pinecone/core-2020-05-10-deduplication huggingface dataset:
Two New Human T-Lymphotropic Virus Type I Phylogenetic Subtypes in Seroindeterminates, a Mbuti Pygmy and a Gabonese, Have Closest Relatives among African STLV-I Strains

AbstractSix new HTLV-I strains from seroindeterminate individuals were analyzed: four from Gabon, one from a Mbuti Efe pygmy in Congo (formerly Zaire), and one from a Congolese patient residing in Belgium. The LTR andenvregions were sequenced and phylogenetic analyses were performed to characterize the new strains. Nucleotide divergence and phylogeny results showed that four of the new strains belong to the HTLV-Ib Central African subtype. The other two strains, one from the Efe pygmy and one from Gabon, lie on distinct branches of the LTR andenvtrees with respect to the four major HTLV-I subtypes. Despite the low bootstrap values, likelihood mapping analyses proved that these strains can be considered two new HTLV-I molecular subtypes, putatively named HTLV-Ie and HTLV-If. A relation exists in the phylogenetic trees and in the likelihood maps between the new subtypes and African STLV-I strains fromPapiospp. andCercopithecusspp., suggesting one or more interspecies transmission events in the past. This study demonstrates that the phylogenetic subtyping of HTLV-I in the African continent is far from being completed and that samples presenting an indeterminate serology can potentially belong to new subtypes in humans. In addition, present day serological tests do not reliably type strains within the HTLV-Ib Central African subtype
Different Evolution of Simian Immunodeficiency Virus in a Natural Host and a New Host

AbstractTo address the mechanisms of host–virus adaptation and pathogenesis of lentiviral infections, we compared the evolution of the same isolate of simian immunodeficiency virus (SIVsmm9) in two different situations: nonpathogenic infection of its natural host, the sooty mangabey, and AIDS-inducing infection of a new host, the rhesus macaque. Samples were obtained at 6, 12, and 23 or 30 months postinfection from three animals of each species. Sequences were derived from the V1 and V2 domains of the surface glycoprotein. In the macaques, we observed specific variations absent from all mangabey samples, indicating that different host species select different virus variants. In the macaques, we also observed a different shape in the phylogenetic tree, a lower divergence of sibling sequences, and a lower synonymous/nonsynonymous change ratio than in the mangabeys. This suggests that the viral population is larger and submitted to weaker selection pressures when host–virus adaptation is achieved, such as in the mangabey
A Cell Surface Protein with Herpesvirus Entry Activity (HveB) Confers Susceptibility to Infection by Mutants of Herpes Simplex Virus Type 1, Herpes Simplex Virus Type 2, and Pseudorabies Virus

AbstractCertain mutant strains of herpes simplex virus type 1 (HSV-1) are unable to infect cells in which entry is dependent on HVEM, the previously described herpesvirus entry mediator designated here as herpesvirus entry protein A (HveA). These mutant viruses can infect other cells where entry is apparently dependent on other co-receptors. The mutant virus HSV-1(KOS)Rid1 was used to screen a human cDNA expression library for ability of transfected plasmids to convert resistant Chinese hamster ovary cells to susceptibility to virus entry. A plasmid expressing the previously described poliovirus receptor-related protein 2 (Prr2) was isolated on the basis of this activity. This protein, designated here as HveB, was shown to mediate the entry of three mutant HSV-1 strains that cannot use HVEM as co-receptor, but not wild-type HSV-1 strains. HveB also mediated the entry of HSV-2 and pseudorabies virus but not bovine herpesvirus type 1. HveB was expressed in some human neuronal cell lines, fibroblastic cells, keratinocytes, and primary activated T lymphocytes. Antibodies specific for HveB blocked infection of HveB-expressing CHO cells and a human fibroblastic cell strain HEL299. Differences in ability of HSV-1 and HSV-2 strains to use HveB for entry should influence the types of cells that can be infected and thereby account in part for serotype and strain differences in tissue tropism and pathogenicity
Genome Instability in BVDV: An Examination of the Sequence and Structural Influences on RNA Recombination

