P Simmonds

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. 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
  2. pmc Reconstructing the origins of human hepatitis viruses
    P Simmonds
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    Philos Trans R Soc Lond B Biol Sci 356:1013-26. 2001
  3. pmc Genetics, recombination and clinical features of human rhinovirus species C (HRV-C) infections; interactions of HRV-C with other respiratory viruses
    Anne Wisdom
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    PLoS ONE 4:e8518. 2009
  4. pmc Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types
    Chloe L McIntyre
    Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
    J Gen Virol 94:1791-806. 2013
  5. pmc Nonprimate hepaciviruses in domestic horses, United kingdom
    Sinéad Lyons
    University of Edinburgh, Edinburgh, Scotland, UK
    Emerg Infect Dis 18:1976-82. 2012
  6. pmc The influence of viral RNA secondary structure on interactions with innate host cell defences
    Jeroen Witteveldt
    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
    Nucleic Acids Res 42:3314-29. 2014
  7. pmc The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
    Nicky J Atkinson
    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
    Nucleic Acids Res 42:4527-45. 2014
  8. pmc Changing epidemiology of human parvovirus 4 infection in sub-Saharan Africa
    Colin P Sharp
    University of Edinburgh, Edinburgh, Scotland, UK
    Emerg Infect Dis 16:1605-7. 2010
  9. pmc Absence of detectable replication of human bocavirus species 2 in respiratory tract
    Thaweesak Chieochansin
    Chulalongkorn University and Hospital, Bangkok, Thailand
    Emerg Infect Dis 15:1503-5. 2009
  10. pmc Influence of genome-scale RNA structure disruption on the replication of murine norovirus--similar replication kinetics in cell culture but attenuation of viral fitness in vivo
    Nora McFadden
    Division of Infection and Immunity, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
    Nucleic Acids Res 41:6316-31. 2013

Research Grants

Detail Information

Publications112 found, 100 shown here

  1. 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...
  2. pmc Reconstructing the origins of human hepatitis viruses
    P Simmonds
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    Philos Trans R Soc Lond B Biol Sci 356:1013-26. 2001
    ..Large population sizes and intense selection pressures that optimize fitness may be additional factors that set virus evolution apart from that of their hosts...
  3. pmc Genetics, recombination and clinical features of human rhinovirus species C (HRV-C) infections; interactions of HRV-C with other respiratory viruses
    Anne Wisdom
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    PLoS ONE 4:e8518. 2009
    ..HRV-C's disease associations, its prevalence and evidence for interfering effects on other respiratory viruses mandates incorporation of rhinoviruses into future diagnostic virology screening...
  4. pmc Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types
    Chloe L McIntyre
    Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
    J Gen Virol 94:1791-806. 2013
    ..Genotypic assignment and identification of HRV types will be of considerable value in the future investigation of type-associated differences in disease outcomes, transmission and epidemiology. ..
  5. pmc Nonprimate hepaciviruses in domestic horses, United kingdom
    Sinéad Lyons
    University of Edinburgh, Edinburgh, Scotland, UK
    Emerg Infect Dis 18:1976-82. 2012
    ..Disease associations and host range of nonprimate hepaciviruses warrant further investigation...
  6. pmc The influence of viral RNA secondary structure on interactions with innate host cell defences
    Jeroen Witteveldt
    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
    Nucleic Acids Res 42:3314-29. 2014
    ..This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses. ..
  7. pmc The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
    Nicky J Atkinson
    Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
    Nucleic Acids Res 42:4527-45. 2014
    ....
  8. pmc Changing epidemiology of human parvovirus 4 infection in sub-Saharan Africa
    Colin P Sharp
    University of Edinburgh, Edinburgh, Scotland, UK
    Emerg Infect Dis 16:1605-7. 2010
    ....
  9. pmc Absence of detectable replication of human bocavirus species 2 in respiratory tract
    Thaweesak Chieochansin
    Chulalongkorn University and Hospital, Bangkok, Thailand
    Emerg Infect Dis 15:1503-5. 2009
    ..Frequent HBoV-2 detection in fecal samples indicated widespread circulation in the United Kingdom and Thailand, but its lack of detection among 6,524 respiratory samples indicates likely differences from HBoV-1 in tropism/pathogenesis...
