Irianingsih S H, Wuryastuty H, Wasito R, Wibawa H, Rasa F S Tjatur, Poermadjaja B
Doctoral Study Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.
Disease Investigation Centre Wates, Yogyakarta, Indonesia.
Vet World. 2019 Jul;12(7):1108-1115. doi: 10.14202/vetworld.2019.1108-1115. Epub 2019 Jul 25.
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.
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.
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.
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.
此前一项研究以贝加毒株作为牛病毒性腹泻病毒1型（BVDV-1a）的参考毒株，基于部分NS5B基因将印度尼西亚的BVDV-1分为BVDV-1a至BVDV-1d亚型。实际上，它与澳大利亚的贝加样毒株一起被归类为BVDV-1c。已对来自雅加达、西爪哇省和中爪哇省的分离株进行了BVDV基因分型，但东爪哇省的分离株尚未进行基因分型。本研究旨在分析感染牛的NS5B基因核苷酸结合口袋中的遗传变异性和氨基酸残基。
样本取自血清库，这些血清来自2013年至2017年对牛进行BVDV抗原检测的主动和被动监测。分别使用酶联免疫吸附测定（ELISA）和巢式多重聚合酶链反应（PCR）检测p80抗体和进行BVDV基因分型。我们定义了15个用于NS5B部分测序的巢式PCR产物。使用比例计算从每个地点和年份选取那些现场样本作为代表性样本。使用BLAST和MEGA 6版本对部分NS5B基因进行同源性和系统发育分析。
基于以360个核苷酸作为部分NS5B基因的系统发育树分析，来自中爪哇省和东爪哇省的印度尼西亚BVDV-1分离株被细分为BVDV-1a（n = 9）、BVDV-1b（n = 1）和BVDV-1c（n = 5）。在本研究中，将BVDV-1a、-1b和-1c亚型与BVDV基因库数据进行同源性比较，发现分别为90 - 93%、93%和92 - 95%，平均成对距离为0.207。基于编码的RNA依赖性RNA聚合酶核苷酸结合口袋中三个氨基酸残基R283、R285和I287的序列，所有BVDV分离株在R283K处均出现一个点突变。
本研究揭示了印度尼西亚中爪哇省和东爪哇省感染牛的BVDV的遗传变异性、BVDV-1a、BVDV-1b、BVDV-1c亚型以及R283K残基处的一个点突变。
