Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Virus Integration”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources
PubMed2006

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.

Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have established the Influenza Virus Database (IVDB) to integrate information and create an analysis platform for genetic, genomic, and phylogenetic studies of the virus. IVDB hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. Our Q-Filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity. IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships. A search system has been developed for users to retrieve a combination of different data types by setting search options. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to pre-computed alignments and polymorphisms of IV genes and proteins, and presents the results as SNP distribution plots and minor allele distributions. IVDB is publicly available at http://influenza.genomics.org.cn.

Databases, Genetic↗
PubMed2004

Rapid determination of Epstein-Barr virus latent or lytic infection in single human cells using in situ hybridization.

Epstein-Barr (EBV) virus is associated with malignancies such as lymphoma and carcinoma. Infection of cells with EBV may result in either lytic infection with production of viral particles, characterized by the presence of linear DNA forms, or latent infection, characterized by either episomal or integrated DNA forms. To examine whether the different lytic and latent EBV DNA forms can reliably be distinguished in single human cells, in situ hybridization was performed in EBV-positive cell lines. Immunocytochemistry and Southern blot analysis were performed supplementary to in situ hybridization. In latent infection, three in situ hybridization patterns were observed: large-disperse (episomal), small-punctate (integrated) and combined (both), signal types 1, 2 and 3 respectively. These were associated with expression of latent membrane protein 1, but not with Z fragment of Epstein-Barr replication activator or viral capsid antigen. In lytic infection, three additional in situ hybridization patterns were observed: nuclear membrane associated, bubble (filling up the nucleus) and spillover (covering the lysed cells) signals types 4, 5 and 6 respectively. Signal types 4 and 5 were associated with expression of latent membrane protein 1 and Z fragment of Epstein-Barr replication activator but not viral capsid antigen, whereas type 6 was associated with expression of viral capsid antigen only. Southern blot analysis confirmed these results; however, low copy numbers of integrated virus were often missed by Southern blot, confirming that in situ hybridization is more sensitive in determining the presence of all types of EBV DNA. In situ hybridization may prove useful in rapidly screening large series of tissue microarrays and other clinical specimens for the presence of lytic or latent EBV.

Blotting, Southern↗
PubMed1984

Several classes of retroviruses are produced by an AKR mouse T lymphoma cell line.

Characterization of the viruses produced by the spontaneous T lymphoma cell line SL3 is presented. Using supernatant fluids or direct co-cultivation of cells, the SL3 cell line was found to produce replication-defective viruses in excess of replication-competent viruses. The replication-competent viruses released were predominantly those negative in the XC plaque assay (XC-); XC+ viruses represented a minor population. However, when the SL3-derived viruses were passed in mouse embryo fibroblasts, XC- viruses were rarely recovered, and XC+ viruses were readily isolated. These viruses were all ecotropic and lymphomagenic. Viruses with dual host range and non-oncogenic ecotropic viruses were not isolated from the lymphoma cells. Two replication-defective viruses from SL3 cells were studied. Both could be rescued by non-oncogenic retroviruses and were then lymphomagenic. One defective virus appeared related to XC+ viruses. In these studies, the XC+ and XC- viruses appeared to represent two different interference classes using separate cell receptors. Taken together, these experiments show that the SL3 T lymphoma cells replicate a variety of viruses most of which are lymphomagenic. Virus replication and/or virus integration may be the means of maintaining the malignant phenotype of these T lymphoma cells.

Animals↗
PubMed1985

Molecular and immunologic analysis of a chronic lymphocytic leukemia case with antibodies against human T-cell leukemia virus.

The human T-cell leukemia virus type-I (HTLV-I) is a unique, exogenous, horizontally transmitted retrovirus which is T-cell tropic, and has been associated with a specific type of aggressive leukemia/lymphoma of mature T-cell origin. In a survey of lymphoid malignancies in Jamaica, antibodies to HTLV-I were also found in 6 of 17 patients with chronic lymphocytic leukemia (CLL), raising the possibility of an etiologic relationship. Further studies were undertaken on one of these patients to clarify the nature of the disease and possible virus relationship. Cell surface marker analysis of her peripheral blood cells documented that the majority of circulating lymphocytes were B-cells. DNA-cloned probe analysis with a complete HTLV-I proviral genome of these peripheral malignant B-cells, was negative for integrated virus. A T-cell line was established in culture from her peripheral blood. The presence of HTLV-I in the cultured T-cell line was established by the detection of expressed viral specific gag protein p-19 and proviral DNA. Thus, a B-cell lymphoid malignancy can occur in the presence of HTLV-I infected T-cells, suggesting the possibility of an indirect leukemogenic mechanism.

