viral genome

Summary

Summary: The complete genetic complement contained in a DNA or RNA molecule in a virus.

Top Publications

  1. pmc Metagenomic analyses of an uncultured viral community from human feces
    Mya Breitbart
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    J Bacteriol 185:6220-3. 2003
  2. pmc Production of infectious hepatitis C virus in tissue culture from a cloned viral genome
    Takaji Wakita
    Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo 183 8526, Japan
    Nat Med 11:791-6. 2005
  3. ncbi Genetic content of wild-type human cytomegalovirus
    Aidan Dolan
    MRC Virology Unit, Institute of Virology, Church Street, Glasgow G11 5JR, UK
    J Gen Virol 85:1301-12. 2004
  4. ncbi RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates
    Andreas Pichlmair
    Immunobiology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3PX, UK
    Science 314:997-1001. 2006
  5. doi Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
    Gavin J D Smith
    State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
    Nature 459:1122-5. 2009
  6. pmc High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    Kevin A Wilkinson
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS Biol 6:e96. 2008
  7. pmc Coding potential of laboratory and clinical strains of human cytomegalovirus
    Eain Murphy
    Department of Molecular Biology, Princeton University, Princeton, NJ 80544, USA
    Proc Natl Acad Sci U S A 100:14976-81. 2003
  8. ncbi Viral metagenomics
    Robert A Edwards
    Department of Biology, Center for Microbial Sciences, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
    Nat Rev Microbiol 3:504-10. 2005
  9. pmc Recombination patterns in aphthoviruses mirror those found in other picornaviruses
    Livio Heath
    Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa
    J Virol 80:11827-32. 2006
  10. pmc Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant
    Anatoly Urisman
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Pathog 2:e25. 2006

Research Grants

  1. Roles for microRNA-122 in hepatitis C virus RNA amplification
    Peter Sarnow; Fiscal Year: 2013
  2. Structure and Function of the Hepatitis C Virus Genome
    Peter Sarnow; Fiscal Year: 2013
  3. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
  4. Regulation of KSHV Latency
    Paul M Lieberman; Fiscal Year: 2013
  5. Regulation of HIV-1 by Rad51 in CNS cells
    Kamel Khalili; Fiscal Year: 2013
  6. Roles of Host Kinases in Paramyxovirus RNA Synthesis
    Biao He; Fiscal Year: 2010
  7. Viral And host mechanisms that tilt the HSV lytic/latent balance
    Donald M Coen; Fiscal Year: 2013
  8. Mechanistic Studies of HCV E2
    Joseph Marcotrigiano; Fiscal Year: 2013
  9. Mechanisms of ENaC Inhibition by Replicating Influenza Virus: Role of M2 Protein
    Sadis Matalon; Fiscal Year: 2012
  10. Peptide inhbitors of influenza entry-FAST TRACK
    Russell B Wilson; Fiscal Year: 2011

Detail Information

Publications398 found, 100 shown here

  1. pmc Metagenomic analyses of an uncultured viral community from human feces
    Mya Breitbart
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    J Bacteriol 185:6220-3. 2003
    ..Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes...
  2. pmc Production of infectious hepatitis C virus in tissue culture from a cloned viral genome
    Takaji Wakita
    Department of Microbiology, Tokyo Metropolitan Institute for Neuroscience, Tokyo 183 8526, Japan
    Nat Med 11:791-6. 2005
    ..The cell culture-generated HCV is infectious for chimpanzee. This system provides a powerful tool for studying the viral life cycle and developing antiviral strategies...
  3. ncbi Genetic content of wild-type human cytomegalovirus
    Aidan Dolan
    MRC Virology Unit, Institute of Virology, Church Street, Glasgow G11 5JR, UK
    J Gen Virol 85:1301-12. 2004
    ..The case in support of a lack of protein-coding potential in the region between UL105 and UL111A was also strengthened...
  4. ncbi RIG-I-mediated antiviral responses to single-stranded RNA bearing 5'-phosphates
    Andreas Pichlmair
    Immunobiology Laboratory, Cancer Research UK, London Research Institute, London WC2A 3PX, UK
    Science 314:997-1001. 2006
    ....
  5. doi Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
    Gavin J D Smith
    State Key Laboratory of Emerging Infectious Diseases and Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
    Nature 459:1122-5. 2009
    ..Our results highlight the need for systematic surveillance of influenza in swine, and provide evidence that the mixing of new genetic elements in swine can result in the emergence of viruses with pandemic potential in humans...
  6. pmc High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    Kevin A Wilkinson
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS Biol 6:e96. 2008
    ..We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles...
  7. pmc Coding potential of laboratory and clinical strains of human cytomegalovirus
    Eain Murphy
    Department of Molecular Biology, Princeton University, Princeton, NJ 80544, USA
    Proc Natl Acad Sci U S A 100:14976-81. 2003
    ..Multiple sequence alignments revealed substantial variation in the amino acid sequences encoded by many of the conserved ORFs...
  8. ncbi Viral metagenomics
    Robert A Edwards
    Department of Biology, Center for Microbial Sciences, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
    Nat Rev Microbiol 3:504-10. 2005
    ..Metagenomic analyses of uncultured viral communities circumvent these limitations and can provide insights into the composition and structure of environmental viral communities...
  9. pmc Recombination patterns in aphthoviruses mirror those found in other picornaviruses
    Livio Heath
    Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa
    J Virol 80:11827-32. 2006
    ....
  10. pmc Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant
    Anatoly Urisman
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Pathog 2:e25. 2006
    ..5%) among 66 RQ and RR cases. The full-length viral genome was cloned and sequenced independently from three positive QQ cases...
  11. pmc Common origin of four diverse families of large eukaryotic DNA viruses
    L M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Virol 75:11720-34. 2001
    ..The results of genome comparison allow a tentative reconstruction of the ancestral viral genome and suggest that the common ancestor of all of these viral families was a nucleocytoplasmic virus with an ..
  12. pmc Clonal integration of a polyomavirus in human Merkel cell carcinoma
    Huichen Feng
    Molecular Virology Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Suite 1 8, Pittsburgh, PA 15213, USA
    Science 319:1096-100. 2008
    ..Thus, MCV may be a contributing factor in the pathogenesis of MCC...
  13. ncbi The extent of codon usage bias in human RNA viruses and its evolutionary origin
    Gareth M Jenkins
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Virus Res 92:1-7. 2003
    ..However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in ..
  14. pmc The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages
    Tony Kwan
    Targanta Therapeutics, 7170 Frederick Banting, Second Floor, Ville Saint Laurent, QC, Canada H4S 2A1
    Proc Natl Acad Sci U S A 102:5174-9. 2005
    ..These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity...
  15. pmc Comparative genomics of foot-and-mouth disease virus
    C Carrillo
    Department of Pathobiology and Veterinary Science, University of Connecticut, 61 N Eagleville Road, Unit 3089, Storrs, CT 06269 3089, USA
    J Virol 79:6487-504. 2005
    ..Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission...
  16. ncbi The 1.2-megabase genome sequence of Mimivirus
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Science 306:1344-50. 2004
    ..This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes...
  17. pmc Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin
    Morris S Jones
    Clinical Investigation Facility, David Grant USAF Medical Center, 101 Bodin Circle, Travis AFB, CA 94535, USA
    J Clin Microbiol 45:2144-50. 2007
    ..Nearly full-length viral genome sequencing and phylogenetic analysis demonstrate that this virus is a member of the Cardiovirus genus of the ..
