藏猪呼吸道疾病临床样本中病毒的宏基因组学分析

doi:10.11843/j.issn.0366-6964.2023.09.023

摘要/Abstract

摘要： 为了解我国川西高原地区藏猪呼吸道疾病综合征(porcine respiratory disease complex, PRDC)相关病毒的种类和流行情况,本研究从四川省甘孜藏族自治州地区采集藏猪呼吸道样本共计119份,其中健康藏猪鼻拭子66份(来自6个猪场),PRDC明显症状的藏猪鼻拭子、肺组织及肺泡灌洗液53份(11个猪场)。将健康组和发病组样本制成两个pool样提取总核酸反转录成cDNA,建库后使用Illunima novaseq测序。经序列分析表明,健康藏猪呼吸道样品主要以细菌噬菌体为主,动物相关病毒仅检测到疱疹病毒科(Herpesviridae)的mardivirus。发病组样本的病毒种群包括14个病毒科的16种病毒,可引起PRDC的病毒有猪圆环病毒2型(PCV-2)、细环病毒(TTSuV)、猪细胞巨化病毒(PCMV)和非洲猪瘟病毒(ASFV)等。使用SOAPdenovo软件组装出两株PCV-2,三株TTSuV和一株Porprismacovirus的全基因组。遗传演化分析结果显示,两株PCV-2属于PCV-2d亚型,三株TTSuV均属于k2型,其中SCgz-1属于k2b亚型,SCgz-2和SCgz-3属于k2a亚型。Porprismacovirus毒株与越南的人源Human 16806x66_213毒株聚为单独一分支,而与猪源毒株则遗传距离较远。RDP4重组分析显示,该毒株为人源Human 16806x66_213毒株和猪源Porcine 17668x82_593毒株的重组毒株,该重组方式在国际上未见报道。本研究首次对川西高原地区藏猪的呼吸道相关病毒开展调查研究,发现藏猪呼吸道疾病相关病毒种类繁多,并存在不同家畜间、人和家畜间跨种传播的可能,应予以更多关注。同时,本研究也为藏猪呼吸道疾病的防控提供参考。

关键词: 藏猪, 呼吸道疾病综合征, 病毒宏基因组, 重组分析

Abstract: To investigate the species and prevalence of viruses related to porcine respiratory disease complex (PRDC) in Tibetan pigs in western Sichuan province, 119 respiratory samples from Tibetan pigs were collected from Ganzi Tibetan Autonomous Prefecture of Sichuan province, including 66 nose swabs from healthy pigs (from 6 pig farms) and 53 nose swabs, lung tissues and alveolar lavage fluid (from 11 pig farms) from diseased pigs with obvious symptoms of PRDC. Samples from healthy group and diseased group were mixed into two pools, respectively, then the total nucleic acid were extracted and cDNAs were generated using reverse transcription. Finally, two mixed pooled samples were sent to company for library construction and Illunima novaseq sequencing. Sequence analysis showed that the respiratory samples from healthy Tibetan pigs were mainly bacteriophages, and only the mardivirus of Herpesviridae that had been identified to be related to animal viruses. 16 distinct viruses in 14 virus families were identified in the diseased group. The viruses that had been associated with PRDC include porcine circovirus type 2 (PCV-2), Torque teno sus virus (TTSuV), porcine cytomegalovirus (PCMV), and African swine fever virus (ASFV). The whole genome of two PCV-2 strains, three TTSuV strains and one Porprismacovirus strain were assembled using SOAPdenovo software. Phylogenetic analysis showed that two PCV-2 strains belonged to PCV-2d subtypes, respectively, and three TTSuV strains belonged to k2 genotype, among which SCgz-1 belonged to k2b subgenotype, SCgz-2 and SCgz-3 belonged to k2a subgenotype. The Porprismacovirus strain was clustered into a single glade with Human 16806x66_213 strain from Vietnam, and showed a distant genetic relationship with the swine-origin Porprismacovirus. Recombination analysis using RDP4 software showed that the virus was a recombinant strain between Human 16806x66_213 and Porcine 17668x82_593, which had not been reported internationally. Our study investigated the respiratory related viruses of Tibetan pigs in plateau region for the first time. The results showed that a variety of respiratory disease related viruses were found in Tibetan pigs, which may be transmitted among different livestock, or human and livestock,which needs more attention. Our study provides reference for the prevention and control of respiratory diseases in Tibetan pigs.

Key words: Tibetan pig, porcine respiratory disease complex, virus metagenome, recombination analysis

中图分类号:

S858.285.3

范燕迪, 杨丹娇, 叶忠明, 张敏, 蓝岚, 王靖皓, 周菡, 康润敏, 于吉锋, 张志东, 李彦敏, 周泷. 藏猪呼吸道疾病临床样本中病毒的宏基因组学分析[J]. 畜牧兽医学报, 2023, 54(9): 3836-3847.

FAN Yandi, YANG Danjiao, YE Zhongming, ZHANG Min, LAN Lan, WANG Jinghao, ZHOU Han, KANG Runmin, YU Jifeng, ZHANG Zhidong, LI Yanmin, ZHOU Long. Metagenomic Analysis of Viruses in Clinical Samples of Respiratory Diseases in Tibetan Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3836-3847.

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