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Volume 101,
Issue 3,
2020
Volume 101, Issue 3, 2020
- ICTV Virus Taxonomy Profile
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ICTV Virus Taxonomy Profile: Spiraviridae
More LessThe family Spiraviridae includes viruses that replicate in hyperthermophilic archaea from the genus Aeropyrum . The non-enveloped, hollow, cylindrical virions are formed from a coiling fibre that consists of two intertwining halves of a single circular nucleoprotein filament. A short appendage protrudes from each end of the cylindrical virion. The genome is circular, positive-sense, single-stranded DNA of 24 893 nucleotides. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Spiraviridae, which is available at ictv.global/report/spiraviridae.
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- Animal
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- Negative-strand RNA Virus
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Identification of amino acid residues involved in the interaction between peste-des-petits-ruminants virus haemagglutinin protein and cellular receptors
More LessPeste-des-petits-ruminants virus (PPRV) haemagglutinin (H) protein mediates binding to cellular receptors and then initiates virus entry. To identify the key residues of PPRV H (Hv) protein of the Nigeria 75/1 strain involved in binding to receptors, interaction of the Hv and mutated Hv (mHv) proteins with receptors (SLAM and Nectin 4) and their mutants (mSLAM1, mSLAM2, mSLAM3 and mNectin 4) was investigated using surface plasmon resonance imaging (SPRi) and coimmunoprecipitation (co-IP) assays. The results showed that the Hv protein failed to interact with mSLAM3, but interacted at a strong or medium intensity with SLAM, mSLAM2, Nectin 4 and mNectin 4, and at a low level with mSLAM1. The mHv protein was unable to interact with SLAM and its mutants, but bound to Nectin 4 and mNectin 4 with medium and weak intensity, respectively. Further analysis showed that the Hv protein could precipitate mSLAM1, mSLAM2 and mNectin 4, but not mSLAM3. The mHv protein failed to coprecipitate with SLAM and its mutants. The binding activities of mNectin 4 and Nectin 4 to mHv were less than 30.36 and 51.94 % of the wild-type levels, respectively. Based on the results obtained, amino acids at positions R389, L464, I498, R503, R533, Y541, Y543, F552 and Y553 of H protein and I61, H62, L64, K76, K78, E123, H130, I210, A211, S226 and R227 in SLAM were identified to be essential for the specificity of H–SLAM interaction, while the critical residues of H–Nectin 4 interaction require further study. These findings would improve our understanding of the invasive mechanisms of PPRV.
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- Positive-strand RNA Virus
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Phenotypic analysis of mutations at residue 146 provides insights into the relationship between NS5A hyperphosphorylation and hepatitis C virus genome replication
More LessThe hepatitis C virus genotype 2a isolate, JFH-1, exhibits much more efficient genome replication than other isolates. Although basic replication mechanisms must be conserved, this raises the question of whether the regulation of replication might exhibit isolate- and/or genotype-specific characteristics. Exemplifying this, the phenotype of NS5A hyperphosphorylation is genotype-dependent; in genotype 1b a loss of hyperphosphorylation correlates with an enhancement of replication. In contrast, the replication of JFH-1 is not regulated by hyperphosphorylation. We previously identified a novel phosphorylation site in JFH-1 NS5A: S146. A phosphomimetic substitution (S146D) had no effect on replication but correlated with a loss of hyperphosphorylation. In genotype 1b, residue 146 is alanine and we therefore investigated whether the substitution of A146 with a phosphorylatable (S), or phosphomimetic, residue would recapitulate the JFH-1 phenotype, decoupling hyperphosphorylation from replication. This was not the case, as A146D exhibited both a loss of hyperphosphorylation and a reduction in replication, accompanied by a perinuclear restriction of replication complexes, reductions in lipid droplet and PI4P lipid accumulation, and a disruption of NS5A dimerization. In contrast, the S232I culture-adaptive mutation in the low-complexity sequence I (LCSI) also exhibited a loss of hyperphosphorylation, but was associated with an increase in replication. Taken together, these data imply that hyperphosphorylation does not directly regulate replication. In contrast, the loss of hyperphosphorylation is a consequence of perturbing genome replication and NS5A function. Furthermore, we show that mutations in either domain I or LCSI of NS5A can disrupt hyperphosphorylation, demonstrating that multiple parameters influence the phosphorylation status of NS5A.
