학술논문
Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.
Document Type
Academic Journal
Author
Vandenbogaert M; Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.; Kwasiborski A; Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.; Gonofio E; Institut Pasteur de Bangui, Bangui, Central African Republic.; Descorps-Declère S; Centre of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France.; Selekon B; Institut Pasteur de Bangui, Bangui, Central African Republic.; Nkili Meyong AA; Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.; Ouilibona RS; Institut Pasteur de Bangui, Bangui, Central African Republic.; Gessain A; Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, UMR3569, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS, Paris, France.; Manuguerra JC; Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.; Caro V; Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.; Nakoune E; Institut Pasteur de Bangui, Bangui, Central African Republic.; Berthet N; Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France. nicolas.berthet@pasteur.fr.; The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai-Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, No. 320 Yueyang Road, XuHui District, Shanghai, 200031, China. nicolas.berthet@pasteur.fr.
Source
Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
Subject
Language
English
Abstract
Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease. In this study, we evaluated the use of the MinION real-time sequencer as well as different polishing tools on MinION-sequenced genome for sequencing the MPXV genome originating from a pustular lesion in the context of an epidemic in a remote area of the Central African Republic. The reads corresponding to the MPXV genome were identified using two taxonomic classifiers, Kraken2 and Kaiju. Assembly of these reads led to a complete sequence of 196,956 bases, which is 6322 bases longer than the sequence previously obtained with Illumina sequencing from the same sample. The comparison of the two sequences showed mainly indels at the homopolymeric regions. However, the combined use of Canu with specific polishing tools such as Medaka and Homopolish was the best combination that reduced their numbers without adding mismatches. Although MinION sequencing is known to introduce a number of characteristic errors compared to Illumina sequencing, the new polishing tools allow a better-quality MinION-sequenced genome, thus to be used to help determine strain origin through phylogenetic analysis.
(© 2022. The Author(s).)
(© 2022. The Author(s).)