牛病毒性腹泻病毒1 (BVDV-1)和BVDV-2适当亚型分型的新基因组靶点

IF 1.9 4区 医学 Q3 GENETICS & HEREDITY
Virus Genes Pub Date : 2023-12-01 Epub Date: 2023-08-17 DOI:10.1007/s11262-023-02022-x
Carolina Isabela Mucellini, José Valter Joaquim Silva Júnior, Pablo Sebastian Britto de Oliveira, Rudi Weiblen, Eduardo Furtado Flores
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引用次数: 0

摘要

全基因组系统发育分析是牛病毒性腹泻病毒1型(BVDV-1)和BVDV-2亚型分型最合适的策略,但在许多实验室并不可行。因此,BVDV分离株/菌株经常基于单个基因组区域(主要是5'非翻译区(UTR))的分析进行亚型分型。然而,这种方法可能导致不准确和/或缺乏统计支持的病毒分类。在此,我们描述了新的引物集合,其扩增子可以很容易地测序并用于BVDV亚型。首先,对先前被描述为BVDV亚型最合适目标的基因组区域进行分析,以设计高覆盖率的引物。对这些扩增子进行了计算机分析,以确定它们是否适合再现118个BVDV-1和88个BVDV-2完整/接近完整基因组(CNCGs)的系统发育分类(GenBank)。该分析还考虑了引物hcv90 - 368,324 -326和BP189-389 (5'UTR)可扩增的区域,这些引物已用于BVDV的诊断和/或分类。在确认引物扩增子分析与CNCGs分析的一致性后,我们对rt - pcr进行了优化,并评估了其扩增BVDV分离株/菌株的性能(n = 35, BVDV-1;BVDV-2 n = 33)。在BVDV分型的潜在靶点中,我们设计了NS3-NS4A (BVDV-1) (526 bp扩增子)和NS5B (BVDV-2) (728 bp扩增子)的高覆盖率引物。基于这些区域的分类完全再现了所有cncg的亚型。另一方面,基于引物HCV90-368、324-326和BP189-389推定扩增子的亚型分析显示与CNCG分析相关的差异。NS3-NS4A和NS5B引物也可以扩增所有BVDV分离株/株。最后,我们建议在未来的bvdv系统发育和流行病学研究中使用这些引物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Novel genomic targets for proper subtyping of bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2.

Novel genomic targets for proper subtyping of bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2.

Whole-genome phylogenetic analysis, the most suitable strategy for subtyping bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, is not feasible for many laboratories. Consequently, BVDV isolates/strains have been frequently subtyped based on analysis of single genomic regions, mainly the 5' untranslated region (UTR). This approach, however, may lead to inaccurate and/or poorly statistically supported viral classification. Herein, we describe novel primer sets whose amplicons may be easily sequenced and used for BVDV subtyping. Initially, genomic regions previously described as the most suitable targets for BVDV subtyping were analyzed for design of high-coverage primers. The putative amplicons were analyzed in silico for their suitability to reproduce the phylogenetic classification of 118 BVDV-1 and 88 BVDV-2 complete/near-complete genomes (CNCGs) (GenBank). This analysis was also performed considering the region amplifiable by primers HCV90-368, 324-326 and BP189-389 (5'UTR), which have been used for BVDV diagnosis and/or classification. After confirming the agreement between the analyses of our primers' amplicon versus the CNCGs, we optimized the RT-PCRs and evaluated their performance for amplification of BVDV isolates/strains (n = 35 for BVDV-1; n = 33 for BVDV-2). Among the potential targets for BVDV subtyping, we designed high-coverage primers for NS3-NS4A (BVDV-1) (526 bp amplicon) and NS5B (BVDV-2) (728 bp). The classification based on these regions fully reproduced the subtyping of all CNCGs. On the other hand, subtyping based on the putative amplicons from primers HCV90-368, 324-326 and BP189-389 showed disagreements in relation the CNCG analysis. The NS3-NS4A and NS5B primers also allowed the amplification of all BVDV isolates/strains tested. Finally, we suggest the use of these primers in future phylogenetic and epidemiological studies of BVDVs.

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来源期刊
Virus Genes
Virus Genes 医学-病毒学
CiteScore
3.30
自引率
0.00%
发文量
76
审稿时长
3 months
期刊介绍: Viruses are convenient models for the elucidation of life processes. The study of viruses is again on the cutting edge of biological sciences: systems biology, genomics, proteomics, metagenomics, using the newest most powerful tools. Huge amounts of new details on virus interactions with the cell, other pathogens and the hosts – animal (including human), insect, fungal, plant, bacterial, and archaeal - and their role in infection and disease are forthcoming in perplexing details requiring analysis and comments. Virus Genes is dedicated to the publication of studies on the structure and function of viruses and their genes, the molecular and systems interactions with the host and all applications derived thereof, providing a forum for the analysis of data and discussion of its implications, and the development of new hypotheses.
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