P Simmonds

The University of Edinburgh, Edinburgh, Scotland, United Kingdom

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Publications (225)1708.84 Total impact

  • D. Smith · H. Harvala · A. Bradley-Stewart · R. Gunson · P. Simmonds ·

  • D. Smith · K. Templeton · P. Simmonds ·

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    ABSTRACT: Human enteroviruses (EV) and parechoviruses (HPeV) within the family Picornaviridae are the most common causes of viral central nervous system (CNS)-associated infections including meningitis and neonatal sepsis-like disease. The frequencies of EV and HPeV types identified in clinical specimens collected in Scotland over an eight-year period were compared to those identified in sewage surveillance established in Edinburgh. Of the 35 different EV types belonging to four EV species (A to D) and the four HPeV types detected in this study, HPeV3 was identified as the most prevalent picornavirus in cerebrospinal fluid samples, followed by species B EV. Interestingly, over half of EV and all HPeV CNS-associated infections were observed in young infants (younger than three months). Detection of species A EV including coxsackievirus A6 and EV71 in clinical samples and sewage indicates that these viruses are already widely circulating in Scotland. Furthermore, species C EV were frequently identified EV in sewage screening but they were not present in any of 606 EV-positive clinical samples studied, indicating their likely lower pathogenicity. Picornavirus surveillance is important not only for monitoring the changing epidemiology of these infections but also for the rapid identification of spread of emerging EV and/or HPeV types.
    Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin 04/2014; 19(15). DOI:10.2807/1560-7917.ES2014.19.15.20772 · 5.72 Impact Factor
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    ABSTRACT: In January to February 2014, 16 hand, foot and mouth disease (HFMD) cases were identified in Edinburgh, United Kingdom. All presented with atypical features, with most (n=13) resembling eczema herpeticum or chickenpox. Coxsackievirus A6 (CV-A6) was identified in all the typed cases (n=11). As atypical forms of HFMD associated with CV-A6 are likely to emerge throughout Europe, clinicians should be alert to unusual clinical presentations of HFMD and virologists aware of effective diagnostic testing and enterovirus typing methods.
    Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin 03/2014; 19(12). DOI:10.2807/1560-7917.ES2014.19.12.20745 · 5.72 Impact Factor
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    P. Whitaker · C. McIntyre · A. Shah · T. Hale · C. Etherington · P. Simmonds · D. Peckham ·

    Journal of Cystic Fibrosis 06/2013; 12:S89. DOI:10.1016/S1569-1993(13)60301-X · 3.48 Impact Factor
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    ABSTRACT: Human rhinoviruses (HRVs) can be divided into three species; HRV-A to HRV-C. Up to 148 different HRV (sero)types have been identified to date. Because of sequence similarity between 5'-NCR of HRVs and enteroviruses (EVs), it is problematic to design EV-specific RT-PCR assays. The aims of this study were to assess the rate of false-detection of different rhinoviruses by EV RT-PCR, and to evaluate the diagnostic and clinical significance of such cross-reactivity. In vitro RNA transcripts of HRV A-C created from cDNA templates were quantified spectrophotometrically. Six hundred twenty-one stool samples screened as part of routine diagnostic for EV, 17 EV-positive stool samples referred for typing, 288 stool samples submitted for gastroenteritis investigations, and 1,500 CSF samples were included in the study. EV-specific RT-PCR detected RNA transcripts of HRV-A1b, HRV-B14, and HRV-Crpat18 but with 10-1,000 reduced sensitivity compared to EV transcripts. Screening fecal samples by EV RT-PCR identified 13 positive samples identified subsequently as rhinoviruses; a further 26 HRV-positive samples were identified by nested HRV RT-PCR. All individuals were hospitalized and presented mostly with diarrhea. A total of 26 HRV types were identified (HRV-A: 46%; HRV-B: 13%; HRV-C: 41%). Results confirm that EV-specific RT-PCR can detect HRVs, and at a practical level, identify potential problems of interpretation if fecal samples are used for surrogate screening in cases of suspected viral meningitis. 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.
