A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
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A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. / Forth, Jan H.; Forth, Leonie F.; King, Jacqueline; Groza, Oxana; Hübner, Alexandra; Olesen, Ann Sofie; Höper, Dirk; Dixon, Linda K.; Netherton, Christopher L.; Rasmussen, Thomas Bruun; Blome, Sandra; Pohlmann, Anne; Beer, Martin.
I: Viruses, Bind 11, Nr. 9, 846, 2019.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
AU - Forth, Jan H.
AU - Forth, Leonie F.
AU - King, Jacqueline
AU - Groza, Oxana
AU - Hübner, Alexandra
AU - Olesen, Ann Sofie
AU - Höper, Dirk
AU - Dixon, Linda K.
AU - Netherton, Christopher L.
AU - Rasmussen, Thomas Bruun
AU - Blome, Sandra
AU - Pohlmann, Anne
AU - Beer, Martin
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - African swine fever virus (ASFV)
KW - Nanopore sequencing
KW - next-generation sequencing (NGS)
KW - target enrichment
KW - whole-genome sequencing
U2 - 10.3390/v11090846
DO - 10.3390/v11090846
M3 - Journal article
C2 - 31514438
AN - SCOPUS:85072148177
VL - 11
JO - Viruses
JF - Viruses
SN - 1999-4915
IS - 9
M1 - 846
ER -
ID: 227873181