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R esearch
(Published online:
10-09-2015)
5.
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
Ravi
Kumar:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; Department of
Biotechnology, Graphic Era University, Dehradun, Uttarakhand,
India; kravi2509@gmail.com
Kaushal
Kishor Rajak:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; Kaushal Kishor Rajak,
e-mail: kaushalvirol@gmail.com
Tribhuwan Chandra:
Department of Biotechnology, Graphic Era University, Dehradun,
Uttarakhand, India; tribhuwan.chandra@gmail.com
Dhanavelu Muthuchelvan:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; drchelva@gmail.com
Arpit
Saxena:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; arpitsxena@gmail.com
Dheeraj
Chaudhary:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; dheeraj.int600@gmail.com
Ajay
Kumar:
Division of Virology, Indian Veterinary Research Institute,
Mukteswar, Nainital, Uttarakhand, India; dr.ajayyadav@hotmail.com
Awadh
Bihari Pandey: Division of Virology, Indian Veterinary
Research Institute, Mukteswar, Nainital, Uttarakhand, India;
abpandey58@rediffmail.com
Received: 20-05-2015, Revised: 31-07-2015, Accepted: 08-08-2015,
Published online: 10-09-2015
Corresponding author:
Kaushal Kishor Rajak, e-mail: kaushalvirol@gmail.com
Citation:
Kumar R, Rajak KK,
Chandra T, Muthuchelvan D, Saxena A, Chaudhary D, Kumar A, Pandey
AB (2015) Sequence-based comparative study of classical swine
fever virus genogroup 2.2 isolate with pestivirus reference
strains, Veterinary World 8(9):1059-1062.
Abstract
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.
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