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Application and Analysis of Metatranscriptomic Sequencing Technology in the Identification of a Co-infection Event Involving European and American Genotypes of PRRSV
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Xiaolong XU1, 2, 3, Pandan CHEN1, 2, 3, Yuanyuan FU1, 2, 3, Dan XU1, 2, 3, Heng WANG1, 2, 3, Lang GONG1, 2, 3, Guihong ZHANG1, 2, 3, Yankuo SUN1, 2, 3
Acta Veterinaria et Zootechnica Sinica | 2026, 57(3) : 1649 - 1660
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Acta Veterinaria et Zootechnica Sinica | 2026, 57(3): 1649-1660
• PREVENTIVE VETERINARY MEDICINE •
Application and Analysis of Metatranscriptomic Sequencing Technology in the Identification of a Co-infection Event Involving European and American Genotypes of PRRSV
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Xiaolong XU1, 2, 3, Pandan CHEN1, 2, 3, Yuanyuan FU1, 2, 3, Dan XU1, 2, 3, Heng WANG1, 2, 3, Lang GONG1, 2, 3, Guihong ZHANG1, 2, 3, Yankuo SUN1, 2, 3
Affiliations
  • 1.College of Veterinary Medicine，South China Agricultural University/Key Laboratory of Prevention and Control of Animal-borne Zoonoses in Guangdong Province，Guangzhou 510642，China
  • 2.Collaborative Laboratory for Porcine Reproductive Disorders，Guangzhou 510642，China
  • 3.Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology，Maoming 525000，China
Published: 2026-03-23 doi: 10.11843/j.issn.0366-6964.2026.03.040
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This study aimed to evaluate the application of metatranscriptomic sequencing technology for the identification of a co-infection event involving European and North American genotypes of PRRSV. A PRRSV-positive serum sample was collected from a swine farm in Guangxi Zhuang Autonomous Region. The complete genome sequence of the virus was obtained using metatranscriptomic sequencing， and further subjected to phylogenetic and recombination analysis. Complete genome sequences of both PRRSV1-GXHZ-202408 （15 076 bp） and PRRSV2-GXHZ-202408 （14 989 bp） were successfully recovered. Phylogenetic analysis revealed that PRRSV1-GXHZ-202408 formed a novel subclade with its closest relative SC-2020-1 （GenBank： MW115431； 90.45% nucleotide identity）， while PRRSV2-GXHZ-202408 clustered within the NADC30-like group （Lineage 1.8）， sharing 88.63% nucleotide identity with the prototype NADC30 strain （MH500776）. Notably， recombination events were identified in both strains： PRRSV1-GXHZ-202408 originated from an SC-2020-1 backbone with recombination breakpoints in NSP1-NSP2 （650-2 050 nt） and ORF6 （14 131-14 570 nt） involving LV4.2.1 （AY588319） and HKEU16 （EU076704）， whereas PRRSV2-GXHZ-202408 arose from recombination between NADC30 （MH500776， major parent） and JXA1 （EF112445， minor parent） in the NSP3-NSP9 region （5 331-8 081 nt）.In this study， metatranscriptomic sequencing was employed to not only definitively identify co-circulation of PRRSV1 and PRRSV2 in the swine farm， but also to obtain complete viral genomes and precisely characterize the genetic features of circulating strains. This approach clearly analyzed the epidemic dynamics of PRRSV in the swine farm， demonstrating that metatranscriptomic sequencing serves as a powerful tool for precise prevention and control of PRRS.

porcine reproductive and respiratory syndrome virus  /  co-infection  /  metatranscriptomic sequencing  /  genomic characterization
许小龙, 陈盼丹, 符媛媛, 许丹, 王衡, 龚浪, 张桂红, 孙彦阔. 基于宏转录组测序技术对一起欧洲型和美洲型PRRSV混合感染事件的鉴定和分析. 畜牧兽医学报, 2026 , 57 (3) : 1649 -1660 . DOI: 10.11843/j.issn.0366-6964.2026.03.040
Xiaolong XU, Pandan CHEN, Yuanyuan FU, Dan XU, Heng WANG, Lang GONG, Guihong ZHANG, Yankuo SUN. Application and Analysis of Metatranscriptomic Sequencing Technology in the Identification of a Co-infection Event Involving European and American Genotypes of PRRSV[J]. Acta Veterinaria et Zootechnica Sinica, 2026 , 57 (3) : 1649 -1660 . DOI: 10.11843/j.issn.0366-6964.2026.03.040
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Year 2026 volume 57 Issue 3
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Article Info
doi: 10.11843/j.issn.0366-6964.2026.03.040
  • Receive Date：2025-05-06
  • Online Date：2026-09-16
  • Published：2026-03-23
Article Data
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History
  • Received：2025-05-06
Funding
Affiliations
    1.College of Veterinary Medicine，South China Agricultural University/Key Laboratory of Prevention and Control of Animal-borne Zoonoses in Guangdong Province，Guangzhou 510642，China
    2.Collaborative Laboratory for Porcine Reproductive Disorders，Guangzhou 510642，China
    3.Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology，Maoming 525000，China

Corresponding:

SUN Yankuo， E-mail：
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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