bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and phylogenetic characterization of a humanT-cell leukaemia virus type I isolate from a native inhabitant (Rapa Nui) of Easter Island
Authors: Ohkura Sadayuki , Yamashita Masahiro , Cartier Luis , Gutierrez Tanabe David , Hayami Masanori , Sonoda Shunro , Tajima Kazuo
Published: August 2015

Human T-cell leukaemia virus type I (HTLV-I) is endemic in Melanesia, one of the three ethnogeographic regions of the Pacific; in the other two regions, Polynesia and Micronesia, the incidence of the virus is relatively low. In an effort to gain new insights into the prevalence of HTLV-I in the Pacific region, we did a seroepidemiological survey on Easter Island, which is located on the eastern edge of Polynesia. Of 138 subjects surveyed, including 108 Rapa Nui (the native inhabitants of this island), we identified one HTLV-I-seropositive Rapa Nui. The new HTLV-I isolate derived from this carrier (E-12) was phylogenetically analysed to ascertain the origin and past dissemination of HTLV-I in the island. The analysis demonstrated that isolate E-12 belongs to subgroup A of the Cosmopolitan group, and that it differs from HTLV-Is found in Melanesia, which are highly divergent variants. In subgroup A, E-12 grouped with South American HTLV-Is including those from Amerindians. This result suggests that this isolate originated in South America rather than in Melanesia.
Detection and characterization of proteins encoded by the second ORF of the M2 gene of pneumoviruses
Authors: Ahmadian G. , Chambers P. , Easton A. J.
Published: August 2015

The nucleotide sequence of the M2 gene of pneumonia virus of mice (PVM) was determined. The sequence showed that the gene encoded a protein of 176 amino acids with a predicted molecular mass of 20165 Da from a major ORF, which is smaller than the equivalent proteins encoded by human, bovine and ovine respiratory syncytial (RS) viruses. The PVM M2 protein is conserved, having 41% similarity to the equivalent human RS virus protein. In common with the M2 genes of the RS viruses and avian pneumovirus (APV), the PVM mRNA also contained a second ORF (ORF2) that partially overlaps the first ORF and which is capable of encoding a 98 residue polypeptide. No significant sequence identity could be detected between the putative M2 ORF2 proteins of PVM, APV and the RS viruses. The expression of the M2 ORF2 proteins of the pneumoviruses was investigated by using monospecific antisera raised against GST fusion proteins. Western blot analysis demonstrated the presence of polypeptides encoded by M2 ORF2 of PVM and RS virus corresponding with those predicted by in vitro translation studies, but this was not the case for APV. The PVM polypeptide was present as three distinct products in vivo. The PVM and RS virus polypeptides were also detected in cells by immunofluorescence, which showed that both were present in the cytoplasm with a degree of localization in inclusion bodies. No APV M2 ORF2 protein could be detected in vivo. The RS virus M2 ORF2 polypeptide was shown to accumulate during infection and the potential implications of this are discussed.
Latency-associated transcripts of equine herpesvirus type 4 in trigeminal ganglia of naturally infected horses
Authors: Borchers Kerstin , Wolfinger Uta , Ludwig Hanns
Published: August 2015

Equine herpesvirus type 4 (EHV-4) is a major respiratory pathogen of horses. Unlike most other members of the Alphaherpesvirinae, EHV-4 was regarded as non-neurotropic. Here, neural and lymphoid tissues of 17 horses have been analysed post-mortem. EHV-4 DNA was detected in 11 cases (65%) by PCR, exclusively in the trigeminal ganglia. In order to define the transcriptional activity, RNA preparations of 10 EHV-4 DNA-positive ganglia were investigated by nested RT–PCR. EHV-4-specific transcripts derived from genes 63 [herpes simplex virus type 1 (HSV-1) ICP0 gene homologue] and 64 (HSV-1 ICP4 gene homologue) were detected in six trigeminal ganglia. In one other case, only gene 64-specific transcripts were present. All of the transcripts proved to be antisense orientated when a strand-specific RT–PCR was applied. Type-specific primers for gene 33 (encoding glycoprotein B) served to detect transcripts of an acute EHV-4-infection, which were found in only one of the six ganglia positive for gene 63- and gene 64-specific transcripts. Overall, these studies clearly demonstrate that EHV-4 is latent in trigeminal ganglia.
DNA sequence of the UL6 to UL20 genes of infectious laryngotracheitis virus and characterization of the UL10 gene product as a nonglycosylated and nonessential virion protein
Authors: Fuchs Walter , Mettenleiter Thomas C.
Published: August 2015

