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Volume 85,
Issue 9,
2004
Volume 85, Issue 9, 2004
- Review
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Hepatitis C virus NS5A: tales of a promiscuous protein
More LessThe non-structural 5A (NS5A) protein of hepatitis C virus (HCV) has been the subject of intensive research over the last decade. It is generally accepted that NS5A is a pleiotropic protein with key roles in both viral RNA replication and modulation of the physiology of the host cell. Our understanding of the role of NS5A in the virus life cycle has been hampered by the lack of a robust in vitro system for the study of HCV replication, although the recent development of the subgenomic replicon has at least allowed us to begin to dissect the involvement of NS5A in the process of viral RNA replication. Early studies into the effects of NS5A on cell physiology relied on expression of NS5A either alone or in the context of other non-structural proteins; the advent of the replicon system has allowed the extrapolation of these studies to a more physiologically relevant cellular context. Despite recent progress, this field is controversial, and there is much work to be accomplished before we fully understand the many functions of this protein. In this article, the current state of our knowledge of NS5A, discussing in detail its direct involvement in virus replication, together with its role in modulating the cellular environment to favour virus replication and persistence, are reviewed. The effects of NS5A on interferon signalling, and the regulation of cell growth and apoptosis are highlighted, demonstrating that this protein is indeed of critical importance for HCV and is worthy of further investigation.
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- Animal
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- RNA viruses
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Fusion PCR generated Japanese encephalitis virus/dengue 4 virus chimera exhibits lack of neuroinvasiveness, attenuated neurovirulence, and a dual-flavi immune response in mice
The first flavivirus chimera encoding dengue 4 virus (D4) PrM and E structural proteins in a Japanese encephalitis virus (JEV) backbone was successfully generated using the long-PCR based cDNA-fragment stitching (LPCRcFS) technique, demonstrating the technique's applicability for rapid preparation of flavivirus chimeras. The JEV/D4 chimera multiplied at levels equal to JEV and D4 in the mosquito cell line C6/36, while in a mouse neuronal cell line (N2a) JEV replicated efficiently, but JEV/D4 and D4 did not. In mouse challenge experiments, JEV/D4 showed a lack of neuroinvasiveness similar to D4 when inoculated intraperitoneally, but demonstrated attenuated neurovirulence (LD50=3·17×104 f.f.u.) when inoculated intracranially. It was also noted that mice receiving intraperitoneal challenge with JEV/D4 possessed D4-specific neutralization antibody and in addition clearly showed resistance to JEV intraperitoneal challenge (at 100×LD50). This suggests that immunity to anti-JEV non-structural protein(s) offers protection against JEV infection in vivo. Dengue secondary infection was also simulated by challenging mice pre-immunized with dengue 2 virus, with D4 or JEV/D4. Mice showed higher secondary antibody response to challenge with JEV/D4 than to D4, at 210 000 and 37 000 averaged ELISA units, respectively. Taken together, aside from demonstrating the LPCRcFS technique, it could be concluded that the PrM and E proteins are the major determinant of neuroinvasiveness for JEV. It is also expected that the JEV/D4 chimera with its pathogenicity in mice and atypical immune profile, could have applications in dengue prophylactic research, in vivo efficacy assessment of dengue vaccines and development of animal research on models of dengue secondary infection.
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Expression of hepatitis C virus proteins in epithelial intestinal cells in vivo
Previous work on hepatitis C virus (HCV) led to the discovery of a new form of virus particle associating virus and lipoprotein elements. These hybrid particles (LVP for lipo-viro-particles) are enriched in triglycerides and contain at least apolipoprotein B (apoB), HCV RNA and core protein. These findings suggest that LVP synthesis could occur in liver and intestine, the two main organs specialized in the production of apoB-containing lipoprotein. To identify the site of LVP production, the genetic diversity and phylogenetic relationship of HCV quasispecies from purified LVP, whole serum and liver biopsies from chronically infected patients were studied. HCV quasispecies from LVP and liver differed significantly, suggesting that LVP were not predominantly synthesized in the liver but might also originate in the intestine. The authors therefore searched for the presence of HCV in the small intestine. Paraffin-embedded intestinal biopsies from 10 chronically HCV-infected patients and from 12 HCV RNA-negative controls (10 anti-HCV antibody-negative and two anti-HCV antibody-positive patients) were tested for HCV protein expression. HCV NS3 and NS5A proteins were stained in small intestine epithelial cells in four of the 10 chronically infected patients, and not in controls. Cells expressing HCV proteins were apoB-producing enterocytes but not mucus-secreting cells. These data indicate that the small intestine can be infected by HCV, and identify this organ as a potential reservoir and replication site. This further emphasizes the interaction between lipoprotein metabolism and HCV, and offers new insights into hepatitis C infection and pathophysiology.