  18. pmc Frequency and dynamics of recombination within different species of human enteroviruses
    Peter Simmonds
    Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 80:483-93. 2006
    ....
  19. ncbi Nidovirales: evolving the largest RNA virus genome
    Alexander E Gorbalenya
    Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC E4 P, P O Box 9600, 2300 RC Leiden, The Netherlands
    Virus Res 117:17-37. 2006
    ..The acquisition of these enzymes may have improved the low fidelity of RNA replication to allow genome expansion and give rise to the ancestors of small and, subsequently, large nidoviruses...
  20. pmc Cloning of a human parvovirus by molecular screening of respiratory tract samples
    Tobias Allander
    Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
    Proc Natl Acad Sci U S A 102:12891-6. 2005
    ..We suggest that a systematic exploration of the viruses that infect humans, "the human virome," can be initiated...
  21. ncbi Metagenomic analysis of coastal RNA virus communities
    Alexander I Culley
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Science 312:1795-8. 2006
    ..Our results show that the oceans are a reservoir of previously unknown RNA viruses...
  22. pmc Metagenomic characterization of Chesapeake Bay virioplankton
    Shellie R Bench
    College of Marine and Earth Studies, University of Delaware, Newark, Delaware 19711, USA
    Appl Environ Microbiol 73:7629-41. 2007
    ..Furthermore, the low frequency of psbD homologs in the library supports the prediction that Chesapeake Bay cyanophage populations are dominated by Podoviridae...
  23. pmc Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage
    R W Hendrix
    Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
    Proc Natl Acad Sci U S A 96:2192-7. 1999
    ....
  24. doi Cloning and sequencing of a highly productive, endotheliotropic virus strain derived from human cytomegalovirus TB40/E
    Christian Sinzger
    Institut fur Medizinische Virologie, Eberhard Karls Universitat, Tubingen, Germany
    J Gen Virol 89:359-68. 2008
    ..The results also suggest BAC cloning as a suitable method for selection of genetically defined virus clones...
  25. pmc Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts
    Matthew B Sullivan
    Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Biol 4:e234. 2006
    ..This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution...
  26. pmc Interferon modulation of cellular microRNAs as an antiviral mechanism
    Irene M Pedersen
    Department of Molecular Biology, University of California San Diego, La Jolla, California 92093, USA
    Nature 449:919-22. 2007
    ..Therefore, our findings strongly support the notion that mammalian organisms too, through the interferon system, use cellular miRNAs to combat viral infections...
  27. ncbi Different trajectories of parallel evolution during viral adaptation
    H A Wichman
    Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
    Science 285:422-4. 1999
    ..However, the order of these changes differed between replicates, and parallel substitutions did not reflect the changes with the largest beneficial effects or indicate a common trajectory of adaptation...
  28. pmc Viral genome sequencing by random priming methods
    Appolinaire Djikeng
    Viral Genomics Group, J, Craig Venter Institute, Rockville, MD 20850, USA
    BMC Genomics 9:5. 2008
    ..Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing.
  29. pmc Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis
    Xiaopeng Qi
    Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
    PLoS ONE 4:e4971. 2009
    ..Our data raised the interesting possibility for viral siRNA-mediated virus-host interactions that may contribute to viral pathogenicity and host specificity...
  30. ncbi Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus
    Jun Han
    Department of Veterinary and Biomedical Sciences, 205 Veterinary Science Building, 1971 Commonwealth Avenue, University of Minnesota, Saint Paul, MN 55108, USA
    Virus Res 122:175-82. 2006
    ..S., Wang, Y., Liu, H., 2005. Non-structural protein 2 mutants of PRRSV strain VR-2332 infectious clone based on deletions seen in RFLP184 isolates are viable. In: PRRS International Symposium Proceedings, vol. 8, Saint Louis, MO]...
  31. pmc Human papillomaviruses activate the ATM DNA damage pathway for viral genome amplification upon differentiation
    Cary A Moody
    Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
    PLoS Pathog 5:e1000605. 2009
    ..The infectious HPV life cycle is closely linked to the differentiation state of the host epithelia, with viral genome amplification, late gene expression and virion production restricted to suprabasal cells...
  32. pmc HIV-1 encoded candidate micro-RNAs and their cellular targets
    Yamina Bennasser
    Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892 0460, USA
    Retrovirology 1:43. 2004
    ..We propose that HIV has evolved to use vmiRNAs as a means to regulate cellular milieu for its benefit...
  33. ncbi The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome
    Andrew J Davison
    MRC Virology Unit, Institute of Virology, Church Street, Glasgow G11 5JR, UK
    J Gen Virol 84:17-28. 2003
    ..wild-type human cytomegalovirus (HCMV) is incompletely understood, on account of the size and complexity of the viral genome and because laboratory strains have undergone deletions and rearrangements during adaptation to growth in ..
  34. pmc A single mutation in chikungunya virus affects vector specificity and epidemic potential
    Konstantin A Tsetsarkin
    Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
    PLoS Pathog 3:e201. 2007
    ..Due to the widespread distribution of Ae. albopictus, this mutation increases the potential for CHIKV to permanently extend its range into Europe and the Americas...
  35. pmc Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity
    Robert Belshaw
    Department of Biological Sciences, Imperial College, Ascot, Berks, United Kingdom
    J Virol 79:12507-14. 2005
    ..This view of the family from a population perspective rather than a genome perspective will inform the current debate about a possible role of HERV-K(HML2) in human disease...
  36. pmc Restriction of foamy viruses by APOBEC cytidine deaminases
    Frédéric Delebecque
    Virus and Immunity Group, URA CNRS 1930, Institut Pasteur, 75724 Paris Cedex 15, France
    J Virol 80:605-14. 2006
    ..This antiviral activity is associated with cytidine editing of the viral genome. Both molecular FV clones and primary uncloned viruses were susceptible to APOBEC3G, and viral infectivity was ..
  37. doi Laboratory procedures to generate viral metagenomes
    Rebecca V Thurber
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nat Protoc 4:470-83. 2009
    ..Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in approximately 1 week...
  38. pmc Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?
    Tulio de Oliveira
    HIV Molecular Virology and Bioinformatics Laboratory, Africa Centre for Health and Population Studies, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu Natal, Durban 4013, South Africa
    Genetics 167:1047-58. 2004
    ..Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process...
  39. ncbi Hepatitis E virus (HEV): molecular cloning and sequencing of the full-length viral genome
    A W Tam
    Molecular Virology Department, Genelabs Incorporated, Redwood City, California 94063
    Virology 185:120-31. 1991
    ..These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family...
  40. pmc Genomic epidemiology of a dengue virus epidemic in urban Singapore
    Mark J Schreiber
    Novartis Institute for Tropical Diseases, Chromos, Singapore
    J Virol 83:4163-73. 2009
    ....
  41. pmc Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
    J Virol 79:884-95. 2005
    ..13 x 10(6) copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans...
  42. pmc Horizontal gene transfer and the evolution of microvirid coliphage genomes
    D R Rokyta
    Department of Biological Sciences, University of Idaho, Moscow, ID 83844 3051, USA
    J Bacteriol 188:1134-42. 2006
    ..Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages...
