Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Programa de Pós-graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil; Setor de Virologia, Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, Brazil; Departamento de Microbiologia e Parasitologia, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
Infect Genet Evol. 2021 Aug;92:104891. doi: 10.1016/j.meegid.2021.104891. Epub 2021 May 2.
Bovine viral diarrhea virus-1 (BVDV-1, Pestivirus A) and BVDV-2 (Pestivirus B) have been clustered into 21 and 4 subtypes, respectively. This genetic diversity, in addition to the lack of consensus on which genomic region to use for BVDV subtyping, has resulted in conflicting classifications depending on the target analyzed. Here, we investigated which genes or UTRs would reproduce the phylogeny obtained by complete genome (CG) analyses. The study was carried out with 91 (BVDV-1) and 85 (BVDV-2) CG available on GenBank database. The viruses were subtyped by analyzing their CG, as well as their individual genes and UTRs (complete 3' and 5'UTRs, and partial 5'UTR); and the phylogeny results were compared to each other. The sequences were aligned using the ClustalW multiple method (BioEdit Alignment Editor software, v.7.0.5.3) and the phylogenetic analyses were performed by the Maximum Likelihood method (MEGA-X software, v.10.2.4), with 1000 bootstrap replicates. The best analysis model for each gene/UTR was defined using the jModelTest software. The geodesic distance between the CG (reference) and individual genes/UTRs trees was also calculated (TreeCmp software, v.2.0). In general, 3'UTR-based analyses, followed by 5'UTR, presented the least reliable subtyping results. Regarding BVDV-1, phylogeny based on C, E, E1, E2, p7, NS2, NS3, NS4B, NS5A and NS5B was consistent with that of CG. In contrast, analyses performed with individual BVDV-2 genes showed at least one different clustering from the phylogeny based on the CG. After analyzing the geodesic distance between the CG and genes/UTRs trees, we observed that NS4B (for BVDV-1) and NS5A (BVDV-2) presented the closest topology and edge length to the CG analyses. Finally, comparing the phylogeny performed with the CG and the genes/UTRs, as well as the geodesic distance between them, we understand that NS4B and NS5A represent the most suitable targets for BVDV-1 and -2 subtyping, respectively, and may be considered in future phylogenetic studies.
牛病毒性腹泻病毒-1（BVDV-1，瘟病毒 A）和 BVDV-2（瘟病毒 B）分别被聚类为 21 个和 4 个亚型。这种遗传多样性，再加上缺乏共识，即应该使用基因组的哪个区域进行 BVDV 亚型分类，导致了根据分析目标的不同而出现相互矛盾的分类。在这里，我们研究了哪些基因或 UTR 可以重现通过完整基因组（CG）分析获得的系统发育。该研究使用了 GenBank 数据库中可用的 91 个（BVDV-1）和 85 个（BVDV-2）CG 进行。通过分析其 CG 以及单个基因和 UTR（完整的 3'和 5'UTR 以及部分 5'UTR）对病毒进行了分型；并将彼此的系统发育结果进行了比较。使用 ClustalW 多重方法（BioEdit Alignment Editor 软件，v.7.0.5.3）对序列进行比对，并使用最大似然法（MEGA-X 软件，v.10.2.4）进行系统发育分析，使用 1000 次重复进行 bootstrap。使用 jModelTest 软件定义了每个基因/UTR 的最佳分析模型。还计算了 CG（参考）与单个基因/UTR 树之间的测地线距离（TreeCmp 软件，v.2.0）。一般来说，基于 3'UTR 的分析，其次是 5'UTR，结果最不可靠。关于 BVDV-1，基于 C、E、E1、E2、p7、NS2、NS3、NS4B、NS5A 和 NS5B 的系统发育与 CG 一致。相反，使用单独的 BVDV-2 基因进行的分析显示，与基于 CG 的系统发育至少有一个聚类不同。在分析 CG 与基因/UTR 树之间的测地线距离后，我们观察到 NS4B（BVDV-1）和 NS5A（BVDV-2）与 CG 分析的拓扑结构和边缘长度最接近。最后，比较 CG 与基因/UTR 进行的系统发育以及它们之间的测地线距离，我们了解到 NS4B 和 NS5A 分别是 BVDV-1 和 -2 亚型最适合的靶标，可以在未来的系统发育研究中考虑。
