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.
Highlights
Viral metagenomics and high-throughput sequencing technology have allowed the detection and characterisation of novel viruses
A study utilizing high-throughput sequencing to characterise the fecal virome of diarrheic and healthy piglets showed that healthy piglets shed an average of 4.2 different mammalian viruses and an average of 5.4 mammalian viruses were shed by the diarrheic piglets [5]
We show that a number of different single-stranded DNA viruses are circulating in pig populations in Sweden apart from the previously well-known porcine circovirus type 2 (PCV2), TTSuV1 and 2
Summary
Viral metagenomics and high-throughput sequencing technology have allowed the detection and characterisation of novel viruses. It has for instance showed that different wildlife reservoirs such as bats have a very diverse virome including mammalian viruses of both human and animal relevance [3]. Metagenomic studies have demonstrated a high diversity of viruses in mammalians such as the pig [4, 5]. A study utilizing high-throughput sequencing to characterise the fecal virome of diarrheic and healthy piglets showed that healthy piglets shed an average of 4.2 different mammalian viruses and an average of 5.4 mammalian viruses were shed by the diarrheic piglets [5]. Similar results have been seen in humans as well as in other animal species, including horses [6] and turkeys [7], indicating that the presence of several viruses in an individual is common
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