    Journal of Medical Virology 03/2012; 84(3):536-42. DOI:10.1002/jmv.23203 · 2.35 Impact Factor
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    ABSTRACT: SUMMARYNorovirus (NoV) is a leading cause of outbreaks of gastroenteritis worldwide, and a major burden for healthcare facilities. This study investigated the NoV genotypes responsible for outbreaks in Edinburgh healthcare facilities between June 2008 and July 2011, and studied their temporal distribution to enable a better understanding of the epidemiology of the outbreaks. A total of 287 samples positive for NoV genogroup II (GII) RNA by reverse transcription-polymerase chain reaction (RT-PCR) during routine diagnostic testing were investigated. Nested RT-PCR (nRT-PCR) and sequencing was used to genotype the NoV strains. Overall, a total of 69 NoV strains belonging to six different genoclusters (GII.1, GII.2, GII.3, GII.4, GII.6, GII.13) were detected. The predominant genotype was GII.4 that included four variants, GII.4 2006a, GII.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.
    Epidemiology and Infection 02/2012; 140(12):1-9. DOI:10.1017/S0950268812000052 · 2.54 Impact Factor
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    ABSTRACT: Enterovirus 71 (EV71) is responsible for frequent large-scale outbreaks of hand, foot, and mouth disease worldwide and represent a major etiological agent of severe, sometimes fatal neurological disease. EV71 variants have been classified into three genogroups (GgA, GgB, and GgC), and the latter two are further subdivided into subgenogroups B1 to B5 and C1 to C5. To investigate the dual roles of recombination and evolution in the epidemiology and transmission of EV71 worldwide, we performed a large-scale genetic analysis of isolates (n = 308) collected from 19 countries worldwide over a 40-year period. A series of recombination events occurred over this period, which have been identified through incongruities in sequence grouping between the VP1 and 3Dpol regions. Eleven 3Dpol clades were identified, each specific to EV71 and associated with specific subgenogroups but interspersed phylogenetically with clades of coxsackievirus A16 and other EV species A serotypes. The likelihood of recombination increased with VP1 sequence divergence; mean half-lives for EV71 recombinant forms (RFs) of 6 and 9 years for GgB and GgC overlapped with those observed for the EV-B serotypes, echovirus 9 (E9), E30, and E11, respectively (1.3 to 9.8 years). Furthermore, within genogroups, sporadic recombination events occurred, such as the linkage of two B4 variants to RF-W instead of RF-A and of two C4 variants to RF-H. Intriguingly, recombination events occurred as a founding event of most subgenogroups immediately preceding their lineage expansion and global emergence. The possibility that recombination contributed to their subsequent spread through improved fitness requires further biological and immunological characterization.
    Journal of Virology 12/2011; 86(5):2676-85. DOI:10.1128/JVI.06065-11 · 4.44 Impact Factor
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    ABSTRACT: Nitrous oxide (N2O) emissions weighted by ozone depletion potential currently dominate emissions of ozone depleting substances, and N2O is now the third most significant long-lived anthropogenic greenhouse gas after CO2 and CH4. Despite its impact on stratospheric ozone destruction, it is not regulated under the Montreal Protocol, and global observations show a continuous N2O mole fraction increase of 0.2 to 0.3% per year. Sinks and sources of N2O still have large uncertainties but previous studies have estimated that soil emissions share more than a half of the global total. Because the variability in soil emissions could potentially have important implications for regional and global climate, and vice versa, it is essential to better understand the processes and feedbacks associated with soil N2O emissions. To achieve this goal and quantify global soil N2O emissions, we have included nitrification-denitrification processes (DNDC) into the Community Land Model (CLM) version 3.5. Using three different bias-corrected, reanalysis-based meteorological datasets (NCC, CAS and GOLD), we constructed a suite of global gridded soil N2O emissions estimates from 1975 through the mid-2000s. We evaluate our global soil N2O flux estimates against: 1) an existing emissions inventory (GEIA), 2) another process model (NASA-CASA), and 3) observations from an existing forest N2O flux dataset in the Amazon and in the United States. Both the global and regional totals agree well and the model reproduces the observed seasonal cycles of N2O emissions. Next, we input these emission estimates to a 3-dimensional atmospheric chemical transport model - the Model for OZone And Related Tracers (MOZART) version 4 - to analyze the impact of monthly and inter-annual variability in soil emissions on atmospheric observations. Using these emissions as an initial estimate, we also determine new regional and global N2O emissions by inverse modeling from 1995 through 2009. Data from the Advanced Global Atmospheric Gases Experiment (AGAGE), National Oceanic and Atmospheric Administration (NOAA), the Commonwealth Scientific and Industrial Research Organization (CSIRO), National Institute for Environmental Studies (NIES), as well as Tohoku University are used after having been averaged into monthly mean values with associated uncertainties. This combination of process-based and inverse estimation allows new insights into the drivers of seasonal and inter-annual variability of this important atmospheric constituent.