  43. ncbi Genetic diversity and evolution of hepatitis C virus--15 years on
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Gen Virol 85:3173-88. 2004
    ..These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses...
  44. pmc Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses
    Peter Simmonds
    Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 80:11124-40. 2006
    ..Overall, this study identifies common themes in the diversification process generating picornavirus serotypes that contribute to understanding of their evolution and pathogenicity...
  45. pmc Efficient infection by a recombinant Kaposi's sarcoma-associated herpesvirus cloned in a bacterial artificial chromosome: application for genetic analysis
    Fu Chun Zhou
    Department of Pediatrics, The University of Texas Health Science Center at San Antonio, 78229, USA
    J Virol 76:6185-96. 2002
    ..BAC36 virions established stable latent infection in 293 cells, harboring 1 to 2 copies of viral genome per cell and expressing viral latent proteins, with approximately 0...
  46. doi The virophage as a unique parasite of the giant mimivirus
    Bernard La Scola
    URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculte de Medecine, Universite de la Mediterranee, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
    Nature 455:100-4. 2008
    ..Considering its functional analogy with bacteriophages, we classify this virus as a virophage. The virophage could be a vehicle mediating lateral gene transfer between giant viruses...
  47. pmc The polycomb group protein Bmi1 binds to the herpes simplex virus 1 latent genome and maintains repressive histone marks during latency
    Dacia L Kwiatkowski
    Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, 32610 0266, USA
    J Virol 83:8173-81. 2009
    ..To our knowledge, these are the first data demonstrating that a virus can repress its gene transcription to enter latency by exploiting the mechanism of Polycomb-mediated repression...
  48. ncbi Polydnavirus genomes reflect their dual roles as mutualists and pathogens
    Bruce A Webb
    Department of Entomology, University of Kentucky, Lexington, KY 40506, USA
    Virology 347:160-74. 2006
    ....
  49. ncbi On the classification and nomenclature of baculoviruses: a proposal for revision
    J A Jehle
    Abteilung Phytomedizin, DLR Rheinpfalz, Neustadt Wstr, Germany
    Arch Virol 151:1257-66. 2006
    ....
  50. ncbi Genome sequence of a polydnavirus: insights into symbiotic virus evolution
    Eric Espagne
    Institut de Recherche sur la Biologie de l Insecte, CNRS UMR 6035, UFR Sciences et Techniques, Parc de Grandmont, 37200 Tours, France
    Science 306:286-9. 2004
    ..by a parasitoid wasp revealed a complex organization, resembling a eukaryote genomic region more than a viral genome. Although endocellular symbiont genomes have undergone a dramatic loss of genes, the evolution of symbiotic ..
  51. ncbi Complete genome sequences of all members of the species Human enterovirus A
    M Steven Oberste
    Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G 17, Atlanta, GA 30333, USA
    J Gen Virol 85:1597-607. 2004
    ..CVA6-Gdula clearly contains sequences that are also present in CVA10-Kowalik and CVA12-Texas-12, suggesting that these three strains have a shared evolutionary history despite their lack of similarity in the capsid region...
  52. pmc Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, EH9 1QH
    RNA 10:1337-51. 2004
    ..These findings potentially reconcile the rapid evolution of RNA viruses over short periods with the documented examples of extreme conservatism evident from their intimate coevolution with their hosts...
  53. doi Biodiversity and biogeography of phages in modern stromatolites and thrombolites
    Christelle Desnues
    Department of Biology, San Diego State University, San Diego, California 92182, USA
    Nature 452:340-3. 2008
    ..Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community...
  54. ncbi Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage phiPVL carrying Panton-Valentine leukocidin genes
    J Kaneko
    Department of Applied Biological Chemistry, Faculty of Agriculture, Tohoku University, Sendai 981 8555, Japan
    Gene 215:57-67. 1998
    ..aureus bacteriophages. The phiPVL genome was found to integrate into an ORF encoding an unknown protein comprising 725 amino acid residues with two leucine zipper-like motifs...
  55. pmc A highly prevalent and genetically diversified Picornaviridae genus in South Asian children
    Amit Kapoor
    Blood Systems Research Institute, San Francisco CA 94118, USA
    Proc Natl Acad Sci U S A 105:20482-7. 2008
    ....
  56. pmc Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs
    Livia Donaire
    Departamento de Biología de Plantas, Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, 28040 Madrid, Spain
    J Virol 82:5167-77. 2008
    ..or in combination, viral templates to promote synthesis of siRNAs of both polarities from all regions of the viral genome. The heterogeneous distribution profile of TRV siRNAs reveals differential contributions throughout the TRV ..
  57. ncbi Identification of a new human coronavirus
    Lia van der Hoek
    Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
    Nat Med 10:368-73. 2004
    ..The viral genome contains distinctive features, including a unique N-terminal fragment within the spike protein...
  58. doi The pathogenicity determinant of Citrus tristeza virus causing the seedling yellows syndrome maps at the 3'-terminal region of the viral genome
    Maria R Albiach-Marti
    Instituto Valenciano de Investigaciones Agrarias, Centro de Proteccion Vegetal y Biotecnologia, Crta Moncada Náquera Km 4 5, Moncada, 46113 Valencia, Spain
    Mol Plant Pathol 11:55-67. 2010
    ....
  59. pmc Evidence of recombination among enteroviruses
    J Santti
    MediCity Research Laboratory and Department of Virology, University of Turku, FIN 20520 Turku, National Public Health Institute, FIN 00300 Helsinki, Finland
    J Virol 73:8741-9. 1999
    ..Recombination breakpoints were detected in all genomic regions except the capsid protein coding region. Our results suggest that recombination is a significant and relatively frequent mechanism in the evolution of enterovirus genomes...
  60. pmc AP-1 homolog BZLF1 of Epstein-Barr virus has two essential functions dependent on the epigenetic state of the viral genome
    Markus Kalla
    Department of Gene Vectors, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, 81377 Munich, Germany
    Proc Natl Acad Sci U S A 107:850-5. 2010
    ..Our data indicate that the viral BZLF1 protein is crucial both to establish latency and to escape from it. Our data also indicate that EBV has evolved to appropriate its host's mode of methylating DNA for its own epigenetic regulation...
  61. pmc Evaluation of the lytic origins of replication of Kaposi's sarcoma-associated virus/human herpesvirus 8 in the context of the viral genome
    Yiyang Xu
    University of Nevada, Reno, Department of Microbiology, 1664 North Virginia Street, Howard Bldg 210, Reno, NV 89557, USA
    J Virol 80:9905-9. 2006
    ..origins, it is limited in its ability to evaluate the activity of replication origins in the context of the viral genome. To this end, we investigated the ability of a recombinant HHV8 bacterial artificial chromosome (BAC) to ..
  62. ncbi Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome
    Qin Yu
    Infectious Disease Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Struct Mol Biol 11:435-42. 2004
    ..We propose that the requirement for ssDNA accounts for the minus-strand mutations, the 5'-->3' graded frequency of deamination and the rare C-->T mutations...
  63. pmc Genome delivery and ion channel properties are altered in VP4 mutants of poliovirus
    Pranav Danthi
    Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock 72205, USA
    J Virol 77:5266-74. 2003
    ..Finally, uncoating and/or cytoplasmic delivery of the viral genome is altered in the 4028T mutants: the 4028T...