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GB virus B infection of the common marmoset (Callithrix jacchus) and associated liver pathology
More LessGB virus B (GBV-B) is a flavivirus that is related closely to hepatitis C virus (HCV) and induces an acute hepatitis when inoculated into several species of New World primates. Common marmosets (Callithrix jacchus) are a widely available, non-endangered primate species that is susceptible to GBV-B infection and develops a characteristic acute hepatitis. Here, animals were found to be susceptible to serially passaged serum and GBV-B transcripts. Hepatic pathology and peripheral viraemia could be quantified biochemically, immunophenotypically and morphologically, and persisted for periods of up to 6 months in some animals. Hepatitis was characterized by a marked influx of CD3+ CD8+ T lymphocytes and CD20+ B cells within the first 2 months of primary infection. The results of this study document the marmoset as another small, non-human primate species in which the pathogenesis of GBV-B can be studied and used as a surrogate model of HCV infection for investigation of pathogenesis and antiviral drug development.
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Sialic acid acts as a receptor for equine rhinitis A virus binding and infection
More LessEquine rhinitis A virus (ERAV) is a member of the genus Aphthovirus, family Picornaviridae, and causes respiratory disease in horses worldwide. To characterize the putative receptor molecule(s) of the ERAV isolate 393/76 (ERAV.393/76) on the surface of Vero and other cells, an assay was developed to measure the binding of purified biotinylated ERAV.393/76 virions to cells by flow cytometry. Using this assay, the level of binding to different cell types correlated with the relative infectivity of ERAV in each cell type. In particular, equine fetal kidney cells, mouse fibroblast cells, rabbit kidney-13 and Crandell feline kidney cells bound virus at high levels and produced high virus yields (⩾107 TCID50 ml−1). Madin–Darby bovine kidney and baby hamster kidney cells showed little or no binding of virus, producing yields of ⩽101·8 TCID50 ml−1. Treatment of Vero and other cells with sodium periodate and the metabolic inhibitors tunicamycin, benzyl N-acetyl-α-d-galactosamide, d,l-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol and proteases indicated that part of the receptor-binding and entry complex for ERAV.393/76 is on N-linked carbohydrates and that the carbohydrate is likely to be present on a protein rather than a lipid backbone. The effect of carbohydrate-specific lectins and neuraminidases on ERAV.393/76 binding and infection of Vero and other cell types implicated α2,3-linked sialic acid residues on the carbohydrate complex in the binding and infection of ERAV.
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Identification of a neutralizing epitope in the βE–βF loop of VP1 of equine rhinitis A virus, defined by a neutralization-resistant variant
More LessEquine rhinitis A virus strain 393/76 (ERAV.393/76) was passaged in the presence of post-infection ERAV.393/76 equine polyclonal antiserum (EPA). Viruses with increased resistance to neutralization by EPA were obtained after 15 passages. Compared with the parent virus, five plaque-purified, neutralization-resistant mutant viruses, in addition to the non-plaque-purified viruses that were examined, had a Glu→Lys change at position 658, which is located in the predicted βE–βF (EF) loop of VP1. Rabbit antiserum was prepared against the isolated EF loop of ERAV.393/76 VP1 expressed as a fusion protein with glutathione S-transferase. This antiserum bound to purified ERAV.393/76 in Western blots, but not to the neutralization-resistant mutant virus or to ERAV.PERV/62, a naturally occurring ERAV strain that has a Lys residue at position 658. These results suggest that the EF loop of VP1 is involved in a neutralization epitope of ERAV.