AbstractThe cytopathogenic biotype of the pestivirus, bovine viral diarrhea virus, is frequently a product of nonhomologous recombination in the region of the genome encoding the viral NS2-NS3 proteins. The possibility that sequences or structures in this region contributed to a hotspot for RNA recombination was examined. A PCR-based strategy was used to examine viral genomic RNA isolated from tissue samples of cattle persistently infected with the noncytopathogenic biotype of the virus. Analysis of two different regions of the viral genome revealed that recombination was not restricted to particular sequences. Alignment of the genomic sequences undergoing recombination and examination of the predicted secondary structures of the participating RNAs revealed that the dissociation of partial, newly synthesized negative strand RNAs from the positive strand template occurred at many different sites on the molecule. Similarly, it appeared that the reassociation of the RNA polymerase complex with a second positive strand template was frequently influenced by short regions of homology between the nascent RNA strand and open secondary structures in the template molecule
A Novel Human DnaJ Protein, hTid-1, a Homolog of the Drosophila Tumor Suppressor Protein Tid56, Can Interact with the Human Papillomavirus Type 16 E7 Oncoprotein

AbstractWe have cloned hTid-1, a human homolog of the Drosophila tumor suppressor protein Tid56, by virtue of its ability to form complexes with the human papillomavirus E7 oncoprotein. The carboxyl terminal cysteine-rich metal binding domain of E7 is the major determinant for interaction with hTid-1. The carboxyl terminus of E7 is essential for the functional and structural integrity of E7 and has previously been shown to function as a multimerization domain. The hTid-1 protein is a member of the DnaJ-family of chaperones. Its mRNA is widely expressed in human tissues, including the HPV-18-positive cervical carcinoma cell line HeLa and human genital keratinocytes, the normal host cells of the HPVs. The hTid-1 gene has been mapped to the short arm of chromosome 16. The large tumor antigens of polyomaviruses encode functional J-domains that are important for viral replication as well as cellular transformation. The ability of HPV E7 to interact with a cellular DnaJ protein suggests that these two viral oncoproteins may target common regulatory pathways through J-domains
ATP-Reactive Sites in the Bacteriophage λ Packaging Protein Terminase Lie in the N-Termini of Its Subunits, gpA and gpNu1

AbstractATP-reactive sites in terminase and its subunits have been successfully identified using three different affinity analogs of ATP (2- and 8-azidoATP and FITC). GpA, the larger subunit of terminase, was shown to have a higher affinity for these analogs than gpNu1, the smaller subunit. The suitability of these reagents as affinity analogs of ATP was demonstrated by ATP protection experiments andin vitroassays done with the modified proteins. These analogs were thus shown to modify the ATP-reactive sites. The results obtained from these experiments also indicate the importance of subunit–subunit interactions in the holoenzyme. Terminase, gpA, and gpNu1 were modified with these analogs and the ATP-reactive sites were identified by isolating the modified peptide by reverse-phase chromatography. The sequence analysis of the modified peptides indicates a region including amino acids 18–35 in the N-terminus of gpNu1 and a region including amino acids 59–85 in the N-terminus of gpA as being the ATP-reactive sites
Substrate, Inhibitor, or Antibody Stabilizes the Glu 119 Gly Mutant Influenza Virus Neuraminidase

AbstractWe have previously reported the isolation and characterization of an influenza virus variant with decreased sensitivity to the neuraminidase-specific inhibitor zanamivir. This variant, which has a mutation in the active site, Glu 119 Gly (E119G), has the same specific activity as the wild-type neuraminidase (NA), but is inherently unstable, as measured by loss of both enzyme activity and NC10 monoclonal antibody reactivity. However, despite the instability of the NA, replication of the virus in liquid culture is not adversely affected. We demonstrate here that in addition to enhanced temperature sensitivity the mutant NA was significantly more sensitive to formaldehyde and to specimen preparation for electron microscopy. Substrate, inhibitor, or monoclonal antibodies stabilized the NA against all methods of denaturation. These results suggest that the instability of the variant is primarily at the level of polypeptide chain folding rather than at the level of association of monomers into tetramers. Furthermore the presence of high levels of substrate, either cell or virus associated, may be sufficient to stabilize the NA during virus replication
Characterization of the Nucleic Acid Binding Properties of Tomato Spotted Wilt Virus Nucleocapsid Protein

