Results 41 to 50 of about 2,869 (209)

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, Joëlle Barido-Sottani, Denise Kühnert, Timothy G. Vaughan, Tanja Stadler   +4 more
doaj   +1 more source

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   +3 more sources

Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018

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, Zaydah R. de Laurent, Gilbert K. Kikwai, Lillian M. Mayieka, Melvin Ochieng, Nicola F. Müller, Nancy A. Otieno, Gideon O. Emukule, Elizabeth A. Hunsperger, Rebecca Garten, John R. Barnes, Sandra S. Chaves, D. James Nokes, Charles N. Agoti   +13 more
doaj   +1 more source

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, Sonia Benito, Vanessa Montero, María Teresa Cuevas, Aurora Fernández-García, Aurora Fernández-García, Mónica Sánchez-Martínez, Elena García-Bodas, Francisco Díez-Fuertes, Horacio Gil, Horacio Gil, Javier Cañada, Cristina Carrera, Jesús Martínez-López, Marcos Sintes, Lucía Pérez-Álvarez, Michael M. Thomson, The Spanish Group for the Study of New HIV Diagnoses, Josefa Muñoz, María Carmen Nieto, María Zuriñe Zubero, Silvia Hernáez-Crespo, Luis Elorduy Otazua, Leyre López Soria, Koldo Agirrebengoa, María José López de Goicoechea, José Mayo, Gustavo Cilla, Julio Arrizabalaga, José Antonio Iribarren, María Jesús Bustinduy, María Julia Echevarría, María Jesús Lezaun, José Joaquín Portu, Carmen Gómez-González, Ana Mariño, Patricia Ordóñez, Hortensia Álvarez, Nieves Valcarce, Ángeles Cañizares, María Ángeles Castro, María Amparo Coira, José López-Álvarez, Ramón Rabunal, Juan García-Costa, Ricardo Fernández-Rodríguez, Raúl Rodríguez-Pérez, Jorge Guitián, Antonio Ocampo, Celia Miralles, Sonia Pérez-Castro, Matilde Trigo, Julio Diz-Arén, María Ángeles Pallarés, Carmen Ezpeleta Baquedano, Aitziber Aguinaga, María Gracia Ruiz de Alda, Jorge del Romero, Carmen Rodríguez, Mar Vera, Óscar Ayerdi, María Isabel García-Arata, Santiago Prieto-Menchero, Esther Culebras, Iciar Rodríguez-Avial, Raquel Téllez, Miguel Górgolas, Manuel Fernández-Guerrero, Olalla Calabia, Rosa García-Delgado, Sara María Quevedo, Lucía Puente, Manuel Álamo, Alfonso Alfange, Sara de la Fuente, Carmen Hinojosa, Carlos Dueñas, Begoña Monteagudo, Edita Sánchez, Carmen Ramos Sánchez, Pablo Bachiller, Helmuth Guillén, Teresa Martínez-Domínguez, Rosa Martínez-González, José Ramón Blanco, Miriam Blasco, Ana María Martínez-Sapiña, Diego Ortega Larrea, César Gómez-Hernando, José Largo-Pau, Fernando Buñuel, Ana Infante   +91 more
doaj   +1 more source

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, Erik M. Volz, Katia Koelle   +2 more
openaire   +4 more sources

Phylodynamics and movement of Phycodnaviruses among aquatic environments [PDF]

, 2011
Phycodnaviruses have a significant role in modulating the dynamics of phytoplankton, thereby influencing community structure and succession, nutrient cycles and potentially atmospheric composition because phytoplankton fix about half the carbon dioxide ...
Paolo M de A Zanotto, Zanotto, Paolo Marinho de Andrade, Hillândia B da Cunha, Manuela V Gimenes, Curtis A Suttle, Cunha, Hillândia Brandão da, Dolores U Mehnert, Suttle, Curtis A., da Cunha, Hillandia B., Mehnert, Dolores Ursula, Gimenes, Manuela V.   +10 more
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Whole genome sequencing reveals local transmission patterns of mycobacterium bovis in sympatric cattle and badger populations [PDF]

, 2012
Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely ...
O'Hare, Anthony, Stanley McDowell, Mallon Tom, Orton, Richard, Mallon, Tom, Biek, R., O'Hare, A., Robin A. Skuce (116935), Kao, R.R., Skuce, Robin A, Tom Mallon, David Wright, Orton Richard J., Kao, Rowland R., Rowland R Kao, McCormick, Carl, Wright David, Biek Roman, Hannah Trewby (116929), Richard J. Orton (116918), Skuce Robin A., Hannah Trewby, McDowell, S., Kao Rowland R., Kao, Rowland R, Trewby, Hannah, Carl McCormick, Skuce, Robin A., Tom Mallon (116914), McCormick, C., David Wright (116911), Mallon, T., Roman Biek (21981), Roman Biek, Wright, D., McCormick Carl, Richard J Orton, McDowell, Stanley, Trewby Hannah, Orton, Richard J., Anthony O'Hare (116908), O'Hare Anthony, McDowell Stanley, Trewby, H., Robin A Skuce, Wright, David; id_orcid, Biek, Roman, Carl McCormick (116915), Stanley McDowell (116923), Wright, David, Orton, R.J., Rowland R. Kao (116940), Skuce, R.A., Anthony O'Hare   +53 more
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Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina [PDF]

, 2020
BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) phylodynamics can be used to monitor epidemic trends and help target prevention through identification and characterization of transmission clusters. METHODS: We analyzed HIV-1 pol sequences sampled
Dennis, A.M., Sebastian, J., Hué, S., Eron, J.J., Levintow, S., Miller, W.C., Billock, R.   +6 more
core   +1 more source

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, Suchard, Marc A., Rambaut, Andrew, Lemey, Philippe   +3 more
openaire   +6 more sources

Update on the Phylodynamic and Genetic Variability of Marburg Virus

Viruses, 2023
The COVID-19 pandemic has not only strained healthcare systems in Africa but has also intensified the impact of emerging and re-emerging diseases. Specifically in Equatorial Guinea, mirroring the situation in other African countries, unique zoonotic outbreaks have occurred during this challenging period. One notable resurgence is Marburg virus disease (
Fabio Scarpa, Liliana Bazzani, Marta Giovanetti, Alessandra Ciccozzi, Francesca Benedetti, Davide Zella, Daria Sanna, Marco Casu, Alessandra Borsetti, Eleonora Cella, Stefano Pascarella, Antonello Maruotti, Massimo Ciccozzi   +12 more
openaire   +3 more sources