title: Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany.
abstract: Classical swine fever (CSF) has caused significant economic losses in industrialized pig production, and is still present in some European countries. Recent CSF outbreaks in Europe were mainly associated with strains of genogroup 2 (subgroup 2.3). Although there are extensive datasets regarding 2.3 strains, there is very little information available on longer fragments or whole classical swine fever virus (CSFV) genomes. Furthermore, there are no detailed analyses of the molecular epidemiology of CSFV wild boar isolates available. Nevertheless, complete genome sequences are supportive in phylogenetic analyses, especially in affected wild boar populations. Here, German CSFV strains of subgroup 2.3 were fully sequenced using two different approaches: (i) a universal panel of CSFV primers that were developed to amplify the complete genome in overlapping fragments for chain-terminator sequencing; and (ii) generation of a single full-length amplicon of the CSFV genome obtained by long-range RT-PCR for deep sequencing with next-generation sequencing technology. In total, five different strains of CSFV subgroup 2.3 were completely sequenced using these newly developed protocols. The approach was used to study virus spread and evolutionary history in German wild boar. For the first time, the results of our study clearly argue for the possibility of a long-term persistence of genotype 2.3 CSFV strains in affected regions at an almost undetectable level, even after long-term oral vaccination campaigns with intensive monitoring. Hence, regional persistence in wild boar populations has to be taken into account as an important factor in the continual outbreaks in affected areas.
authors.affiliation: Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany.
authors.forename: Immanuel
authors.initials: I
authors.lastname: Leifer
authors.forename: Bernd
authors.initials: B
authors.lastname: Hoffmann
authors.forename: Dirk
authors.initials: D
authors.lastname: Höper
authors.forename: Thomas
authors.initials: T
authors.lastname: Bruun Rasmussen
authors.forename: Sandra
authors.initials: S
authors.lastname: Blome
authors.forename: Günter
authors.initials: G
authors.lastname: Strebelow
authors.forename: Detlef
authors.initials: D
authors.lastname: Höreth-Böntgen
authors.forename: Christoph
authors.initials: C
authors.lastname: Staubach
authors.forename: Martin
authors.initials: M
authors.lastname: Beer
mesh_terms: D000818:Animals; D006691:Classical Swine Fever / Q000453:epidemiology* / Q000821:virology*; D006692:Classical Swine Fever Virus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral; D005858:Germany / Q000453:epidemiology; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D034421:Sus scrofa / Q000821:virology*; D014611:Vaccination / Q000379:methods; D014765:Viral Vaccines / Q000008:administration & dosage / Q000276:immunology
chemical_list: D017931:DNA Primers; D012367:RNA, Viral; D014765:Viral Vaccines