  64. ncbi Strand-specific compositional asymmetries in double-stranded DNA viruses
    A Grigoriev
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    Virus Res 60:1-19. 1999
    ..Use of cumulative skew plots for genome comparisons is demonstrated on the example of herpes simplex virus...
  65. pmc Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform
    Graham F Hatfull
    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
    PLoS Genet 2:e92. 2006
    ....
  66. ncbi The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance
    Lone Simonsen
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:1811-20. 2007
    ..belonged to a single lineage (the "N-lineage") characterized by 17 amino acid replacements across the viral genome. Further, our analysis revealed that the genesis of the N-lineage was due to a 4+4 segment reassortment event ..
  67. pmc Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population
    Marco Vignuzzi
    Department of Microbiology and Immunology, University of California, San Francisco, California 94143 2280, USA
    Nature 439:344-8. 2006
    ..Our study provides direct evidence for a fundamental prediction of the quasispecies theory and establishes a link between mutation rate, population dynamics and pathogenesis...
  68. doi Single-molecule DNA sequencing of a viral genome
    TIMOTHY D HARRIS
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, USA
    Science 320:106-9. 2008
    ..This demonstrates a strategy for high-throughput low-cost resequencing...
  69. pmc The marine viromes of four oceanic regions
    Florent E Angly
    Department of Biology, San Diego State University, San Diego, California, USA
    PLoS Biol 4:e368. 2006
    ..These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure...
  70. pmc Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome
    Vasily Tcherepanov
    Department of Microbiology and Biochemistry, University of Victoria, Victoria, BC, V8W 3P6, Canada
    BMC Genomics 7:150. 2006
    ....
  71. pmc The West Nile virus mutant spectrum is host-dependant and a determinant of mortality in mice
    Greta V S Jerzak
    The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Rd, Slingerlands, NY 12159, USA
    Virology 360:469-76. 2007
    ..These studies suggest that mosquitoes serve as sources for WNV genetic diversity, that birds are selective sieves, and that both the consensus sequence and the mutant spectrum contribute to WNV phenotype...
  72. pmc A full-genome phylogenetic analysis of varicella-zoster virus reveals a novel origin of replication-based genotyping scheme and evidence of recombination between major circulating clades
    Geoffrey A Peters
    National Microbiology Laboratory, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
    J Virol 80:9850-60. 2006
    ..The very low rate of single-nucleotide polymorphisms scattered across the genome made full-genome sequencing the only definitive method for identifying specific VZV recombination events...
  73. pmc Interaction of JC virus agno protein with T antigen modulates transcription and replication of the viral genome in glial cells
    M Safak
    Laboratory of Molecular Neurovirology, Center for Neurovirology and Cancer Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    J Virol 75:1476-86. 2001
    ..Here, we investigated the functional role of JCV Agno protein on transcription and replication of the viral genome in glial cells...
  74. pmc Bacteriophage genomics
    Graham F Hatfull
    Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA
    Curr Opin Microbiol 11:447-53. 2008
    ..With an estimated 10(31) bacterial and archael viruses in the biosphere, our view of the virosphere will draw into sharper focus as further bacteriophage genomes are characterized...
  75. doi Divergent picornavirus IRES elements
    Graham J Belsham
    National Veterinary Institute, Technical University of Denmark, Lindholm, DK 4771 Kalvehave, Denmark
    Virus Res 139:183-92. 2009
    ..The selection of the initiation codon by these distinct IRES elements is also discussed...
  76. pmc The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy
    Sherwood R Casjens
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
    J Bacteriol 187:1091-104. 2005
    ..Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence...
  77. ncbi Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus
    Juliana Velasco de Castro Oliveira
    Laboratório de Evolução Molecular e Bionformática, Departamento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, SP, Brazil
    J Gen Virol 87:3233-50. 2006
    ..fumiferana MNPV), sharing eight defining genes, and the Autographa californica MNPV (AcMNPV) lineage (AcMNPV, Rachiplusia ou NPV and Bombyx mori NPV), sharing nine defining genes...
  78. doi Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools
    Rob Lavigne
    Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B 3001, Belgium
    Res Microbiol 159:406-14. 2008
    ..Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes...
  79. ncbi The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution
    U A Gompels
    Department of Clinical Sciences, London School of Hygiene and Tropical Medicine, University of London, United Kingdom
    Virology 209:29-51. 1995
    ....
  80. ncbi The genome sequence and evolution of baculoviruses
    Elisabeth A Herniou
    Department of Biological Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, United Kingdom
    Annu Rev Entomol 48:211-34. 2003
    ..Examination of gene order conservation revealed a core gene cluster of four genes, helicase, lef-5, ac96, and 38K(ac98), whose relative positions are conserved in all baculovirus genomes...
  81. ncbi RNA virus mutations and fitness for survival
    E Domingo
    Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco, Spain
    Annu Rev Microbiol 51:151-78. 1997
    ..Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections...
  82. ncbi Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy
    Michael M Thomson
    Department of Viral Pathogenesis, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Ctra Majadahonda Pozuelo, 28220, Madrid, Majadahonda, Spain
    Lancet Infect Dis 2:461-71. 2002
    ....
  83. doi Relevance of RNA structure for the activity of picornavirus IRES elements
    Olga Fernandez-Miragall
    Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas Universidad Autonoma de Madrid, Cantoblanco 28049, Madrid, Spain
    Virus Res 139:172-82. 2009
    ....
  84. pmc Cloning the vaccinia virus genome as a bacterial artificial chromosome in Escherichia coli and recovery of infectious virus in mammalian cells
    Arban Domi
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 0445, USA
    Proc Natl Acad Sci U S A 99:12415-20. 2002
    ..Rescue of infectious VAC was consistently achieved by transfecting the VAC-BAC plasmids into mammalian cells that were infected with a helper nonreplicating fowlpox virus...
  85. ncbi Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
    Tong Zhou
    Key Laboratory of Molecular and Biomolecular Electronics of the Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China
    Biosystems 81:77-86. 2005
    ..However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes...
  86. pmc The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
    Nilu Goonetilleke
    Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, England, UK
    J Exp Med 206:1253-72. 2009
    ..These included clusters of mutations in envelope that were targeted by NAbs, a few isolated sites that reverted to the consensus sequence, and bystander mutations in linkage with T cell-driven escape...
  87. ncbi Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages
    H Brussow
    Nestle Research Centre, Nestec Ltd, CH 1000 Lausanne 26, Switzerland
    Mol Microbiol 39:213-22. 2001
    ..We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web-like phylogenies...
  88. ncbi A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase
    Alice K Inoue-Nagata
    Embrapa Hortaliças, Virology, Km 9, BR060, C Postal 218, 70359 970 Brasília, DF, Brazil
    J Virol Methods 116:209-11. 2004
    ..The use of this enzyme simplified the cloning steps and increased the cloning efficiency of the complete genome of a circular plant DNA virus...
  89. pmc Rapid genome sequencing of RNA viruses
    Tetsuya Mizutani
    Department of Virology 1, National Institute of Infectious Diseases, Musashimurayama City, Tokyo, Japan
    Emerg Infect Dis 13:322-4. 2007
    ..This method affords new opportunities to address the challenges of unknown or untypeable emerging viruses...
  90. pmc Construction and characterization of infectious intragenotypic and intergenotypic hepatitis C virus chimeras
    Thomas Pietschmann
    Department of Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
    Proc Natl Acad Sci U S A 103:7408-13. 2006
    ..Finally, we describe an E1-specific antiserum capable of neutralizing infectivity of all HCV chimeras...
