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

The potential RNA structures of the 5' and 3' untranslated regions (UTRs) and cis-acting replication elements (CREs) of a novel pasivirus (PaV) genotype (family Picornaviridae) were analysed. PaV-A3 (KM259923) was identified in a faecal sample from a domestic pig in Hungary with posterior paraplegia of unknown etiology. Based on likely structural features of the 5' UTR, the pasiviruses were inferred to possess Hepacivirus/Pestivirus-like type-IV IRES. The pasivirus CRE was mapped to the 2B genome region, similar to Ljungan virus. The secondary RNA structure of the pasivirus 3' UTR was structurally similar to that of human parechoviruses. The genome, CRE, and 3' UTR of pasiviruses provide further evidence of the common origin of the members of the genera Parechovirus and Pasivirus, although their different 5' UTR IRES types suggest that a recombination event occurred during the divergence these viruses.

Virulence Traits of Inpatient Campylobacter jejuni Isolates, and a Transcriptomic Approach to Identify Potential Genes Maintaining Intracellular Survival.

There are still major gaps in our understanding of the bacterial factors that influence the outcomes of human Campylobacter jejuni infection. The aim of this study was to compare the virulence-associated features of 192 human C. jejuni strains isolated from hospitalized patients with diarrhoea (150/192, 78.1%), bloody diarrhoea (23/192, 11.9%), gastroenteritis (3/192, 1.6%), ulcerative colitis (3/192, 1.5%), and stomach ache (2/192, 1.0%). Traits were analysed with genotypic and phenotypic methods, including PCR and extracellular matrix protein (ECMP) binding, adhesion, and invasion capacities. Results were studied alongside patient symptoms, but no distinct links with them could be determined. Since the capacity of C. jejuni to invade host epithelial cells is one of its most enigmatic attributes, a high throughput transcriptomic analysis was performed in the third hour of internalization with a C. jejuni strain originally isolated from bloody diarrhoea. Characteristic groups of genes were significantly upregulated, outlining a survival strategy of internalized C. jejuni comprising genes related (1) to oxidative stress; (2) to a protective sheath formed by the capsule, LOS, N-, and O- glycosylation systems; (3) to dynamic metabolic activity supported by different translocases and the membrane-integrated component of the flagellar apparatus; and (4) to hitherto unknown genes.

[The clinical significance of severe human parechovirus infections in newborns and infants in Hungary]. / A humán parechovírusok klinikai jelentosége súlyos újszülött- és csecsemokori fertozésekben hazánkban.

INTRODUCTION: Most human parechovirus (HPeV, family Picornaviridae) infections are asymptomatic but may cause gastroenteritis in children. New reports show that HPeVs can be associated with severe central nervous system symptoms and sepsis-like syndromes in infants. The clinical significance of HPeVs in Hungary has not been investigated before. AIM: The aim of this study was to detect genotype HPeV in faecal samples of children and analysis of the clinical symptoms. METHOD: For the detection and genotyping of HPeV strains, reverse transcription-polymerase chain reaction and sequencing methods were used from faecal samples of children with gastroenteritis divided into three groups: group A) hospitalised children younger than 10 years (n = 75); group B) 0-12 months infants (n = 237) and group C) children less than 18 years of age with sepsis-like/neurological symptoms (n = 105) were tested. RESULTS: Three HPeV positive samples (3/75, 4%) were found in group A, two of them belong to the HPeV type 1, the third was non-typeable. All positive samples were from infants of 7 to 11 months of age. In group B, HPeV was detected in 6.8% (16/237) of the samples. Five were HPeV1, six were HPeV3 and five were non-typeable. While most of the infants with HPeV1 (4/5) did not require hospitalisation, 83% of the HPeV3 infected infants (5/6) did. Five (4.8%) HPeV strains detected from children less than 18 years of age with sepsis-like/neurological symptoms (group C) belonged to HPeV1 (three) and HPeV3 (two). All positive samples were from hospitalised infants less than 2 months of age. CONCLUSION: HPeV1 infections are less severe in infants than HPeV3 infections. The leading symptom of HPeV1 was diarrhoea, although in infants less than 1-2 months neurological symptoms (somnolence, lassitude) were also present. HPeV3 infections were more common among newborns. The main symptoms of severe HPeV3 infection are: gastroenteritis (7/8), fever ≥38 °C (6/7), loss of appetite (6/7), rash (4/7), somnolence/lassitude (3/7), sepsis-like syndrome (3/7) and respiratory symptoms (2/7). Orv Hetil. 2019; 160(10): 386-395.

Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken.

Picobirnaviruses (PBVs) of family Picobirnaviridae have bisegmented (S1 and S2 segments), double-stranded RNA genomes. In this study a total of N = 12 complete chicken PBVs (ChPBV) segments (N = 5 of S1 and N = 7 of S2, Acc. Nos.: MH425579-90) were determined using viral metagenomic and RT-PCR techniques from a single cloacal sample of a diarrheic chicken. The identified ChPBV segments are unrelated to each other and distant from all of the currently known PBVs. In silico sequence analyses revealed the presence of conserved prokaryotic Shine-Dalgarno-like (SD-like) sequences upstream of the three presumed open reading frames (ORFs) of the S1 and a single presumed ORF of the S2 segments. According to the results of expression analyses in E. coli using 6xHis-tagged recombinant ChPBV segment 1 construct and Western blot these SD-like sequences are functional in vivo suggesting that S1 of study PBVs can contain three ORFs and supporting the bacteriophage-nature of PBVs.

A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera.

In this study all currently known chicken picornaviruses including a novel one (chicken phacovirus 1, KT880670) were identified by viral metagenomic and RT-PCR methods from a single specimen of a diarrheic chicken suffering from a total of eight picornavirus co-infections, in Hungary. The complete genomes of six picornaviruses were determined and their genomic and phylogenetic characteristics and UTR RNA structural models analyzed in details. Picornaviruses belonged to genera Sicinivirus (the first complete genome), Gallivirus, Tremovirus, Avisivirus and "Orivirus" (two potential genotypes). In addition, the unassigned phacoviruses were also detected in multiple samples of chickens in the USA. Multiple co-infections promote and facilitate the recombination and evolution of picornaviruses and eventually could contribute to the severity of the diarrhea in chicken, in one of the most important food sources of humans.