  • E.R. Gaunt · H Harvala · C McIntyre · K.E. Templeton · P Simmonds ·
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    ABSTRACT: The most common acute infections occur in the respiratory tract. Recent discoveries of several novel viruses have markedly increased the repertoire of agents understood to cause presentations of acute respiratory disease. Further understanding is needed of the relative importance of newly discovered pathogens in the clinical setting to provide clinicians with an indication of appropriate diagnostic and therapeutic targets. To address this, quantification of the disease burden of respiratory viruses in hospitalized patients was undertaken. Disease burden caused by respiratory viruses in hospitalized patients was quantified using the World Health Organization endorsed DALY model. Diagnostic testing results from samples collected over three years for adenovirus (AdV), influenzas A and B, parainfluenza viruses 1, 2 and 3 (PIV-1, -2 and -3), respiratory syncytial virus (HRSV), and previously published retrospective screening for human metapneumovirus, rhinoviruses, and four respiratory coronaviruses were applied to the DALY model. Disability weights were calculated per 1000 hospitalized patients in age banded groups. Strikingly different disease burden profiles were observed in children and adults. Adenoviruses were among the leading cause of respiratory presentations in children but not adults. HRSV and influenza A were consistently one of the greatest causes of disease regardless of sampled population. Rhinoviruses and PIV-3 were significant pathogens in all groups except those aged 16-64 years. In immunocompromised patients rhinoviruses were the leading viral cause of disease. These analyses provide a framework which can be used to identify where finite resources should be directed in respiratory therapeutics and vaccine development.
    Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 08/2011; 52(3):215-21. DOI:10.1016/j.jcv.2011.07.017 · 3.02 Impact Factor
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    Journal of Clinical Virology 08/2011; 51(4):286. DOI:10.1016/j.jcv.2011.05.010 · 3.02 Impact Factor
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    ABSTRACT: The relationship between virus evolution and recombination in species B human enteroviruses was investigated through large-scale genetic analysis of echovirus type 9 (E9) and E11 isolates (n = 85 and 116) from 16 European, African, and Asian countries between 1995 and 2008. Cluster 1 E9 isolates and genotype D5 and A E11 isolates showed evidence of frequent recombination between the VP1 and 3Dpol regions, the latter falling into 23 (E9) and 43 (E11) clades interspersed phylogenetically with 46 3Dpol clades of E30 and with those of other species B serotypes. Remarkably, only 2 of the 112 3Dpol clades were shared by more than one serotype (E11 and E30), demonstrating an extremely large and genetically heterogeneous recombination pool of species B nonstructural-region variants. The likelihood of recombination increased with geographical separation and time, and both were correlated with VP1 divergence, whose substitution rates allowed recombination half-lives of 1.3, 9.8, and 3.1 years, respectively, for E9, E11, and E30 to be calculated. These marked differences in recombination dynamics matched epidemiological patterns of periodic epidemic cycles of 2 to 3 (E9) and 5 to 6 (E30) years and the longer-term endemic pattern of E11 infections. Phylotemporal analysis using a Bayesian Markov chain Monte Carlo method, which placed recombination events within the evolutionary reconstruction of VP1, showed a close relationship with VP1 lineage expansion, with defined recombination events that correlated with their epidemiological periodicity. Whether recombination events contribute directly to changes in transmissibility that drive epidemic behavior or occur stochastically during periodic population bottlenecks is an unresolved issue vital to future understanding of enterovirus molecular epidemiology and pathogenesis.
