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

Jan H Forth, Leonie F Forth, Jacqueline King, Oxana Groza, Alexandra Hübner, Ann Sofie Olesen, Dirk Höper, Linda K Dixon, Christopher L Netherton, Thomas Bruun Rasmussen, Sandra Blome*, Anne Pohlmann, Martin Beer

*Corresponding author for this work

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Abstract

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

Cite this

Forth, J. H., Forth, L. F., King, J., Groza, O., Hübner, A., Olesen, A. S., ... Beer, M. (2019). A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses, 11(9), [846]. https://doi.org/10.3390/v11090846
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. / A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. In: Viruses. 2019 ; Vol. 11, No. 9.
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title = "A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences",
abstract = "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.",
author = "Forth, {Jan H} and Forth, {Leonie F} and Jacqueline King and Oxana Groza and Alexandra H{\"u}bner and Olesen, {Ann Sofie} and Dirk H{\"o}per and Dixon, {Linda K} and Netherton, {Christopher L} and Rasmussen, {Thomas Bruun} and Sandra Blome and Anne Pohlmann and Martin Beer",
year = "2019",
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Forth, JH, Forth, LF, King, J, Groza, O, Hübner, A, Olesen, AS, Höper, D, Dixon, LK, Netherton, CL, Rasmussen, TB, Blome, S, Pohlmann, A & Beer, M 2019, 'A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences', Viruses, vol. 11, no. 9, 846. https://doi.org/10.3390/v11090846

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.

In: Viruses, Vol. 11, No. 9, 846, 2019.

Research output: Contribution to journalJournal articleResearchpeer-review

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.

U2 - 10.3390/v11090846

DO - 10.3390/v11090846

M3 - Journal article

VL - 11

JO - Viruses

JF - Viruses

SN - 1999-4915

IS - 9

M1 - 846

ER -