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.

Truncation and Sequence Shuffling of Segment 6 Generate Replication-Competent Neuraminidase-Negative Influenza H5N1 Viruses

“…EscEgg50A and CoEgg50 were sequenced with a Genome Sequencer FLX (GS FLX) instrument (Roche, Mannheim, Germany) according to the protocol of Höper and coworkers (13) with the modifications of Leifer and colleagues (14). In addition, EscEgg50A was sequenced after preparation of a randomly primed cDNA sequencing library for Titanium sequencing with the GS FLX instrument according to the manufacturer's protocol.…”

Mixed Triple: Allied Viruses in Unique Recent Isolates of Highly Virulent Type 2 Bovine Viral Diarrhea Virus Detected by Deep Sequencing

“…The observed unique adaptive mutations in the p7-NS2 region are remarkable, since the p7-encoding genome part, in general, appears to be highly conserved in all pestiviruses (39). Only these very specific single nucleotide polymorphisms (SNPs) allowed the detection and differentiation of the duplicated genome parts by deep sequencing.…”

Farmer perceptions of classical swine fever outbreak in communal pig production systems of South Africa

“…Delays in detecting outbreak of contagious diseases like CSF (Ruggli et al, 1996;Liu et al, 2009;Podgórska and Stadejek, 2010) will result in the virus travelling long distances affecting many pigs hence increased costs of controlling the disease (Edwards et al, 2000;Leifer et al, 2005;Rowlands et al, 2008).…”

“…There is risk of disease outbreak if farmers are left to restock using some of the pigs that were hid during the culling exercise. Future outbreaks of contagious diseases such as CSF (Ruggli et al, 1996;Liu et al, 2009;Podgórska and Stadejek, 2010) should be avoided since it has a huge financial implication on the national economy economy as the government struggles to control the disease (Edwards et al, 2000;Leifer et al, 2005;Rowlands et al, 2008). For example, the South African government paid more than R200 million to compensate the more than 83 000 affected farmers (National African Farmers Union (NAFU), 2007).…”