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- Small DNA Viruses
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Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers
Introduction. Cervical cancer is caused by human papillomavirus (HPV), but some cases may test HPV-negative. We previously tested 2850 Swedish cases and found that 394/2850 (13.8 %) cases tested HPV DNA-negative by PCR. Sequencing is the most thorough method to assess HPV status.
Aim. We wished to assess whether deep sequencing might detect HPV sequences among these HPV-negative cervical cancer specimens, and to increase the likelihood of detecting transcriptionally active infections.
Methodology. Out of the 2850 cancer cases, we sequenced a random sample of 92 HPV PCR-negative cervical cancers and 34 HPV PCR-positive cervical cancers. Four pools of blank blocks were sequenced as negative controls. To enrich for mRNA – a hallmark of active viral infection – the samples were extracted, reverse-transcribed, rRNA-depleted and then sequenced using the NovaSeq 6000 system (Illumina, USA). High-quality reads were aligned to the human genome and non-human reads were queried against HPV proteins.
Results. We obtained a median of 23 million paired reads per sample. HPV was detected in 31/34 HPV PCR-positive cases. Among cases negative for HPV by PCR, 48/92 (52.2 %) contained HPV sequences, with HPV33 being the most commonly detected type among these (14/48 cases, 29.2 %). Comparison of the ratio of exon and intron sequences found that the sequenced material contained both DNA and RNA. Splice junctions were detected in 12 cases.
Conclusion. Apparently, some cervical cancers contain HPV that is difficult to detect by PCR. Sequencing may be a helpful tool for additional quality assurance for HPV testing methods.
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Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences
More LessHepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A–I), and a putative 10th genotype (J), characterized thus far. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level. All of the generated data, including the alignments, phylogenies and chosen reference sequences, are available online (https://doi.org/10.6084/m9.figshare.8851946) as a simple open-access resource.
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- Large DNA Viruses
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Differential upregulation of host cell protein kinases by the replication of α-, β- and γ-herpesviruses provides a signature of virus-specific signalling
Infections with human herpesviruses share several molecular characteristics, but the diversified medical outcomes are distinct to viral subfamilies and species. Notably, both clinical and molecular correlates of infection are a challenging field and distinct patterns of virus–host interaction have rarely been defined; this study therefore focuses on the search for virus-specific molecular indicators. As previous studies have demonstrated the impact of herpesvirus infections on changes in host signalling pathways, we illustrate virus-modulated expression levels of individual cellular protein kinases. Current data reveal (i) α-, β- and γ-herpesvirus-specific patterns of kinase modulation as well as (ii) differential levels of up-/downregulated kinase expression and phosphorylation, which collectively suggest (iii) defined signalling patterns specific for the various viruses (VSS) that may prove useful for defining molecular indicators. Combined, the study confirms the correlation between herpesviral replication and modulation of signalling kinases, possibly exploitable for the in vitro characterization of viral infections.