  10. pmc Influence of genome-scale RNA structure disruption on the replication of murine norovirus--similar replication kinetics in cell culture but attenuation of viral fitness in vivo
    Nora McFadden
    Division of Infection and Immunity, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
    Nucleic Acids Res 41:6316-31. 2013
    ..GORS plays no role in basic replication of MNV but potentially contributes to viral fitness and persistence in vivo. ..
  11. pmc Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla--selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses
    Peter Simmonds
    Division of Infection and Immunity, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
    BMC Genomics 14:610. 2013
    ....
  12. doi request reprint The origin of hepatitis C virus
    Peter Simmonds
    Roslin Institute University of Edinburgh Easter Bush, Edinburgh, UK
    Curr Top Microbiol Immunol 369:1-15. 2013
    ..Further research on a much wider range of mammals is needed to better understand the true genetic diversity of HCV-like viruses and their host ranges in the search for the ultimate origin of HCV in humans...
  13. pmc Independent evolution of macrophage-tropism and increased charge between HIV-1 R5 envelopes present in brain and immune tissue
    Maria Paz Gonzalez-Perez
    Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01605 2377, USA
    Retrovirology 9:20. 2012
    ..To further investigate the tropism and charge of HIV-1 viruses in late disease, we evaluated the properties of HIV-1 envelopes amplified from immune and brain tissues of AIDS patients with neurological complications...
  14. pmc SSE: a nucleotide and amino acid sequence analysis platform
    Peter Simmonds
    Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Main Road, Edinburgh EH9 3JT, UK
    BMC Res Notes 5:50. 2012
    ..abstract:..
  15. pmc Variation in HIV-1 R5 macrophage-tropism correlates with sensitivity to reagents that block envelope: CD4 interactions but not with sensitivity to other entry inhibitors
    Paul J Peters
    Center for AIDS Research, Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, 373 Plantation Street, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Retrovirology 5:5. 2008
    ..These R5 envelopes conferred a wide range of macrophage tropism and included highly macrophage-tropic variants from brain and non-macrophage-tropic variants from lymph node...
  16. ncbi request reprint A third genotype of the human parvovirus PARV4 in sub-Saharan Africa
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Gen Virol 89:2299-302. 2008
    ....
  17. pmc Parenteral transmission of the novel human parvovirus PARV4
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, Scotland, United Kingdom
    Emerg Infect Dis 13:1386-8. 2007
    ..Predominantly parenteral routes of transmission were demonstrated by infection restricted to injection drug users and persons with hemophilia and absence of infection in homosexual men with AIDS and low-risk controls...
  18. ncbi request reprint Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    Hepatology 42:962-73. 2005
    ..In conclusion, these proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future...
  19. 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...
  20. 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
    ....
  21. ncbi request reprint 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...
  22. pmc Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, EH9 1QH, UK
    Nucleic Acids Res 36:2530-46. 2008
    ..This study provides comprehensive bioinformatic resources for future functional studies of MNV and other caliciviruses...
  23. pmc Recombination in the genesis and evolution of hepatitis B virus genotypes
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 79:15467-76. 2005
    ....
  24. doi request reprint Proposals for the classification of human rhinovirus species C into genotypically assigned types
    Peter Simmonds
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, UK
    J Gen Virol 91:2409-19. 2010
    ....
  25. ncbi request reprint Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity
    P Simmonds
    Department of Medical Microbiology, University of Edinburgh, UK
    J Gen Virol 77:3013-24. 1996
    ..Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus...
  26. ncbi request reprint Transfusion virology: progress and challenges
    P Simmonds
    Department of Medical Microbiology, University of Edinburgh, UK
    Blood Rev 12:171-7. 1998
    ..Establishing a framework for PCR-based screening would also enable the testing for others such as hepatitis A virus, parvovirus B19 and GBV-C/HGV for which serological detection methods cannot be or have not been developed...
  27. ncbi request reprint Viral heterogeneity of the hepatitis C virus
    P Simmonds
    Department of Medical Microbiology, University of Edinburgh, UK
    J Hepatol 31:54-60. 1999
    ....
  28. pmc Structural constraints on RNA virus evolution
    P Simmonds
    Department of Medical Microbiology, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
    J Virol 73:5787-94. 1999
    ..This places a major restriction on the use of nucleotide or amino acid sequence comparisons to calculate times of divergence of other viruses evolving under the same structural constraints as GB viruses...