The 24 kbp KpnI restriction fragment A from the unique long genome region of infectious laryngotracheitis virus (ILTV, gallid herpesvirus-1) has been sequenced. The analysed region contains 14 open reading frames sharing homology with conserved alphaherpesvirus genes. Arrangement of the UL6 to UL20 homologues of ILTV is almost identical to that found in the herpes simplex virus type 1 genome. As in other herpesviruses the UL15 gene consists of two exons and is expressed from a spliced mRNA. However, the UL16 gene, which is usually localized within the intron sequence of UL15, is not conserved at this position of the ILTV genome. Another unique feature is the absence of any putative N-glycosylation motifs within the deduced ILTV UL10 gene product, which is the homologue of the conserved herpesvirus glycoprotein M. After preparation of a monospecific antiserum, two distinct UL10 proteins with apparent molecular masses of 36 and 31 kDa were identified in ILTV-infected cells as well as in purified virions. None of these UL10 gene products is modified by N- or O-linked glycosylation. Isolation of a green fluorescent protein-expressing UL10 deletion mutant of ILTV revealed that this gene is not required for virus replication in cell culture.
Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships
Authors: Cabauatan Pepito Q. , Melcher Ulrich , Ishikawa Koichi , Omura Toshihiro , Hibino Hiroyuki , Koganezawa Hiroki , Azzam Ossmat
Published: August 2015

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host
Authors: Ambrós S. , Hernández C. , Flores R.
Published: August 2015

Viroids, small single-stranded circular RNAs endowed with autonomous replication, are unique systems to conduct evolutionary studies of complete RNA genomes. The primary structure of 36 progeny variants of peach latent mosaic viroid (PLMVd), evolved from inoculations of the peach indicator GF-305 with four individual PLMVd cDNAs differing in their pathogenicity, has been determined. Most progeny variants had unique sequences, revealing that the extremely heterogeneous character of PLMVd natural isolates most probably results from the intrinsic ability of this RNA to accumulate changes, rather than from repeated inoculations of the same individual trees under field conditions. The structure of the populations derived from single PLMVd sequences differed according to the observed phenotype. Variant gds6 induced a reproducible symptomatic infection and gave rise to a more uniform progeny that preserves some parental features, whereas variant gds15, which induced a variable phenotype, showed a more complex behaviour, generating two distinct progenies in symptomatic and asymptomatic individual plants. Progenies derived from variants esc10 and ls11, which incited latent infections, followed a similar evolutionary pattern, leading to a population structure consisting of two main groups of variants, one of which was formed by variants closely related to the parental sequence. The evolution rate exhibited by PLMVd, considerably higher than that reported for potato spindle tuber viroid, may contribute to the fluctuating symptomatology of the severe PLMVd natural isolates. However, the polymorphism observed in PLMVd progenies does preserve some structural and functional elements previously proposed for this viroid, supporting the fact that they act as constraints limiting the genetic divergence of PLMVd quasispecies generated de novo.
Identification and functional analysis of a putative non-hr origin of DNA replication from the Spodoptera littoralis type B multinucleocapsid nucleopolyhedrovirus
Authors: Huang Jianhe , Levin David B.
Published: August 2015

A putative non-hrorigin of DNA replication was identified in theSpodoptera littoralismultinucleocapsid nucleopolyhedrovirus (SpliNPV) genome by transient replication assays. The putative SpliNPVoriwas mapped to thePstI-J fragment between 75·1–77·9 map units in the SpliNPV genome. While the DNA sequence of the putative SpliNPVorialigned with regions within the non-hr oris ofAutographa californica,Orgyia pseudotsugataandSpodoptera exiguamultinucleocapsid nucleopolyhedroviruses, it has limited DNA sequence identity with these elements. The sequence of the putative SpliNPV non-hrorifragment contains a unique distribution of imperfect palindromes, multiple direct repeats and putative transcription factor-binding sites. Transient expression assays indicated that the putative SpliNPVorifragment repressed SpliNPVlef-3promoter-mediated luciferase reporter gene expression. However, the putative SpliNPVorifragment itself was capable of directing luciferase expression in the absence of a recognizable baculovirus promoter element in an orientation-independent fashion, suggesting that DNA sequence motifs within its sequence can activate transcription. Gel mobility shift analyses confirmed that proteins within nuclear extracts from both uninfected and virus-infected cells bound with specificity to the putative SpliNPVorifragment.
PrP (prion) gene expression in sheep may be modulated by alternative polyadenylation of its messenger RNA
Authors: Goldmann Wilfred , O’Neill Gerard , Cheung Foo , Charleson Fiona , Ford Peter , Hunter Nora
Published: August 2015

Scrapie-associated fibrils and their major protein component, PrP or prion protein, accumulate in the brains and some other tissues of all species affected by transmissible spongiform encephalopathies or prion diseases. To investigate the role of PrP gene expression in the hosts of these diseases, we have analysed some characteristics of PrP gene RNA transcripts in sheep and cattle tissues and made comparisons with PrP RNA transcripts in human and mouse tissues. Two PrP messenger RNAs of 4·6 kb and 2·1 kb, the result of alternative polyadenylation, were found first in sheep peripheral tissues and also occurred at low levels in sheep brain and bovine tissues, but not in human and mouse tissues. Our results from transfection assays of murine neuroblastoma cells with constructs expressing different regions of ovine PrP messenger RNA revealed the presence of sequences in the 3′ untranslated region of the gene that modulate protein synthesis.
Clearance of infection in cats naturally infected with feline coronaviruses is associated with an anti-S glycoprotein antibody response
Authors: Gonon V. , Duquesne V. , Klonjkowski B. , Monteil M. , Aubert A. , Eloit M.
Published: August 2015

