Detection of novel viruses in porcine fecal samples from China

Abstract

BackgroundPigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs.FindingsTotal nucleic acid was extracted from stool samples of healthy piglets and randomly amplified. The amplified materials were pooled and processed using a high-throughput pyrosequencing technique. The raw sequences were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatics pipeline. The unique reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and parechoviruses. Specific primers were synthesized to assess the prevalence of the viruses in healthy piglets. Our results indicate extremely high rates of positivity.ConclusionsSeveral novel astroviruses, bocaviruses and Ljungan-like viruses were identified in stool samples from healthy pigs. The rates of isolation for the new viruses were high. The high detection rate, diverse sequences and categories indicate that pigs are well-established reservoirs for and likely sources of different enteric viruses.

Identification of a Novel Picornavirus in Healthy Piglets and Seroepidemiological Evidence of Its Presence in Humans

“…To determine the full-length genomic sequence of PLV-CHN, primers were initially designed based on contigs obtained by 454 high-throughput sequencing [19]. Further synthesis was based on newly amplified PLV-CHN sequences.…”

“…However, these characteristics require further study and no human LV seroprevalence data are available. In the present study, we report the complete nucleotide sequence of a novel parechovirus-like virus (PLV-CHN), which was identified by 454 high-throughput sequencing of fecal samples from healthy piglets as described in our previous study [19]. The molecular epidemiology of the virus in healthy piglets and in children's fecal and cerebrospinal fluid (CSF) samples was investigated using RT-PCR.…”

Secondary structure analysis of swine pasivirus (family Picornaviridae) RNA reveals a type-IV IRES and a parechovirus-like 3’ UTR organization

“…Secondary structure analysis of the RNA genome of pasiviruses, including a novel Hungarian genotype, provided further evidence supporting a common origin of the members of the genera Parechovirus and Pasivirus with the exception of the IRES types [1,12,13]. Although earlier analyses of pasivirus sequences did not reveal any signs of recombination [1][2][3], different IRES types in parecho-and pasiviruses suggest a recombination event in the 5' UTR/P1 region. Currently, seven picornavirus genera (Cardiovirus, Enterovirus, Teschovirus, Sapelovirus, Senecavirus, Kobuvirus and Pasivirus) include viruses that are known to be capable of infecting swine.…”

“…The same virus was also identified among healthy swine in China [2,3]. The pasiviruses (PaV) are related to the human parechoviruses and Ljungan virus, making up the genus Parechovirus [1].…”

“…The pasiviruses (PaV) are related to the human parechoviruses and Ljungan virus, making up the genus Parechovirus [1]. The viral polyprotein, the proteolytic cleavage sites, the genome organization, and the phylogenetic relationships of the pasiviruses were analyzed previously [1][2][3], but potential RNA structure including the 5' and 3' untranslated regions (UTRs) and the cis-acting replication element (CRE) of the pasivirus genome were not described. In this study, the secondary RNA structure of a pasivirus was analysed using the genome sequence of a novel pasivirus genotype (KM259923) from Hungary.…”