  29. ncbi request reprint The origin and evolution of hepatitis viruses in humans
    P Simmonds
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Gen Virol 82:693-712. 2001
    ..Large population sizes and intense selection pressures that optimize fitness may be the factors that set virus evolution apart from that of their hosts...
  30. pmc Evolutionary dynamics and temporal/geographical correlates of recombination in the human enterovirus echovirus types 9, 11, and 30
    E C McWilliam Leitch
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 84:9292-300. 2010
    ....
  31. doi request reprint Recombination dynamics of human parechoviruses: investigation of type-specific differences in frequency and epidemiological correlates
    J Calvert
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, UK
    J Gen Virol 91:1229-38. 2010
    ..Future investigation of the epidemiological and biological opportunities and constraints on intertypic recombination will provide more information about its influence on the longer term evolution and pathogenicity of parechoviruses...
  32. pmc Screening respiratory samples for detection of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity of HRV species C
    A Wisdom
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Clin Microbiol 47:3958-67. 2009
    ..The study demonstrates the extraordinary genetic diversity of HRVs, their rapid population turnover, and their extensive involvement in childhood respiratory disease...
  33. pmc Infection of the CD45RA+ (naive) subset of peripheral CD8+ lymphocytes by human immunodeficiency virus type 1 in vivo
    S McBreen
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Edinburgh EH9 1QH, United Kingdom
    J Virol 75:4091-102. 2001
    ..Destruction of cells destined to become CD8+ lymphocytes may be a major factor in the decline in CD8+ lymphocyte frequencies and function on disease progression and may contribute directly to the observed immunodeficiency in AIDS...
  34. pmc Activated peripheral CD8 lymphocytes express CD4 in vivo and are targets for infection by human immunodeficiency virus type 1
    S Imlach
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 75:11555-64. 2001
    ....
  35. ncbi request reprint Discrimination of hepatitis G virus/GBV-C geographical variants by analysis of the 5' non-coding region
    D B Smith
    Department of Medical Microbiology, University of Edinburgh, Medical School, UK
    J Gen Virol 78:1533-42. 1997
    ..The relatively low level of amino acid sequence variation observed between these geographically and phylogenetically defined groups of variants suggests that they are unlikely to display significant biological differences...
  36. ncbi request reprint Variation of the hepatitis C virus 5' non-coding region: implications for secondary structure, virus detection and typing. The International HCV Collaborative Study Group
    D B Smith
    Department of Medical Microbiology, University of Edinburgh, Medical School, UK
    J Gen Virol 76:1749-61. 1995
    ..Other sites of variation suggest minor modifications to this model and have implications for the probable functions of the 5'NCR...
  37. ncbi request reprint The origin of hepatitis C virus genotypes
    D B Smith
    Department of Medical Microbiology, University of Edinburgh, Medical School, UK
    J Gen Virol 78:321-8. 1997
    ..Estimation of the time of origin of the major HCV genotypes (types 1-6) is problematic, but our data and analogy with other viruses suggest that divergence occurred at least 500-2000 years ago...
  38. ncbi request reprint HIV encephalitis, proviral load and dementia in drug users and homosexuals with AIDS. Effect of neocortical involvement
    J E Bell
    Department of Pathology, University of Edinburgh, UK
    Brain 121:2043-52. 1998
    ..These findings suggest that neocortical productive HIV infection is a significant factor in AIDS-related dementia, although this may reflect merely a higher overall viral burden in the brain...
  39. ncbi request reprint An immune control model for viral replication in the CNS during presymptomatic HIV infection
    M McCrossan
    Centre for Infectious Diseases, Western General Hospital, Edinburgh, UK
    Brain 129:503-16. 2006
    ..Neurological complications in AIDS occur when this control breaks down, due to systemic immunosuppression from HIV that destroys CD8 lymphocyte function and/or through the evolution of more aggressive neuropathogenic variants...
  40. pmc The association of recombination events in the founding and emergence of subgenogroup evolutionary lineages of human enterovirus 71
    E C McWilliam Leitch
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    J Virol 86:2676-85. 2012
    ..The possibility that recombination contributed to their subsequent spread through improved fitness requires further biological and immunological characterization...
  41. pmc Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system
    T H Wang
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 75:11686-99. 2001
    ..This study provides the basis for future investigation of possible phenotypic similarities that underline the shared distributions of HIV variants infecting microglia and tissue macrophages outside the CNS...