AbstractTomato spotted wilt tospovirus (TSWV) is the type member of the plant-infecting viruses of the genusTospovirusin the family Bunyaviridae. The three TSWV RNAs are encapsidated with nucleocapsid (N) protein to form ribonucleoprotein (RNP) which serves as the template for viral transcription and replication. Regions of the open reading frame coding for the N protein on the small (S) RNA were subcloned into pET protein expression vectors and expressed inEscherichia coliBL21 (DE3) cells. Full-length N, N amino and carboxy halves, and two N carboxy-terminal regions were expressed and isolated by metal chelate affinity chromatography. The N protein, both of its halves and the extreme carboxy-terminal region, bound cooperatively and irrespective of sequence to radiolabeled single-stranded RNA produced by runoff transcription of clones of either TSWV S RNA or cowpea chlorotic mottle virus RNA3. N protein did not bind to radiolabeled double-stranded TSWV RNA. The density of the synthetic RNase-sensitive N protein–RNA complexes was 1.32 g/ml, similar to the density of authentic Bunyaviridae RNPs. These studies are the first to indicate differences in the nucleic acid binding abilities ofTospovirusandHantavirusnucleocapsid proteins, the only characterized nucleocapsid proteins of the family Bunyaviridae
Rice Tungro Spherical Virus Polyprotein Processing: Identification of a Virus-Encoded Protease and Mutational Analysis of Putative Cleavage Sites

AbstractRice tungro spherical virus encodes a large polyprotein containing motifs with sequence similarity to viral serine-like proteases and RNA polymerases. Polyclonal antisera raised against domains of the putative protease and polymerase in fusion with glutathioneS-transferase detected a protein of about 35 kDa and, in very low amounts, a protein of about 70 kDa, respectively, in extracts from infected plants. Inin vitrotranscription/translation systems and inEscherichia coliwe demonstrated a proteolytic activity in the C-terminal region of the polyprotein. This protease rapidly cleaved its polyprotein precursorsin vitro.Mutating a potential cleavage site located N-terminal to the protease domain, Gln2526-Asp2527, diminished processing. The transversion mutation at the putative C-terminal cleavage site of the protease, at Gln2852-Ala2853, led to a delayed and partial processing
Detection of Infectious Adeno-Associated Virus Particles in Human Cervical Biopsies

AbstractRecently we reported that DNA of the human oncogenic papillomaviruses (HPV) and the tumor suppressive human helper virus-dependent parvoviruses, adeno-associated viruses type 2 (AAV-2), colocalize in cervical epithelium. To analyze whether infectious AAV particles are present in cervical tissue, we examined cervical biopsies from 36 patients with HPV-related lesions (squamous intraepithelial lesions) for the presence of AAV DNA and of infectious AAV. From each patient specimens from the lesion and from adjacent normal epithelium were analyzed. After PCR analysis AAV DNA-containing samples were purified by CsCl gradient centrifugation. The presence of AAV virions in CsCl gradients was analyzed and infectivity of AAV was determined. In addition, the biopsies were tested for the presence of HPV DNA. AAV DNA could be detected in biopsies from 23 of 36 patients. AAV particles were found in 11 AAV DNA-positive biopsies from 7 patients (lesions and/or normal tissue, respectively). AAV particles were found to be infectious virions in 10 of the 11 cases. These results demonstrate for the first time that infectious AAV can be isolated from human cervical biopsies, indicating a possible sexual transmission of AAV
The E5 Oncoprotein of Human Papillomavirus Type 16 Enhances Endothelin-1-Induced Keratinocyte Growth

