Sequence-based comparative study of classical swine fever virus genogroup 2.2 isolate with pestivirus reference strains

Ravi Kumar, Kaushal Kishor Rajak, Tribhuwan Chandra, Dhanavelu Muthuchelvan, Arpit Saxena, Dheeraj Chaudhary, Ajay Kumar and Awadh Bihari Pandey

Veterinary World, 8(9): 1059-1062

   doi: 10.14202/vetworld.2015.1059-1062

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Abstract

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Aim: This study was undertaken with the aim to compare and establish the genetic relatedness between classical swine fever virus (CSFV) genogroup 2.2 isolate and pestivirus reference strains.

Materials and Methods: The available complete genome sequences of CSFV/IND/UK/LAL-290 strain and other pestivirus reference strains were retrieved from GenBank. The complete genome sequence, complete open reading frame, 5’ and 3’ non-coding region (NCR) sequences were analyzed and compared with reference pestiviruses strains. Clustal W model in MegAlign program of Lasergene 6.0 software was used for analysis of genetic heterogeneity. Phylogenetic analysis was carried out using MEGA 6.06 software package.

Results: The complete genome sequence alignment of CSFV/IND/UK/LAL-290 isolate and reference pestivirus strains showed 58.9-72% identities at the nucleotide level and 50.3-76.9% at amino acid level. Sequence homology of 5’ and 3’ NCRs was found to be 64.1-82.3% and 22.9-71.4%, respectively. In phylogenetic analysis, overall tree topology was found similar irrespective of sequences used in this study; however, whole genome phylogeny of pestivirus formed two main clusters, which further distinguished into the monophyletic clade of each pestivirus species. CSFV/IND/UK/LAL-290 isolate placed with the CSFV Eystrup strain in the same clade with close proximity to border disease virus and Aydin strains.

Conclusion: CSFV/IND/UK/LAL-290 exhibited the analogous genomic organization to those of all reference pestivirus strains. Based on sequence identity and phylogenetic analysis, the isolate showed close homology to Aydin/04-TR virus and distantly related to Bungowannah virus.

Keywords: classical swine fever virus, genogroup, genome, pestivirus, phylogenetic tree, sequence.