  42. doi request reprint Direct identification of human enterovirus serotypes in cerebrospinal fluid by amplification and sequencing of the VP1 region
    E C McWilliam Leitch
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, EH9 1QH, UK
    J Clin Virol 44:119-24. 2009
    ..Serotype identification is currently problematic following the widespread adoption of polymerase chain reaction (PCR)-based methods for HEV detection in place of virus culture...
  43. doi request reprint High detection frequency and viral loads of human rhinovirus species A to C in fecal samples; diagnostic and clinical implications
    H Harvala
    Specialist Virology Centre, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
    J Med Virol 84:536-42. 2012
    ..High detection frequencies (10%) and viral loads in stool samples provide evidence for enteric replication of HRV, and its association with enteric disease requires further etiological studies...
  44. ncbi request reprint Geographic and species association of hepatitis B virus genotypes in non-human primates
    S E Starkman
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh, EH9 1QH, UK
    Virology 314:381-93. 2003
    ..These new findings have a number of implication for understanding the origins and epidemiology of HBV infection in non-human primates...
  45. doi request reprint Specific association of human parechovirus type 3 with sepsis and fever in young infants, as identified by direct typing of cerebrospinal fluid samples
    H Harvala
    Specialist Virology Centre, Royal Infirmary of Edinburgh, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
    J Infect Dis 199:1753-60. 2009
    ..We determined the relative importance of these viruses and the specific HPeV types involved in the development of central nervous system-associated disease...
  46. ncbi request reprint Influence of HAART on HIV-related CNS disease and neuroinflammation
    I C Anthony
    Neuropathology Unit, University of Edinburgh, Alexander Donald Building, Western General Hospital, Edinburgh, Scotland
    J Neuropathol Exp Neurol 64:529-36. 2005
    ..We conclude that there is a surprising degree of ongoing neuroinflammation in HAART-treated patients, particularly in the hippocampus. This may pose a threat for the future health of individuals maintained long-term on HAART therapy...
  47. doi request reprint Molecular epidemiology of norovirus in Edinburgh healthcare facilities, Scotland 2007-2011
    G McAllister
    Specialist Virology Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
    Epidemiol Infect 140:2273-81. 2012
    ..4 2006b, GII.4 2007 and GII.4 2010. Importantly, increases in NoV activity coincided with the emergence of new GII.4 strains, highlighting the need for an active surveillance system to allow the rapid identification of new strains...
  48. ncbi request reprint Development of multiplexed nucleic acid testing for human immunodeficiency virus type 1 and hepatitis C virus
    A Cleland
    PCR Reference Unit, Scottish National Blood Transfusion Service, Summerhall Place, Edinburgh, UK
    Vox Sang 81:93-101. 2001
    ..CONCLUSION: We have developed a highly sensitive multiplexed PCR for HIV-1 and HCV RNA screening that can be introduced into current PCR-based blood donor screening at minimal cost and without significant operational changes...
  49. ncbi request reprint Phylogenetic analysis of GBV-C/hepatitis G virus
    D B Smith
    Department of Medical Microbiology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Gen Virol 81:769-80. 2000
    ..The geographical distribution of virus variants is consistent with a long evolutionary history that may parallel that of pre-historic human migrations, implying that the long-term evolution of this RNA virus is extremely slow...
  50. ncbi request reprint Distribution of TT virus (TTV), TTV-like minivirus, and related viruses in humans and nonhuman primates
    K Thom
    TTI Theme Group, Scottish National Blood Transfusion Service, University of Edinburgh, Teviot Place, EH8 9AG Scotland, Edinburgh, UK
    Virology 306:324-33. 2003
    ..These findings support the hypothesis for the co-evolution of TTV-like viruses with their hosts over the period of primate speciation, potentially analogous to the evolution of primate herpesviruses...
  51. ncbi request reprint Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3' end of the hepatitis G virus/GB-virus C genome
    N M Cuceanu
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Gen Virol 82:713-22. 2001
    ..The prediction of similar structures in the same region of hepatitis C virus may allow the functions of these structures to be determined with a more tractable experimental model...
