Molecular Diversity of Partial-Length Genomic Segment 2 of Human Picobirnavirus

Abstract

Objectives: This study was carried out in order to evaluate the efficacy of the recently developed picobirnavirus (PBV) sets of primers and to establish the phylogenetic relationships of Argentine strains with PBV strains isolated in China and the USA. Methods: Thirteen fecal specimens tested as positive for PBV by polyacrylamide gel electrophoresis were analyzed by reverse transcription-polymerase chain reaction assays using primers target to the genomic segments 2 of PBV strains isolated in China and the USA. The amplicons were sequenced and analyzed. Results: Primers derived from the China strain produced amplicons in only 4 of the 13 specimens (30.76%). No sample was revealed as positive with the primers derived from the US strain. DNA sequencing of polymerase chain reaction products differed in nucleic acid and amino acid sequences by 13.9–42.28% and 18.1–51.1%, respectively. Despite this strain diversity, three domains of conserved nucleotide sequences as well as the amino acid motif D-S-D typical of RNA-dependent RNA polymerase gene of double-strand RNA viruses were identified. Comparatively, these conserved regions were also identified in homologous PBV strains from the USA and China. Phylogenetic analysis showed no time or geographic clustering. Conclusions: These findings provide evidence that PBV may represent an emerging heterogeneous group of viruses.

Molecular Characterization of Porcine Picobirnaviruses and Development of a Specific Reverse Transcription-PCR Assay

“…The deduced amino acid sequences showed that all the clones encoded the conserved residues D-S-D and clone PBV2-POR encoded additionally the conserved residues SG-T-E, corresponding, respectively, to motifs 1 and 2 of the RNA-dependent RNA polymerases of dsRNA viruses (6), thus confirming previous results obtained with human PBV which postulated that genomic segment 2 encodes the polymerase of these viruses (23,27,29).…”

“…The larger RNA segment, or segment 1, contains two open reading frames encoding 224 and 552 amino acids, while the small RNA segment, or segment 2, contains a single open reading frame encoding 534 amino acids (29). The small segment encodes amino acid motifs typical of those encoded by the RNA-dependent RNA polymerase genes (23,27,29). Because of its genomic and morphological characteristics, this novel group of viruses is a likely candidate for a new taxon.…”

“…PBV have been identified in fecal samples of humans practically worldwide (2,4,5,8,10,20,23,25,27), in feces of a wide variety of farm mammals and birds, including pigs (3,9,12,21,26), calves (7), rabbits (11,14,22), and chickens (19), and even in feces of wild animals keep in captivity (16,24,30). Despite the numerous reports of the presence of PBV in fecal samples from vertebrates, the pathogenicity of these viruses has not been established.…”

“…Epidemiological studies carried out in several countries have made it clear that human PBV strains are highly diverse and can be grouped into at least two genogroups (2,5,23,27). PBV sequences from pigs have recently been described (3), being genetically related to the human genogroup I.…”

“…Clone PBV2-POR was left out of the analysis, since mostly PBV sequences containing RNA polymerase motif 1 were available in GenBank. The phylogenetic analysis included sequences from 19 human strains, 18 representative of genogroup I (2,23,27,29), and 43 recently reported sequences from porcine picobirnaviruses isolated in Hungary, also classified as genogroup I (3). Figure 1 shows a phylogenetic tree based on a 168-nucleotides fragment which included clones PBV1-POR, PVB3-POR, and PBV4-POR.…”