Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA.
Prev Vet Med. 2024 May;226:106186. doi: 10.1016/j.prevetmed.2024.106186. Epub 2024 Mar 16.
Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 - 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% - 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% - 10.5%), L5 (0.0% - 14.4%), L8 (0.0% - 1.3%), and L1F (0.0% - 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher's exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.
猪繁殖与呼吸综合征病毒（PRRSV）是养猪业中最重要的病毒之一，由于其高突变和重组率以及复杂性，一直难以控制。本回顾性研究旨在描述和比较在个体农场、生产系统和区域水平上获得的 PRRSV 谱系的分布。2017 年至 2021 年间，俄亥俄州立区域实验室（俄亥俄州农业局动物疾病诊断中心（ODA-ADDL））提供了 PRRSV-2（类型 2）序列（n=482），这些序列来自俄亥俄州和邻近州的养猪场，包括印第安纳州、密歇根州、宾夕法尼亚州和西弗吉尼亚州。此外，还有一个合作的养猪生产系统提供了额外的序列（n=138）。使用 Geneious Prime®上的 MUSCLE 算法对齐了 PRRSV-2 序列的 ORF5 区以及 PRRSV 活疫苗株（n=6）和谱系锚定（n=169）。对测序的 PRRSV-2 进行了分类，使其与最相似的谱系锚定/疫苗株一致。在所有序列（n=620）中，有 29.8%（185/620）与疫苗株的同一性≥98.0%，其中 93.5%（173/185）和 6.5%（12/185）与 L5 Ingelvac PRRS® MLV 和 L8 Fostera® PRRS 疫苗株完全一致，因此被排除在分析之外。在五年的区域水平上，排名前五的最常见谱系包括 L1A、L5、L1H、L1C 和 L8。在具有生产系统已知的非疫苗序列中，L1A 序列在五个系统中被最多识别（64.3%-100.0%），其次是 L1H（0.0%-28.6%）、L1C（0.0%-10.5%）、L5（0.0%-14.4%）、L8（0.0%-1.3%）和 L1F（0.0%-0.5%）。此外，在具有前提识别的非疫苗序列中（n=262），来自五个个体农场的大多数序列要么被归类为 L1A 要么为 L5。在三个农场中同时存在 L1A 和 L5 序列，而一个农场提交的样本则包含 L1A、L1H 和 L5 序列。此外，非疫苗序列的谱系分类结果与其限制性片段长度多态性（RFLP）模式相关（Fisher 精确检验，p<0.05）。总体而言，我们的结果表明，个体农场和生产系统水平的 PRRSV-2 谱系模式不一定与区域水平的模式相对应，这突出了个体农场和系统在塑造这些水平内 PRRSV 发生的重要性，并强调了在农场和系统内进行监测和早期检测的重要目标，以便准确了解 PRRSV-2 谱系的发生和出现。