  52. pmc Analysis of genetic diversity and sites of recombination in human rhinovirus species C
    Chloe L McIntyre
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    J Virol 84:10297-310. 2010
    ..The extensive sequence data from multiple genome regions of HRV-C and analyses of recombination in the current study will assist future formulation of consensus criteria for HRV-C type assignment and identification...
  53. pmc Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses
    Matthew Davis
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 82:11824-36. 2008
    ..Bioinformatic and physical characterization methods both identified fundamental differences in the configurations of viral genomic RNA that may modify their interactions with host cell defenses and their ability to persist...
  54. pmc Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method
    E R Gaunt
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Clin Microbiol 48:2940-7. 2010
    ....
  55. pmc Transmission networks and population turnover of echovirus 30
    E C McWilliam Leitch
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 83:2109-18. 2009
    ....
  56. ncbi request reprint Sequence diversity of TT virus in geographically dispersed human populations
    L E Prescott
    Department of Medical Microbiology, University of Edinburgh, UK
    J Gen Virol 80:1751-8. 1999
    ..This study provides an indication of the extreme sequence diversity of TTV, a characteristic which is untypical of parvoviruses...
  57. ncbi request reprint Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods
    A Tuplin
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK
    J Gen Virol 85:3037-47. 2004
    ....
  58. ncbi request reprint Comparison of tissue distribution, persistence, and molecular epidemiology of parvovirus B19 and novel human parvoviruses PARV4 and human bocavirus
    Ashleigh Manning
    Centre for Infectious Diseases, Western General Hospital, University of Edinburgh, Edinburgh, EH9 1QH, United Kingdom
    J Infect Dis 195:1345-52. 2007
    ..We investigated the frequencies of persistence, tissue distribution, and influence of immunosuppression on replication of these viruses...
  59. pmc High frequencies of exposure to the novel human parvovirus PARV4 in hemophiliacs and injection drug users, as detected by a serological assay for PARV4 antibodies
    Colin P Sharp
    Centre for Infectious Diseases, University of Edinburgh, Edinburgh, United Kingdom
    J Infect Dis 200:1119-25. 2009
    ....
  60. pmc Widespread infection with homologues of human parvoviruses B19, PARV4, and human bocavirus of chimpanzees and gorillas in the wild
    Colin P Sharp
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, Scotland, UK
    J Virol 84:10289-96. 2010
    ..This study provides the first evidence for widespread circulation of parvoviruses in primates and enables future investigations of their epidemiology, host specificity, and (co)evolutionary histories...
  61. pmc Development of an intergenotypic hepatitis C virus (HCV) cell culture method to assess antiviral susceptibilities and resistance development of HCV NS3 protease genes from HCV genotypes 1 to 6
    Ingrid Imhof
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 84:4597-610. 2010
    ..The system will allow future comprehensive phenotypic characterization of naturally occurring and treatment-induced mutations for PIs in trial or entering clinical use...
  62. ncbi request reprint The UK blood transfusion service: over a (patent) barrel?
    P Simmonds
    Laboratory for Clinical and Molecular Biology, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
    Lancet 359:1713-4. 2002
  63. ncbi request reprint Atypical hand, foot, and mouth disease associated with coxsackievirus A6 infection, Edinburgh, United Kingdom, January to February 2014
    C Sinclair
    Department of Dermatology, Lauriston Building, Edinburgh, United Kingdom
    Euro Surveill 19:20745. 2014
    ....
  64. ncbi request reprint No evidence for an association between infections with WU and KI polyomaviruses and respiratory disease
    P Norja
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Clin Virol 40:307-11. 2007
    ..To investigate their potential role in respiratory disease, we determined their frequencies of detection, clinical presentations and epidemiological characteristics among samples referred for diagnostic respiratory virus testing...
  65. ncbi request reprint Genetic heterogeneity of HIV type 1 subtypes in Kimpese, rural Democratic Republic of Congo
    J L Mokili
    Department of Medical Microbiology, University of Edinburgh, UK
    AIDS Res Hum Retroviruses 15:655-64. 1999
    ..These results are relevant for the molecular epidemiology of HIV-1 in Africa and for the design of a future vaccine against HIV-1 in this region...
  66. ncbi request reprint A genetic analysis of hepatitis C virus transmission between injection drug users
    Alexandra Cochrane
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Edinburgh, United Kingdom
    J Infect Dis 186:1212-21. 2002
    ..The degree of city-specific segregation of HCV subtype 1a sequences was linearly related to that of subtype 3a, indicating that these subtypes have spread through similar transmission networks...