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Feedback inhibition of bovine herpesvirus 5 replication by dual-copy bhv5-miR-B10-3p
More LessBovine herpesvirus 5 (BoHV-5) is a pathogen of cattle responsible for fatal meningoencephalitis. Like alpha herpesvirus subfamily members, BoHV-5 also encodes microRNA in lytic infections of epithelial cells. BoHV-5-miR-B10 was the most abundant miRNA detected in a high-throughput sequencing study. Here, we evaluated the kinetics of miR-B10 expression after BoHV-5 productive infection by stem-loop real-time quantitative PCR. miR-B10 candidate target sites in the virus were predicted, and BoHV-5 UL39 was confirmed as a target gene by dual-luciferase assay with the design of an miR-B10 tough decoy (TuD). The UL39 gene encoding ribonucleotide reductase (RR) large subunit plays an important role in the early stage of BoHV-5 lytic infection. As BoHV-5-miR-B10 is located in internal and terminal repeat regions, we generated a TuD gene-integrated BoHV-5 strain, which effectively down-regulated miR-B10-3p. Strikingly, the suppression of miR-B10-3p significantly improved BoHV-5 replication. Taking these findings together, our study established an efficient method to deliver and express TuD RNA for viral miRNA suppression, and demonstrated that virus-encoded miRNA suppresses viral-genome biogenesis with a feedback mode, which might serve as a brake for viral replication. Herpesviruses infect humans and a variety of animals. Almost all herpesviruses can encode miRNAs, but the functions of these miRNAs remain to be elucidated. Most herpesvirus-encoded miRNA harbours dual copies, which is difficult to be deleted by current genetic modulation. Here, we developed an efficient method to deliver and express TuD RNA to efficiently suppress viral miRNA with multiple copies. Using this method, we demonstrated for the first time that viral miRNA feedback regulates viral replication by suppressing the expression of RR.
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- Retrovirus
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GGERV20, a recently integrated, segregating endogenous retrovirus in Gallus gallus
More LessEndogenous retroviruses (ERVs) are widespread in vertebrate genomes. The recent availability of whole eukaryotic genomes has enabled their characterization in many organisms, including Gallus gallus (red jungle fowl), the progenitor of the domesticated chicken. Our bioinformatics analysis of a G. gallus ERV previously designated GGERV20 identified 35 proviruses with complete long terminal repeats (LTRs) and gag-pol open reading frames (ORFs) in the Genome Reference Consortium Chicken Build 6a, of which 8 showed potential for translation of functional retroviral polyproteins, including the integrase and reverse transcriptase enzymes. No elements were discovered with an env gene. Fifteen loci had LTR sequences with 100 % identity, indicative of recent integration. Chicken embryo fibroblast RNA-seq datasets showed reads representing the entire length of the GGERV20 provirus, supporting their potential for expressing viral proteins. To investigate the possibility that GGERV20 elements may not be fixed in the genome, we assessed the integration status of five loci in a meat-type chicken. PCRs targeting a GGERV20 locus on G. gallus chromosome one (GGERV201-1) reproducibly amplified both LTRs and the preintegration state, indicating that the bird from which the DNA was sampled was hemizygous at this locus. The four other loci examined only produced the preintegration state amplicons. These results reveal that GGERV20 is not fixed in the G. gallus population, and taken together with the lack of mutations seen in several provirus LTRs and their transcriptional activity, suggest that GGERV20 retroviruses have recently been and continue to be active in the chicken genome.
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- Insect
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- DNA Virus
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Bombyx mori nucleopolyhedrovirus F-like protein Bm14 is a type I integral membrane protein that facilitates ODV attachment to the midgut epithelial cells
More LessOur previous study showed that the Bombyx mori nucleopolyhedrovirus (BmNPV) F-like protein Bm14 is intrinsically related to the production of occlusion bodies, occlusion-derived virus (ODV) embedding and virulence in infected larvae. However, the exact mechanism by which Bm14 affects primary infection remains unknown. In this report, we characterized the detailed distribution and topology of Bm14 in occlusion bodies (OBs) and ODVs, and then further investigated the functional role of Bm14 in primary infection. A combination of Western blot and immunoelectron microscopy showed that Bm14 is mainly present on the surface of ODVs within OBs, but rarely in the OB matrix. Further phase separation and topology analysis of Bm14 by selective permeabilization revealed that Bm14 is a type I integral membrane protein with an N-terminus hidden in the endoplasmic reticulum (ER) lumen and a C-terminus exposed to the cytosol. In vivo assays demonstrated that the disruption of bm14 impaired the interactions of ODV with midgut epithelia, resulting in delayed spread in larval tissues. As the essential trigger of primary infection, some per os infectivity factors (PIFs) were verified to interact with Bm14 via a series of coimmunoprecipitation analyses. Further partially denaturing SDS-PAGE and BN-PAGE assays clearly showed that the deletion of bm14 did not affect the formation and presence of the PIF complex. In conclusion, Bm14 functions as a type I integral membrane protein to regulate ODV attachment to the midgut epithelial cells.