  91. ncbi A newly discovered human pneumovirus isolated from young children with respiratory tract disease
    B G van den Hoogen
    Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
    Nat Med 7:719-24. 2001
    ..Serological studies showed that by the age of five years, virtually all children in the Netherlands have been exposed to human metapneumovirus and that the virus has been circulating in humans for at least 50 years...
  92. pmc Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus
    Christopher A Desjardins
    The Institute for Genomic Research, J Craig Venter Institute, Rockville, Maryland, USA
    BMC Microbiol 7:61. 2007
    ..Here we describe a 223 kbp region of Glyptapanteles indiensis genomic DNA which contains a part of the G. indiensis bracovirus (GiBV) proviral genome...
  93. pmc Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virol J 6:223. 2009
    ....
  94. ncbi Targets for human encoded microRNAs in HIV genes
    Manoj Hariharan
    G N Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    Biochem Biophys Res Commun 337:1214-8. 2005
    ..This is the first report of human microRNAs which can target crucial HIV-1 genes including the nef gene, which plays an important role in delayed disease progression...
  95. pmc Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA
    Takeshi Saito
    Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98195 7650, USA
    Nature 454:523-7. 2008
    ....
  96. pmc Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin
    Melinda J Mayer
    Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom
    J Bacteriol 190:6734-40. 2008
    ..To investigate a method for the protected delivery and production of the lysin in the gastrointestinal tract, we demonstrated the expression of active CD27L endolysin in the lactic acid bacterium Lactococcus lactis MG1363...
  97. ncbi Here a virus, there a virus, everywhere the same virus?
    Mya Breitbart
    Biology Department, LS301, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182 USA
    Trends Microbiol 13:278-84. 2005
    ..Together, these findings suggest that viral diversity could be high on a local scale but relatively limited globally. Also, by moving between environments, viruses can facilitate horizontal gene transfer...
  98. pmc Identification of a novel polyomavirus from patients with acute respiratory tract infections
    Anne M Gaynor
    Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Pathog 3:e64. 2007
    ..The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen...
  99. pmc Possible role of dimerization in human immunodeficiency virus type 1 genome RNA packaging
    Jun ichi Sakuragi
    Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita City, Japan
    J Virol 77:4060-9. 2003
    ..Therefore, it is suggested that RNA dimerization is a part of RNA packaging, which requires multiple steps...
  100. pmc Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica
    Dennis H Bamford
    Department of Biological and Environmental Sciences, P O Box 56 Viikinkaari 5, University of Helsinki, FIN 00014 Helsinki, Finland
    J Virol 79:9097-107. 2005
    ....
  101. pmc The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1
    Andre Villegas
    Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, 110 Stone Road West, Guelph, ON, N1G 3W4, Canada
    Virol J 6:41. 2009
    ....

Research Grants94

  1. Roles for microRNA-122 in hepatitis C virus RNA amplification
    Peter Sarnow; Fiscal Year: 2013
    ..two molecules of a liver-specific microRNA, miR-122, resulting in a novel, unprecedented upregulation of the viral genome. Sequestration of miR-122 in HCV-infected cultured cells or in livers of infected chimpanzees leads to a ..
  2. Structure and Function of the Hepatitis C Virus Genome
    Peter Sarnow; Fiscal Year: 2013
    ..functions as an internal ribosome entry site (IRES) that can directly recruit 40S ribosomal subunits to the viral genome. Specifically, we will employ biochemical, NMR and single-molecule fluorescence approaches to explore the ..
  3. Regulation of EBV Latency by EBNA1
    Paul M Lieberman; Fiscal Year: 2013
    ..We now propose to advance these studies to better understand the role of EBNA1 in viral genome maintenance and host-cell survival during latent infection...
  4. Regulation of KSHV Latency
    Paul M Lieberman; Fiscal Year: 2013
    ..Latent infection is characterized by the transcription of several viral genes associated with viral genome stability and host-cell survival...
  5. Regulation of HIV-1 by Rad51 in CNS cells
    Kamel Khalili; Fiscal Year: 2013
    ..system with HIV-1 can trigger a cascade of defense mechanisms that are aimed at blocking expression of the viral genome at various stages of its life cycle...
  6. Roles of Host Kinases in Paramyxovirus RNA Synthesis
    Biao He; Fiscal Year: 2010
    ..RNA synthesis using a mini-genome replicon system, mutating these putative CKII phosphorylation sites within a viral genome has no effect on viral RNA synthesis, leading to the theory that phosphorylation, at least phosphorylation by ..
  7. Viral And host mechanisms that tilt the HSV lytic/latent balance
    Donald M Coen; Fiscal Year: 2013
    ..of trigeminal ganglia: LAT acts as a long noncoding RNA that recruits histone-modifying complexes to the viral genome, b...
  8. Mechanistic Studies of HCV E2
    Joseph Marcotrigiano; Fiscal Year: 2013
    ..and other flaviviruses, HCV infection requires fusion between viral and host cell membrane before the viral genome can be released into the host cell cytosol...
  9. Mechanisms of ENaC Inhibition by Replicating Influenza Virus: Role of M2 Protein
    Sadis Matalon; Fiscal Year: 2012
    ..the rational basis for the development of new therapeutic strategies, against a highly conserved region of the viral genome to knockdown M2 expression, and thus broadly and effectively decrease flu induced pulmonary edema and ..
  10. Peptide inhbitors of influenza entry-FAST TRACK
    Russell B Wilson; Fiscal Year: 2011
    ..a myxovirus that readily develops new strains through a process of reassortment and mutation of the segmented viral genome. Highly virulent strains of type A influenza virus can produce epidemics and pandemics...
  11. Molecular Biology of Eukaryotic Viruses
    Bert L Semler; Fiscal Year: 2012
    ..The research programs of faculty participants include the study of viral genome replication, viral-specific transcription, RNA processing, viral translation and protein processing, assembly ..
  12. Novel vaccine to CMV based on a disc virus
    Alistair McGregor; Fiscal Year: 2010
    ..be further augmented by introducing a second copy of the major neutralizing antigen, glycoprotein gB, into the viral genome. We also hypothesize that the co-administration of the vaccine strain with a pro-inflammatory cytokine (IL-12) ..
  13. Antisense Mediated Treatment of Hepatitis B Virus Infection
    STEFAN FRANK WIELAND; Fiscal Year: 2013
    ..I have extensive experience using HBV transgenic mice that express and replicate HBV from an integrated viral genome to study viral gene expression, replication, virus production and inhibition of these steps by interferon-..
  14. Identification and characterization of inhibitors for hantavirus replication
    MOHAMMAD AYOUB MIR; Fiscal Year: 2013
    ..N protein also plays a key role in encapsidation and packaging of viral genome. All minus stranded, segmented RNA viruses have genome segments that are found in "panhandle" conformation via ..
  15. Retroviral Subversion of ERAD and Intrinsic Immunity
    JAQUELIN PAGE DUDLEY; Fiscal Year: 2013
    ..We propose that MMTV is the first virus to antagonize AID to avoid both viral genome mutation and maturation of the MMTV-specific antibody response...
  16. Encapsidation of the poxvirus genome
    Paula Traktman; Fiscal Year: 2012
    ..At its essence, a productive viral infection requires that the viral genome be efficiently replicated and packaged into nascent, infectious virions...