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Sequence and secondary structure requirements in a highly conserved element for foot-and-mouth disease virus internal ribosome entry site activity and eIF4G binding
More LessFoot-and-mouth disease virus (FMDV) and other picornaviruses initiate translation of their positive-strand RNA genomes at the highly structured internal ribosome entry site (IRES), which mediates ribosome recruitment to an internal site of the virus RNA. This process is facilitated by eukaryotic translation initiation factors (eIFs), such as eIF4G and eIF4B. In the eIF4G-binding site, a characteristic, discontinuous sequence element is highly conserved within the cardio- and aphthovirus subgroup (including FMDV) of the picornaviruses. This conserved element was mutated in order to investigate its primary sequence and secondary structure requirements for IRES function. Both binding of eIF4G to the IRES and IRES-directed translation are seriously impaired by mutations in two unpaired dinucleotide stretches that are exposed from the double-stranded (ds)RNA. In the base-paired regions of the conserved element, maintenance of the double-stranded secondary structure is essential, whilst in some cases, the primary sequence within the dsRNA regions is also important for IRES function. Extra eIF4F added to the translation reaction does not restore full IRES activity or eIF4G binding, indicating that disturbances in the structure of this conserved element cannot be overcome by increased initiation factor concentrations.
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Quantitative analysis of foot-and-mouth disease virus RNA loads in bovine tissues: implications for the site of viral persistence
More LessTo understand better the pathogenesis of foot-and-mouth disease (FMD), the levels of viral RNA in various bovine tissues during the acute and persistent stages of FMD virus (FMDV) infection were investigated by using quantitative RT-PCR. The viral RNA levels in the tissues examined had peaked by day 1 post-infection (p.i.) and were markedly different among the tissues examined. The epithelium collected from sites of lesion development, i.e. the interdigital area and coronary band on the feet, and the tongue, contained the highest level of viral RNA, indicating the predominant tissue sites of viral infection and amplification during the acute stage of infection. Clearance of viral RNA from most of the tissues occurred relatively rapidly and the rate of clearance was largely independent of the level of viral RNA. The viral RNA load in most of the tissues declined slower than in serum, in which viral clearance is rapid. Beyond 28 days p.i., a proportion of pharyngeal region tissues (soft palate, pharynx, tonsil and mandibular lymph node) from infected animals still contained a detectable level of viral RNA, while viral RNA in non-pharyngeal region tissues was generally only detectable for variable periods ranging from 4 to 14 days p.i. The presence of viral RNA in dorsal soft palate tissue had a good correlation with the presence of infectious virus in oesophageal-pharyngeal fluid (OP-fluid) samples, a finding indicative of the specific tissue sites of FMDV persistence.
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Enterovirus 68 is associated with respiratory illness and shares biological features with both the enteroviruses and the rhinoviruses
Enterovirus (EV) 68 was originally isolated in California in 1962 from four children with respiratory illness. Since that time, reports of EV68 isolation have been very uncommon. Between 1989 and 2003, 12 additional EV68 clinical isolates were identified and characterized, all of which were obtained from respiratory specimens of patients with respiratory tract illnesses. No EV68 isolates from enteric specimens have been identified from these same laboratories. These recent isolates, as well as the original California strains and human rhinovirus (HRV) 87 (recently shown to be an isolate of EV68 and distinct from the other human rhinoviruses), were compared by partial nucleotide sequencing in three genomic regions (partial sequencing of the 5′-non-translated region and 3D polymerase gene, and complete sequencing of the VP1 capsid gene). The EV68 isolates, including HRV87, were monophyletic in all three regions of the genome. EV68 isolates and HRV87 grew poorly at 37 °C relative to growth at 33 °C and their titres were reduced by incubation at pH 3·0, whereas the control enterovirus, echovirus 11, grew equally well at 33 and 37 °C and its titre was not affected by treatment at pH 3·0. Acid lability and a lower optimum growth temperature are characteristic features of the human rhinoviruses. It is concluded that EV68 is primarily an agent of respiratory disease and that it shares important biological and molecular properties with both the enteroviruses and the rhinoviruses.
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Downmodulation of CD3ε expression in CD8α + β − T cells of feline immunodeficiency virus-infected cats
Feline immunodeficiency virus (FIV) infection in cats is associated with an increase of feline CD (fCD)8α + β − and fCD8α + β low cells in peripheral blood. To investigate these cells in more detail, an anti-fCD3ε mAb, termed NZM1, was generated, which recognizes the extracellular epitope of the fCD3ε molecule. The anti-fCD3ε mAb proved to be more suitable for identifying feline T cells than the anti-fCD5 one, which has been used as a pan-T-cell reagent in cats, because of the presence of fCD5+fCD3ε − cells among lymphocytes. Although the fCD8α + β − and fCD8α + β low cells in the FIV-infected cats expressed fCD3ε, a subset of fCD8α + β − cells expressed fCD3ε antigen at a lower level than the T cells whose phenotype was fCD4+, or fCD8α + β low. The lower expression of fCD3ε may be associated with the immune status of fCD8α + β − T cells.