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- RNA Virus
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Season- and caste-specific variation in RNA viruses in the invasive Argentine ant European supercolony
More LessThe Argentine ant (Linepithema humile, Mayr) is a highly invasive species. Recently, several RNA viruses have been identified in samples from invasive Argentine ant colonies. Using quantitative PCR, we investigated variation in the levels of these viruses in the main European supercolony over the course of a year. We discovered that virus prevalence and amounts of viral RNA were affected by season and caste: ants had more virus types during warm versus cold months, and queens had more virus types and higher virus prevalence than did workers or males. This seasonal variation was largely due to the appearance of positive-strand RNA viruses in the summer and their subsequent disappearance in the winter. The prevalences of positive-strand RNA viruses were positively correlated with worker foraging activity. We hypothesise that during warmer months, ants are more active and more numerous and, as a result, they have more conspecific and heterospecific interactions that promote virus transmission.
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- Plant
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- RNA Virus
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Analysis of tomato spotted wilt virus RNA-dependent RNA polymerase adaptative evolution and constrained domains using homology protein structure modelling
More LessTomato spotted wilt virus (TSWV; genus Orthotospovirus, family Tospoviridae) has a huge impact on a large range of plants worldwide. In this study, we determined the sequence of the large (L) RNA segment that encodes the RNA-dependent RNA polymerase (RdRp) from a TSWV isolate (LYE51) collected in the south of France. Analysis of the phylogenetic relationships of TSWV–LYE51 with other TSWV isolates shows that it is closely related to other European isolates. A 3D model of TSWV-LYE51 RdRp was built by homology with the RdRp structure of the La Crosse virus (genus Orthobunyavirus, family Peribunyaviridae). Finally, an analysis of positive and negative selection was carried out on 30 TSWV full-length RNA L sequences and compared with the phylogeny and the protein structure data. We showed that the seven codons that are under positive selection are distributed all along the RdRp gene. By contrast, the codons associated with negative selection are especially concentrated in three highly constrained domains: the endonuclease in charge of the cap-snatching mechanism, the thumb domain and the mid domain. Those three domains could constitute good candidates to look for host targets on which genetic resistance by loss of susceptibility could be developed.
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- TSE Agents
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In vitro detection of haematogenous prions in white-tailed deer orally dosed with low concentrations of chronic wasting disease
Infectivity associated with prion disease has been demonstrated in blood throughout the course of disease, yet the ability to detect blood-borne prions by in vitro methods remains challenging. We capitalized on longitudinal pathogenesis studies of chronic wasting disease (CWD) conducted in the native host to examine haematogenous prion load by real-time quaking-induced conversion (RT-QuIC) and protein misfolding cyclic amplification. Our study demonstrated in vitro detection of amyloid seeding activity (prions) in buffy-coat cells harvested from deer orally dosed with low concentrations of CWD positive (+) brain (1 gr and 300 ng) or saliva (300 ng RT-QuIC equivalent). These findings make possible the longitudinal assessment of prion disease and deeper investigation of the role haematogenous prions play in prion pathogenesis.
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Volumes and issues
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Volume 106 (2025)
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Volume 105 (2024)
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Volume 104 (2023)
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Volume 103 (2022)
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Volume 102 (2021)
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Volume 101 (2020)
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Volume 100 (2019)
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Volume 99 (2018)
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Volume 98 (2017)
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Volume 97 (2016)
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Volume 96 (2015)
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Volume 95 (2014)
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Volume 93 (2012)
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Volume 7 (1970)
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Volume 6 (1970)
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Volume 5 (1969)
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Volume 4 (1969)
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Volume 3 (1968)
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Volume 2 (1968)
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Volume 1 (1967)
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