  17. The influenza A virus nucleoprotein: structure and function
    Yizhi Jane Tao; Fiscal Year: 2012
    ..NP is abundantly made in infected cells, and is essential for important viral processes such as viral genome trafficking, viral RNA replication, and virus assembly...
  18. Intracellular immunization strategy in inhibit HCV related liver cancer
    Srikanta Dash; Fiscal Year: 2010
    ..HCV NS3 protein, which has multiple enzymatic activities (protease, helicase and NTPase) that are crucial for viral genome replication...
  19. ASM Conference on Viral Genome Replication
    Sean P J Whelan; Fiscal Year: 2011
    ..Funds are requested to provide partial support for a new American Society of Microbiology conference on Viral Genome Replication, which will be held from February 6-9, 2011 in Banff, Alberta...
  20. LANA and Cellular Gene Expression
    ROLF F RENNE; Fiscal Year: 2013
    ..SA2: Study LANA's contribution to the epigenetic state of the viral genome and transcriptional regulation of both host and viral genes during the establishment of latency...
  21. BETR Therapy for Herpesvirus-Associated Tumors
    Martin G Pomper; Fiscal Year: 2013
    ..Because the viral genome is latent, it must be activated using a pharmacologic inducer such as bortezomib...
  22. Viral Gene Expression to Therapeutic Levels in Models of Heart Failure
    Joseph E Rabinowitz; Fiscal Year: 2012
    ..Quantification of luciferase expression and viral genome copy (vg) number in the heart after delivery of equivalent numbers of viral particles demonstrates that AAV9 ..
  23. Assay Development for Inhibitors of KSHV
    Paul M Lieberman; Fiscal Year: 2010
    ..Disruption of LANA by siRNA depletion or gene deletion blocks viral genome persistence during latent infection...
  24. GENETICS OF HERPESVIRUS TRANSFORMATION
    David M Knipe; Fiscal Year: 2013
    ..Define the mechanisms of chromatin regulation on viral DNA through targeting of the viral genome to the nuclear lamina in studies to determine the viral and host gene products needed for peripheral targeting ..
  25. Surrogate endpoints for correlating protective immunity in response to influenza
    Gary Fujii; Fiscal Year: 2010
    ..Rapid mutations and rearrangements of the viral genome allow the virus to evade host immune responses, making the frequent development of vaccines to new viral ..
  26. Generation and Evaluation of KSHV VLPs as Vaccines
    GARY S contact HAYWARD; Fiscal Year: 2010
    ..because of the large size and complexity of this virus, as well as the fact that as a tumor forming virus the viral genome and oncogenes would have to be absent or removed...
  27. Papillomavirus E2 Functions: Cellular Regulation and Effectors
    Peter M Howley; Fiscal Year: 2013
    ..a transcription factor that can activate viral transcription through E2 responsive elements located within the viral genome. E2 has additional functions however, and can serve either as a transactivator or a repressor of viral ..
  28. Mechanism of RNA synthesis and 5'-capping by dengue virus NS5 polymerase
    Kyung H Choi; Fiscal Year: 2013
    ..and helicase as well as other viral and unidentified cellular proteins, is responsible for copying the viral genome. During replication, 5'-RNA capping of the nascent strand occurs along with RNA synthesis...
  29. Structural Studies of Alphavirus Membrane Fusion In Situ
    Wei Zhang; Fiscal Year: 2010
    ..environment in the endosome induces fusion of the viral and endosomal membranes, allowing delivery of the viral genome into the cytoplasm of the infected cell...
  30. Novel Tetravalent Vaccines for Dengue Virus
    ROBERT GERALD WHALEN; Fiscal Year: 2013
    ..multiprotein structures that mimic the organization and conformation of authentic native viruses but lack the viral genome. Past experience with approved vaccines (HBV, HPV) has shown that recombinant VLPs are potent immunogens and ..
  31. Interconnectivity between genome packagaing and other viral functions
    A L Rao; Fiscal Year: 2010
    ..This system not only allowed efficient expression of viral genome components either autonomously or synchronously in plant cells, but also effectively uncoupled replication from ..
  32. Release and trafficking of JC polyomavirus genomes and implications in AIDS
    CHRISTIAN DOUGLAS STUART NELSON; Fiscal Year: 2012
    ..project proposes to increase our understanding of JCV pathogenesis, by studying exposure and delivery of the viral genome to the host cell nucleus...
  33. Chromatin and Herpes Simplex Virus Latency
    David M Knipe; Fiscal Year: 2013
    ..b. LAT acts as a long noncoding RNA that recruits histone-modifying complexes to the viral genome. c...
  34. The Viral Life Cycle of Human Endogenous Retrovirus Type K
    Derek Dube; Fiscal Year: 2013
    ..the nucleic acid constituents of HERV-K viral genomes, clarify the mechanism by which HERV-K packages its viral genome, and ascertain the importance of viral DNA genomes on the historical infection process of HERV-K...
  35. KSHV Lytic DNA Replication and its Control Mechanism
    Subhash C Verma; Fiscal Year: 2013
    ..analysis of the replicated DNA (SMARD), will determine preferentially used replication initiation origin for viral genome replication in various cell backgrounds...
  36. Analysis of Coronavirus-Host Cell Interactions
    Shinji Makino; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): The translation of the viral genome begins immediately after coronavirus (CoV) infection to produce two large polyproteins that are processed into 15 or 16 mature, nonstructural proteins...
  37. A new synergy for flavivirus therapy: RNAi enhancement and viral mutagens
    KATHRYN ALYCE HANLEY; Fiscal Year: 2012
    ..eukaryotes that acts by targeting small interfering RNA's (siRNA's) to complementary regions in the viral genome;genomes bound to siRNA's are marked for cleavage and degradation...
  38. Targeting the DNA Damage Response for the Treatment of Herpes Simplex Labialis
    WILLIAM DONEGAN; Fiscal Year: 2013
    ..validity to this hypothesis by analyzing the impact of ATM activation on the chromatin packaging state of the viral genome. We will also evaluate how recombination of the viral genome is impacted by ATM activity...
  39. Genetic Analysis of Molecular Interactions in Coronavirus Replication
    PAUL SCOTT MASTERS; Fiscal Year: 2013
    ..crucial role of N protein in the initiation of coronavirus infection, which, we hypothesize, is to deliver the viral genome to the nascent replication-transcription complex...
  40. Dengue Virus Genome Encapsidation and Its Interplay with Host Lipid Droplets
    Andrea Gamarnik; Fiscal Year: 2013
    ..The viral genome is an RNA molecule that plays multiple roles during viral replication...
  41. hnRNP A1 inhibition of HIV-1 replication
    Massimo Caputi; Fiscal Year: 2011
    ..Transcription and processing of the viral genome involves interactions between viral RNA sequences, viral proteins and host cell factors, which may constitute ..
  42. Viral evolution in peropheral macrophages and brain during progression to AIDS
    Marco Salemi; Fiscal Year: 2013
    ..3kb fragment, including gp160, nef and 5'LTR, of the viral genome, as well as some full-length genomes from selected tissues...
  43. Chronic CMV infection in the elderly: diagnosis and link to chronic inflammation
    Sean X Leng; Fiscal Year: 2013
    ..CMV biology indicates that while most people are exposed to the virus, CMV can persist in some with the viral genome (DNA) harbored in peripheral blood monocytes, representing a chronic infection...