AbstractHuman keratinocytes express ETAreceptors and produce endothelin-1 (ET-1), which stimulates growth response. Previously, we reported that a twofold increase in ETAreceptors is present in human papillomavirus type 16 (HPV16) immortalized keratinocytes and that ET-1 induces enhanced proliferative response in these cell lines compared to normal cells. The present studies examine whether the E5 gene of HPV16 is responsible for the enhanced activity of ET-1 in HPV-transfected keratinocytes. The presence of the E5 gene in growth factor-starved keratinocytes induced the DNA synthesis and enhanced the mitogenic activity of ET-1 or epidermal growth factor. The selection of primary keratinocytes in growth factor-free medium with the addition of ET-1 as a growth factor showed that E5-transfected keratinocytes were able to grow and to form a higher number of larger colonies with respect to untransfected cells. This effect seems to be related to the interaction of E5 with the mitogenic signaling pathway of ET-1 rather than to an increase in the expression of the receptors for ET-1. In conclusion, our data demonstrate that E5 enhances ligand signaling in keratinocytes outside the EGF pathway by the amplification of the proliferative effect of ET-1/ETAreceptor signaling
Epstein–Barr Virus DNase Contains Two Nuclear Localization Signals, Which Are Different in Sensitivity to the Hydrophobic Regions

AbstractThe DNase of Epstein–Barr virus (EBV) is a 470-amino-acid protein which possesses both endonuclease and exonuclease activities and accepts both double-stranded DNA and single-stranded DNA as substrates. It has been reported that this protein may be found in the nucleus and/or cytoplasm of infected cells. In this study, using cell fractionation and immunoblotting to determine the distribution of EBV DNase in Akata cells stimulated with anti-human immunoglobulin G antibody (anti-IgG), the DNase was found to be located predominantly in the nucleus. To map the signals in DNase which mediate its nuclear localization, we monitored the nuclear transport of fusion proteins consisting of various fragments of EBV DNase linked to a cytoplasmic protein, β-galactosidase (β-Gal). The results demonstrated that two regions of the DNase with nuclear localization signal (NLS) activity, designated NLS-A (amino acids 239–266) and NLS-B (amino acids 291–306), were able independently to localize the β-Gal to the nuclei of HEp-2 and HeLa cells. Five basic residues (R or K) were found in each NLS and distributed differently in primary structure. The basic domains and flanking residues of NLS-A and NLS-B are250YKRPCKRSFIRFI262and294LKDVRKRKLGPGH306, respectively. Further examination of these sequences revealed that NLS-A contains bulky aromatic amino acids (Y and F) which may diminish its capacity to act as a strong NLS and lacks the typical proline and glycine helix-breakers. However, NLS-B contains typical proline and glycine helix-breakers and the histidine residue at amino acid 306 is required for NLS activity. In addition, two hydrophobic regions within the DNase were found to inhibit the function of NLS-A but not NLS-B, suggesting that these two domains are different types of NLSs and differ in their sensitivity to hydrophobic regions in the context of protein structure
Herpes Simplex Virus Type 1 VP26 Is Not Essential for Replication in Cell Culture but Influences Production of Infectious Virus in the Nervous System of Infected Mice

AbstractVP26 is the smallest capsid protein of herpes simplex virus type 1 and is encoded by the UL35 open reading frame. It resides on the outer capsid surface, interacting with VP5 in a one to one stoichiometry in the hexons that comprise capsids. A null mutation in the gene encoding VP26 was generated and transferred into the KOS genome. Recombinant viruses were isolated on Vero cells, which indicated that the absence of VP26 was not required for growth of the virus in cell culture. This was confirmed by the characterization of the VP26 null mutant, designated KΔ26Z. The yield of virus from KΔ26Z-infected Vero cells was decreased only twofold relative to wild-type-infected cells, as judged by the burst size. All three types of capsids (A, B, and C) were observed after sedimentation analysis of KΔ26Z-infected cell extracts. These capsids were similar in composition to wild-type capsids except for the absence of VP26. The mouse ocular model was used to determine if VP26 played a major rolein vivo. The yield of the mutant virus relative to wild-type virus was decreased twofold in the eye; however, the mutant virus yields were decreased 30- to 100-fold in the trigeminal ganglia. Reactivation of the mutant virus as determined by cocultivation assays was also reduced. To determine the effect of VP26 on capsid translocation, the VP26 null mutation was transferred into a virus specifiying a thymidine kinase mutation that by itself is transported to the trigeminal ganglia but whose DNA is not replicated in the ganglia. Using quantitative PCR assays the number of viral genomes detected in the ganglia was similar in the presence or the absence of VP26. Therefore, VP26 does not appear to aid in the translocation of the virus capsid from the mouse eye to the trigeminal ganglia but is important for infectious virus production in the ganglia
Productive Infection of Epstein–Barr Virus (EBV) in EBV-Genome-Positive Epithelial Cell Lines (GT38 and GT39) Derived from Gastric Tissues