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Macaques infected long-term with attenuated simian immunodeficiency virus (SIVmac) remain resistant to wild-type challenge, despite declining cytotoxic T lymphocyte responses to an immunodominant epitope
To further investigate mechanisms of protective immunity that are induced by live, attenuated simian immunodeficiency virus (SIV), three macaques were infected with SIVmacGX2, a nef-disrupted molecular clone. In two of these animals, which expressed the MamuA*01 major histocompatibility complex class I allele, loss of functional activity against an SIV-Gag-encoded immunodominant cytotoxic T lymphocyte (CTL) epitope was observed following prolonged infection. Nonetheless, all three animals were resistant to challenge with an uncloned pool of wild-type SIVmac, whereas four naïve controls became infected. Tetramer staining revealed the rapid generation of CD8+ T-cell responses against gag- and tat-encoded immunodominant epitopes in MamuA*01+ challenge controls. The dynamics of these T-cell responses to the wild-type virus were similar to those observed following primary infection of the vaccine group with attenuated virus. In contrast, neither tetramer staining nor gamma interferon ELISpot assay revealed an immediate, systemic, anamnestic response in the wild-type-challenged, attenuated SIV-infected animals. Functional CTL capacity had not been lost in this group, as lytic activity was still evident 17 weeks after challenge. Both attenuated and wild-type viruses induced a disseminated CD8+ T-cell response, which was of a higher magnitude in lymphoid tissues than in the periphery. These results suggest that, at least as measured in the periphery, protection against wild-type infection that is induced by live, attenuated SIV is not dependent on a rechallenge-driven expansion of immunodominant epitope-specific CD8+ T cells and, therefore, pre-existing activity may be sufficient to prevent superinfection.
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Inhibition of human immunodeficiency virus type 1 replication by Z-100, an immunomodulator extracted from human-type tubercle bacilli, in macrophages
Z-100 is an arabinomannan extracted from Mycobacterium tuberculosis that has various immunomodulatory activities, such as the induction of interleukin 12, interferon gamma (IFN-γ) and β-chemokines. The effects of Z-100 on human immunodeficiency virus type 1 (HIV-1) replication in human monocyte-derived macrophages (MDMs) are investigated in this paper. In MDMs, Z-100 markedly suppressed the replication of not only macrophage-tropic (M-tropic) HIV-1 strain (HIV-1JR-CSF), but also HIV-1 pseudotypes that possessed amphotropic Moloney murine leukemia virus or vesicular stomatitis virus G envelopes. Z-100 was found to inhibit HIV-1 expression, even when added 24 h after infection. In addition, it substantially inhibited the expression of the pNL43lucΔenv vector (in which the env gene is defective and the nef gene is replaced with the firefly luciferase gene) when this vector was transfected directly into MDMs. These findings suggest that Z-100 inhibits virus replication, mainly at HIV-1 transcription. However, Z-100 also downregulated expression of the cell surface receptors CD4 and CCR5 in MDMs, suggesting some inhibitory effect on HIV-1 entry. Further experiments revealed that Z-100 induced IFN-β production in these cells, resulting in induction of the 16-kDa CCAAT/enhancer binding protein (C/EBP) β transcription factor that represses HIV-1 long terminal repeat transcription. These effects were alleviated by SB 203580, a specific inhibitor of p38 mitogen-activated protein kinases (MAPK), indicating that the p38 MAPK signalling pathway was involved in Z-100-induced repression of HIV-1 replication in MDMs. These findings suggest that Z-100 might be a useful immunomodulator for control of HIV-1 infection.
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- DNA viruses
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Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1
The 36 001 base pair DNA sequence of human adenovirus serotype 1 (HAdV-1) has been determined, using a ‘leveraged primer sequencing strategy’ to generate high quality sequences economically. This annotated genome (GenBank AF534906) confirms anticipated similarity to closely related species C (formerly subgroup), human adenoviruses HAdV-2 and -5, and near identity with earlier reports of sequences representing parts of the HAdV-1 genome. A first round of HAdV-1 sequence data acquisition used PCR amplification and sequencing primers from sequences common to the genomes of HAdV-2 and -5. The subsequent rounds of sequencing used primers derived from the newly generated data. Corroborative re-sequencing with primers selected from this HAdV-1 dataset generated sparsely tiled arrays of high quality sequencing ladders spanning both complementary strands of the HAdV-1 genome. These strategies allow for rapid and accurate low-pass sequencing of genomes. Such rapid genome determinations facilitate the development of specific probes for differentiation of family, serotype, subtype and strain (e.g. pathogen genome signatures). These will be used to monitor epidemic outbreaks of acute respiratory disease in a defined test bed by the Epidemic Outbreak Surveillance (EOS) project.