We have investigated by Western blotting the antibody responses against the three major structural proteins in cats naturally infected with feline coronaviruses that cleared virus infection (group I), established chronic asymptomatic infection (group II) or were sick (group III). The cats of group I developed an anti-S glycoprotein response that was, relative to the anti-M glycoprotein response, at least 30-fold higher than that of chronically infected cats from groups II and III. These results suggest that the anti-S glycoprotein response against antigenic domains revealed by Western blot is associated with clearance of the virus after natural infection, and is not a risk factor for the establishment of a chronic infection.
Phylogenetic analysis of GB viruses A and C: evidence for cospeciation between virus isolates and their primate hosts
Authors: Charrel Rémi N. , De Micco Philippe , de Lamballerie Xavier
Published: August 2015

GB viruses A and C (GBV-A and GBV-C) have been isolated from humans and non-human primates. Phylogenetic analysis based on full-length polyproteins suggests that these two viruses have a common ancestor. It has now been determined that analysis of subgenomic amino acid sequences in the E2 and NS5 regions of GBV-A and a 345 nucleotide segment in the 5′ non-coding (5′NC) region was able to reproduce the phylogenetic relationships obtained by complete polyprotein sequences analysis. Using 5′NC sequences from databases, GBV-A isolates were discriminated into eight genetic groups, each one closely associated with specific primate hosts. Phylogenetic analyses performed on sequences from the ϵ-globin genes of primate hosts on one hand and complete polyprotein sequences from GBV-A and GBV-C isolates on the other suggest that a mechanism of cospeciation could be involved in virus evolution over a period of 35 million years.
A study of primary neuronal infection by mutants of herpes simplex virus type 1 lacking dispensable and non-dispensable glycoproteins
Authors: Babic N. , Rodger G. , Arthur J. , Minson A. C.
Published: August 2015

Cultures of primary rat dorsal root ganglia neurones were inoculated with various doses of herpes simplex virus mutants deficient in glycoproteins B, D, H, C, G, E, I or J, and the proportion of infected neurones was determined. The behaviour of these mutants on primary neurones was broadly similar to their behaviour on fibroblasts or epithelial cells. Thus, virions lacking the ‘non-dispensable’ glycoproteins B, D or H were incapable of infecting primary neurones, whereas mutants lacking glycoproteins G, E, I or J infected primary neurones with the same efficiency as wild-type virions. Two independently derived mutants lacking gC displayed a marginal phenotype, infecting neurones with a five- to tenfold reduced efficiency relative to wild-type virus and relative to non-neuronal cells in the same cultures. We conclude that the virion glycoprotein requirements for infection of mammalian neurones are similar to those required for infection of fibroblasts and epithelial cells but that glycoprotein C may enhance infection of neurones.
Human papillomavirus type 16 E2-specific T-helper lymphocyte responses in patients with cervical intraepithelial neoplasia
Authors: Bontkes Hetty J. , de Gruijl Tanja D. , Bijl Astrid , Verheijen René H. M. , Meijer Chris J. L. M. , Scheper Rik J. , Stern Peter L. , Burns Julie E. , Maitland Norman J. , Walboomers Jan M. M.
Published: August 2015

T-cell-mediated immune responses against mucosal oncogenic types of human papillomaviruses (HPV) are thought to play a role in the control of the virus infection and its associated cervical lesions. The in vitro production of interleukin-2 by T-helper (Th) cells in response to the C-terminal and N-terminal domains of the HPV-16 E2 protein was determined in 74 women with cytological evidence of premalignant cervical epithelial neoplasia who participated in a non-intervention follow-up (FU) study. Cross-sectional analysis at the end of FU showed that Th cell responses against the C-terminal domain were associated with evidence of previous or present HPV-16 infection as compared to patients with no evidence of any HPV infection (18·9% versus 0%, P=0·039). Th cell responses against the N-terminal domain were not associated with evidence of HPV-16 infection. No association with disease outcome was observed with Th cell responses against either of the E2 protein domains. However, longitudinal analysis revealed that Th cell responses against the C-terminal domain frequently occur at the time of virus clearance. Whether these responses are responsible for the clearance of the virus is not known.
Cys9, Cys104 and Cys207 of simian virus 40 Vp1 are essential for inter-pentamer disulfide-linkage and stabilization in cell-free lysates
Authors: Jao Christine C. , Weidman Mary K. , Perez Ana R. , Gharakhanian Editte
Published: August 2015

Previous studies have implicated disulfide bonds between Vp1 molecules in the stabilization of the simian virus 40 (SV40) capsid. To identify the cysteine residues involved in intermolecular disulfide interactions, systematic oligo-directed mutagenesis of cysteine codons to serine codons was initiated. Wild-type and mutant Vp1 proteins were produced in rabbit reticulocyte lysates and were allowed to interact post-translationally. Disulfide-linked Vp1 complexes were assessed via non-reducing SDS–PAGE and via sucrose-gradient sedimentation. Wild-type Vp1 forms 7S pentamers followed by 12S disulfide-linked multi-pentameric complexes in cell-free lysates. Mutagenesis of all seven cysteine codons abolished Vp1 12S complexes, but did not affect pentamer formation. A quadruple Vp1 mutant at Cys49, Cys87, Cys254and Cys267continued to form 12S complexes, whereas the major products of the Cys9, Cys104and Cys207triple mutant Vp1 were 7S pentamers. Single and double mutant Vp1 proteins at the three cysteines affected continued to form 12S complexes, but to a lesser extent. Thus, inter-pentamer disulfide bonds at Cys9, Cys104and Cys207are essential and sufficient for stabilization of Vp1 complexes in cell-free lysates. These results are in agreement with previous structural studies of SV40 that implicated the same three residues in disulfide linkage in the capsid. Possible parameters for the involvement of the three cysteines are discussed.
The bulk of the phosphorylation of human respiratory syncytial virus phosphoprotein is not essential but modulates viral RNA transcription and replication
Authors: Villanueva Nieves , Hardy Richard , Asenjo Ana , Yu Qingzhong , Wertz Gail
Published: August 2015

