Genomic surveillance highlights key VP4/VP7 regions, dominant genotypes, and reassortment in bovine rotaviruses among diarrheic calves in China

doi:10.1016/j.jia.2025.10.003

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Min Sun¹^,³^,⁴^,^5*, Xinru Sun¹^,^2*, Li Mao¹^,³^,⁵, Jinzhu Zhou¹^,³^,⁵, Xuehan Zhang¹^,³^,⁵, Xuejiao Zhu¹^,³^,⁵, Ran Tao¹^,³^,⁵, Baochao Fan¹^,³^,⁴^,⁵, Zihao Pan⁴, Sizhu Suolang^2#, Bin Li¹^,³^,⁴^,^5#

¹ Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture/Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China

² Animal Science College, Xizang Agricultural and Animal Husbandry University, Nyingchi 860000, China

³ GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China

⁴ College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China

⁵ Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225000, China

Highlights

1. A 21.46% detection rate of bovine RVs in diarrheic calves across 15 provinces in China during 2022-2023 shows clear seasonality and geographic patterns.

2. Key genomic regions in VP4/VP7 genes were identified for precise genotyping, and the genotypes of G6, G10, P[1], P[5], and P[11] are widely distributed in China.

3. A novel G10P[11] strain provides evidence of complex reassortment and ongoing evolution of bovine RVs.

Abstract
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摘要

牛轮状病毒是引起犊牛腹泻的重要病原之一，且在特定情况下对公共卫生安全构成潜在威胁。已知该病毒至少包含13种P基因型与15种G基因型，其高度的遗传多样性为建立精准检测技术、获取可靠临床数据带来了巨大挑战。因此，深入解析牛轮状病毒的流行病学特征与基因组进化规律，对于制定科学有效的疫情防控策略具有至关重要的意义。本研究以2022-2023年间中国腹泻犊牛为研究对象，系统探究牛轮状病毒的流行规律、基因特征及进化机制。我们通过对全国15个省份的犊牛腹泻病料进行监测分析，结果显示牛轮状病毒总体阳性率达21.46%，且在流行过程中呈现出明显的季节特征与地理分布差异。为进一步明确病毒进化规律，我们对来源于不同国家和地区的VP4基因（决定P基因型）和VP7基因（决定G基因型）序列展开全面比对分析，鉴定出VP4基因的310-595 bp区域及VP7基因的260-631 bp区域，在不同基因型毒株中具有高度的序列特异性与进化关联性，可作为评估牛轮状病毒进化机制的精准靶标。系统进化分析结果表明，我国当前流行毒株以G6型与P[1]型为优势基因型，同时G10型、P[5]型和P[11]型等基因型分布广泛，反映出病毒基因型的丰富性与流行的广泛性。为深入探究病毒进化动态，我们进一步对CHN/HLJ/N3/2023/G10P [11] 毒株进行全基因组分析，发现了该毒株基因组存在属间重配，提示牛轮状病毒在基因组水平上持续进化，为理解病毒进化机制提供了依据。综上所述，本研究通过基因组监测与系统进化分析，揭示了2022-2023年我国牛轮状病毒的流行规律，明确了VP4及VP7基因中用于进化分析的精确靶标，鉴定出的具有重配特征的G10P[11]型毒株，为后续开展牛轮状病毒快速基因分型研究与病毒进化机制探索奠定了坚实的理论基础，为制定针对性防控策略提供重要的科学依据。

Abstract

Bovine rotaviruses (RVs) have been confirmed as the important pathogen responsible for calf diarrhea, and in some instances posing a significant threat to public health. The genetic diversity of bovine RVs with at least thirteen P and fifteen G genotypes poses challenges to establish accurate detection methods and collect convincing clinical data, emphasizing the importance of understanding the epidemiological and genomic characteristics for combatting outbreaks. In the present study, the prevalence of bovine RVs in diarrheic calves across 15 provinces in China during 2022-2023 was monitored at a rate of 21.46%, and exhibits certain levels of seasonality and geographic specificity. By a comprehensive analysis based on 62 entire VP4 (determining P genotype) and 84 entire VP7 (determining G genotype) genes, two specific regions within the VP4 and VP7 genes, ranging from 310 to 595 bp and 260 to 631 bp, respectively, were identified as more accurate targets for assessing the evolutionary mechanisms of bovine RVs. Genotyping and phylogenetic analysis based on these genomic segments revealed the complexity of bovine RVs epidemics in China, with the dominant genotypes being G6 and P[1], and other genotypes such as G10, P[5], and P[11] being widely distributed. Further analysis in strain CHN/HLJ/N3/2023/G10P[11] provided evidence of multiple-genera reassortant and ongoing evolution of rotaviruses at the whole genome level. This comprehensive research brings valuable insights into the genetic patterns of bovine RVs, and such understanding is essential for addressing the challenges posed by the diverse genotypes of bovine RVs, which can significantly contribute to effective control measures against outbreaks in bovine populations.

Keywords: Bovine rotavirus prevalence genotyping molecular characteristics whole-genome analysis

Online: 01 October 2025

Fund:

This work was supported by the National Key Research and Development Program of China (2023YFD1801302), the Jiangsu Provincial Natural Science Fund for Excellent Young (BK20230077), the Jiangsu Agriculture Science and Technology Innovation Fund (CX(23)1029), Jiangsu Provincial Key Research and Development Program (Modern Agriculture, BE2023317), National Natural Science Foundation of China (32102568 and 32302892), S&T Program of Hebei, China (21322401D).

About author: #Correspondence Bin Li, E-mail: libinana@126.com; Sizhu Suolang, E-mail: xzslsz@163.com *These authors contribute equally to this work.

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Min Sun, Xinru Sun, Li Mao, Jinzhu Zhou, Xuehan Zhang, Xuejiao Zhu, Ran Tao, Baochao Fan, Zihao Pan, Sizhu Suolang, Bin Li. 2025. Genomic surveillance highlights key VP4/VP7 regions, dominant genotypes, and reassortment in bovine rotaviruses among diarrheic calves in China. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.10.003

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