  67. ncbi request reprint HIV and drug misuse in the Edinburgh cohort
    Jeanne E Bell
    Department of Neuropathology, University of Edinburgh, Western General Hospital, United Kingdom
    J Acquir Immune Defic Syndr 31:S35-42. 2002
    ..Collections of clinically well-characterized HIV-infected tissues such as those in the Edinburgh Brain Bank are a vital resource to support ongoing studies of viral pathogenesis in the CNS and interactions with drug abuse...
  68. ncbi request reprint Impact of HIV on regional & cellular organisation of the brain
    Jeanne E Bell
    Neuropathology Unit, University of Edinburgh, UK
    Curr HIV Res 4:249-57. 2006
    ..The cause of HIV associated dementia and cognitive disability remains poorly understood. Perhaps most significantly, the long-term consequences of clinically occult brain infection are unknown and will require further investigation...
  69. pmc Antiviral RNA interference responses induced by Semliki Forest virus infection of mosquito cells: characterization, origin, and frequency-dependent functions of virus-derived small interfering RNAs
    Ricky W C Siu
    The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Edinburgh EH9 1QH, Scotland, United Kingdom
    J Virol 85:2907-17. 2011
    ..Hot-spot viRNAs were found to be significantly less efficient at mediating antiviral RNAi than cold-spot viRNAs, pointing toward a nucleic acid-based viral decoy mechanism to evade the RNAi response...
  70. pmc Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus
    Andrew Tuplin
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Scotland
    RNA 8:824-41. 2002
    ....
  71. ncbi request reprint Clinical perspectives of emerging pathogens in bleeding disorders
    Christopher A Ludlam
    University of Edinburgh, Edinburgh, UK
    Lancet 367:252-61. 2006
    ..Such recombinant products have extended the safety profile of their predecessors by ensuring that all reagents used for cell culture, purification steps, and stabilisation and storage buffers are completely independent of human plasma...
  72. doi request reprint Incidence, molecular epidemiology and clinical presentations of human metapneumovirus; assessment of its importance as a diagnostic screening target
    Eleanor Gaunt
    Centre for Infectious Diseases, University of Edinburgh, Edinburgh, United Kingdom
    J Clin Virol 46:318-24. 2009
    ..Human metapneumovirus (HMPV) is a recently discovered human paramyxovirus associated with a spectrum of respiratory symptoms from the common cold to pneumonia and bronchiolitis...
  73. ncbi request reprint Virus immunocapture provides evidence of CD8 lymphocyte-derived HIV-1 in vivo
    Gareth J Hughes
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, UK
    AIDS 21:1507-13. 2007
    ....
  74. pmc High levels of human immunodeficiency virus infection of CD8 lymphocytes expressing CD4 in vivo
    Alexandra Cochrane
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Edinburgh EH9 1QH, United Kingdom
    J Virol 78:9862-71. 2004
    ..The high level of infection of CD8bright CD4dim lymphocytes could have a direct role in the decline in CD8 lymphocyte function that accompanies HIV disease progression...
  75. ncbi request reprint HIV-1-infected CD8+CD4+ T cells decay in vivo at a similar rate to infected CD4 T cells during HAART
    Gareth J Hughes
    Centre for Infectious Diseases, University of Edinburgh, Edinburgh, UK
    AIDS 22:57-65. 2008
    ..To investigate the potential for CD4+CD8+ T cells [CD8 double positive (CD8 DP)] T cells to form a reservoir of HIV-1 following HAART through measurement of the rate of decay of infected CD4/CD8 DP T cells...
  76. ncbi request reprint Does drug abuse alter microglial phenotype and cell turnover in the context of advancing HIV infection?
    I C Anthony
    Neuropathology Unit, University of Edinburgh, Alexander Donald Building, Western General Hospital, Edinburgh EH4 2XU, UK
    Neuropathol Appl Neurobiol 31:325-38. 2005
    ....
  77. ncbi request reprint Relationship of Nef-positive and GFAP-reactive astrocytes to drug use in early and late HIV infection
    C E Anderson
    Department of Pathology and Laboratory for Clinical and Molecular Virology, University of Edinburgh, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, Scotland, UK
    Neuropathol Appl Neurobiol 29:378-88. 2003
    ..However, the number of GFAP-positive astrocytes was neither increased in pre-AIDS nor in drug abuse, in contrast with microglia which we have shown previously to be up-regulated in both states...