  44. RASCAL: a new tropism determinant encoded by human cytomegalovirus?
    Laura Hertel; Fiscal Year: 2012
    ..cell types by enhancing trafficking of penetrated virions towards the nucleus, or the nuclear deposition of the viral genome during entry, two critical steps for the establishment of productive infections in EPC, EC and DC...
  45. Regulation of DNA Metabolism During Herpes Simplex Virus-1 Infection
    KEVIN FRANCIS BRYANT; Fiscal Year: 2010
    ..that chromatin-remodeling proteins play a role in HSV-1 biology by remodeling the chromatin state of the viral genome and that viral proteins regulate the activity of these cellular enzymes...
  46. Dendritic Cell Restriction and Innate Immune Sensing of HIV Infection
    Dan Littman; Fiscal Year: 2011
    ..are resistant to productive viral replication due to a block that occurs before reverse transcription of the viral genome can be completed...
  47. Interdisciplinary Training in Virology and Gene Therapy
    Ren Sun; Fiscal Year: 2013
    ..The research interests of our faculty encompass viral entry, viral gene expression regulation, replication of viral genome, cell biology during viral infection, viral particle assembly, viral carcinogenesis and viral immunology, as ..
  48. Cellular mechanisms of transcriptional regulation near DNA double-strand breaks
    Nabil Sayed; Fiscal Year: 2013
    ..by ICP0, a viral protein produced during HSV-1 infection to counteract ND10 silencing mechanisms and promote viral genome transcription and replication...
  49. Transcriptomic and Proteomic Approaches to Discovering Viral Causes for Human Hem
    Yuan Chang; Fiscal Year: 2013
    ..studies showing that MCV, a common commensal skin infection, initiates tumors after specific mutations to the viral genome. This is a new mechanism for carcinogenesis that will not necessarily be found through cancer cell genome ..
  50. RNA processing in non-segmented minus-strand RNA viruses
    Sean P J Whelan; Fiscal Year: 2013
    ..Understanding how those activities are controlled to ensure that the viral genome is expressed is of intrinsic interest and has the potential to impact the development of antiviral drugs and ..
  51. Hepatitis C Virus Replication and Intracellular Membrane Rearrangement
    Kouacou Konan; Fiscal Year: 2009
    ..Various reports have shown that the web contains HCV nonstructural proteins as well as the viral genome, suggesting that this novel membrane might be the site where HCV genome replication occurs...
  52. Epigenetic determinants of Epstein-Barr virus and cellular DNA in oral diseases
    SHANNON CELESTE KENNEY; Fiscal Year: 2013
    ..by Z versus R, b) epithelial differentiation regulates EBV reactivation at least partially via effects on viral genome methylation and 5-hmC modification, and c) EBV+ NPC tumors only occur in undifferentiated epithelial cells that ..
  53. Molecular biology of viral capsids
    CHENG C KAO; Fiscal Year: 2013
    ..have many essential roles during a virus infection, from the regulation of translation to the protection of the viral genome against cellular innate immune detection...
  54. Vif Antagonism: Lead Discovery and SAR
    Tariq M Rana; Fiscal Year: 2013
    ..A3G incorporation into virions leading to less infectious viruses, and enhanced cytidine deamination of the viral genome. These studies provide the first evidence that the HIV-1 Vif-A3G axis is a valid target for developing small ..
  55. VACCINIA DNA REPLICATION
    Paula Traktman; Fiscal Year: 2013
    ..DNA ligase and the G5 protein, which has homology to FEN1 nucleases, in the replication and maturation of the viral genome. AIM III: Analysis of the assembly and structure of viral replication factories...
  56. Mechanisms of Epstein-Barr Virus Persistence
    Jeffery T Sample; Fiscal Year: 2013
    ..The EBNAs primarily function as transcription factors (EBNA1 is also the viral genome-maintenance protein) to promote virus persistence through their regulation of cellular and viral latency-gene ..
  57. Genome Persistence of KSHV
    Erle S Robertson; Fiscal Year: 2013
    ..a number of chromosomal proteins which are important for tethering the viral proteins and segregation of the viral genome to new daughter cells...
  58. REPRESSION AND ACTIVATION OF PERSISTING HSV GENOMES
    Neal A DeLuca; Fiscal Year: 2013
    ..The repression seen during latency is due to the chromatinization the viral genome. The repressors that mediate and maintain chromatin on the viral genome are not known...
  59. Rational Design of Live Attenuated Influenza A Vaccine Candidates
    Eckard Wimmer; Fiscal Year: 2013
    ..Attenuation in our system is achieved via designing hundreds of synonymous nucleotide changes across the viral genome. This rational gene design approach allows Codagenix Inc...
  60. The Role of Host-Encoded microRNAs in Maintaining Measles Virus Persistence
    Glenn F Rall; Fiscal Year: 2013
    ..be placed on genes within interferon signaling pathways (Aim 1), and those miRs that may directly bind to the viral genome (Aim 2)...
  61. HPV Persistence and Head and Neck Cancer
    LUBOMIR TUREK; Fiscal Year: 2013
    ..In clinical cancer specimens, the viral genome often is disrupted and integrated in the cellular genome...
  62. T-antigen Binding to the Merkel Cell Carcinoma Virus Origin
    ALEX ANDREW BOHM; Fiscal Year: 2010
    ..for origin recognition, DNA melting and the recruitment of host cell proteins that initiate replication of the viral genome. Previously we have determined crystal structures of the T-antigen domain that binds the GAGGC sequence from ..
  63. Inhibitors of Kaposi???s Sarcoma Herpesvirus
    Kenneth M Kaye; Fiscal Year: 2011
    ..KSHV latently infects tumor cells. In latent infection, the viral genome persists in tumor cells as a multiple copy, extrachromosomal plasmid (episome)...
  64. Role of DNA damage in the early steps of HSV infection and latency in neurons
    Matthew D Weitzman; Fiscal Year: 2013
    ..is to define the role of the DNA damage response in circularization and nucleosome deposition on the incoming viral genome at the earliest stages of infection, and to determine how this impacts the decision to form lytic or latent HSV ..
  65. Mechanism of Brd4-mediated papillomavirus host interactions
    Jianxin You; Fiscal Year: 2013
    ..HPV life cycle that is tightly linked to the differentiation program of host epithelium, E2 ensures that the viral genome is established, replicated and maintained in the early-infected basal epithelial cells...
  66. Role of HIV-1 IN during reverse transcription and uncoating
    Samson A Chow; Fiscal Year: 2013
    ..Retroviral integrase (IN) catalyzes the essential step of integrating the double-stranded DNA copy of the viral genome into the chromosome of an infected cell...
  67. Discovery of Anti-HBV cccDNA Compounds from a Unique Natural Products Collection
    Andrea Cuconati; Fiscal Year: 2013
    ..from a stably integrated, linear, inducible HBV genome (transgene), leading to replication of full-length viral genome and cccDNA formation;subsequently, intact HBeAg RNA and protein are only made from transcripts produced from ..
  68. Structure and Function of Flaviviruses
    Michael G Rossmann; Fiscal Year: 2013
    ..This should initiate fusion with the host cell endoplasmi membrane during endocytosis and, eventually, trigger release of the viral genome into the host cell's cytoplasm.
