A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences
Închide
Conţinutul numărului revistei
Articolul precedent
Articolul urmator
478 0
SM ISO690:2012
FORTH, Jan H., FORTH, Leonie F., KING, Jacqueline, GROZA, Oxana, HUBNER, Alexandra, OLESEN, Ann Sofie, HOPER, 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, nr. 9(11), p. 0. ISSN 1999-4915. DOI: https://doi.org/10.3390/v11090846
EXPORT metadate:
Google Scholar
Crossref
CERIF

DataCite
Dublin Core
Viruses
Numărul 9(11) / 2019 / ISSN 1999-4915

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

DOI:https://doi.org/10.3390/v11090846

Pag. 0-0

Forth Jan H.1, Forth Leonie F.1, King Jacqueline1, Groza Oxana2, Hubner Alexandra1, Olesen Ann Sofie3, Hoper Dirk1, Dixon Linda K.4, Netherton Christopher L.4, Rasmussen Thomas Bruun5, Blome Sandra1, Pohlmann Anne1, Beer Martin1
 
1 Friedrich-Loeffler-Institut, Germany,
2 Republican Center for Veterinary Diagnostic,
3 Copenhagen University, Blegdamsvej, Copenhagen, Denmark,
4 The Pirbright Institute, UK,
5 Technical University of Denmark
 
 
Disponibil în IBN: 2 octombrie 2019


Rezumat

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.

Cuvinte-cheie
African swine fever virus (ASFV), next-generation sequencing (NGS), whole-genome sequencing, Nanopore sequencing, target enrichment