使用Nextclade进行基于PRRSV-2ORF5的快速血统分类
Michael A Zeller1, Jennifer Chang2, Giovani Trevisan1
1Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States.
Frontiers in veterinary science
|September 30, 2024
概括
猪生殖和呼吸系统综合征病毒2型 (PRRSV-2) 的新遗传命名法使标准化血统分类成为可能. 该系统与Nextclade集成,有助于识别突变并将菌株与疫苗进行比较,以改善猪健康管理.
科学领域:
- 兽医病毒学 兽医病毒学
- 分子流行病学分子流行病学
- 生物信息学是一种生物信息学.
背景情况:
- 猪生殖和呼吸系统综合征病毒 (PRRSV) 对猪健康和农业经济构成重大全球威胁.
- 现有的PRRSV-2遗传特征是分散的,阻碍了有效的全球监测和控制策略.
- 标准化遗传命名对于一致的PRRSV-2血统识别和跟踪至关重要.
研究的目的:
- 建立和实施基于PRRSV-2 ORF5的基因谱系的标准遗传命名法.
- 为快速的PRRSV-2血统分类和分析开发一个用户友好的生物信息学工具.
- 为了促进当代PRRSV-2菌株与历史数据和疫苗序列的比较.
主要方法:
- 开发基于PRRSV-2 ORF5的基因命名法,扩展以前的分类.
- 创建一个支架序列数据集,包括历史/当代菌株和疫苗,用于Nextclade v3.0.0.
- 使用Augur管道与DQ478308.1作为基因分析和分类器生成的参考.
主要成果:
- 现在可以通过Nextstrain和PRRSView获得PRRSV-2 ORF5谱系分配的功能Nextclade分类器.
- 该分类器提供了遗传学分类,序列指标 (质量,突变) 和机密的用户分析.
- 提交的序列是基因排列的,允许与参考病毒,疫苗菌株和元数据进行比较.
结论:
- 实施的Nextclade工作流提供了一种标准化和高效的PRRSV-2血统分类方法.
- 该工具有助于识别关键突变,并将当前的PRRSV-2菌株与相关疫苗进行比较.
- 通过这种标准化分类系统,可以支持加强PRRSV-2的监测和控制策略.
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