The ability of variants of the human respiratory syncytial virus (HRSV) phosphoprotein (P protein) to support RNA transcription and replication has been studied by using HRSV-based subgenomic replicons. The serine residues normally phosphorylated in P during HRSV infection have been replaced by other residues. The results indicate that the bulk of phosphorylation of P (98%) is not essential for viral RNA transcription or replication but that phosphorylation can modulate these processes.
Linkage of an alphavirus host-range restriction to the carbohydrate-processing phenotypes of the host cell
Authors: Boehme Karl W. , Williams Jacqueline C. , Johnston Robert E. , Heidner Hans W.
Published: August 2015

The Sindbis virus mutant NE2G216 retains PE2 in place of E2 in its virion structure. NE2G216 is a host-range mutant that replicates with near-normal kinetics in vertebrate cells, but displays severely restricted growth in cultured mosquito cells (C6/36) due to defects in the virus maturation process. In this study we tested the hypothesis that the host-range phenotype of NE2G216 was linked to the differences in carbohydrate-processing phenotypes between vertebrate and arthropod cells. Arthropod cell-derived glycoproteins are distinguishable from those synthesized in vertebrate cells by the absence of complex- and hybrid-typeN-linked oligosaccharides. To test our hypothesis we compared the growth of the wild-type virus, TRSB, NE2G216 and three PE2-containing, C6/36 cell-adapted variants, in vertebrate cells treated with 1-deoxymannojirimycin (1-dMM). 1-dMM inhibits the Golgi α-mannosidase I enzyme and limits oligosaccharide processing to high-mannose forms (Man8–9GlcNAc2). The growth of TRSB was not restricted by the action of 1-dMM; however, NE2G216 was restricted in a dose-dependent manner. In contrast, the growth of each PE2-containing, C6/36 cell-adapted mutant was enhanced by low concentrations of 1-dMM (up to 1500%) and was only slightly affected by the higher concentrations. These results demonstrate that virion maturation functions of NE2G216 are sensitive to the structure ofcis-linked oligosaccharides, and indicate that the carbohydrate-processing phenotypes of the host cell can influence viral host-range and function as a selective pressure in alphavirus evolution.
High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA
Authors: Nelson Gary W. , Stohlman Stephen A. , Tahara Stanley M.
Published: August 2015

The nucleocapsid (N) protein of mouse hepatitis virus (MHV) is the major virion structural protein. It associates with both viral genomic RNA and subgenomic mRNAs and has structural and non-structural roles in replication including viral RNA-dependent RNA transcription, genome replication, encapsidation and translation. These processes all involve RNA–protein interactions between the N protein and viral RNAs. To better understand the RNA-binding properties of this multifunctional protein, the N protein was expressed in Escherichia coli as a chimeric protein fused to glutathione-S-transferase (GST). Biochemical analyses of RNA-binding properties were performed on full-length and partial N protein segments to define the RNA-binding domain. The full-length N protein and the GST–N protein fusion product had similar binding activities with a dissociation constant (K
d) of 14 nM when the MHV 5′-leader sequence was used as ligand. The smallest N protein fragment which retained RNA-binding activity was a 55 aa segment containing residues 177–231 which bound viral RNA with a K
d of 32 nM. A consensus viral sequence recognized by the N protein was inferred from these studies; AAUCYAAAC was identified to be the potential minimum ligand for the N protein. Although the core UCYAA sequence is often tandemly repeated in viral genomes, ligands containing one or more repeats of UCYAA showed no difference in binding to the N protein. Together these data demonstrate a high-affinity, specific interaction between the N protein and a conserved RNA sequence present at the 5′-ends of MHV mRNA.
The entire nucleotide sequence of two hepatitis G virus isolates belonging to a novel genotype: isolation in Myanmar and Vietnam
Authors: Naito Hideo , Hayashi Shigeki , Abe Kenji
Published: August 2015

A novel genotype of hepatitis G virus (HGV) was recently identified in sera of subjects from countries in South-East Asia. These isolates were recovered from serum of Myanmarese (designated HGV-MY14) and Vietnamese (designated HGV-VT48) subjects, respectively. To characterize the viral genome in more detail, the full-length nucleotide sequence of the two different HGV isolates belonging to the novel genotype was cloned. Both HGV isolates were composed of 9228 nt and had a single open reading frame spanning 8529 nt and encoding 2843 aa residues. The isolates differed from previously reported HGV/GBV-C isolates types 1 to 3 by 13–15% (nucleotide sequence) and 4–6% (amino acid sequence). The putative core region of both isolates was not clearly identifiable as it consisted of only 16 aa residues. Based on phylogenetic analysis of full-length genome sequences and 5′-UTR sequences, HGV-MY14 and HGV-VT48 isolates can be classified as a novel genotype, designated type 4.
Interactions in vivo between the proteins of infectious bursal disease virus: capsid protein VP3 interacts with the RNA-dependent RNA polymerase, VP1
Authors: Tacken Mirriam G. J. , Rottier Peter J. M. , Gielkens Arno L. J. , Peeters Ben P. H.
Published: August 2015