AbstractWe characterized the expression of Epstein–Barr virus (EBV) on two epithelial cell lines, GT38 and GT39, derived from human gastric tissues. The EBV nuclear antigen (EBNA) was detected in all cells of both cell lines. The EBV immediate-early BZLF1 protein (ZEBRA), the early antigen diffuse component (EA-D), and one of the EBV envelope proteins (gp350/220) were expressed spontaneously in small proportions in the cells. EBNA1, EBNA2, latent membrane protein 1, ZEBRA, and EA-D molecules were then observed by Western blotting in the cells. The lytic cycle was enhanced with treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA) orn-butyrate. The virus particles were observed in the TPA treated GT38 cells by electron microscopy. Infectious EBV was detected with the transformation of cord blood lymphocytes and also with the induction of early antigen to Raji cells by the supernatants of both cell lines. A major single and minor multiple fused terminal fragments and a ladder of smaller fragments of the EBV genome were detected with aXhoI probe in both cell lines. These epithelial cell lines and viruses will be useful in studying their association with EBV in gastric epithelial cells
Detection and Molecular Characterisation of Feline Foamy Virus Serotypes in Naturally Infected Cats

AbstractThe characterisation of two distinct feline foamy virus sequence groupings in the external surface portion of the viralenvgene are reported. Although amino acid identities in the Gag nucleocapsid, Pol protease, and Env transmembrane domains were greater than 92% in the 12 proviral sequences examined, two distinct sequence groups were observed in the Env surface (SU) protein. Only 57% amino acid identity was observed in the Env SU between the two groups designated FUV7-like or 951-like, while within these groups >97% identity was found. Isolates FUV7 and 951 represent two serogroups previously characterised by Floweret al.(1985). A 100% correlation was found among FeFV seroreactivity, virus isolation, and detection of viral DNA in feline leucocytes using a single round of PCR amplification. Serum neutralisation assays using autologous virus, as well as isolates 951 and FUV7, revealed that viruses with FUV7-like sequences were in a single neutralisation group and viruses with 951-like sequences were in a single neutralisation group. Based on these results, group-specific PCRs were developed, using the same sense primer with an antisense primer specific for each group. Using this PCR, no evidence of superinfection of any cat with virus from both serogroups was detected
The Upstream Direct Repeat Sequence of Prague A Rous Sarcoma Virus Is Deficient in Mediating Efficient Gag Assembly and Particle Release

AbstractRous sarcoma virus (RSV) contains two ∼135-nt imperfect direct repeats composed of smaller repeats, dr1 (∼100 nt) and dr2 (∼36 nt), that are between theenvandsrcgenes and downstream ofsrcin the 3′ untranslated region, respectively. It has previously been shown that a Prague A RSV mutant in which both dr1 sequences are deleted is defective at several points in the virus life cycle, including unspliced RNA andenvmRNA stability, unspliced RNA transport, and virus particle assembly. A defect in unspliced RNA transport occurs because a cytoplasmic transport element is present within the dr1. We have suggested that the defect of particle production may arise from the failure of the unspliced RNA to be targeted to sites in the cytoplasm where its translation is favorable for Gag protein assembly. In this report, we have further investigated the function of the direct repeats by comparing virus mutants containing either a single upstream or downstream dr1 sequence. Both mutants were delayed in replication compared to the wild-type; the mutant with a single upstream dr1 (ΔDDR) is significantly more defective than the mutant with a single downstream dr1 (ΔUDR). While both mutants appear capable of efficiently transporting unspliced RNA to the cytoplasm, the ΔDDR mutant with only the upstream dr1 is defective in its ability to support Gag assembly and particle release. The replication defect cannot be repaired by placing the upstream dr1 at the location of the downstream dr1 in the 3′ untranslated region. A single point mutation in the upstream dr1 (U to C) restored replication and particle production to near normal levels. The results suggest that unspliced RNA transport and Gag assembly functions may be mediated by different elements within the dr1 and that the Prague A upstream dr1 is defective in the latter but not the former function