bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hot-spot variations of Kaposi’s sarcoma-associated herpesvirus latent nuclear antigen and application in genotyping by PCR–RFLP
Authors: Zhang Yan-Jin , Deng Jian-Hong , Rabkin Charles , Gao Shou-Jiang 
Published: August 2015

Kaposi’s sarcoma-associated herpesvirus (KSHV, human herpesvirus-8) is aetiologically associated with Kaposi’s sarcoma and several other lymphoproliferative disorders. The latent nuclear antigen (LNA) encoded by KSHV ORF73 has important functions in virus latent infection and shows molecular polymorphism. Sequence variations were identified in the internal repeat domain (IRD) of ORF73. DNA sequencing of ORF73 from one KSHV-infected cell line, PK-1, revealed that there were 558 bp (30·2%) deletions and 66 (3·6%) point mutations located mainly in repeat region 2, the glutamine-rich region of ORF73 IRD, compared with ORF73 of BC-1 KSHV. Similar sequence variations of ORF73 were also identified in two other isolates. None of the sequence variations caused any translational frame-shift in these four KSHV isolates examined, suggesting that LNA has a conservative function in virus latent infection. The frequent sequence variations in repeat region 2 of ORF73 IRD were also identified by PCR–RFLP genotyping in 26 KSHV isolates, suggesting that this region is a ‘hot-spot’ for genetic variations. Each Kaposi’s sarcoma lesion sample contained one virus genotype with a unique RFLP pattern, indicating that in vivo KSHV infection was established with single predominate genotypes, which was further supported by the presence of invariable genotypes in multifocal lesions from individual KS patients. Four KSHV subtypes were classified based on the RFLP patterns that represent the patterns of DNA sequence variations in the ORF73 IRD. PCR–RFLP genotyping is capable of identifying LNA genetic variations and differentiating individual KSHV isolates, and thus may be useful for KSHV molecular epidemiology studies.
The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome
Authors: Chen Xinwen , IJkel Wilfred F. J. , Tarchini Renato , Sun Xiulian , Sandbrink Hans , Wang Hualin , Peters Sander , Zuidema Douwe , Lankhorst René Klein , Vlak Just M. , Hu Zhihong 
Published: August 2015

The nucleotide sequence of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) DNA genome was determined and analysed. The circular genome encompasses 131403 bp, has a G+C content of 39·1 mol% and contains five homologous regions with a unique pattern of repeats. Computer-assisted analysis revealed 135 putative ORFs of 150 nt or larger; 100 ORFs have homologues in Autographa californica multicapsid NPV (AcMNPV) and a further 15 ORFs have homologues in other baculoviruses such as Lymantria dispar MNPV (LdMNPV), Spodoptera exigua MNPV (SeMNPV) and Xestia c-nigrum granulovirus (XcGV). Twenty ORFs are unique to HaSNPV without homologues in GenBank. Among the six previously sequenced baculoviruses, AcMNPV, Bombyx mori NPV (BmNPV), Orgyia pseudotsugata MNPV (OpMNPV), SeMNPV, LdMNPV and XcGV, 65 ORFs are conserved and hence are considered as core baculovirus genes. The mean overall amino acid identity of HaSNPV ORFs was the highest with SeMNPV and LdMNPV homologues. Other than three ‘baculovirus repeat ORFs’ (bro) and two ‘inhibitor of apoptosis’ (iap) genes, no duplicated ORFs were found. A putative ORF showing similarity to poly(ADP-ribose) glycohydrolases (parg) was newly identified. The HaSNPV genome lacks a homologue of the major budded virus (BV) glycoprotein gene, gp64, of AcMNPV, BmNPV and OpMNPV. Instead, a homologue of SeMNPV ORF8, encoding the major BV envelope protein, has been identified. GeneParityPlot analysis suggests that HaSNPV, SeMNPV and LdMNPV (group II) have structural genomic features in common and are distinct from the group I NPVs and from the granuloviruses. Cluster alignment between group I and group II baculoviruses suggests that they have a common ancestor.
The open reading frame 1-encoded (‘36K’) protein of Carnation Italian ringspot virus localizes to mitochondria
Authors: Rubino L. , Weber-Lotfi F. , Dietrich A. , Stussi-Garaud C. , Russo M. 
Published: August 2015

