Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
J Vet Diagn Invest. 2021 Sep;33(5):920-931. doi: 10.1177/10406387211027221. Epub 2021 Jun 28.
The genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) increases over time. In 1998, restriction-fragment length polymorphism (RFLP) pattern analysis was introduced to differentiate PRRSV wild-type strains from VR2332, a reference strain from which a commercial vaccine (Ingelvac PRRS MLV) was derived. We have characterized here the PRRSV genetic diversity within selected RFLP families over time and U.S. geographic space, using available ISU-VDL data from 2007 to 2019. The 40,454 ORF5 sequences recovered corresponded to 228 distinct RFLPs. Four RFLPs [2-5-2 (21.2%), 1-7-4 (15.6%), 1-4-4 (11.8%), and 1-8-4 (9.9%)] represented 58.5% of all ORF5 sequences and were used for cluster analysis. Over time, there was increased detection of RFLPs 2-5-2, 1-7-4, 1-3-4, 1-3-2, and 1-12-4; decreased detection of 1-4-2, 1-18-4, 1-18-2, and 1-2-2; and different detection trends for 1-8-4, 1-4-4, 1-26-1, 1-22-2, and 1-2-4. An over-time cluster analysis revealed a single cluster for RFLP 2-5-2, supporting that sequences within RFLP 2-5-2 are still relatively conserved. For 1-7-4, 1-4-4, and 1-8-4, there were multiple clusters. State-wise cluster analysis demonstrated 4 main clusters for RFLP 1-7-4 and 1-8-4, and 6 for RFLP 1-4-4. For the other RFLPs, there was a significant genetic difference within them, particularly between states. RFLP typing is limited in its ability to discriminate among different strains of PRRSV. Understanding the magnitude of genetic divergence within RFLPs helps develop PRRSV regional control programs, placement, herd immunization strategies, and design of appropriate animal movements across borders to minimize the risk of PRRSV transmission.
猪繁殖与呼吸综合征病毒（PRRSV）的遗传多样性随时间而增加。1998 年，限制性片段长度多态性（RFLP）分析模式被引入，以区分 PRRSV 野生型毒株和 VR2332，后者是一种商业疫苗（Ingelvac PRRS MLV）的来源。我们使用 2007 年至 2019 年可用的 ISU-VDL 数据，对特定 RFLP 家族内的 PRRSV 遗传多样性进行了时间和美国地理空间的特征描述。回收的 40454 个 ORF5 序列对应于 228 个不同的 RFLP。4 种 RFLP[2-5-2（21.2%）、1-7-4（15.6%）、1-4-4（11.8%）和 1-8-4（9.9%）]代表了所有 ORF5 序列的 58.5%，并用于聚类分析。随着时间的推移，RFLP 2-5-2、1-7-4、1-3-4、1-3-2 和 1-12-4 的检测率增加；RFLP 1-4-2、1-18-4、1-18-2 和 1-2-2 的检测率降低；而 1-8-4、1-4-4、1-26-1、1-22-2 和 1-2-4 的检测趋势则不同。随时间的聚类分析显示，RFLP 2-5-2 为单一聚类，支持 RFLP 2-5-2 内的序列仍然相对保守。对于 1-7-4、1-4-4 和 1-8-4，存在多个聚类。州级聚类分析显示，RFLP 1-7-4 和 1-8-4 有 4 个主要聚类，RFLP 1-4-4 有 6 个聚类。对于其他 RFLP，它们内部存在显著的遗传差异，特别是各州之间。RFLP 分型在区分 PRRSV 的不同毒株方面能力有限。了解 RFLP 内遗传分歧的程度有助于制定 PRRSV 区域控制计划、定位、群体免疫策略以及设计跨越边境的适当动物流动，以最大限度地降低 PRRSV 传播的风险。
