Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs

Abstract

The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs. The aim is to increase knowledge of potential viruses, apart from porcine circovirus type 2 (PCV2), involved in PMWS development as well as to increase knowledge on the virome of healthy individuals. In healthy individuals, a diverse viral flora was seen with several different viruses present simultaneously. The majority of the identified viruses were small linear and circular DNA viruses, such as different circoviruses, anelloviruses and bocaviruses. In the pigs suffering from PMWS, PCV2 sequences were, as expected, detected to a high extent but other viruses were also identified in the background of PCV2. Apart from DNA viruses also RNA viruses were identified, among them were a porcine pestivirus showing high similarity to a recently (in 2015) discovered atypical porcine pestivirus in the US. Majority of the viruses identified in the background of PCV2 in PMWS pigs could also be identified in the healthy pigs. PCV2 sequences were also identified in the healthy pigs but to a much lower extent than in PMWS affected pigs. Although the method used here is not quantitative the very clear difference in amount of PCV2 sequences in PMWS affected pigs and healthy pigs most likely reflect the very strong replication of PCV2 known to be a hallmark of PMWS. Taken together, these findings illustrate that pigs appear to have a considerable viral flora consisting to a large extent of small single-stranded and circular DNA viruses. Future research on these types of viruses will help to better understand the role that these ubiquitous viruses may have on health and disease of pigs. We also demonstrate for the first time, in Europe, the presence of a novel porcine pestivirus.

Virus Metagenomics in Farm Animals: A Systematic Review

“…Surveillance of livestock and the surrounding environment is a hallmark of early detection but is currently targeted to known risks.Advances in Next-Generation Sequencing (NGS) technologies and rapid development of bioinformatics and computational tools offer new opportunities for EID surveillance in quality and in scale. Particularly, metagenomic NGS (mNGS) allows unbiased detection of all microbes and viruses in a sample, showing potential for timely detection of rare or novel infectious etiologies, as well as for surveillance of foodborne and waterborne viruses [20][21][22][23][24][25][26]. However, the use of mNGS as a potential surveillance tool requires a deeper understanding of what is "normal" diversity in humans [27], as well as wildlife [28,29] and farm animals [30].…”

The porcine virome and xenotransplantation

“…Viral metagenomics analysis in healthy and pigs suffering from the postweaning multisystemic wasting syndrome (PMWS) showed that pigs have a considerable viral flora consisting mainly of small single-stranded and circular DNA viruses [13]. Although many viruses were also detected in the healthy pigs, the number of porcine circovirus 2 (PCV2) had increased considerably in the PMWS pigs.…”

Antibody Titers from Finisher Populations with Persistent/Latent PCV2 Infection Before, During and After the PCV2-SD Epizootic

“…PCV2 can be detected in both healthy and diseased pigs [1] and is found in the lymphatic system in most pigs [2,3].…”