The localization of the 36 kDa (‘36K’) protein encoded by open reading frame 1 of Carnation Italian ringspot virus was studied in infected cells and in cells transiently expressing the 36K protein fused to green fluorescent protein (GFP). Subcellular fractionation demonstrated that the 36K protein accumulated in fractions containing mostly mitochondria. Fluorescence microscopy of transiently transformed cells showed that the 36K–GFP fusion protein accumulated in structures which could be stained with the mitochondrial-specific dye MitoTracker. However, these structures were larger than normal mitochondria and were irregular in shape and distribution in the cytoplasm. Electron microscopy showed severe alterations of mitochondria, which were often clumped. The stroma was more electron-opaque, the cristae were irregularly shaped, the intermembrane space was enlarged and the outer membrane was covered with an electron-dense amorphous material whose nature could not be determined. The organelle-targeted 36K protein seems to promote the overgrowth of the mitochondrial outer membrane.
Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant ‘potex-like’ viruses
Authors: Howitt Robyn L. J. , Beever Ross E. , Pearson Michael N. , Forster Richard L. S. 
Published: August 2015

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus Botrytis cinerea. The mycovirus Botrytis virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3′ terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant ‘tymo-’ and ‘potex-like’ viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in ‘tymo-’ and ‘potex-like’ replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant ‘potex-like’ viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3′-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant ‘potex-like’ virus group.
Genetic identification and characterization of a novel virus related to human hepatitis E virus from chickens with hepatitis–splenomegaly syndrome in the United States
Authors: Haqshenas G. , Shivaprasad H. L. , Woolcock P. R. , Read D. H. , Meng X. J. 
Published: August 2015

Hepatitis–splenomegaly (HS) syndrome is an emerging disease in chickens in North America; the cause of this disease is unknown. In this study, the genetic identification and characterization of a novel virus related to human hepatitis E virus (HEV) isolated from bile samples of chickens with HS syndrome is reported. Based upon the similar genomic organization and significant sequence identity of this virus with HEV, the virus has been tentatively named avian HEV in order to distinguish it from human and swine HEV. Electron microscopy revealed that avian HEV is a non-enveloped virus particle of 30–35 nm in diameter. The sequence of the 3′ half of the viral genome (∼4 kb) was determined. Sequence analyses revealed that this genomic region contains the complete 3′ non-coding region, the complete genes from open reading frames (ORFs) 2 and 3, the complete RNA-dependent RNA polymerase (RdRp) gene and a partial helicase gene from ORF 1. The helicase gene is the most conserved gene between avian HEV and other HEV strains, displaying 58–61% aa and 57–60% nt sequence identities. The RdRp gene of avian HEV shares 47–50% aa and 52–53% nt sequence identities and the putative capsid gene (ORF 2) of avian HEV shares 48–49% aa and 48–51% nt sequence identities with the corresponding regions of other known HEV strains. Phylogenetic analysis indicates that avian HEV is genetically related to, but distinct from, other known HEV strains. This discovery has important implications for HEV animal models, nomenclature and natural history.
Identification and ultrastructural characterization of a novel virus from fish
Authors: Granzow Harald , Weiland Frank , Fichtner Dieter , Schütze Heike , Karger Axel , Mundt Egbert , Dresenkamp Barbara , Martin Petra , Mettenleiter Thomas C. 
Published: August 2015

