Eurosurveillance · 2024 · 43 citations · 11 references
Life SciencesInfectious DiseasesMicrobiologyMedical MicrobiologyMolecular VirologyVirologyAnimal VirusesPhylogenetic EpidemiologySequence-based EpidemiologyViral GenomicsViral InfectionsViral ZoonosesGenomic Epidemiology Of ZoonosesLineage AssignmentMolecular Epidemiology PhylogeneticsPhylogenetic Tracing Of TransmissionPhylogenomics Of Viruses
Between January and August 2024, mpox cases have been reported in nearly all provinces of the Democratic Republic of the Congo (DRC). Monkeypox virus genome sequences were obtained from 11 mpox cases' samples, collected in July-August 2024 in several health zones of Kinshasa. Characterisation of the sequences showed subclades Ia and Ib co-circulating in the Limete health zone, while phylogenetic analyses suggested multiple introductions of the two subclades in Kinshasa. This illustrates the growing complexity of Clade I mpox outbreaks in DRC.
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fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen, Yanqing Zhou, Yaru Chen et al. · Bioinformatics · 2018 · 29.7K citations · Full text
Minimap2: pairwise alignment for nucleotide sequences
Heng Li · Bioinformatics · 2018 · 16.8K citations · Full text
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler et al. · Molecular Biology and Evolution · 2017 · 11K citations · Full text