Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020.
Molecular Evolution of Porcine Reproductive and Respiratory Syndrome Virus Field Strains from Two Swine Production Systems in the Midwestern United States from 2001 to 2020.
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DOI：
10.1128/spectrum.02634-21
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发表时间：
2022-06-29
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
--
作者：
猪繁殖与呼吸综合征病毒(PRRSV)对美国养猪业构成广泛的经济威胁。PRRSV基因和抗原的高度变异性对现有的疫苗接种计划提出了挑战。我们对2001年至2020年从美国中西部两个猪肉生产系统管理的300个养殖场检测到的1931株PRRSV-2毒株的ORF5序列进行了评估，以评估异源PRRSV-2毒株的遗传多样性和分子特征。对ORF5序列进行系统发育分析，并使用全球PRRSV分类系统进行分类。对ORF5编码的GP5的N-糖基化和全局和局部选择压力进行了估算。将PRRSV-2序列分为谱系5(L5；n = 438[22.7%])和谱系1(L1；n = 1,493[77.3%])。L1菌株属于三个亚类：L1a(n = 1,225[63.4%])、L1B(n = 69[3.6%])和L1C/D(n = 199[10.3%])。预测了10个N-糖基化位点，并在大多数gp5序列中检测到N44和N51位(n = 1,801[93.3%])。观察到分支特异的N-糖基化位点：L1a的第57位，L1B的第33位，L1C/D的第30位和第34位，L5的第30位和第33位。在L5和L1的显著正选择下，我们分别确定了GP5中的9个和19个位点。第13个、第151个和第200个正选择位点为L5所独有。N-糖基化和正选择位点的异质性可能有助于改变在这些猪生产系统中循环的PRRSV-2毒株的进化过程。L1a和L5菌株因其广泛的正选择位点和较高的位点特定选择压力而在适应当前猪群体方面表现出卓越的表现。重要性猪繁殖与呼吸综合征病毒(PRRSV)以其高度的遗传和抗原变异性而闻名。在这项研究中，我们评估了2001年至2020年在美国中西部两个养猪系统中流行的PRRSV-2毒株的ORF5序列。根据亲缘关系将所有野毒株分为四大类群，其中一类与英格尔瓦克PRRS MLV毒株关系密切。在这里，我们系统地比较了不同群体之间在ORF5多态、N-糖基化位点以及局部和全球进化动力学方面的差异。大多数氨基酸序列(n = 1,801，93.3%)中共有44和51位的N-糖基化。我们发现，与L1菌株相比，L5序列具有更大的正选择压力。我们的发现将对PRRSV-2的进化机制提供有价值的见解，这些分子变化可能导致英格尔瓦克PRRS MLV疫苗的效果不佳。
Porcine reproductive and respiratory syndrome virus (PRRSV) poses an extensive economic threat to the United States swine industry. The high degree of PRRSV genetic and antigenic variability challenges existing vaccination programs. We evaluated the ORF5 sequence of 1,931 PRRSV-2 strains detected from >300 farms managed by two pork production systems in the midwestern United States from 2001 to 2020 to assess the genetic diversity and molecular characteristics of heterologous PRRSV-2 strains. Phylogenetic analysis was performed on ORF5 sequences and classified using the global PRRSV classification system. N-glycosylation and the global and local selection pressure in the putative GP5 encoded by ORF5 were estimated. The PRRSV-2 sequences were classified into lineage 5 (L5; n = 438[22.7%]) or lineage 1 (L1; n = 1,493[77.3%]). The L1 strains belonged to one of three subclades: L1A (n = 1,225[63.4%]), L1B (n = 69[3.6%]), and L1C/D (n = 199[10.3%]). 10 N-glycosylation sites were predicted, and positions N44 and N51 were detected in most GP5 sequences (n = 1,801[93.3%]). Clade-specific N-glycosylation sites were observed: 57th in L1A, 33rd in L1B, 30th and 34th in L1C/D, and 30th and 33rd in L5. We identified nine and 19 sites in GP5 under significant positive selection in L5 and L1, respectively. The 13th, 151st, and 200th positive selection sites were exclusive to L5. Heterogeneity of N-glycosylation and positive selection sites may contribute to varying the evolutionary processes of PRRSV-2 strains circulating in these swine production systems. L1A and L5 strains denoted excellence in adaptation to the current swine population by their extensive positive selection sites with higher site-specific selection pressure. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is known for its high genetic and antigenic variability. In this study, we evaluated the ORF5 sequences of PRRSV-2 strains circulating in two swine production systems in the midwestern United States from 2001 to 2020. All the field strains were classified into four major groups based on genetic relatedness, where one group is closely related to the Ingelvac PRRS MLV strain. Here, we systematically compared differences in the ORF5 polymorphisms, N-glycosylation sites, and local and global evolutionary dynamics between different groups. Sites 44 and 51 were common for N-glycosylation in most amino acid sequences (n = 1,801, 93.3%). We identified that the L5 sequences had more positive selection pressure compared to the L1 strains. Our findings will provide valuable insights into the evolutionary mechanisms of PRRSV-2 and these molecular changes may lead to suboptimal effectiveness of Ingelvac PRRS MLV vaccine.
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