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Journal of Integrative Agriculture
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Genetic diversity and recombination analysis of NADC34-like porcine reproductive and respiratory syndrome viruses

Zhengqin Ye1, Wenqiang Wang1, Zhenbang Zhu1, Wei Wen1, Hu Suk Lee2, 3, Xiangdong Li1#

1Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China

2 International Livestock Research Institute, Hanoi, 112000, Vietnam

3College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea

 Highlights 

Recombinant variants represent a substantial proportion (56.8%) of the analyzed NADC34-like PRRSV strains.

12 consistent recombinant patterns (R1-R12) were defined across 176 NADC34-like whole-genome sequences.

Recombination hotspots in Chinese strains shifted from structural genes to ORF1a after 2020.

Lineage 1.8 is the primary minor parent driving NADC34-like genetic diversification.

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摘要  

猪繁殖与呼吸综合征(PRRS)是威胁全球养猪业的重要疫病。近年来,NADC34-like毒株因其复杂的重组背景和多变的致病性备受关注。本研究旨在通过全球视野下的全基因组分析,明确NADC34-like毒株的遗传多样性、时空分布特征及重组规律,为该毒株的精准防控提供理论依据。本研究从GenBank数据库中检索并筛选了截至20256月的1,598PRRSV全基因组序列,最终聚焦于来自中国、美国和韩国的176NADC34-like毒株序列。利用IQ-TREE软件构建最大似然系统发育树进行分类研究;采用RDP4(集成7种算法)及Simplot软件对重组事件进行系统鉴定与验证;并结合时间与地理信息,分析了不同国家毒株重组热点的演化趋势。遗传分类显示,NADC34-like毒株内平均核苷酸距离为5.68%,而与其他谱系距离均超过14.89%。重组分析发现,在176条毒株中,重组毒株占比56.82%100/176),已成为该亚群的主要存在形式。研究界定了12种重组模式(R1–R12),其中NADC34-R1是美国最流行的模式,且具有明显的地域聚集性。发现中国NADC34-like毒株的重组热点存在显著的时空转移:2017-2019年重组多发生于结构蛋白区(ORFs 2-7),而2020年后则主要集中在ORF1a区域,这与美国和韩国毒株持续集中于ORF1ab的特征显著不同。谱系1.8Lineage 1.8)被鉴定为全球范围内最主要的次要亲本贡献者(占比54.84%),是驱动该毒株遗传多样化的核心引擎。NADC34-like PRRSV在全球范围内呈现高度的遗传多样性和复杂的区域演化特征。虽然重组模式与毒株毒力间的直接联系尚待明确,但重组株的广泛流行及其演化热点的漂移提示该毒株具有极强的环境适应性。首次在全球尺度下对NADC34-like毒株进行了系统的全基因组重组模式分类,确立了R1-R12评价框架。揭示了中国毒株重组热点从结构基因向非结构基因区转移的独特演化规律。明确了Lineage 1.8作为通用亲本在驱动全球NADC34-like毒株多样性中的关键作用。



Online: 07 January 2026  
Fund: 

This work was supported by the National Natural Science Foundation of China-CGIAR (32361143511), Jiangsu Innovative and Entrepreneurial Talent Team Project (JSSCTD202224), the 111 Project D18007, and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

About author:  Zhengqin Ye, E-mail: yezhengqin@126.com; Wenqiang Wang, E-mail: wqwang@yzu.edu.cn; Zhenbang Zhu, E-mail: 007583@yzu.edu.cn; Wei Wen, E-mail: 008634@yzu.edu.cn; Hu Suk Lee, E-mail:hs.lee@cnu.ac.kr; #Correspondence Xiangdong Li, E-mail: 007352@yzu.edu.cn *These authors contributed equally to this study.

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