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Efficient internalization into low-passage glioma cell lines using adenoviruses other than type 5: an approach for improvement of gene delivery to brain tumours
More LessThere is a need for improvement of the commonly used adenovirus vectors based on serotype 5. This study was performed on three adenovirus serotypes with a CAR-binding motif (Ad4p, Ad5p and Ad17p) and three non-CAR-binding serotypes (Ad11p, Ad16p and Ad21p). The capacity of these alternative adenovirus vector candidates to deliver DNA into low-passage glioma cell lines from seven different donors was evaluated. The non-CAR-binding serotype Ad16p was the most efficient serotype with regard to import of its DNA, as well as initiation of hexon protein expression. Ad16p established hexon expression in 60–80 % of the cell population in gliomas from all donors tested. The other non-CAR-binding serotypes, Ad11p and Ad21p, showed hexon expression in 25–60 and 40–80 % of cells, respectively. The corresponding figure for the best CAR-binding serotype, Ad5p, was only 25–65 %, indicating greater variability between cells from different donors than serotype Ad16p had. The other CAR-binding serotypes, Ad4p and Ad17p, were refractory to some of the gliomas, giving a maximum of only 45 and 40 % hexon expression, respectively, in the most permissive cells. Interestingly, the transduction capacity of the CAR-binding serotypes was not correlated to the level of CAR expression on the cells.
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Transcriptional downregulation of DC-SIGN in human herpesvirus 6-infected dendritic cells
DC-SIGN expressed on dendritic cells (DCs) efficiently binds and transmits various pathogens, including human immunodeficiency virus, to lymphoid tissues and permissive cells. Consequently, alteration of DC-SIGN expression may affect susceptibility and resistance to pathogens. The present study shows that infection with human herpesvirus 6 (HHV-6) induces downregulation of DC-SIGN expression on immature DCs. Expression levels of DC-SIGN mRNA and intracellular protein appeared to decrease following infection with HHV-6, indicating that downregulation of surface DC-SIGN occurs at the transcriptional level. Downregulation of DC-SIGN was not induced by inoculation of UV-inactivated HHV-6 or culture supernatant of HHV-6-infected DCs, indicating that replication of HHV-6 in DCs is required for downregulation of DC-SIGN. The present study demonstrates for the first time that expression of DC-SIGN is altered at the transcriptional level by virus infection.
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Detection of antibodies against a human papillomavirus (HPV) type 16 peptide that differentiate high-risk from low-risk HPV-associated low-grade squamous intraepithelial lesions
A nonapeptide (16L1) was derived from the human papillomavirus type 16 (HPV-16) major capsid protein and tested for detection of potential cross-reactive serum IgG and cervical IgA antibodies in low- and high-risk HPV-associated low-grade squamous intraepithelial lesions (LSIL) and cervical cancer patients by ELISA. The IgG response was similar in women with low-risk HPV-associated LSIL and controls (P=0·1). In contrast, more than 90 % of patients with high-risk HPV-associated LSIL were seropositive. Although tumours from cancer patients were all positive for the presence of high-risk HPV DNA, the level of seropositivity decreased significantly in this group (P<0·0001). Cervical IgA antibodies were also detected in a significantly high proportion of women with high-risk HPV-associated LSIL compared with controls. However, the proportion of IgA-positive patients was lower than the proportion of IgG seropositives. In conclusion, the 16L1 peptide appears to be a high-risk type-common epitope that induces cross-reactive antibodies in high-risk, but not low-risk, HPV-associated LSIL patients, allowing differentiation of high- and low-risk infected women at this stage of infection.
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Analysis of 15 novel full-length BK virus sequences from three individuals: evidence of a high intra-strain genetic diversity
More LessTo determine the variability of BK virus (BKV) in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKVCAP), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKVHI) and one healthy control subject (BKVHC), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKVCAP proteins did not suggest any structural differences on the surface of the viral particles compared with BKVHI and BKVHC clones. No amino acid changes common to most BKVCAP clones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKVCAP clones, with a mean difference of 0·29 % per site compared with 0·16 % for BKVHI and 0·14 % for BKVHC. The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKVCAP clones differed at 0·55 % of sites, implying a rate of nucleotide substitution of approximately 5×10−5 substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.