    Journal of Virology 09/2010; 84(18):9292-300. DOI:10.1128/JVI.00783-10 · 4.44 Impact Factor
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    E R Gaunt · A Hardie · E C J Claas · P Simmonds · K E Templeton ·
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    ABSTRACT: Four human coronaviruses (HCoV-229E, HCoV-HKU1, HCoV-NL63, and HCoV-OC43) are associated with a range of respiratory outcomes, including bronchiolitis and pneumonia. Their epidemiologies and clinical characteristics are poorly described and are often reliant on case reports. To address these problems, we conducted a large-scale comprehensive screening for all four coronaviruses by analysis of 11,661 diagnostic respiratory samples collected in Edinburgh, United Kingdom, over 3 years between July 2006 and June 2009 using a novel four-way multiplex real-time reverse transcription-PCR (RT-PCR) assay. Coronaviruses were detected in 0.3 to 0.85% of samples in all age groups. Generally, coronaviruses displayed marked winter seasonality between the months of December and April and were not detected in summer months, which is comparable to the pattern seen with influenza viruses. HCoV-229E was the exception; detection was confined to the winter of 2008 and was sporadic in the following year. There were additional longer-term differences in detection frequencies between seasons, with HCoV-OC43 predominant in the first and third seasons and HCoV-HKU1 dominating in the second (see Results for definitions of seasons). A total of 11 to 41% of coronaviruses detected were in samples testing positive for other respiratory viruses, although clinical presentations of coronavirus monoinfections were comparable to those of viruses which have an established role in respiratory disease, such as respiratory syncytial virus, influenza virus, and parainfluenza viruses. The novel multiplex assay for real-time pan-coronavirus detection enhances respiratory virus diagnosis, overcomes potential diagnostic problems arising through seasonal variation in coronavirus frequency, and provides novel insights into the epidemiology and clinical implications of coronaviruses.
    Journal of clinical microbiology 08/2010; 48(8):2940-7. DOI:10.1128/JCM.00636-10 · 3.99 Impact Factor
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    ABSTRACT: Human parechoviruses (HPeVs) are highly prevalent RNA viruses classified in the family Picornaviridae. Several antigenically distinct types circulate in human populations worldwide, whilst recombination additionally contributes to the genetic heterogeneity of the virus. To investigate factors influencing the likelihood of recombination and to compare its dynamics among types, 154 variants collected from four widely geographically separated referral centres (UK, The Netherlands, Thailand and Brazil) were typed by VP3/VP1 amplification/sequencing with recombination groups assigned by analysis of 3Dpol sequences. HPeV1B and HPeV3 were the most frequently detected types in each referral region, but with marked geographical differences in the frequencies of different recombinant forms (RFs) of types 1B, 5 and 6. HPeV1B showed more frequent recombination than HPeV3, in terms both of evolutionary divergence and of temporal/geographical indicators of population separation. HPeV1 variants showing between 10 and 20% divergence in VP3/VP1 almost invariably fell into different recombination groups, compared with only one-third of similarly divergent HPeV3 variants. Substitution rates calculated by beast in the VP3/VP1 region of HPeV1 and HPeV3 allowed half-lives of the RFs of 4 and 20 years, respectively, to be calculated, estimates fitting closely with their observed lifespans based on population sampling. The variability in recombination dynamics between HPeV1B and HPeV3 offers an intriguing link with their markedly different seasonal patterns of transmission, age distributions of infection and clinical outcomes. 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.
    Journal of General Virology 05/2010; 91(Pt 5):1229-38. DOI:10.1099/vir.0.018747-0 · 3.18 Impact Factor
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    ABSTRACT: Mace Head is situated at the extreme west end of mainland Europe and is having relatively clean environment, best suited for the study of base line surface ozone trend and seasonal sycle. About 20 years of ozone data from Mace Hread are analyzed to investigate the surface ozone concentration, long term trend, and seasonal changes. Hourly ozone data is used to calculate daily mean concentration and daily mean daytime concentration. To decompose the ozone concentration in long term trend and seasonal variation, a technique based on locally- weighted regression smoothing is used. Ozone concentrations is found to be increasing and particularly in 2006 surface ozone levels were higher than recent years. Hourly ozone exceeded 90 ppb and 8 hourly mean EPA (Environmental Protection Agency) target value of 60 ppb exceeded at the station. Seasonal component is found to be increasing both sides i.e. spring time maxima and summer time minima but is most pronounced towards the positive side (Spring-Maxima). Mace head has shown very slow but increasing annual trend. For detailed analysis back trajectories are calculated to investigate the impact of air-mass origin on the behaviour of seasonal and trend components.