Little is known about the intermolecular interactions between the viral proteins of infectious bursal disease virus (IBDV). By using the yeast two-hybrid system, which allows the detection of protein–protein interactions in vivo, all possible interactions were tested by fusing the viral proteins to the LexA DNA-binding domain and the B42 transactivation domain. A heterologous interaction between VP1 and VP3, and homologous interactions of pVP2, VP3, VP5 and possibly VP1, were found by co-expression of the fusion proteins in Saccharomyces cerevisiae. The presence of the VP1–VP3 complex in IBDV-infected cells was confirmed by co-immunoprecipitation studies. Kinetic analyses showed that the complex of VP1 and VP3 is formed in the cytoplasm and eventually is released into the cell-culture medium, indicating that VP1–VP3 complexes are present in mature virions. In IBDV-infected cells, VP1 was present in two forms of 90 and 95 kDa. Whereas VP3 initially interacted with both the 90 and 95 kDa proteins, later it interacted exclusively with the 95 kDa protein both in infected cells and in the culture supernatant. These results suggest that the VP1–VP3 complex is involved in replication and packaging of the IBDV genome.
High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution
Authors: Bousalem M. , Douzery E. J. P. , Fargette D.
Published: August 2015

To evaluate the genetic diversity and understand the evolution ofYam mosaic virus(YMV), a highly destructive pathogen of yam (Dioscoreasp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscoreaalata, the complexDioscoreacayenensis–DioscorearotundataandDioscoreatrifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3′-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complexD.cayenensis–D.rotundata, followed by independent transfers toD.alataandD.trifidaduring virus evolution.
Cloning and epitope mapping of a functional partial fusion receptor for human cytomegalovirus gH
Authors: Baldwin Brenda R. , Zhang Chen-Ou , Keay Susan
Published: August 2015

A cDNA clone encoding a partial putative human cytomegalovirus (HCMV) gH fusion receptor (CMVFR) was previously identified. In this report, the cDNA sequence of CMVFR was determined and the role of this CMVFR in HCMV/cell fusion was confirmed by rendering fusion-incompetent MOLT-4 cells susceptible to fusion following transfection with receptor cDNA. Blocking experiments using recombinant gH or either of two MAbs (against recombinant gH or purified viral gH:gL) provided additional evidence for the role of gH binding to this protein in virus fusion. An HCMV-binding domain of 12 aa in the middle hydrophilic region of CMVFR was identified by fusion blocking studies using synthetic receptor peptides. The 1368 bp cDNA of CMVFR contained a predicted ORF of 345 aa with two potential membrane-spanning domains and several possible nuclear localization signals. A search of sequence databases indicated that CMVFR is a novel protein. Further characterization of this cell membrane protein that confers susceptibility to fusion with the viral envelope should provide important information about the mechanism by which HCMV infects cells.
Transactivation activity of the human cytomegalovirus IE2 protein occurs at steps subsequent to TATA box-binding protein recruitment
Authors: Kim Jong-Mook , Hong Youngtae , Jeang Kuan-Teh , Kim Sunyoung
Published: August 2015

The IE2 protein of human cytomegalovirus transactivates viral and cellular promoters through a wide variety of cis-elements, but the mechanism of its action has not been well characterized. Here, IE2–Sp1 synergy and IE2–TATA box-binding protein (TBP) interaction are examined by artificial recruitment of either Sp1 or TBP to the promoter. It was found that IE2 could cooperate with DNA-bound Sp1. A 117 amino acid glutamine-rich fragment of Sp1, which can interact with Drosophila TAFII110 and human TAFII130, was sufficient for the augmentation of IE2-driven transactivation. In binding assays in vitro, IE2 interacted directly with the C-terminal region of Sp1, which contains the zinc finger DNA-binding domain, but not with its transactivation domain, suggesting that synergy between IE2 and the transactivation domain of Sp1 might be mediated by other proteins such as TAF or TBP. It was also found that TBP recruitment to the promoter markedly increased IE2-mediated transactivation. Thus, IE2 acts synergistically with DNA-bound Sp1 and DNA-bound TBP. These results suggest that, in human cytomegalovirus IE2 transactivation, Sp1 functions at an early step such as recruitment of TBP and IE2 acts to accelerate rate-limiting steps after TBP recruitment.
A new genotype of hepatitis B virus: complete genome and phylogenetic relatedness
Authors: Stuyver Lieven , De Gendt Sija , Van Geyt Caroline , Zoulim Fabien , Fried Michael , Schinazi Raymond F. , Rossau Rudi
Published: August 2015

