Results 1 to 10 of about 2,682 (195)

Human Immunodeficiency Virus-1 Diversity in the Moscow Region, Russia: Phylodynamics of the Most Common Subtypes

Frontiers in Microbiology, 2019
This study analyzes the HIV-1 subtype diversity and its phylodynamics in Moscow region, which is the most densely populated area of Russia characterized by high rates of internal and external migration.
Aleksey Lebedev, Elena Kazennova, Marina Bobkova   +2 more
exaly   +3 more sources

Genetic Diversity and Phylodynamics of Avian Coronaviruses in Egyptian Wild Birds

Viruses, 2019
Avian coronaviruses (ACoVs) are continuously evolving and causing serious economic consequences in the poultry industry and around the globe. Owing to their extensive genetic diversity and high mutation rates, controlling ACoVs has become a challenge. In
Mohammed A Rohaim, Rania F El Naggar, Mahmoud Bayoumi   +2 more
exaly   +3 more sources

PhyloCNN: Improving Tree Representation and Neural Network Architecture for Deep Learning from Trees in Phylodynamics and Diversification Studies [PDF]

Systematic Biology
Olivier Gascuel, Gascuel Olivier
exaly   +2 more sources

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

Nature Communications, 2022
Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics.
J. Voznica, A. Zhukova, V. Boskova, E. Saulnier, F. Lemoine, M. Moslonka-Lefebvre, O. Gascuel   +6 more
doaj   +1 more source

Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics

Viruses, 2022
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses.
Muhammad Dilshad Hussain, Tahir Farooq, Xi Chen, Tong Jiang, Lianyi Zang, Muhammad Taimoor Shakeel, Tao Zhou   +6 more
doaj   +1 more source

Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa

Viruses, 2022
The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 incidence.
Emma Pujol-Hodge, Jesus F. Salazar-Gonzalez, Deogratius Ssemwanga, Edwin D. Charlebois, James Ayieko, Heather E. Grant, Teri Liegler, Katherine E. Atkins, Pontiano Kaleebu, Moses R. Kamya, Maya Petersen, Diane V. Havlir, Andrew J. Leigh Brown   +12 more
doaj   +1 more source

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

eLife, 2023
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated ...
Hugo G Castelán-Sánchez, Luis Delaye, Rhys PD Inward, Simon Dellicour, Bernardo Gutierrez, Natalia Martinez de la Vina, Celia Boukadida, Oliver G Pybus, Guillermo de Anda Jáuregui, Plinio Guzmán, Marisol Flores-Garrido, Óscar Fontanelli, Maribel Hernández Rosales, Amilcar Meneses, Gabriela Olmedo-Alvarez, Alfredo Heriberto Herrera-Estrella, Alejandro Sánchez-Flores, José Esteban Muñoz-Medina, Andreu Comas-García, Bruno Gómez-Gil, Selene Zárate, Blanca Taboada, Susana López, Carlos F Arias, Moritz UG Kraemer, Antonio Lazcano, Marina Escalera Zamudio   +26 more
doaj   +1 more source

Infectious disease phylodynamics with occurrence data

Methods in Ecology and Evolution, 2021
Phylodynamic models use pathogen genome sequence data to infer epidemiological dynamics. With the increasing genomic surveillance of pathogens, especially during the SARS‐CoV‐2 pandemic, new practical questions about their use are emerging.
Leo A. Featherstone, Francesca Di Giallonardo, Edward C. Holmes, Timothy G. Vaughan, Sebastián Duchêne   +4 more
doaj   +1 more source

Porcine Reproductive and Respiratory Syndrome (PRRS) Epidemiology in an Integrated Pig Company of Northern Italy: A Multilevel Threat Requiring Multilevel Interventions

Viruses, 2021
Porcine reproductive and respiratory syndrome (PRRS) is probably the most relevant viral disease affecting pig farming. Despite the remarkable efforts paid in terms of vaccination administration and biosecurity, eradication and long-term control have ...
Giovanni Franzo, Giacomo Barbierato, Patrizia Pesente, Matteo Legnardi, Claudia Maria Tucciarone, Giampietro Sandri, Michele Drigo   +6 more
doaj   +1 more source

Retrospective Characterization of the 2006–2007 Swine Vesicular Disease Epidemic in Northern Italy by Whole Genome Sequence Analysis

Viruses, 2021
Advances in the epidemiological tracing of pathogen transmission have been largely driven by the increasing characterisation of whole-genome sequence data obtained at a finer resolution from infectious disease outbreaks.
Giulia Pezzoni, Arianna Bregoli, Chiara Chiapponi, Santina Grazioli, Antonello Di Nardo, Emiliana Brocchi   +5 more
doaj   +1 more source