    Journal of Geophysical Research Atmospheres 01/2010; 115(D19). · 3.43 Impact Factor
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    ABSTRACT: To investigate the frequency of oseltamivir resistance in circulating strains of the 2009 influenza A(H1N1) pandemic virus in Scotland, 1,802 samples from 1,608 infected hospitalised patients were screened by the H275Y discriminatory RT-PCR. Among these, we identified 10 patients who developed the H275Y mutation. All of them were immunocompromised and were under treatment or had been treated previously with oseltamivir.
    Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin 01/2010; 15(14). · 5.72 Impact Factor
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    A Wisdom · E C McWilliam Leitch · E Gaunt · H Harvala · P Simmonds ·
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    ABSTRACT: Rhinovirus infections are the most common cause of viral illness in humans, and there is increasing evidence of their etiological role in severe acute respiratory tract infections (ARTIs). Human rhinoviruses (HRVs) are classified into two species, species A and B, which contain over 100 serotypes, and a recently discovered genetically heterogeneous third species (HRV species C). To investigate their diversity and population turnover, screening for the detection and the genetic characterization of HRV variants in diagnostic respiratory samples was performed by using nested primers for the efficient amplification of the VP4-VP2 region of HRV (and enterovirus) species and serotype identification. HRV species A, B, and C variants were detected in 14%, 1.8%, and 6.8%, respectively, of 456 diagnostic respiratory samples from 345 subjects (6 samples also contained enteroviruses), predominantly among children under age 10 years. HRV species A and B variants were remarkably heterogeneous, with 22 and 6 different serotypes, respectively, detected among 73 positive samples. Similarly, by using a pairwise distance threshold of 0.1, species C variants occurring worldwide were provisionally assigned to 47 different types, of which 15 were present among samples from Edinburgh, United Kingdom. There was a rapid turnover of variants, with only 5 of 43 serotypes detected during both sampling periods. By using divergence thresholds and phylogenetic analysis, several species A and C variants could provisionally be assigned to new types. An initial investigation of the clinical differences between rhinovirus species found HRV species C to be nearly twice as frequently associated with ARTIs than other rhinovirus species, which matches the frequencies of detection of respiratory syncytial virus. The study demonstrates the extraordinary genetic diversity of HRVs, their rapid population turnover, and their extensive involvement in childhood respiratory disease.
    Journal of clinical microbiology 10/2009; 47(12):3958-67. DOI:10.1128/JCM.00993-09 · 3.99 Impact Factor
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    ABSTRACT: Human parechoviruses (HPeVs) are highly prevalent pathogens among very young children. Although originally classified into two serologically distinct types, HPeV1 and -2, recent analyses of variants collected worldwide have revealed the existence of 12 further types classified genetically by sequence comparisons of complete genome sequences or the capsid (VP1) gene. To investigate the nature of HPeV evolution, its population dynamics and recombination breakpoints, this study generated 18 full-length genomic sequences of the most commonly circulating genotypes, HPeV1 and -3, collected over a time span of 14 years from The Netherlands. By inclusion of previously published full-length sequences, 35 sequences were analysed in total. Analysis of contemporary strains of HPeV1 and those most similar to the prototype strain (Harris) showed that HPeV1 variants fall into two genetically distinct clusters that are much more divergent from each other than those observed within other HPeV types. Future classification criteria for HPeVs may require modification to accommodate the occurrence of variants with intermediate degrees of diversity within types. Recombination was frequently observed among HPeV1, -4, -5 and -6, but was much more restricted among HPeV3 strains. Favoured sites for recombination were found to flank the capsid region, and further sites were found within the non-structural region, P2. In contrast to other HPeV types, the majority of the HPeV3 sequences remained monophyletic across the genome, a possible reflection of its lower diversity and potentially more recent emergence than other HPeV types, or biological and/or epidemiological constraints that limit opportunities for co-infections with potential recombination partners.
