Abstract:
UNLABELLED:We searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV18 integrated in HeLa cells were also present in some samples. We hypothesize that HPV18 sequences in these non-cervical samples are due to nucleic acid contamination from HeLa cells. This finding highlights the problems that contamination presents in computational virus detection pipelines. IMPORTANCE:Viruses associated with cancer can be detected by searching tumor sequence databases. Several studies involving searches of the TCGA database have reported the presence of HPV18, a known cause of cervical cancer, in a small number of additional cancers, including those of the rectum, kidney, and colon. We have determined that the sequences related to HPV18 in non-cervical samples are due to nucleic acid contamination from HeLa cells. To our knowledge, this is the first report of the misidentification of viruses in next-generation sequencing data of tumors due to contamination with a cancer cell line. These results raise awareness of the difficulty of accurately identifying viruses in human sequence databases.
journal_name
J Viroljournal_title
Journal of virologyauthors
Cantalupo PG,Katz JP,Pipas JMdoi
10.1128/JVI.03365-14subject
Has Abstractpub_date
2015-04-01 00:00:00pages
4051-7issue
8eissn
0022-538Xissn
1098-5514pii
JVI.03365-14journal_volume
89pub_type
杂志文章abstract::Hantavirus pulmonary syndrome (HPS) is a severe respiratory disease which is thought to result from a dysregulated immune response to infection with pathogenic hantaviruses, such as Sin Nombre virus or Andes virus (ANDV). Other New World hantaviruses, such as Prospect Hill virus (PHV), have not been associated with hu...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02402-06
更新日期:2007-03-01 00:00:00
abstract::We sequenced the genes coding for the two neutralization proteins, VP4 and VP7, of human rotavirus strains L26 and L27 with subgroup I specificity but the long RNA pattern. The deduced VP7 amino acid sequence of strains L26 and L27 showed a low homology (73.6 to 81.9%) to those of rotavirus strains of the established ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.64.11.5640-5644.1990
更新日期:1990-11-01 00:00:00
abstract::Upon stimulation with alpha/beta interferon, rat cells synthesize three Mx proteins. Sequence analysis of corresponding cDNAs reveals that these three proteins are derived from three distinct genes. One of the rat cDNAs is termed Mx1 because it is most closely related to the mouse Mx1 cDNA and because it codes for a n...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.64.12.6263-6269.1990
更新日期:1990-12-01 00:00:00
abstract::The mature virion of the alphaherpesvirus pseudorabies virus (PrV) contains a minimum of 31 structural proteins which are recruited into the virus particle by a network of protein-protein interactions which is only incompletely understood. We show here that deletion of the tegument protein pUL21 resulted in a drastic ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01801-06
更新日期:2007-01-01 00:00:00
abstract::The regressing and conventional strains of Friend virus were compared by neutralization assays, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and tryptic peptide mapping of the individual viral components. Neutralization rates of the two viruses differed in the presence of monospecific anti-gp70 antiserum...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.33.3.1083-1096.1980
更新日期:1980-03-01 00:00:00
abstract::Borna disease virus infection of neonatal rats results in a characteristic behavioral syndrome and apoptosis of subsets of neurons in the hippocampus and cerebellum (neonatal Borna disease [NBD]). The cellular mechanisms leading to neurodevelopmental damage in NBD have not been fully elucidated. Insights into this mod...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00836-06
更新日期:2006-09-01 00:00:00
abstract::Human T-cell lymphotropic virus type 1 (HTLV-1) is the etiological agent involved in the disease HTLV-1-associated myelopathy, or tropical spastic paraparesis (HAM/TSP). The pathogenesis of HAM/TSP is poorly understood, but it is probable that viral infection has an indirect, deleterious effect on neural function. In ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.70.12.8727-8736.1996
更新日期:1996-12-01 00:00:00
abstract::Here, we report that specific manipulations of the cellular response to virus infection can cause prevention of apoptosis and consequent establishment of persistent infection. Infection of several human cell lines with Sendai virus (SeV) or human parainfluenza virus 3, two prototypic paramyxoviruses, caused slow apopt...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.02536-07