  69. KSHV Genome Replication during Primary Infection
    Subhash C Verma; Fiscal Year: 2013
    ..Interestingly, latent virus replicates only once per cell cycle thus suggests tat viral genome amplifies during primary infection before establishing latency...
  70. RNA As A Therapeutic Target
    Webster L Santos; Fiscal Year: 2013
    ..TAR and RRE RNAs are well-conserved noncoding sequences in the viral genome with defined targetable structures...
  71. TARGETED siRNA DELIVERY AS AN ANTI-HIV MICROBICIDE
    DEREK MICHAEL DYKXHOORN; Fiscal Year: 2013
    ..Therefore, even if therapeutic approaches can inhibit new virus production, the viral genome remains intact and competent...
  72. CD8 T Cell Response to Murine Cytomegalovirus
    Ann B Hill; Fiscal Year: 2013
    ..use an iterative process of organ digestion, cell sorting and bioassays to identify the cells that carry the viral genome and the cells that present antigen to T cells...
  73. Transforming Mechanisms of Merkel Cell Polyoma Virus
    James A DeCaprio; Fiscal Year: 2013
    ..susceptible to transformation by MCPyV since no other human tumor has been reported to contain integrated MCPyV viral genome. This proposed project addresses these critical barriers by building on a recent discovery from my research ..
  74. New Models and Treatments for AIDS-related Lymphoma
    SHANNON CELESTE KENNEY; Fiscal Year: 2013
    ..of two EBV latent proteins (LMP1 and LMP2A) for the establishment of lymphomas in the context of an intact viral genome, and in the presence or absence of a functional immune system...
  75. Structure and Function of the Hepatitis C Virus Genome
    PETER contact SARNOW; Fiscal Year: 2010
    ..functions as an internal ribosome entry site (IRES) that can directly recruit 40S ribosomal subunits to the viral genome. Specifically, we will employ biochemical, NMR and single-molecule fluorescence approaches to explore the ..
  76. RNA Structure-Function Relationships in a Dengue Virus Genome
    ELIZABETH ANN DETHOFF; Fiscal Year: 2013
    ..The RNA structures in the viral genome essential for dengue replication are potential targets, but we currently have only a limited knowledge of a few ..
  77. Exploring the role of microtubules in HIV-1 uncoating
    Edward M Campbell; Fiscal Year: 2013
    ..At some point prior to the nuclear import of the viral genome, the virus undergoes the poorly understood process of uncoating, defined as the disassembly of the assembled ..
  78. Targeting the epigenome of gammaherpesviruses in oral disease
    Dirk P Dittmer; Fiscal Year: 2013
    ..The gammaherpesviruses establish life-long latency in the host. During latency the viral genome is chromatinized by host factors, and viral gene expression is extremely limited during latency...
  79. Mechanism of HTLV-1 Tax-mediated activation of CDK6 transcription.
    ISABELLE MICHELE LEMASSON; Fiscal Year: 2010
    ..chromosomally integrated HTLV-1 genome and by stimulating cell proliferation, which both serve to replicate the viral genome. Stimulation of cell proliferation is also paramount to the persistence of HTLV-1 infection and is believed to ..
  80. MECHANISM OF LATENCY OF HERPES SIMPLEX VIRUS
    Nigel Fraser; Fiscal Year: 2007
    ..We have previously used mouse model systems of HSV latency to study physical state of the latent viral genome, and to initiate studies on viral gene expression during latency...
  81. Adenovirus Persistence in Human Lymphoid Tissues
    Linda Gooding; Fiscal Year: 2007
    ..quantitation by real time PCR to evaluate the number of virus-containing cells and the number of copies of the viral genome per cell. Specific aim 2 will analyze the viral genome in lymphoid tissues...
  82. Pittsburgh Center for HIV Protein Interactions (PCHPI)
    Angela M Gronenborn; Fiscal Year: 2013
    ..with the host after engagement of cell surface receptors and membrane fusion and before integration of the viral genome into that of the host, the so called "early events"...
  83. An HBV polymerase RNA binding assay suitable for inhibitor screening
    Feng Cao; Fiscal Year: 2009
    ..DHBV) reverse transcriptase that together form the site where the enzyme first binds to the RNA form of the viral genome. Disrupting RNA binding at the T3:RT1 site blocks reverse transcription...
  84. Transduction of the Mouse Auditory System with AAV
    DIANA LURIE; Fiscal Year: 2003
    ..In contrast, AAV is particularly attractive as a gene delivery system because 96% of its viral genome has been removed...
  85. MECHANISTIC STUDIES ON VIRAL ASSEMBLY
    CARLOS CATALANO; Fiscal Year: 1999
    ..One of the final steps in viral assembly is the packaging of the viral genome into a protective protein coat known as the capsid, or head...
  86. HSV LATENCY AND MECHANISMS OF GENE SILENCING
    Joseph Glorioso; Fiscal Year: 2000
    ..be inoculated into the hippocampus of rat brain and the activity of the promoters relative to the number of viral genome equivalents will be determined by RT-PCR...
  87. A Synthetic Human Cytomegalovirus Vaccine Platform
    Sanjay Vashee; Fiscal Year: 2013
    ..clones of CMV directly from sequence information without prior tissue culture, b) result in the largest viral genome synthesized to date, c) revolutionize the genetic manipulation of herpesviral genomes as well as that of other ..
  88. Developing a yeast system to study virus-host interactions in Mononegavirales
    VALERY GRDZELISHVILI; Fiscal Year: 2009
    ..and optimize a unique yeast system for systematic identification and characterization of host factors of viral genome replication and gene expression in nonsegmented negative-strand (NNS) RNA viruses (taxonomic order ..
  89. PATHOGENESIS OF FELINE LEUKEMIA VIRUS INDUCED AIDS
    Edward Hoover; Fiscal Year: 1993
    ..which coexisted with a genetically closely related, highly replication competent but apathogenic common from viral genome (clone 61C s the prototype), which coexisted with a genetically closely related, highly replication competent ..
  90. Alteration of Rb in HTLV-1 transformed cells
    Fatah Kashanchi; Fiscal Year: 2005
    ..Tax, the viral oncoprotein encoded within the pX region of the viral genome, is considered a major contributor to cell cycle deregulation in HTLV-I transformed cells by targeting such ..
  91. Biochemical and structural characterization of self-assembling viral particles
    REBECCA ETHEL TAUROG; Fiscal Year: 2010
    ..The virus is composed of a coat protein wrapped around the linear dsDNA viral genome;at the termini of the virion are a plug and three tail fibers...
  92. MOLECULAR RECOGNITION OF HIV1 PRIMER TRNA LYS
    Karin Musier Forsyth; Fiscal Year: 2001
    ..transcription, the 18 nucleotides at the 3' end of this tRNA are annealed to a complementary sequence on the viral genome called the primer binding site (PBS)...
  93. Antiviral Compounds for Human Papillomavirus 16
    Christopher Fisher; Fiscal Year: 2005
    ..One reason for the lack of treatment alternatives is the small size of the viral genome, and the corresponding lack of antivirai targets...
  94. Role of Targeted Mutations in ViF on SHIV Pathogenesis
    Edward Stephens; Fiscal Year: 2006
    ..DNA and studies suggest that this could be a mechanism for the introduction of genetic variation in the viral genome. Domains have now been identified on the Vif protein that interact with the APOBEC3G and the interact with the ..