Aged↗
PubMed1987

Multiple integration site of hepatitis B virus DNA in hepatocellular carcinoma and chronic active hepatitis tissues from children.

Attention was directed to hepatitis B virus (HBV) integration in tissues obtained from an hepatocellular carcinoma (HCC) of an 11-year-old boy and from the liver of his 6-year-old brother, who had chronic active hepatitis. Multiple HBV DNA integration sites were demonstrated in both tissues. Cell population(s) in the HCC and liver from the patient with chronic active hepatitis were assumed to be heterogeneous with regard to HBV integration. The integrated forms in the two tissues showed similar genetic organization without gross rearrangement. The location of one of the virus-chromosomal junctions was restricted to the 5'-end region of the minus-strand DNA of HBV. The experimental results support our previous model for the mechanism of HBV integration, in which minus-strand replicative intermediates integrate into chromosomal DNA. The integrated HBV DNAs were conserved in the same region of the viral genome, spanning from the C gene through the S gene to the X gene, which contains intrinsic promoter-enhancer sequences.

Base Sequence↗
PubMed1991

Genes encoding ligands for deletion of V beta 11 T cells cosegregate with mammary tumour virus genomes.

The T-cell receptor (TCR) repertoire is selected in the thymus after rearrangement of genes encoding TCR alpha and beta chains. Selection is based on the recognition by newly emergent T cells of self-ligands associated with molecules of the major histocompatibility complex: some combinations result in positive selection, others in negative selection. Negative selection, or clonal deletion, is an important mechanism for eliminating autoreactive T cells. A group of self-ligands involved in clonal deletion was identified because they, like exogenous superantigens, were recognized by almost all T cells expressing particular TCR V beta genes. V beta 17a T cells are deleted by a tissue-specific ligand; V beta 6, V beta 7, V beta 8.1 and V beta 9 T cells are deleted by the minor lymphocyte-stimulating (Mls) determinant Mls-1a; V beta 3 T cells by Mls-2a and Mls-3a; V beta 11 T cells by ligands encoded by independently segregating genes; and V beta 5 T cells by ligands encoded by two genes. Chromosome mapping using recombinant inbred strains of mice and classic backcrosses show that Mls-1a in DBA/2 mice is encoded on chromosome 1, that one of the two ligand genes for deletion of V beta 5 T cells maps to chromosome 12 and that a ligand gene for V beta 11 deletion is linked to the CD8 locus on chromosome 6. Here we present evidence from three sets of backcross mice for concordance between V beta 11 deletion ligand genes on chromosomes 6, 12 and 14 and endogenous mouse mammary tumour virus integrant (Mtv) genomes.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1994

Susceptibility and resistance to Moloney murine leukemia virus-induced promonocytic leukemia.

Moloney murine leukemia virus (M-MuLV) induces promonocytic leukemias, called MML, in pristane-treated adult mice. These tumors invariably express fused gag-myb mRNA as a consequence of virus integration and activation of the c-myb locus. In the present study it was determined that while BALB/c and DBA/2N mice are highly susceptible, C57BL/6, C3H/He, STS/A, NFS, NIH/Swiss, SJL/J, and NZB mice are strongly resistant to tumor induction. Although C57BL/6 mice were resistant because they were unable to support early virus replication in hematopoietic tissue, NFS and C3H/He mice supported replication and were shown, using RT-PCR, to have cells in the bone marrow and spleen that expressed the aberrant, leukemia-related gag-myb mRNA. This provided evidence that early stages of leukemia were permitted to develop in these mice, but preneoplastic cells were unable to progress to the acute phase. Experiments in which MML was induced by M-MuLV plus pristane treatment in immunodeficient C3H/He nu/nu and sublethally irradiated C3H/He mice suggested that the immune response may play a role in eliminating preleukemic cells in immunocompetent C3H/He. Tumors from these mice had rearrangements at the c-myb locus and expressed gag-myb RNA. It was concluded that, at least in the case of C3H/He mice, resistance is not due to an inability of virus to activate c-myb or to a lack of other tumor promoting events. Rather, leukemia development appears to be restricted by an immune response, presumably T-cell mediated. Evidence is provided that non-H-2 MHC genes are required for resistance in both C57BL/6 and C3H/He mice and that resistance is dominant. This provides an animal model for the study of tumor progression as it relates to the immune response.