During routine investigations on fish, a virus (isolate DF 24/00) with novel morphological features and hitherto undescribed morphogenesis was isolated from a white bream (Blicca bjoerkna L.; Teleostei, order Cypriniformes). Cell-free virions consist of a rod-shaped nucleocapsid (120–150×19–22 nm) similar to that seen in baculoviruses. The virion has a bacilliform shape (170–200×75–88 nm) reminiscent of rhabdoviruses with an envelope containing coronavirus-like spikes (20–25 nm). DF 24/00 replicated well in various fish cell lines. Inhibitor studies with 5-iodo-2′-deoxyuridine indicated that the viral genome consists of RNA and chloroform sensitivity correlated with ultrastructural demonstration of enveloped virions. The buoyant density of the virus determined in sucrose was 1·17–1·19 g/ml. Preliminary biochemical characterization revealed the presence of six antigenic glycoproteins, three of which contain sugars with concanavalin-A specificity. Ultrastructurally, morphogenesis of virus progeny was detected only in the cytoplasm. Nucleocapsids were observed to bud through membranes of the endoplasmic reticulum and/or Golgi apparatus into dilated vesicles. Egress of mature virions occurs primarily by exocytosis and, only very rarely, by budding directly at the plasma membrane. Morphologically similar viruses had previously been isolated from grass carp (Ctenopharyngodon idella), blue crab (Callinectis sapidus), European shore crab (Carcinus maenas) and shrimp (Penaeus monodon). To date, none of them has been classified. In summary, the first characterization of a new virus that might represent a member of a novel virus family that has morphological features resembling those found in rhabdo-, corona- and baculoviruses is presented.
Molecular epidemiology of simian T-lymphotropic virus (STLV) in wild-caught monkeys and apes from Cameroon: a new STLV-1, related to human T-lymphotropic virus subtype F, in a Cercocebus agilis
Authors: Nerrienet Eric , Meertens Laurent , Kfutwah Anfumbom , Foupouapouognigni Yacouba , Gessain Antoine 
Published: August 2015

A serological survey for human T-lymphotropic virus (HTLV)/simian T-lymphotropic virus (STLV) antibodies was performed in 102 wild-caught monkeys and apes from 15 (sub)species originating from Cameroon. Two animals (aMandrillus sphinxand aCercocebus agilis) exhibited a complete HTLV-1 seroreactivity pattern while two others lacked either the p24 (aMandrillus sphinx) or the MTA-1/gp46 bands (aPan troglodytes). Sequence comparison and phylogenetic analyses, using a 522 bpenvgene fragment and the complete LTR, indicated that the two mandrill STLV strains belonged to the HTLV/STLV subtype D clade while the chimpanzee strain clustered in the HTLV/STLV subtype B clade. TheCercocebus agilisSTLV strain, the first one found in this species, was closely related to the two HTLV/STLV subtype F strains. Such data indicate that the African biodiversity of STLV-1 in the wild is far from being known and reinforces the hypothesis of interspecies transmission of STLV-1 from monkeys and apes to humans leading to the present day distribution of HTLV-1 in African inhabitants.
Cis-acting sequences may contribute to size variation in the surface glycoprotein of bovine immunodeficiency virus
Authors: Li Yuxing , Carpenter Susan 
Published: August 2015

Genetic recombination is an important mechanism of retrovirus variation and diversity. Size variation in the surface (SU) glycoprotein, characterized by duplication and insertion, has been observed duringin vivoinfection with several lentiviruses, including bovine immunodeficiency virus (BIV), equine infectious anaemia virus (EIAV) and human immunodeficiency virus type 1. These duplication/insertion events are thought to occur through a mechanism of template switching/strand transfer during reverse transcription. Studies of RNA recombination in a number of virus systems indicate thatcis-acting sequences can modulate the frequency of template switching/strand transfer. The size variable region of EIAV and BIV SU glycoproteins was examined and an AU-rich region and regions of nucleotide sequence identity that may facilitate template switching/strand transfer were identified. Anin vitrostrand transfer assay using donor and acceptor templates derived from the size variable region in BIVenvdetected both precise and imprecise strand transfer products, in addition to full-length products. Sequence analysis of clones obtained from imprecise strand transfer products showed that 87·5% had crossover sites within 10 nt of the crossover site observedin vivo. Mutations in the donor template which altered either the AU-rich region or nucleotide sequence identity dramatically decreased the frequency of imprecise strand transfer. Together, these results suggest thatcis-acting elements can modulate non-homologous recombination events during reverse transcription and may contribute to the genetic and biological diversity of lentivirusesin vivo.
Circulating tumour necrosis factor-α and interferon-γ are detectable during acute and convalescent parvovirus B19 infection and are associated with prolonged and chronic fatigue
Authors: Kerr Jonathan R. , Barah Faraj , Mattey Derek L. , Laing Ian , Hopkins Stephen J. , Hutchinson Ian V. , Tyrrell David A. J. 
Published: August 2015

