Abstract: High?throughput sequencing（HTS）has been increasingly applied in animal disease diagnosis and molecular epidemiological investigations in recent years. In intensive swine production systems，clinical syndromes such as respiratory disease，diarrhea，and reproductive disorders are often associated with multiple co ? infecting pathogens，making comprehensive pathogen identification difficult using conventional targeted diagnostic assays. By enabling large ? scale parallel sequencing of nucleic acids in clinical samples，HTS allows unbiased detection of pathogens and provides high ? resolution genomic information. This capability offers significant advantages for the discovery of emerging pathogens，characterization of mixed infections，analysis of viral genetic variation，and epidemiological source tracing. In this review，we summarize recent advances in the application of HTS technologies for viral detection in swine diseases. Particular attention is given to three major sequencing strategies—Whole?Genome Sequencing（WGS），Metagenomic Next?Generation Sequencing（mNGS），and Targeted Next?Generation Sequencing （tNGS）—and their applications in the detection of major swine viruses. In addition，the potential of HTS for swine disease surveillance and precision disease control is discussed.

Key words: High?throughput sequencing；Swine disease diagnosis；Whole?Genome Sequencing；Metagenomic Next?Generation Sequencing；Targeted Next?Generation Sequencing；Bioinformatics

摘要： 高通量测序（High?Throughput Sequencing，HTS）技术近年来在动物疾病诊断和分子 流行病学研究中得到广泛应用。在规模化养猪生产中，呼吸道疾病、腹泻及繁殖障碍等综合征 常由多种病原体共同感染，而传统靶向检测方法难以全面解析复杂病原谱。HTS通过对样本 核酸进行大规模并行测序，可实现病原体的无偏识别，并获得高分辨率基因组信息，在新发病 原发现、混合感染解析、病毒遗传变异分析及疫情溯源等方面具有重要优势。该文综述了高通 量测序在猪病病毒检测中的研究进展，重点介绍全基因组测序（Whole?Genome Sequencing， WGS）、宏基因组测序（Metagenomic Next?Generation Sequencing，mNGS）和靶向高通量测序 （Targeted Next?Generation Sequencing，tNGS）三种技术策略及其在重要猪病病毒检测中的应 用，并对其在猪群疫病监测与精准防控中的应用前景进行了展望。

关键词: 高通量测序；猪病诊断；全基因组测序；宏基因组测序；靶向高通量测序；生物信息学