Vet World Vol.12 July-2019 Article-27
Research Article
Veterinary World, 12(7): 1108-1115
https://doi.org/10.14202/vetworld.2019.1108-1115
Genetic analysis of NS5B gene from bovine viral diarrhea virus-infected cattle in Central and East Java, Indonesia
2. Disease Investigation Centre Wates, Yogyakarta, Indonesia.
3. Department of Veterinary Internal Medicine, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
4. Department of Veterinary Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
5. Department of Reproduction Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza, P.O. Box 12622, Egypt.
6. Directorate of Animal Health, Directorate General of Livestock Services and Animal Health, Ministry of Agriculture, The Republic of Indonesia, Jakarta, Indonesia.
Background and Aim: A previous study divided Indonesian bovine viral diarrhea virus (BVDV)-1 into subgenotypes BVDV-1a to BVDV-1d based on the partial NS5B gene using strain Bega as reference for BVDV-1a. In fact, it is clustered into BVDV-1c with strain Bega-like Australia. BVDV genotyping has been done on isolates from Jakarta, West and Central Java, but East Java isolates have not been genotyped. This study aimed to analyze genetic variability and amino acid residues in the nucleotide-binding pocket of the NS5B gene from infected cattle.
Materials and Methods: Samples were obtained from the Sera Bank originating from active and passive surveillance of cattle that had been tested for BVDV antigen from 2013 to 2017. Detection of the p80 antibody and BVDV genotyping was carried out using ELISA and nested-multiplex-polymerase chain reaction (PCR), respectively. We defined 15 nested PCR products for partial sequencing of NS5B. Those field samples were selected from each location and year using proportional calculation as a representative sample. Homological and phylogenetic analyses of the partial NS5B gene were performed using BLAST and MEGA version 6.
Results: Based on the phylogenetic tree analysis using 360 nucleotides as the partial NS5B gene, Indonesian BVDV-1 isolates from Central and East Java were subdivided to BVDV-1a (n=9), BVDV-1b (n=1), and BVDV-1c (n=5). In the present study, the homology of BVDV subgenotype -1a, -1b, and -1c was compared to the BVDV GenBank data and found 90-93%, 93%, and 92-95% respectively with the average pairwise distance of 0.207. A point mutation was shown at R283K of all BVDV isolates based on the sequence of three amino acid residues R283, R285, and I287 in the nucleotide-binding pocket as a part of the encoded RNA-dependent RNA polymerase.
Conclusion: This study revealed the genetic variability of BVDV infecting cattle in Central Java and East Java, Indonesia, the subtypes BVDV-1a, BVDV-1b, BVDV-1c, and a point mutation at the R283K residue. Keywords: bovine viral diarrhea virus, NS5B gene, phylogenetic analysis, point mutation, subgenotype.
Keywords: bovine viral diarrhea virus, NS5B gene, phylogenetic analysis, point mutation, subgenotype.
How to cite this article: Irianingsih SH, Wuryastuty H, Wasito R, Wibawa H, Tjatur Rasa FS, Poermadjaja B (2019) Genetic analysis of NS5B gene from bovine viral diarrhea virus-infected cattle in Central and East Java, Indonesia, Veterinary World, 12(7): 1108-1115.
Received: 26-03-2019 Accepted: 13-06-2019 Published online: 25-07-2019
Corresponding author: H. Wuryastuty E-mail: hastari@ugm.ac.id
DOI: 10.14202/vetworld.2019.1108-1115
Copyright: Irianingsih, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.