To investigate whether cytokine responses may have a bearing on the symptoms and outcome of parvovirus B19 infection, circulating cytokines were measured during acute infection (n=51), follow-up of acute infection (n=39) and in normal healthy controls (n=50). At acute B19 virus infection (serum anti-B19 IgM-positive), patients ranged in age from 4 to 54 years, with a mean age of 28·2 years. The male:female ratio was 1:4·1 and symptoms were rash (n=15), arthralgia (n=31), fatigue (n=8), lymphadenopathy (n=4), foetal hydrops (n=3), transient aplastic crisis (n=2), neutropenia (n=2), myelodysplasia (n=1), thrombocytopenia (n=1) and pancytopenia (n=1). Of these patients, 39 were contacted after a follow-up period of 2–37 months (mean of 22·5 months). In comparison with normal controls, detectable IL-6 was associated with acute B19 virus infection (26%;P=0·0003), but not with follow-up (6%;P=0·16). Detection of interferon (IFN)-γ was associated with acute B19 virus infection (67%;P<0·0001) and follow-up (67%;P<0·0001). Detection of tumour necrosis factor (TNF)-α was associated with acute B19 virus infection (49%;P<0·0001) and follow-up (56%;P<0·0001). IL-1β was detected in acute infection (20%), but not at follow-up. At acute B19 virus infection, detection of serum/plasma IL-6 was associated with rheumatoid factor (P=0·038) and IFN-γ (⩾7 pg/ml) was associated with fatigue in those patients of ⩾15 years of age (P=0·022). At follow-up, fatigue was associated with IFN-γ (⩾7 pg/ml) and/or TNF-α (⩾40 pg/ml) (P=0·0275). Prolonged upregulation of serum IFN-γ and TNF-α appears to represent a consistent host response to symptomatic B19 virus infection.
Effects of inactivation of the coat protein and movement genes of Tomato bushy stunt virus on early accumulation of genomic and subgenomic RNAs
Authors: Qiu Wenping , Scholthof Herman B. 
Published: August 2015

Accumulation of RNA of Tomato bushy stunt virus (TBSV) was examined within the first few hours after infection of Nicotiana benthamiana protoplasts to determine the influence of the coat protein (CP), the movement-associated proteins P22 and P19 and RNA sequences at very early stages of replication. The results showed that P19 had no effect on early RNA replication, whereas the absence of CP and/or P22 expression delayed RNA accumulation only marginally. Removal of CP-coding sequences had no added negative effects, but when the deletion extended into the downstream p22 gene, it not only eliminated synthesis of subgenomic RNA2 but also delayed accumulation of genomic RNA by 10 h. At times beyond 20 h post-transfection, RNA accumulated to normal high levels for all mutants. This illustrates that TBSV RNA sequences that have negligible impact on overall RNA levels observed late in infection can actually have pronounced effects at very early stages.
P34.8 (GP37) is not essential for baculovirus replication
Authors: Cheng Xiao-Wen , Krell Peter J. , Arif Basil M. 
Published: August 2015

Previous reports have indicated that p34.8 (gp37) may be essential for the replication of Autographa californica nucleopolyhedrovirus (AcMNPV) because no virus with inactivated p34.8 was isolated. We have ascertained the requirement for this gene by attempting to inactivate it with a large insertion [the gene encoding GFP (green fluorescent protein)] or by deleting all the conserved domains from the open reading frame (ORF). The gene encoding GFP was inserted into the NotI site of the p34.8 ORF and a viral plaque containing the insertion was propagated in SF-21 cells. Similarly, 531 bp (NotI–XbaI) containing all conserved domains were deleted from the ORF. All mutants were authenticated by PCR amplification, restriction endonuclease analysis, DNA sequencing, and Southern and Northern blot analysis. It was found that inactivation of p34.8 of AcUW1-LacZ (AcMNPV containing a lacZ gene in the p10 locus) had no effect on the biological property of virus, such as virulence and kinetics. These two independent methods showed that p34.8 is not essential for replication and that this locus could provide another site for the engineering of baculoviruses.
The tegument protein ppUL25 of human cytomegalovirus (CMV) is a major target antigen for the anti-CMV antibody response
Authors: Lazzarotto Tiziana , Varani Stefania , Gabrielli Liliana , Pignatelli Sara , Landini Maria Paola 
Published: August 2015

