A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

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  • Author: Forth, Jan H

    Friedrich-Loeffler-Institute, Germany

  • Author: Forth, Leonie F

    Friedrich-Loeffler-Institute, Germany

  • Author: King, Jacqueline

    Friedrich-Loeffler-Institute, Germany

  • Author: Groza, Oxana

    Republican Center for Veterinary Diagnostic, Moldova, Republic of

  • Author: Hübner, Alexandra

    Friedrich-Loeffler-Institute, Germany

  • Author: Olesen, Ann Sofie

    University of Copenhagen, Denmark

  • Author: Höper, Dirk

    Friedrich-Loeffler-Institute, Germany

  • Author: Dixon, Linda K

    Pirbright Institute, United Kingdom

  • Author: Netherton, Christopher L

    Pirbright Institute, United Kingdom

  • Author: Rasmussen, Thomas Bruun

    Virology, Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lindholm, 4771, Kalvehave, Denmark

  • Author: Blome, Sandra

    Friedrich-Loeffler-Institute, Germany

  • Author: Pohlmann, Anne

    Friedrich-Loeffler-Institute, Germany

  • Author: Beer, Martin

    Friedrich-Loeffler-Institute, Germany

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African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing. Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.
Original languageEnglish
Article number846
JournalViruses
Volume11
Issue number9
Number of pages18
ISSN1999-4915
DOIs
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

ID: 192715597