The hepatitis B virus (HBV) genotype was determined in a total of 121 plasma samples collected in France and the US from patients chronically infected with HBV. HBV genotype A was predominant in this collection, appearing in 66 samples (54%), while genotypes B, C, D, E and F occurred in 4 (3%), 14 (12%), 23 (19%), 1 (1%) and 0 (0%) of samples, respectively. However, the genotype of a total of 13 (11%) samples (2 from France, 11 from the US) could not be determined with the methodology used. Sequence analysis, and subsequent phylogenetic analysis of the complete genome and the individual open reading frames, showed that the virus isolate from these samples was 3248 bp long and, phylogenetically, did not cluster with any of the known genotypes. This strain was provisionally called HBV genotype G. Virus isolates that were obtained from geographically separated regions like France and the US were closely related to each other. All virus strains analysed contained some characteristic differences when compared to genotype A: a translational stop codon at aa 2 and 28 of the preCore region; a 36 nt (12 aa) insert in the amino-terminal part of the Core antigen (HBcAg); a 2 aa deletion in the carboxy-terminal part of HBcAg; and a 1 aa deletion in the preS1 open reading frame. The deduced amino acid sequence of HBsAg suggests that this newly discovered genotype G strain belongs to serological group adw2.
The replicative capacity of rhesus macaque peripheral blood mononuclear cells for simian immunodeficiency virus in vitro is predictive of the rate of progression to AIDS in vivo
Authors: Seman Amy L. , Pewen William F. , Fresh Lynn F. , Martin Louis N. , Murphey-Corb Michael
Published: August 2015

Survival of rhesus macaques (Macaca mulatta) experimentally infected with simian immunodeficiency virus (SIV) varies significantly from animal to animal. Some animals die within 2 months while others survive for more than 5 years, even when identical inocula are used. This diversity in survival creates a significant problem in the design of therapeutic and vaccine trials using the SIV–macaque model because the use of small numbers of animals may provide results that are misleading. Identifying an in vitro assay that could determine the survival of monkeys prior to infection would prove extremely useful for stratifying experimental groups. Analysis of the survival of a cohort of 59 control animals obtained from over a decade of vaccine and therapeutic trials has demonstrated that the ability of peripheral blood mononuclear cells (PBMC) from a naïve animal to produce virus in vitro was highly predictive of disease progression in vivo following experimental inoculation. Animals classified in vitro as high producers of virus progressed to disease significantly more rapidly than animals classified as either low (P=0·002) or intermediate (P=0·013) producers of virus. The hierarchy of high and low virus production was maintained in purified CD4+ T cell cultures, indicating that this phenotype is an intrinsic property of the CD4+ T cell itself. These findings should significantly aid in the design of vaccine and therapeutic trials using the SIV–macaque model. Furthermore, since these studies suggest that the rate of virus replication is controlled by innate characteristics of the individual, they provide new insight into the pathogenesis of AIDS.
Recombinant human monoclonal antibodies against different conformational epitopes of the E2 envelope glycoprotein of hepatitis C virus that inhibit its interaction with CD81
Authors: Allander Tobias , Drakenberg Katarina , Beyene Aster , Rosa Domenico , Abrignani Sergio , Houghton Michael , Widell Anders , Grillner Lena , Persson Mats A. A.
Published: August 2015

The antibody response to the envelope proteins of hepatitis C virus (HCV) may play an important role in controlling the infection. To allow molecular analyses of protective antibodies, we isolated human monoclonal antibodies to the E2 envelope glycoprotein of HCV from a combinatorial Fab library established from bone marrow of a chronically HCV-infected patient. Anti-E2 reactive clones were selected using recombinant E2 protein. The bone marrow donor carried HCV genotype 2b, and E2 used for selection was of genotype 1a. The antibody clones were expressed as Fab fragments in E. coli, and as Fab fragments and IgG1 in CHO cells. Seven different antibody clones were characterized, and shown to have high affinity for E2, genotype 1a. Three clones also had high affinity for E2 of genotype 1b. They all bind to conformation-dependent epitopes. Five clones compete for the same or overlapping binding sites, while two bind to one or two other epitopes of E2. Four clones corresponding to the different epitopes were tested as purified IgG1 for blocking the CD81–E2 interaction in vitro; all four were positive at 0·3–0·5  μg/ml. Thus, the present results suggest the existence of at least two conserved epitopes in E2 that mediate inhibition of the E2–CD81 interaction, of which one appeared immunodominant in this donor.
Molecular characterization of the first Australian isolate of Japanese encephalitis virus, the FU strain
Authors: Williams David T. , Wang Lin-Fa , Daniels Peter W. , Mackenzie John S.
Published: August 2015

The complete genomic and predicted amino acid sequence of the Japanese encephalitis virus (JEV) FU strain, a human isolate recovered from the first outbreak of Japanese encephalitis in Australian territory, was determined. Comparison of the FU genome with 15 fully sequenced JEV genomes revealed high levels of sequence identity, ranging from 88·7% (GP78) to 89·7% (K94P05) for nucleotides and 96·8% (K94P05) to 98·0% (JaGAr01) for amino acid sequences. A total of 39 unique amino acid differences were found in the FU strain polyprotein. Phylogenetic analyses were performed on all available full-length JEV genomes and a selection of 64 E gene sequences from temporally and geographically diverse JEV strains. For comparison with the E gene phylogeny, phylogenetic analysis using cognate prM gene sequences was also carried out. The FU strain was found to be most closely related to Korean isolate K94P05 in the full-length analysis and to Southeast Asian strains in the E and prM gene analyses. The E gene analysis corresponded well with the prM gene analysis and with previous genotyping studies using the prM gene. The epidemiological implications of this investigation are discussed.
Variations in the major envelope glycoprotein GP5 of Czech strains of porcine reproductive and respiratory syndrome virus
Authors: Indik Stanislav , Valíček Lubomír , Klein Dieter , Klánová Jana
Published: August 2015