3T3 Cells↗
PubMed2003

Bacteriophage MS2: molecular weight and spatial distribution of the protein and RNA components by small-angle neutron scattering and virus counting.

Small-angle neutron scattering (SANS) has been used to extend the structural characterization of the MS2 phage by examining its physical characteristics in solution. Specifically, the contrast variation technique was employed to determine the molecular weight of the individual components of the MS2 virion (protein shell and genomic RNA) and the spatial relationship of the genomic RNA to its protein shell. A consequence of this work was to evaluate a novel particle counting instrument, the integrated virus detection system (IVDS) that, in combination with SANS, has the potential to provide rapid quantitative physical characterization of unidentified viruses and phage.

Electrophoresis, Polyacrylamide Gel↗
PubMed1990

Trans-activation function of a 3' truncated X gene-cell fusion product from integrated hepatitis B virus DNA in chronic hepatitis tissues.

To investigate the expression and transactivation function of the X gene in integrated hepatitis B virus (HBV) DNA from chronic hepatitis tissues, a series of transfectants containing cloned integrated HBV DNAs was made and analyzed for X mRNA expression and trans-activation activity by using a chloramphenicol acetyltransferase assay. Most of the integrated HBV DNAs expressed X mRNA and encoded a product with trans-activation activity in spite of the loss of the 3' end region of the X gene due to integration. From cDNA cloning and sequence analysis of X mRNA transcribed from native or integrated HBV DNA, the X protein was found to be translated from the X open reading frame without splicing. For integrated HBV DNA, transcription was extended to a cellular flanking DNA and an X gene-cell fusion transcript was terminated by using a cellular poly(A) signal. The amino acid sequence deduced from an X-cell fusion transcript indicated truncation of the carboxyl-terminal five amino acids, but the upstream region of seven amino acids conserved among hepadnaviruses was retained in the integrated HBV DNA, suggesting that this conserved region is essential for the transactivation function of the X protein. These findings support the following explanation for hepatocarcinogenesis by HBV DNA integration: the expression of a cellular oncogene(s) is transactivated at the time of chronic infection by the increasing amounts of the integrated HBV gene product(s), such as the X-cell fusion product.

Amino Acid Sequence↗
PubMed1979

Transformation of rat cells by the hybrid virus Ad2(2+) HEY.

A set of four isogenic rat cell lines transformed by Ad22+ HEY have been studied. While all of the cell lines synthesize SV40 T antigen, only one expresses adenovirus 2 T antigen: none expresses SV40 V antigen or adenovirus 2 fibre antigen. Three cell lines contain 1 to 2 virus equivalents of SV40 and adenoviral sequences per diploid quantity of rate cell DNA and the fourth line contains five copies of SV40 and 20 copies of the adenovirus genome. At least three of the cell lines contain DNA sequences from the helper adenovirus 2 in addition to sequences from the Ad2+ HEY genome. The patterns of integrated virus sequences are complex suggesting multiple insertions of both adenovirus and SV40 DNA sequences. SV40 can be rescued from three cell lines by fusion with permissive cells.

Adenoviruses, Human↗
PubMed1993

Analysis of the growth properties and physical state of the human papillomavirus type 16 genome in cell lines derived from primary cervical tumors.

