Results 11 to 20 of about 4,475 (152)

What We Talk About When We Talk About Microbial Species. [PDF]

Mol Ecol
ABSTRACT Genome annotation, alignment and phylogenetics are at the centre of most studies in evolutionary genomics. These techniques function best when rooted in prior work. Genes are mined from new genomes using evidence from old gene models. These genomes are aligned to well‐worn references to create matrices for tree reconstruction.
Narechania A, Gopalakrishnan S, Gilbert MTP.   +2 more
europepmc   +2 more sources

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

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

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

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

Molecular Basis of the Toxigenic Vibrio cholerae O1 Serotype Switch from Ogawa to Inaba in Haiti

Microbiology Spectrum, 2023
Toxigenic Vibrio cholerae O1 serotype Ogawa was introduced involuntarily into Haiti in October 2010, and virtually all of the clinical strains isolated during the first 5 years of the epidemic were Ogawa.
Taylor K. Paisie, Melanie N. Cash, Massimiliano S. Tagliamonte, Afsar Ali, J. Glenn Morris, Marco Salemi, Carla Mavian   +6 more
doaj   +1 more source

Effects of memory on the shapes of simple outbreak trees [PDF]

, 2016
Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission.
Boyd, M, Colijn, C, Kwan, C, Plazzotta, G   +3 more
core   +1 more source

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, Natalya Lebedeva, Fedor Moskaleychik, Alexander Pronin, Elena Kazennova, Marina Bobkova   +5 more
doaj   +1 more source

Phylodynamic Analysis Complements Partner Services by Identifying Acute and Unreported HIV Transmission

Viruses, 2020
Tailoring public health responses to growing HIV transmission clusters depends on accurately mapping the risk network through which it spreads and identifying acute infections that represent the leading edge of cluster growth.
Ellsworth M. Campbell, Anne Patala, Anupama Shankar, Jin-Fen Li, Jeffrey A. Johnson, Emily Westheimer, Cynthia L. Gay, Stephanie E. Cohen, William M. Switzer, Philip J. Peters   +9 more
doaj   +1 more source

An Ecological and Conservation Perspective on Advances in the Applied Virology of Zoonoses

Viruses, 2011
The aim of this manuscript is to describe how modern advances in our knowledge of viruses and viral evolution can be applied to the fields of disease ecology and conservation.
Jonathan H. Epstein, Kurt J. Vandegrift, Nina Wale   +2 more
doaj   +1 more source