更新日期:2008-04-01 00:00:00
abstract::Fanconi anemia (FA) patients have an increased risk for squamous cell carcinomas (SCCs) at sites of predilection for infection with high-risk human papillomavirus (HPV) types, including the oral cavity and the anogenital tract. We show here that activation of the FA pathway is a frequent event in cervical SCCs. We fou...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01121-07
更新日期:2007-12-01 00:00:00
abstract::CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long-range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific site...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01279-19
更新日期:2020-01-06 00:00:00
abstract:UNLABELLED:Influenza virus hemagglutinin (HA) mediates virus entry by binding to cell surface receptors and fusing the viral and endosomal membranes following uptake by endocytosis. The acidic environment of endosomes triggers a large-scale conformational change in the transmembrane subunit of HA (HA2) involving a loop...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00939-15
更新日期:2015-10-01 00:00:00
abstract::During viral infection, inflammation and recovery are tightly controlled by competing proinflammatory and regulatory immune pathways. Respiratory syncytial virus (RSV) is the leading global cause of infantile bronchiolitis, which is associated with recurrent wheeze and asthma diagnosis in later life. Th2-driven diseas...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01295-13
更新日期:2013-10-01 00:00:00
abstract::We investigated the cis-acting sequences involved in termination of vesicular stomatis virus mRNA synthesis by using bicistronic genomic analogs. All of the cis-acting signals necessary for termination reside within the first 13 nucleotides of the 23-nucleotide conserved gene junction. This 13-nucleotide termination s...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.71.11.8718-8725.1997
更新日期:1997-11-01 00:00:00
abstract::The simian virus 40 large T antigen is a promiscuous transcriptional activator of many viral and cellular promoters. We show that the promoter structure necessary for T antigen-mediated transcriptional activation is very simple. A TATA or initiator element is required, in addition to an upstream factor-binding site, w...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.67.11.6682-6688.1993
更新日期:1993-11-01 00:00:00
abstract:UNLABELLED:The distribution of vesicular stomatitis virus (VSV) nucleocapsids in the cytoplasm of infected cells was analyzed by scanning confocal fluorescence microscopy using a newly developed quantitative approach called the border-to-border distribution method. Nucleocapsids were located near the cell nucleus at ea...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00488-16
更新日期:2016-06-10 00:00:00
abstract::The cytotoxic T-lymphocyte (CTL) response to lymphocytic choriomeningitis virus infection determines the outcome of infection. Here we show that this response in BALB/c mice (H-2d), when analyzed both at the primary CTL level and using CTL clones, is predominantly monospecific. The vast majority of CTL have a common s...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.63.10.4303-4310.1989
更新日期:1989-10-01 00:00:00
abstract:UNLABELLED:Herpes simplex virus 1 (HSV-1) glycoprotein B (gB)-specific CD8(+) T cells protect mice from herpes infection and disease. However, whether and which HSV-1 gB-specific CD8(+) T cells play a key role in the "natural" protection seen in HSV-1-seropositive healthy asymptomatic (ASYMP) individuals (who have neve...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.03419-14
更新日期:2015-04-01 00:00:00
abstract::The ability of certain vesicular stomatitis virus (VSV; Indiana serotype) temperature-sensitive (ts) mutants to synthesize intracellular viral complementary RNA (vcRNA) at permissive or nonpermissive temperatures for productive infections has been investigated. Mutants belonging to complementation groups II, III, and ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.20.1.157-169.1976
更新日期:1976-10-01 00:00:00
abstract:UNLABELLED:Uracil DNA glycosylases (UNG) are highly conserved proteins that preserve DNA fidelity by catalyzing the removal of mutagenic uracils. All herpesviruses encode a viral UNG (vUNG), and yet the role of the vUNG in a pathogenic course of gammaherpesvirus infection is not known. First, we demonstrated that the v...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.03111-14
更新日期:2015-03-01 00:00:00
