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Other Double-Stranded RNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Duquerroy et al. (2009) reported the near-atomic x-ray structure of a PBV—an animal dsRNA virus associated with diarrhea and gastroenteritis in humans. To do this, the PBV VLPs were obtained by expressing the rabbit PBV (rPBV) capsid protein gene in insect Sf9 cells by the baculovirus expression system. The structure was resolved to 3.4 Å and showed a simple core capsid with a distinctive icosahedral arrangement, displaying 60 2-fold symmetric dimers of the coat protein with a new 3D fold. As with many nonenveloped animal viruses, the coat underwent an autoproteolytic cleavage, releasing a posttranslationally modified peptide that remained associated with nucleic acid within the capsid. These data showed that the picobirnavirus particles are capable of disrupting biological membranes in vitro, indicating that its simple capsid had evolved animal cell invasion properties (Duquerroy et al. 2009).
Epilogue
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
The actual place of the RNA viruses, including the RNA phages, in the virosphere was defined systematically (Koonin et al. 2015; Krishnamurthy et al. 2016; Shi et al. 2016; Novik et al. 2018). Currently, the Leviviridae and Cystoviridae families remain the only two recognized families of prokaryotic RNA viruses. Siddharth R. Krishnamurthy and David Wang (2018) hypothesized recently that picobirnaviruses, which are bisegmented double-stranded RNA viruses commonly found in animal stool samples, are in fact prokaryotic RNA viruses, since they have never been propagated in cell culture or in an animal model. The authors identified and analyzed the genomes of 38 novel picobirnaviruses and determined that a classical bacterial sequence motif, the ribosomal binding site, is present in the 5′ untranslated regions of all of the novel as well as all previously published picobirnavirus sequences. Among all viruses, enrichment of the ribosome binding site motif was only observed in viral families that infect prokaryotes and not in eukaryotic infecting viral families (Krishnamurthy and Wang 2018). The hypothesis that picobirnaviruses are phages that belong to a novel RNA phage family with a high level of genomic diversity was supported experimentally by Adrianssens et al. (2018).
Assessing the role of intestinal absorption, permeability, and nutrition in AIDS patients
Published in Ronald R. Watson, NUTRIENTS and FOODS in AIDS, 2017
Cytomegalovirus infects the entire gastrointestinal tract and in some patients causes severe small intestinal inflammation. Malabsorption of nutrients may result from small intestinal disease or as a complication of pancreatitis, cholangitis, and papillary stenosis. Several other viruses have been implicated as enteric pathogens in HIV-infected patients. In a study by Grohmann et al.,26 viruses were detected in 35% of 109 fecal specimens from patients with diarrhea but in only 12% of 113 specimens from those without diarrhea. Specimens from patients with diarrhea were more likely than those from patients without diarrhea to have astrovirus, picobirnavirus, calciviruses, including small round structured viruses, and adenoviruses as well as a mixed viral infection. These results suggest that intestinal virus infections may be more common agents of diarrhea in HIV-infected patients than bacterial and parasitic pathogens. An earlier report by Kaljot et al.71 found that enteric viruses were more prevalent in HIV-infected patients, but not associated with diarrhea. No systematic studies are available that have investigated the importance of enteral viruses in the development of malabsorption or other signs of small intestinal dysfunction.
Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes
Published in Expert Review of Molecular Diagnostics, 2019
Xin Li, Susanna K. P. Lau, Patrick C. Y. Woo
In addition to the use of single or multiple gene amplification and sequencing, the use of deep sequencing has helped us make one step further in detection and characterization of emerging microbes causing unexplained infectious disease syndromes. In contrast to PCR/RT-PCR where part of the target gene sequence has to be known for the design of PCR primers, deep sequencing allows detection of microbes when we have minimal idea on which type of microorganism is involved, allowing pathogen identification and typing using a single protocol. For example, using unbiased high-throughput sequencing of random-primer PCR amplification products, increasing numbers of human viruses are identified to account for previously unexplained infectious conditions, including the transplant-associated arenavirus [53], cosavirus [54], klassevirus [55], Saffold virus [56], and novel members of polyomavirus, astrovirus, picobirnavirus, papillomavirus, and bocavirus [57–62]. High-throughput genomic approach also provides a useful tool for outbreak investigation, including identification of the infectious species, strain type, virulence factor, resistance mechanisms and tracking the transmission at hospital, community, or even global scale. In addition, genomic analysis allows the design of target-specific primers for rapid case identification and outbreak control. Well-known examples include hospital outbreaks of Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus, and carbapenem-resistant Klebsiella pneumonia [63–65], and community outbreak of Shiga toxin-producing Escherichia coli O104:H4 in Germany in 2011 [66,67]. The cost of next-generation sequencing (NGS) has decreased dramatically in the past decade, allowing migration of this technology from the research field into the clinical microbiology or public health laboratories. More data on the correlation between metagenomic data and microbial phenotype, as well as lowering the instrument and running cost will enable wider adoption in routine clinical practice.