The major envelope glycoprotein genes (ORF5) of seven Czech isolates of porcine reproductive and respiratory syndrome virus (PRRSV) were amplified and their nucleotide sequences were determined. ORF5 displayed nucleotide and amino acid identities of 87·5–100% and 87·6–100%, respectively, among the isolates. In a phylogenetic tree, all European isolates were grouped in a genotype distinct from that of reference American strains (VR-2332, IAF-Klop). Among the European isolates, two different clades were identified. Two Czech isolates (V-501 and V-503) and Italian strain PRRSV 2156 fell into one clade. The remaining European strains comprised the second clade. Surprisingly, two separately clustered strains (V-501 and V-516) were isolated from the same herd. Additionally, the possible effect of in vitro cultivation on the nucleotide sequence was analysed. Nine point mutations in the ORF5 region resulted from 152 in vitro passages of the V-502 isolate in MARC-145 cells.
Three functionally diverged major structural proteins of white spot syndrome virus evolved by gene duplication
Authors: van Hulten Mariëlle C. W. , Goldbach Rob W. , Vlak Just M.
Published: August 2015

White spot syndrome virus (WSSV) is an invertebrate virus causing considerable mortality in penaeid shrimp. The oval-to-bacilliform shaped virions, isolated from infected Penaeus monodon, contain four major proteins: VP28, VP26, VP24 and VP19 (28, 26, 24 and 19 kDa, respectively). VP26 and VP24 are associated with the nucleocapsid and the remaining two with the envelope. Forty-one N-terminal amino acids of VP24 were determined biochemically allowing the identification of its gene (vp24) in the WSSV genome. Computer-assisted analysis revealed a striking similarity between WSSV VP24, VP26 and VP28 at the amino acid and nucleotide sequence level. This strongly suggests that these structural protein genes may have evolved by gene duplication and subsequently diverged into proteins with different functions in the WSSV virion, i.e. envelope and nucleocapsid. None of these three structural WSSV proteins showed homology to proteins of other viruses including baculoviruses, underscoring the distinct taxonomic position of WSSV among invertebrate viruses.
Isolation of a Spodoptera exigua baculovirus recombinant with a 10·6 kbp genome deletion that retains biological activity
Authors: Dai Xiaojiang , Hajós József P. , Joosten Nina N. , van Oers Monique M. , IJkel Wilfred F. J. , Zuidema Douwe , Pang Yi , Vlak Just M.
Published: August 2015

When Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) is grown in insect cell culture, defective viruses are generated. These viruses lack about 25 kbp of sequence information and are no longer infectious for insects. This makes the engineering of SeMNPV for improved insecticidal activity or as expression vectors difficult to achieve. Recombinants of Autographa californica MNPV have been generated in insects after lipofection with viral DNA and a transfer vector into the haemocoel. In the present study a novel procedure to isolate SeMNPV recombinants was adopted by alternate cloning between insect larvae and cultured cells. The S. exigua cell line Se301 was used to select the putative recombinants by following a green fluorescent protein marker inserted in the p10 locus of SeMNPV. Polyhedra from individual plaques were fed to larvae to select for biological activity. In this way an SeMNPV recombinant (SeXD1) was obtained with the speed of kill improved by about 25%. This recombinant lacked 10593 bp of sequence information, located between 13·7 and 21·6 map units of SeMNPV and including ecdysteroid UDP glucosyl transferase, gp37, chitinase and cathepsin genes, as well as several genes unique to SeMNPV. The result indicated, however, that these genes are dispensable for virus replication both in vitro and in vivo. A mutant with a similar deletion was identified by PCR in the parental wild-type SeMNPV isolate, suggesting that genotypes with differential biological activities exist in field isolates of baculoviruses. The generation of recombinants in vivo, combined with the alternate cloning between insects and insect cells, is likely to be applicable to many baculovirus species in order to obtain biologically active recombinants.
Pyrogenicity of human adenoviruses
Authors: Kato Nobuo
Published: August 2015

High doses (>1·56×107 p.f.u.) of purified preparations of human adenovirus types 3, 5 and 8 exhibited definite pyrogenic activity when injected intravenously into rabbits. Complete pyrogenic tolerance was obtained not only with homologous types but also with heterologous types of adenovirus. No pyrogenic cross-tolerance was observed between each of these three adenovirus types and paramyxovirus pyrogen or bacterial lipopolysaccharide. Adenovirus pyrogenicity was retained after UV-inactivation, whereas it was inactivated by heating at 56 °C for 30 min. Adenovirus pyrogenicity was not neutralized by mixing with homologous type-specific antiserum but non-pyrogenic doses (107 p.f.u.) of adenovirus types 3, 5 and 8 became highly pyrogenic in the presence of type-specific antibodies at the optimal virus:antibody ratio. This enhanced pyrogenicity depended upon the virus–antibody complex. From these results, it is probable that the pyrogenic activity of the virus–antibody complex, rather than the pyrogenic activity of the virions, is the main contributor to fever in adenovirus infection under actual physiological conditions.
VP1 DNA sequences of JC and BK viruses detected in urine of systemic lupus erythematosus patients reveal no differences from strains expressed in normal individuals
Authors: Bendiksen Signy , Rekvig Ole Petter , Van Ghelue Marijke , Moens Ugo
Published: August 2015

