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

GND
106658446X
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. janhendrik.forth@fli.de.
Forth, Jan Hendrik;
GND
1149753951
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. leonie.forth@fli.de.
Forth, Leonie;
GND
1221280147
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. jacqueline.king@fli.de.
King, Jacqueline;
Affiliation
Animal Health Diagnostic Laboratory, Republican Center for Veterinary Diagnostic, str. Murelor, 3, MD-2051, mun. Chișinău, Moldova. crdv@ansa.gov.md.
Groza, Oxana;
GND
1105073327
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. a.huebner87@gmx.de.
Hübner, Alexandra;
Affiliation
Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark. ann.sofie.olesen@sund.ku.dk.
Olesen, Ann Sofie;
GND
132084457
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. dirk.hoeper@fli.de.
Höper, Dirk;
Affiliation
The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK. linda.dixon@pirbright.ac.uk.
Dixon, Linda K;
Affiliation
The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK. christopher.netherton@pirbright.ac.uk.
Netherton, Christopher L;
Affiliation
DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark. tbru@ssi.dk.
Rasmussen, Thomas Bruun;
GND
1019543779
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. sandra.blome@fli.de.
Blome, Sandra;
GND
123110165
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. Anne.pohlmann@fli.de.
Pohlmann, Anne;
GND
1019543523
Affiliation
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany. martin.beer@fli.de.
Beer, Martin

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.

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