Genetic analysis of NS5B gene from bovine viral diarrhea virus-infected cattle in Central and East Java, Indonesia

Abstract

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.

Detection of Pestivirus in small ruminants in Central Java, Indonesia

“…The prevalence of the disease continues to increase over the years. The seropositivity of BVDV-1 among beef, dairy, and breeding cattle populations varies from approximately 46-56.2% [ 15 , 16 ]. Because BVDV-1 from cattle is the only officially recognized pestivirus species in Indonesia, all studies related to this virus are focused on cattle as the natural host and no research on pestiviruses in small ruminants has been conducted.…”

The Epidemiology and Control of Bovine Viral Diarrhoea Virus in Tropical Indonesian Cattle

“…Apart from culture-and protein-based tests, RNA-based tests have also been widely used to detect and characterise Indonesian isolates of BVDV, especially for genotyping [44][45][46]48,49].…”

“…Studies of BVDV subgenotypes in Indonesia mainly used genes NS5B or 5 UTR for analyses, but genes Npro, NS3 and E2 were also used. A study of a 360-nucleotide fragment of the NS5B gene of BVDV indicated that subgenotypes-1a, -1b and -1c were circulating in the Banyumas region, Central Java, during 2013-2016 [45]. The sequences used in this study are accessible in GenBank with the accession numbers MK411754, MK411755, MK411756, MK411757, MK411762, MK411764, MK411765, MK411761 and MK411759 for BVDV-1a, MK 411760 for BVDV-1b and MK411751, MK411763, MK411753, MK411758 and MK411752 for the BVDC-1c genotypes.…”

“…Subgenotypes BVDV-1a and BVDV-1c were detectable in a study of 360 nt fragments of the NS5B gene of BVDV isolates from the Malang and Pasuruan regions of East Java and isolates from the Cilacap, Boyolali and Semarang regions of Central Java [45]. The BVDV isolates of West Java were reported to belong to the genotype BVDV-1, when clustered using 360 nt of partial NS5B gene [46].…”

Genetic recombination of bovine viral diarrhea virus subgenotype -1a and -1c in persistently infected dairy cattle

“…It is believed that there are two main BVDV1 subgenotypes, 1a and 1c (Saepulloh et al 2015; Wuryastuti et al 2015, in addition to other subgenotypes, 1b and 1d (Saepulloh et al 2015). The distribution of three subgenotypes, namely, BVDV 1a, 1b, and 1c, in Central and East Java, Indonesia, re flects the genetic variability of BVDV1 viruses based on partial NS5B genes (Irianingsih et al 2019). Phylogenetic analysis from different regions, specifically 5′ NCR, Npro, E2, NS3, and NS5B3' NCR, of BVDV isolates has been carried out in Japan (Nagai et al 2004) and 5'UTR nd NPro in the UK (Booth et al 2013).…”