Emerging infectious diseases · 2018 · 91 citations · 24 references
Life SciencesInfectious DiseasesMicrobiologyEmerging Infectious DiseasesGenomicsVirologyEmerging Viral DiseasesGenomic EpidemiologyViral EpidemiologyViral GeneticsViral GenomicsViral InfectionsCoxsackievirus InfectionsHand-foot-mouth DiseaseMolecular Epidemiology Of VirusesMolecular Epidemiology PhylogeneticsPhylogenetic Character AnalysisPhylogenetic Diversity AnalysisPhylogenomics Of VirusesVirus Evolutionary Relationships
Hand, foot and mouth disease (HFMD) is a major public health issue in Asia and has global pandemic potential. Coxsackievirus A6 (CV-A6) was detected in 514/2,230 (23%) of HFMD patients admitted to 3 major hospitals in southern Vietnam during 2011-2015. Of these patients, 93 (18%) had severe HFMD. Phylogenetic analysis of 98 genome sequences revealed they belonged to cluster A and had been circulating in Vietnam for 2 years before emergence. CV-A6 movement among localities within Vietnam occurred frequently, whereas viral movement across international borders appeared rare. Skyline plots identified fluctuations in the relative genetic diversity of CV-A6 corresponding to large CV-A6-associated HFMD outbreaks worldwide. These data show that CV-A6 is an emerging pathogen and emphasize the necessity of active surveillance and understanding the mechanisms that shape the pathogen evolution and emergence, which is essential for development and implementation of intervention strategies.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar · Nucleic Acids Research · 2004 · 46.5K citations · Full text
A new method for calculating evolutionary substitution rates
Cecilia Lanave, Giuliano Preparata, Cecilia Sacone et al. · Journal of Molecular Evolution · 1984 · 1.4K citations