We have established three cell lines from keratinizing and nonkeratinizing cervical carcinomas with distinct growth properties in vitro and in vivo. Each cell line contained human papillomavirus type 16 DNA sequences, but the lines differed in the physical state of the viral genome present in the cells. A high copy number of episomal human papillomavirus type 16 DNA sequences was detected in the TC-140 line derived from a keratinizing cervical cancer. This cell line had an aneuploid karyotype, did not grow in soft agarose, and formed benign cystlike nodules in nude mice, similar in morphology to well-differentiated areas of the primary tumor. Only integrated human papillomavirus type 16 sequences were detected in the TC-146A and TC-146B lines established from a nonkeratinizing large-cell cervical carcinoma. These cell lines exhibited reduced sensitivity to transforming growth factor-beta 1 and produced invasive, but not progressively growing, tumors in nude mice. These cell lines should complement existing in vitro models of cervical carcinogenesis and provide useful tools for understanding the importance of virus integration in the transformation process as well as the cellular and molecular basis for tumor progression.

Adult↗
PubMed1994

[Detection of human papillomavirus DNA in formalin fixed invasive squamous cell carcinoma of the larynx with polymerase chain reaction (PCR)].

Approximately 67 different subtypes of HPVs have now been described. Regularly most of the cervical cancers are positive for HPV 16/18. Current research also indicates that HPVs may be involved in the development of benign tumours and also squamous cell cancers of head and neck. Studies establishing the presence of different HPV subtypes in oral cancers and precancers suggest the possibility of the virus as etiological factor in oral carcinogenesis too. In this study the prevalence of HPV 6/11, 16 and 18 infection and other exogenous risk factors like nicotine and alcohol in laryngeal cancers were studied. A total of 100 formalin-fixed and paraffin-embedded cancers, 41 glottic and 59 supraglottic, in patients aged 58 years, were detected by use of the E6 specific PCR for HPV DNA. Significantly more glottic cancers, 26 of 41 (63.4%), were positive for the investigated HPV's. HPV 16 was found in all positive cancers. This predominance of HPV 16 was also present in the supraglottic carcinomas, but only 10.2% (6 of 59) of the these groups were HPV positive. In both groups the patients with HPV 16 and/or 18 positive cancers, the exogenous risk factor was higher than with in HPV 16/18 negative tumours. Following infection, the virus either remains dormant or else undergoes active replication resulting in the synthesis of infectious virus. The integration of virus DNA into the host cell DNA may be the result of action of nicotine and/or alcohol. The integration event is the key of the carcinogenesis. The level of the risk factor in the patients with supraglottic tumours was significantly higher.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1989

The putative oncogene Spi-1: murine chromosomal localization and transcriptional activation in murine acute erythroleukemias.

We have shown previously that spleen focus forming virus integration near the Spi-1 putative oncogene is observed in 95% of erythroid Friend tumors (Moreau-Gachelin et al., 1988). Here we describe how the proviral insertion in the Spi-1 domain is associated with the enhanced transcription of a 1.4 kb mRNA normally expressed at a low level in normal cells. The gene is localized on murine chromosome 2, band E3. The structure of the Spi-1 gene was determined by sequencing genomic and cDNA clones. The gene has an open reading frame encoding a protein of 218 amino acids, extending over five exons. Proviruses always integrate outside, upstream and in the opposite orientation of the protein-encoding domain. This suggests that SFFV integration activates the expression of Spi-2 gene that may contribute to the erythroleukemic process.

Amino Acid Sequence↗
PubMedDate not supplied

[Chronic infection of cells with tick-borne encephalitis virus. Additional characteristics of the provirus].

The paper presents additional characteristics of HEp-2 cells cronically infested with tick-borne encephalitis virus, Sofyin strain (Hep-2-Sof). On the basis of the inhibition analysis, the method of molecular hybridization, and transfection, HEp-2-Sof cells were shown to contain dozens of DNA-transcripts of tick-borne encephalitis virus integrated into nucleoplasm DNA and into the fraction of repeated sequences. Their transcription is mediated by a polymerase sensitive to L-amanitine.

Amantadine↗
PubMed2001

Small tumor virus genomes are integrated near nuclear matrix attachment regions in transformed cells.

