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

Abstract

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

CLC Number:

S858.285.3

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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Metagenomic Analysis of Viruses in Clinical Samples of Respiratory Diseases in Tibetan Pigs

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