A viral protein of approximately 82 kDa is the only structural protein of human cytomegalovirus (CMV) that is strongly immunogenic during natural infection and the corresponding gene of which is still unknown. In this work, strong evidence is presented that this protein is the product of UL25.
Human immunodeficiency virus type 2 lentiviral vectors: packaging signal and splice donor in expression and encapsidation
Authors: D’Costa Jenice , Brown Heidi M. , Kundra Priya , Davis-Warren Alberta , Arya Suresh K. 
Published: August 2015

Retroviral vectors provide the means for gene transfer with long-term expression. The lentivirus subgroup of retroviruses, such as human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2), possesses a number of regulatory and accessory genes and other special elements. These features can be exploited to design vectors for transducing non-dividing as well as dividing cells with the potential for regulated transgene expression. Encapsidation of the transgene RNA in lentiviral vectors is determined by the leader sequence-based multipartite packaging signal. Embedded in the packaging signal is a major splice donor site that, this study shows, is not by itself essential for transgene expression or encapsidation. We designed HIV-2 vectors that contained all the sequence elements thought to be necessary and sufficient for vector RNA encapsidation. Unexpectedly, despite abundant expression, only a small fraction of the transgene RNA was encapsidated and the titre of the vector was low. Redesign of the vector with a mutant splice donor resulted in increased vector RNA encapsidation and yielded vectors with high titre. Inefficient encapsidation by the conventionally designed vector was not due to suboptimal Rev responsive element (RRE)–Rev function. Varying the length of RRE in the vector did not change vector RNA encapsidation, nor did the introduction of a synthetic intron into the mutant vector. The vector RNA with the intact splice donor may have been excessively spliced, decreasing the amount of packageable RNA. A titre of 105 transducing units (TU)/ml was readily obtained for vectors with the neo or GFP transgene, and the vector could be concentrated to a titre of 1–5×107 TU/ml.
Divergent replication kinetics of two phenotypically different parvoviruses of rats
Authors: Ball-Goodrich Lisa J. , Johnson Elizabeth , Jacoby Robert 
Published: August 2015

Rat virus (RV) is an important infectious agent of laboratory rats because of its high prevalence and capacity to disrupt research. Additionally, RV infection serves as a model for characterizing virus–host interactions during acute, persistent and prenatal infection. Our research has examined the pathogenesis of two RV strains, RV-UMass and RV-Y. RV-UMass is more pathogenic, causes a higher level of persistent infection and transmits to the foetus after oronasal inoculation of the pregnant dam. To determine in vitro distinctions between the strains that may account for these differences and to provide a benchmark for characterizing virus replication in vivo, synchronized in vitro replication of both RV strains was defined and compared. The results demonstrated that RV replication has replicative intermediates, virus transcripts and proteins similar to those reported for the prototype parvovirus, minute virus of mice. However, the replicative cycle of RV-UMass was 12 h compared with 24 h for RV-Y, and RV-UMass and RV-Y differed in kinetics of virus DNA replication, transcription and protein accumulation. Additionally, in situ analysis correlated well with kinetics data as determined by Southern and Northern blot analysis. Sequence comparisons between the strains also determined coding differences that may contribute to phenotypic differences.
Determination of the complete nucleotide sequences of RNA1 and RNA2 from greasy grouper (Epinephelus tauvina) nervous necrosis virus, Singapore strain
Authors: Tan Corrina , Huang Bin , Chang Siow Foong , Ngoh Gim Hue , Munday Barry , Chen Shih Chu , Kwang Jimmy 
Published: August 2015

The complete nucleotide sequences of RNA1 and RNA2 from greasy grouper (Epinephelus tauvina) nervous necrosis virus (GGNNV), Singapore strain, were determined. 5′RACE and RNA ligation were used to obtain the complete nucleotide sequences of the 5′ and 3′ non-coding regions (NCRs). GGNNV RNA1 was determined to be 3103 nt long, containing an ORF of 982 aa, while GGNNV RNA2 was determined to be 1433 nt long, containing an ORF of 338 aa. Both GGNNV RNAs are longer than those of other published betanodavirus sequences and the additional nucleotides were located within the NCRs. Analysis of GGNNV RNA2 revealed that it is closely related to redspotted grouper nervous necrosis virus and that both grouper viruses share the same neutralization epitope. Predicted domains for six RNA-dependent RNA polymerase motifs and two putative ORFs (proteins B1 and B2) were confirmed by sequence analysis of GGNNV RNA1.