The ubiquitous human polyomaviruses BK (BKV) and JC (JCV) persist with no adverse effects in immunocompetent individuals. Virus-induced pathogenesis has been linked to virus reactivation during impaired immune conditions. Previous studies have shown a significant difference between the VP1 DNA sequences of JCV obtained from control urine samples and those in progressive multifocal leukoencephalopathy brain samples. This difference could not be detected when comparing normal control urinary JCV DNA with DNA sequences from chronic progressive multiple sclerosis patients. Since BKV and JCV are readily activated in systemic lupus erythematosus (SLE) patients, the presence of specific strains, related to VP1 DNA sequences, was investigated in these patients. VP1 DNA sequences in 100 urine samples from 21 SLE patients and 75 urine samples from 75 healthy pregnant women were analysed and compared to previously reported sequences. The results show that the VP1 sequence profiles of JCV and BKV excreted by SLE patients do not differ significantly from those excreted by immunocompetent individuals. The European JCV subtypes 1A or 1B were represented among all JCV-positive urine specimens, while BKV VP1 sequences showed complete, or almost complete, identity with the MM or JL strains. Different urine samples from the same patient collected over a 1 year period were predominantly stable. BKV VP1 DNA in urine specimens from healthy pregnant women was only detected during the third trimester of their pregnancy. These results argue against SLE-specific JCV and BKV strains and suggest reactivation of the viruses rather than recurrent re-infections of patients with SLE.
Vesicular stomatitis virus and pseudorabies virus induce a vig1/cig5 homologue in mouse dendritic cells via different pathways
Authors: Boudinot Pierre , Riffault Sabine , Salhi Samia , Carrat Charles , Sedlik Christine , Mahmoudi Nassira , Charley Bernard , Benmansour Abdenour
Published: August 2015

The homologous genesvig1andcig5were identified by differential display PCR as virus-induced genes in rainbow trout and humans, respectively. These genes are significantly related to sequences required for the biosynthesis of metal cofactors, but their function remains unknown. In this study, it is shown that the mouse homologue ofvig1/cig5was induced by vesicular stomatitis virus (VSV) and pseudorabies virus (PrV) in mouse spleen cells. Among a collection of cell lines from dendritic, myeloid, lymphoid or fibroblast lineages, only the dendritic cell line, D2SC1, showed expression ofmvigafter virus infection. This dendritic restriction was confirmed by our finding thatmvigwas also induced by both VSV and PrV in CD11c++spleen cells, separated by magnetic purification or derived from bone marrow precursor cells. Similar to the fish rhabdovirus viral haemorrhagic septicaemia virus in trout cells, VSV directly inducedmvigin the dendritic cell line D2SC1, but the PrV-mediated induction required the integrity of the interferon pathway. This result indicates thatmvigis interferon-inducible like its fish and human homologues. Furthermore,mvigwas also induced by LPS in bone marrow-derived cells. Thus,mvigexpression seems to correlate with an activated state of dendritic cells subjected to different pathogen-associated stimuli.
Resistance to Rift Valley fever virus in Rattus norvegicus: genetic variability within certain ‘inbred’ strains
Authors: Ritter Marcus , Bouloy Michèle , Vialat Pierre , Janzen Christian , Haller Otto , Frese Michael
Published: August 2015

Rift Valley fever virus(RVFV) is the causative agent of Rift Valley fever, a widespread disease of domestic animals and humans in sub-Saharan Africa. Laboratory rats have frequently been used as an animal model for studying the pathogenesis of Rift Valley fever. It is shown here that Lewis rats (LEW/mol) are susceptible to infection with RVFV, whereas Wistar–Furth (WF/mol) rats are resistant to RVFV infection. LEW/mol rats developed acute hepatitis and died after infection with RVFV strain ZH548, whereas WF/mol rats survived the infection. Cross-breeding of resistant WF/mol rats with susceptible LEW/mol rats demonstrated that resistance is segregated as a single dominant gene. Primary hepatocytes but not glial cells from WF/mol rats showed the resistant phenotype in cell culture, indicating that resistance was cell type-specific. Moreover, when cultured hepatocytes were stimulated with interferon (IFN) type I there was no indication of a regulatory role of IFN in the RVFV-resistance gene expression in WF/mol rats. Interestingly, previous reports have shown that LEW rats from a different breeding stock (LEW/mai) are resistant to RVFV infections, whereas WF/mai rats are susceptible. Thus, inbred rat strains seem to differ in virus susceptibility depending on their breeding histories. A better genetic characterization of inbred rat strains and a revision in nomenclature is needed to improve animal experimentation in the future.