  78. ncbi request reprint Scottish experience with NAT
    L M Jarvis
    Scottish National Blood Transfusion Service NAT Reference Unit, Royal Dick Veterinary College, University of Edinburgh, Summerhall, Edinburgh, UK
    Transfus Med 12:259-64. 2002
  79. ncbi request reprint A second outbreak of hepatitis C virus infection from anti-D immunoglobulin in Ireland
    D B Smith
    Department of Medical Microbiology, University of Edinburgh, Medical School, Edinburgh, UK
    Vox Sang 76:175-80. 1999
    ..To investigate the infectivity for hepatitis C virus (HCV) of intravenous anti-D immunoglobulin batches manufactured in Ireland between 1991 and 1994...
  80. ncbi request reprint Detection of enterovirus viraemia in blood donors
    J B Welch
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Edinburgh, UK
    Vox Sang 80:211-5. 2001
    ..The frequency of transmission and clinical outcome after exposure to enterovirus-contaminated blood components in recipients is unknown...
  81. pmc Rapid sequence change and geographical spread of human parvovirus B19: comparison of B19 virus evolution in acute and persistent infections
    Päivi Norja
    Center for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom
    J Virol 82:6427-33. 2008
    ..Determining what epidemiological or biological factors led to such a complete and geographically extensive population replacement over this short period is central to further understanding the nature of parvovirus evolution...
  82. ncbi request reprint Frequency, viral loads, and serotype identification of enterovirus infections in Scottish blood donors
    Jon Welch
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, Edinburgh, UK
    Transfusion 43:1060-6. 2003
    ..Positive samples were quantified, and serotypes were identified by nucleotide sequencing of VP1...
  83. ncbi request reprint Does drug abuse influence the microglial response in AIDS and HIV encephalitis?
    Juan Carlos Arango
    School of Molecular and Clinical Medicine, Pathology Neuropathology, University of Edinburgh, Edinburgh, Scotland, UK
    AIDS 18:S69-74. 2004
    ....
  84. ncbi request reprint The effects of illicit drugs on the HIV infected brain
    Iain Crawford Anthony
    Division of Pathology Neuropathology, University of Edinburgh, Alexander Donald Building, Western General Hospital, Edinburgh, EH4 2XU, UK
    Front Biosci 13:1294-307. 2008
    ..The additional impact of intravenous drug abuse on HIV-associated brain disease, then and now, is also reviewed. Predictions for the future are discussed, based on what is known at present and on recently emerging data...
  85. ncbi request reprint Epidemiological profile and clinical associations of human bocavirus and other human parvoviruses
    A Manning
    Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, EH9 IQH, UK
    J Infect Dis 194:1283-90. 2006
    ....
  86. ncbi request reprint Accelerated Tau deposition in the brains of individuals infected with human immunodeficiency virus-1 before and after the advent of highly active anti-retroviral therapy
    Iain C Anthony
    Department of Pathology Neuropathology, University of Edinburgh, Western General Hospital, Alexander Donald Building, EH4 2XU, Edinburgh, UK
    Acta Neuropathol 111:529-38. 2006
    ..Within the age groups studied these significant neuropathological changes remained subclinical and were not yet associated with cognitive impairment...
  87. ncbi request reprint Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations
    Catriona Macfarlane
    Center for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, Scotland EH9 1QH, UK
    J Mol Evol 59:642-56. 2004
    ..These findings denote a recent expansion from Africa. We compare the phylogenetic relationships of HML-2 sequences that are unique to humans and consider whether these elements have played a role in the remodeling of the hominid genome...
  88. doi request reprint Human parechoviruses: biology, epidemiology and clinical significance
    H Harvala
    Specialist Virology Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
    J Clin Virol 45:1-9. 2009
    ..By this means, we will learn much more about the clinical relevance of HPeVs and the association of different HPeV types with specific disease presentations...
  89. ncbi request reprint Phenotypic analysis of peripheral blood gammadelta T lymphocytes and their targeting by human immunodeficiency virus type 1 in vivo
    S Imlach
    Laboratory for Clinical and Molecular Virology, University of Edinburgh, Summerhall, United Kingdom
    Virology 305:415-27. 2003
    ..For each cell type, blocking assays with an anti-CD4 monoclonal antibody indicated that entry was CD4-dependent...