    Journal of General Virology 09/2009; 91(Pt 1):145-54. DOI:10.1099/vir.0.014670-0 · 3.18 Impact Factor
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    ABSTRACT: Background: Many patients with chronic hepatitis C have long periods of normal or near-normal liver enzyme levels, even though histologic alterations have been confirmed. The recommendation today is not to treat this patient group. Methods: In a pilot study 23 hepatitis C virus (HCV) RNA-positive patients with alanine aminotransferase (ALAT) levels less than 1.5 times upper normal limits for at least 6 months on more than three occasions and with histologic liver abnormalities compatible with chronic hepatitis C were treated with 3 MU of interferon-α2b three times a week for 6 months. Results: Nine patients (39%) became HCV RNA-negative in serum during treatment, but only two (8.7%) remained so after 6 months' follow-up. Significantly more patients with genotype other than type 1 became HCV RNA-negative than patients with genotype 1 during treatment (P = 0.005). Conclusions: Patients with low-activity chronic hepatitis C have a response to interferon-alpha treatment similar to that of patients with increased ALAT levels. Genotype seems to influence the rate of response.
    Scandinavian Journal of Gastroenterology 07/2009; 32(12):1256-1260. DOI:10.3109/00365529709028156 · 2.36 Impact Factor
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    ABSTRACT: Human parechoviruses (HPeVs), along with human enteroviruses (HEVs), are associated with neonatal sepsis and meningitis. We determined the relative importance of these viruses and the specific HPeV types involved in the development of central nervous system-associated disease. A total of 1575 cerebrospinal fluid (CSF) samples obtained during 2006-2008 were screened for HPeV by means of nested polymerase chain reaction. All samples for which results were positive were typed by sequencing of viral protein (VP) 3/VP1. Screening for HEV was performed in parallel, as was detection of HPeV in respiratory and fecal surveillance samples, to identify virus types circulating in the general population. HPeV was detected in 14 CSF samples obtained exclusively from young infants (age, <3 months) with sepsis or pyrexia. The frequency of detection of HPeVs varied greatly by year, with the highest frequency (7.2%) noted in 2008 exceeding that of HEVs. Direct typing of CSF samples revealed that all infections were caused by HPeV type 3, a finding that is in contrast to the predominant circulation of HPeV1 in contemporary respiratory and fecal surveillance samples. HPeV was a significant cause of severe sepsis and fever with central nervous system involvement in young infants, rivaling enteroviruses. The specific targeting of young infants by HPeV type 3 may reflect a difference in tissue tropism between virus types or a lack of protection of young infants by maternal antibody consequent to the recent emergence of HPeV.
    The Journal of Infectious Diseases 07/2009; 199(12):1753-60. DOI:10.1086/599094 · 6.00 Impact Factor

Publication Stats

15k Citations
1,708.84 Total Impact Points


  • 1985-2014
    • The University of Edinburgh
      • • Centre for Immunity, Infection and Evolution
      • • Edinburgh Infectious Diseases
      • • Laboratory for Clinical and Molecular Virology
      • • Medical Genetics Unit
      • • Division of Genetics and Genomics
      Edinburgh, Scotland, United Kingdom
  • 2011
    • Instituto de Salud Carlos III
      Madrid, Madrid, Spain
  • 1987-2008
    • University of Bristol
      • School of Chemistry
      Bristol, England, United Kingdom
  • 2001
    • The UK Clinical Virology Network
      Edinburgh, Scotland, United Kingdom
  • 1999
    • Oslo University Hospital
      • Department of Pathology
      Kristiania (historical), Oslo County, Norway
    • Guy's and St Thomas' NHS Foundation Trust
      Londinium, England, United Kingdom
  • 1998
    • Chulalongkorn University
      • Faculty of Medicine
      Bangkok, Bangkok, Thailand
  • 1997
    • Drammen Sykehus
      Drammen, Buskerud, Norway
  • 1995
    • Oxford University Hospitals NHS Trust
      • Department of Gastroenterology
      Oxford, England, United Kingdom