abstract::The small envelope protein of hepatitis B virus is the major component of the viral coat and is also secreted from cells as a 20-nm subviral particle, even in the absence of other viral proteins. Such empty envelope particles are composed of approximately 100 copies of this polypeptide and host-derived lipids and are ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.67.8.4588-4597.1993
更新日期:1993-08-01 00:00:00
abstract::We have measured growth of West Nile virus in mouse primary peritoneal macrophages (resident, thioglycolate elicited, and Mycobacterium bovis BCG activated) and in macrophagelike (P338D1) and nonmacrophage (L929, PS clone D) cell lines infected in the absence or presence of specific antibodies (immunoglobulin G ([IgG]...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.57.3.952-959.1986
更新日期:1986-03-01 00:00:00
abstract::Examination of the interaction between human immunodeficiency virus (HIV) regulatory gene products and the host immune system is fundamental to understanding the pathogenesis of HIV and could reveal possible targets for therapeutic intervention in the treatment of AIDS. The HIV Tat gene is a potential candidate for th...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.69.12.7622-7629.1995
更新日期:1995-12-01 00:00:00
abstract::Satellite RNAs are the smallest infectious agents whose replication is thought to be completely dependent on their helper virus (HV). Here we report that, when expressed autonomously in the absence of HV, a variant of satellite RNA (satRNA) associated with Cucumber mosaic virus strain Q (Q-satRNA) has a propensity to ...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.00018-12
更新日期:2012-05-01 00:00:00
abstract::We have used linker scanning and site-directed mutagenesis in an attempt to distinguish among the known functions of the duck hepatitis B virus large envelope protein, p36. We found that linker-encoded amino acid substitutions in at least one region of the pre-S envelope protein p36 produced defects in both the produc...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.68.7.4565-4571.1994
更新日期:1994-07-01 00:00:00
abstract::High concentrations of either trypsin or chymotrypsin caused nearly complete cleavage of capsid protein VP2 of hepatitis A virus but did not significantly reduce the infectivity, thermostability, or antigenicity of the virus. Chymotrypsin also had a lesser effect on VP1. These findings indicate the presence of a prote...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.65.10.5636-5640.1991
更新日期:1991-10-01 00:00:00
abstract::This study reports the identification and initial characterization of the precursors, modified forms, and oligomers of bovine herpesvirus 1 (BHV-1) gI and gE proteins with polyvalent rabbit serum specific for gI or gE. Our experiments used the Colorado strain of BHV-1 and mutant viruses with insertions of the Escheric...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.70.11.7878-7884.1996
更新日期:1996-11-01 00:00:00
abstract::Bacterial lipopolysaccharide (LPS) induces interferon (IFN) secretion and an antiviral state in murine peritoneal macrophages (PM). These cells secrete predominantly IFN-beta, as shown by neutralization assays with monoclonal antibodies. Secretion of IFN-beta is also induced in PM by IFN-gamma. LPS and IFN-gamma syner...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.63.6.2785-2789.1989
更新日期:1989-06-01 00:00:00
abstract::Sensory neurons within trigeminal ganglia (TG) are the primary site for bovine herpesvirus 1 (BHV-1) latency. During latency, viral gene expression is restricted to the latency-related (LR) gene and the open reading frame ORF-E. We previously constructed an LR mutant virus that expresses LR RNA but not any of the know...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.01009-09
更新日期:2009-09-01 00:00:00
abstract::Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), in combination with proteolytic protection assays, has been used to identify the functional epitope on human immunodeficiency virus envelope glycoprotein gp41 for the broadly neutralizing anti-gp41 human monoclonal antibody 2F5. In this protecti...
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.75.22.10906-10911.2001
更新日期:2001-11-01 00:00:00
abstract::A human endogenous retrovirus-like element (HERV), flanked by long terminal repeats of 502 and 495 nucleotides is inserted into the human pleiotrophin (PTN) gene upstream of the open reading frame. Based on its Glu-tRNA primer binding site specificity and the location within the PTN gene, we named this element HERV-E....
journal_title:Journal of virology
pub_type: 杂志文章
doi:10.1128/JVI.72.7.6065-6072.1998
更新日期:1998-07-01 00:00:00