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Mosaic hepatitis B virus core particles presenting the complete preS sequence of the viral envelope on their surface
The sequence of the preS domain of the hepatitis B virus (HBV, genotype D) envelope was inserted into the major immunodominant region (MIR) of the C-terminally truncated HBV core (HBc) protein. In Escherichia coli, the HBc–preS fusion protein was partially soluble and did not produce particles. Co-expression of the wild-type HBc as a helper protein along with the fusion protein led to the formation of mosaic HBc particles that exhibited HBc, preS1 and preS2 antigenicity. Two alternative combinations of medium- and high-copy plasmids were used for co-expression of fusion and helper proteins, in an attempt to improve mosaic particle production. However, the preS fusion content of the particles remained the same in both expression combinations. In a third co-expression in which the modified HBc helper lacked aa 76–85 in the MIR, the incorporation level of HBc–preS fusion into the particles was noticeably lower. Purified chimeric particles were immunogenic in mice.
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- Plant Viruses
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Geographically and temporally distant natural recombinant isolates of Plum pox virus (PPV) are genetically very similar and form a unique PPV subgroup
Natural recombinant Plum pox virus (PPV) isolates were detected in Albania, Bulgaria, Czech Republic, Germany, Hungary and Slovakia. Despite different geographical origins and dates of isolation, all the recombinant isolates were closely related at the molecular level and shared the same recombination breakpoint as well as a typical signature in their N-terminal coat protein sequence, suggesting a common origin. Biological assays with four recombinant isolates demonstrated their capacity to be aphid-transmitted to various Prunus hosts. One of these isolates had a threonine-to-isoleucine mutation in the conserved PTK motif of its HC-Pro and showed a drastically decreased, although not abolished, aphid transmissibility. The complete genome sequence of one of the recombinant isolates, BOR-3, was determined, as well as some partial sequences in the HC-Pro and P3 genes for additional natural recombinant isolates. Analysis of the phylogenetic relationships between the recombinant isolates and other sequenced PPV isolates confirmed that the recombinant isolates form a phylogenetically homogeneous lineage. In addition, this analysis revealed an ancient recombination event between the PPV-D and M subgroups, with a recombination breakpoint located in the P3 gene. Taken together, these results indicate that recombinant isolates represent an evolutionarily successful, homogeneous group of isolates with a common history and unique founding recombination event. The name PPV-Rec is proposed for this coherent ensemble of isolates.
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Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus
More LessA recombination map of the genome of Turnip mosaic virus (TuMV) was assembled using data from 19 complete genomic sequences, previously reported, and a composite sample of three regions of the genome, one-third in total, of a representative Asia-wide collection of 70 isolates. Thus, a total of 89 isolates of worldwide origin was analysed for recombinants. Eighteen recombination sites were found spaced throughout the 5′ two-thirds of the genome, but there were only two in the 3′ one-third; thus, 24 and 35 % of the P1 and NIa-VPg gene sequences examined were recombinants, whereas only 1 % of the corresponding NIa-Pro and CP gene sequences were recombinants. Recombinants with parents from the same or from different lineages were found, and some recombination sites characterized particular lineages. Most of the strain BR recombinants belonged to the Asian-BR group, as defined previously, and it was concluded that this lineage resulted from a recent migration, whereas many of the strain B recombinants from Asia fell into the world-B group. Again, a large proportion of isolates in this group were recombinants. Some recombination sites were found only in particular lineages, and hence seemed more likely to be the surviving progeny from single recombinational events, rather than the progeny of multiple events occurring at recombination hotspots. It seems that the presence of recombination sites, as well as sequence similarities, may be used to trace the migration and evolution of TuMV.
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Peter J. Walker, Juliana Freitas-Astúa, Nicolas Bejerman, Kim R. Blasdell, Rachel Breyta, Ralf G. Dietzgen, Anthony R. Fooks, Hideki Kondo, Gael Kurath, Ivan V. Kuzmin, Pedro Luis Ramos-González, Mang Shi, David M. Stone, Robert B. Tesh, Noël Tordo, Nikos Vasilakis, Anna E. Whitfield and ICTV Report Consortium
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