More than 15% of human cancers have a viral etiology. In benign lesions induced by the small DNA tumor viruses, viral genomes are typically maintained extrachromosomally. Malignant progression is often associated with viral integration into host cell chromatin. To study the role of viral integration in tumorigenesis, we analyzed the positions of integrated viral genomes in tumors and tumor cell lines induced by the small oncogenic viruses, including the high-risk human papillomaviruses, hepatitis B virus, simian virus 40, and human T-cell leukemia virus type 1. We show that viral integrations in tumor cells lie near cellular sequences identified as nuclear matrix attachment regions (MARs), while integrations in nonneoplastic cells show no significant correlation with these regions. In mammalian cells, the nuclear matrix functions in gene expression and DNA replication. MARs play varied but poorly understood roles in eukaryotic gene expression. Our results suggest that integrated tumor virus genomes are subject to MAR-mediated transcriptional regulation, providing insight into mechanisms of viral carcinogenesis. Furthermore, the viral oncoproteins serve as invaluable tools for the study of mechanisms controlling cellular growth. Similarly, our demonstration that integrated viral genomes may be subject to MAR-mediated transcriptional effects should facilitate elucidation of fundamental mechanisms regulating eukaryotic gene expression.

Attachment Sites, Microbiological↗
PubMed1985

High frequency germline acquisition of ecotropic MuLV proviruses in SWR/J-RF/J hybrid mice.

RF/J mice carry three endogenous ecotropic murine leukemia proviruses designated Emv-1, Emv-16, and Emv-17. Two of these proviruses, Emv-16 and Emv-17, are tightly linked and segregate with the high viremia phenotype in backcrossed mice. During the derivation of an SWR/J strain congenic for Emv-16 and Emv-17, we found that many of the progeny derived from female virus carriers acquired new germline ecotropic proviruses. Additional genetic crosses suggested that these proviruses are acquired early in development by virus infection and that this strain combination is particularly susceptible to these events. The frequency of proviral acquisition was only about 10-fold lower than the frequency of P element acquisition in dysgenic crosses of Drosophila melanogaster. Since virus integration in these hybrids occurs at many different sites, these types of hybrids may ultimately be useful for generating virally induced mutations that are amenable to study at the molecular level.

Animals↗
PubMed1996

Murine leukemia virus infects early bone marrow progenitors in immunocompetent mice.

Chronic murine leukemia viruses (MuLVs) are retroviruses which induce leukemias/lymphomas after long latency periods. The induction of leukemia by MuLVs is complex, requiring multiple steps beginning with infection of an appropriate target cell. A number of investigators have proposed a bone marrow-thymus axis in the development of retrovirus induced T-cell lymphoma in which cells are initially infected in the bone marrow. These bone marrow cells or their progeny migrate to the thymus during the disease process. In our system using adult, immunocompetent BALB.K mice infected with E-55(+) MuLV, a similar pattern is seen; integrated virus is initially detectable in the bone marrow and spleen and only later in the thymus. In order to better understand the leukemic process, we analyzed the bone marrow from adult, immunocompetent BALB.K mice infected with the E-55(+) MuLV in bone marrow colony assays. The results from these assays demonstrate that either a pluripotent progenitor cell or an early progenitor cell is a target in the bone marrow for the virus.

Animals↗
PubMed1994

[Murine leukemia virus Akv promotes bone tumor development in fos-transgenic mice].

Newborn hMT-fos-LTR transgenic C3H mice and their non-transgenic siblings were infected with Akv, derived from the ecotropic provirus of the AKR mouse. Bone sarcomas in non-infected transgenics were observed in 20% (3/15) of females at 448 +/- 25 days and in 8% (1/12) of males at 523 days. Akv-infected transgenics developed bone tumors with higher frequency and at younger age: Females in 69% (20/28) at 268 +/- 122 days, males in 83% (24/29) at 279 +/- 109 days. In the majority of the bone tumors of Akv-infected transgenics (70% in females, 59% in males) cellular atypia was lacking and the histological pattern resembled human parosteal osteosarcoma. Only 50% (12/24) of bone tumors in Akv-infected transgenics revealed newly integrated virus sequences by Southern analysis. PCR analysis detected Akv sequences in DNAs of all tumors. Obviously, the insertion of Akv in a few cells induced the considerably accelerated bone tumor growth.

Animals↗