Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences

Abstract

Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508–3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins Npro, C, Erns, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.

Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1

“…3) whereas in E2 and NS5B tree it has been grouped with 1.2 isolates which shows that grouping of group 1 isolates was not proper. The same observation was also demonstrated by Postel et al [17] for isolates belonging to individual subgenotypes of 1.1, 1.2, 2.1 and 2.3. Due to advantage and disadvantages of each region, Paton et al [16] advised to study different genomic regions whenever new isolates are included in the analyses that fall into new or distinct clusters and also when comparing very similar viruses.…”

“…On the phylogenetic tree, all the Indian isolates were placed in separate cluster from the other members of the 2.2 subgroup from Germany, Austria and Netherlands and had 3.5-10.4 % divergent from them. Interestingly, Indian clade showed a closer phylogenetic relationship to E2-encoding sequences of the Chinese recombinant isolate ''strain 39'' (possessing an E2 gene from an unknown parental 2.2 genotype isolate [17]) at a genetic distances of 3.3-4.6 % than to those of E2-encoding sequences of isolates from Germany(JQ411560), Austria(CSF00740) and Netherlands(AF1829110). Present isolates were 17.1-19.8 % divergent with vaccine strain (HCLV India) and 17.1-24.0, 19.1-24.8 % divergent from the members of the groups 1 and 3 respectively in E2 sequences (Table 1).…”

The Molecular Biology of Pestiviruses

“…The figure was taken from Liu, Xia, Wahlberg, Belak, and Baule (2009). review. For more information on genotypes, we refer to corresponding publications ( Jenckel et al, 2014;Luzzago et al, 2014;Pan et al, 2005;Paton et al, 2000;Postel et al, 2012;Rosamilia et al, 2014).…”

Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China

“…-6]. It has been reported that subgenotype 2.1 isolates are distributed in many Asian and European countries and play a dominant role in CSF outbreaks occurring in China, Korea and other countries [3,5,7,8]. With more sequences of 2.1 isolates deposited in the GenBank database, CSFV subgenotype 2.1 has been further divided into 10 sub-subgenotypes (2.1a-2.1j) based on a nucleotide sequence of 190-nt and the 1,119-nt E2 gene [8].…”

“…The ORF encodes a 3898-amino-acid polyprotein that can be further processed to four structural proteins (Core, E rns , E1, and E2) and eight nonstructural proteins (N pro , P7, NS2, NS3, isolate for GD19/2011 is the sub-subgenotype 2.1a strain Paderborn from Germany [5], and the most distant isolate is the sub-subgenotype 2.1d strain IND/AS/GHY/G4 collected from India [7]. Sequence identity values from the comparison of GD19/2011 and other subgenotype 2.1 isolates at the genome and individual gene levels are shown in Table 1.…”