is H12 IAV.
Zhimin Wan, Qiuqi Kan, Dongchang He, Zhehong Zhao, Jianxi Gong, Wenjie Jiang, Ting Tang, Yafeng Li, Quan Xie, Tuofan Li, Hongxia Shao, Aijian Qin, Jianqiang Ye   +12 more
doaj   +1 more source

cinthylorein/Colombia-COVID-19-phylodynamics: Zenodo

, 2023
making this repository citeable via ...
cinthylorein
core   +1 more source

Phylodynamic applications in 21st century global infectious disease research

Global Health Research and Policy, 2017
Background Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission ...
Brittany D Rife, Carla Mavian, Xinguang Chen, Massimo Ciccozzi, Marco Salemi, Jae Min, Mattia CF Prosperi   +6 more
doaj   +1 more source