  90. ncbi request reprint A CCR5-dependent novel mechanism for type 1 HIV gp120 induced loss of macrophage cell surface CD4
    T J Hewson
    Immunobiology Group, Centre for Inflammation Research and Laboratory for Clinical and Molecular Virology, University of Edinburgh, United Kingdom
    J Immunol 166:4835-42. 2001
    ....
  91. ncbi request reprint Parechoviruses in children: understanding a new infection
    Heli Harvala
    Specialist Virology Centre, Royal Infirmary of Edinburgh, Edinburgh, UK
    Curr Opin Infect Dis 23:224-30. 2010
    ..In this review, we will describe both the disease associations and underlying epidemiological and/or biological basis for the often marked differences in disease outcomes between HPeV types...
  92. doi request reprint Reactivation and mutation of newly discovered WU, KI, and Merkel cell carcinoma polyomaviruses in immunosuppressed individuals
    Colin P Sharp
    Centre for Infectious Diseases, Neuropathology Unit, University of Edinburgh, United Kingdom
    J Infect Dis 199:398-404. 2009
    ..In this study, we investigated whether the recently discovered WU and KI polyomaviruses (WUPyV and KIPyV) and Merkel cell polyomavirus (MCPyV) could, like BKV and JCV, persist, mutate, and reactivate in immunodeficient subjects...
  93. pmc A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame
    Thomas Kuntzen
    Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
    J Med Virol 80:1370-8. 2008
    ..Reference sequences for accurate HCV genotyping are required for optimized treatment, and a better knowledge of the global viral sequence diversity is needed to guide vaccines or new drugs effective in the world wide epidemic...
  94. pmc Biological analysis of human immunodeficiency virus type 1 R5 envelopes amplified from brain and lymph node tissues of AIDS patients with neuropathology reveals two distinct tropism phenotypes and identifies envelopes in the brain that confer an enhanced
    Paul J Peters
    Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester MA 01605, USA
    J Virol 78:6915-26. 2004
    ..These envelopes are able to infect cells that express low levels of CD4 and/or CCR5 and may have adapted for replication in brain macrophages and microglia, which are known to express limited amounts of CD4...
  95. pmc Non-macrophage-tropic human immunodeficiency virus type 1 R5 envelopes predominate in blood, lymph nodes, and semen: implications for transmission and pathogenesis
    Paul J Peters
    Center for AIDS Research, Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St, Biotech II Suite 315, Worcester, MA 01605, USA
    J Virol 80:6324-32. 2006
    ..The extensive variation in R5 tropism reported here is likely to have an important impact on pathogenesis and on the capacity of HIV-1 to transmit...
  96. pmc A comparative method for finding and folding RNA secondary structures within protein-coding regions
    Jakob Skou Pedersen
    Bioinformatics Research Center, Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 550, 8000 Aarhus C, Denmark
    Nucleic Acids Res 32:4925-36. 2004
    ..When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD...
  97. ncbi request reprint A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes
    Carla Kuiken
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
    Hepatology 44:1355-61. 2006
  98. ncbi request reprint The hepatitis C virus epidemic among injecting drug users
    Oliver G Pybus
    Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
    Infect Genet Evol 5:131-9. 2005
    ..The results provide a baseline for prediction of the future course of the HCV epidemic, and its likely response to transmission control policies...
  99. ncbi request reprint First evidence of HIV infection of CD8 lymphocytes expressing CD4 during primary HIV-1 infection
    Alexandra Cochrane
    AIDS 19:1237-9. 2005
  100. pmc A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B
    Sinéad Diviney
    Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
    J Virol 82:9008-22. 2008
    ..Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication...
  101. ncbi request reprint Clinical performance of the LCx HCV RNA quantitative assay
    Rasa Bertuzis
    Abbott Laboratories, D99G AP20, 100 Abbott Park Road, Abbott Park, IL 60064 6015, USA
    J Virol Methods 123:171-8. 2005
    ..0 specimen results were within 1 log, as were 85.6% (237/277) of paired Roche Monitor 2.0 and Bayer specimen results. These data demonstrate that the LCx assay may be used for quantitation of HCV RNA in HCV-infected individuals...

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