Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China

Sinan Qin,Bin Zhang,Hua Yue,Cheng Tang,Kelei Zhou,Wenqiang Ruan

doi:10.1038/s41598-018-31554-8

Abstract

Porcine respiratory disease complex (PRDC), a common piglet disease, causes substantive economic losses in pig farming. To investigate the viral diversity associated with PRDC, the viral communities in serum and nasal swabs from 26 PRDC-affected piglets were investigated using metagenomics. By deep sequencing and de novo assembly, 17 viruses were identified in two pooled libraries (16 viruses from serum, nine from nasal swabs). Porcine circovirus (PCV)-2, porcine reproductive and respiratory syndrome virus (PRRSV) and pseudorabies virus, all commonly associated with PRDC, were identified in the two pooled samples by metagenomics, but most viruses comprised small linear and circular DNAs (e.g. parvoviruses, bocaviruses and circoviruses). PCR was used to compare the detection rates of each virus in the serum samples from 36 PRDC-affected piglets versus 38 location-matched clinically healthy controls. The average virus category per sample was 6.81 for the PRDC-affected piglets and 4.09 for the controls. Single or co-infections with PCV-2 or PRRSV had very high detection rates in the PRDC-affected piglets. Interestingly, porcine parvovirus (PPV)-2, PPV-3, PPV-6 and torque teno sus virus 1a were significantly associated with PRDC. These results illustrate the complexity of viral communities in the PRDC-affected piglets and highlight the candidate viruses associated with it.

Highlights

Porcine respiratory disease complex (PRDC), which causes major losses in the pig farming industry, is characterized by retarded growth performance, increased mortality and antimicrobial use in PRDC-affected pigs, and extra expenditure on control measures against it[1]
Porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2) and swine influenza virus (SIV) are frequently identified as the primary pathogens associated with PRDC, a disease that can lead to severe respiratory distress in pigs[1,5,6]
Sixteen distinct viruses were identified in the serum samples from the diseased piglets (Fig. 1a), which, in order of sequence read abundance, are as follows: porcine parvovirus (PPV) 6 (PPV-6, 46.42% of all reads), PPV-3 (35.04%), PPV-5 (8.18%), PPV-4 (5.41%), PPV-2 (4.03%), porcine pseudorabies virus (PRV, 0.38%), torque teno sus virus 1b (TTSuV-1b, 0.25%), TTSuV-1a (0.07%), porcine kobuvirus (PKV, 0.06%), porcine reproductive and respiratory syndrome virus (PRRSV, 0.04%), porcine circovirus 2 (PCV-2, 0.03%), porcine bocavirus 5 (PBoV-5; 0.03%), ungulate bocaparvovirus 2 (PBoV-1, 0.02%), ungulate bocaparvovirus 5 (PBoV-3, 0.02%), pig stool associated circular ssDNA virus (PigSCV, 0.02%) and porcine cytomegalovirus (PCMV, 0.01%)

Summary

Introduction

Porcine respiratory disease complex (PRDC), which causes major losses in the pig farming industry, is characterized by retarded growth performance, increased mortality and antimicrobial use in PRDC-affected pigs, and extra expenditure on control measures against it[1]. The onset of respiratory disease on piglet farms is thought to be related to the initial stress of piglet transportation to the farms, after which a primary viral insult causes a secondary infection from the bacteria resident in these animals[1,4]. Based on their ability to damage the upper airway epithelium, injure the lung parenchyma and promote secondary bacterial colonization, the primary viral pathogens are able to influence the development and outcome of PRDC5.

Methods

Results

Conclusion