Publications by authors named "Alison Bermingham"

18 Publications

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Middle East Respiratory Syndrome.

N Engl J Med 2017 02;376(6):584-594

From the Departments of Intensive Care (Y.M.A., A. Bouchama), Infection Prevention and Control (H.H.B.), and Pathology and Laboratory (A.H.H.), King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center (Y.M.A., H.H.B., A. Bouchama, A.H.H.), the Department of Intensive Care, Dr. Sulaiman Al-Habib Group Hospitals (A.A.-O.), and Alfaisal University (A.A.-O.) - all in Riyadh, Saudi Arabia; the Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville (F.G.H.); the Department of Viral and Rickettsial Diseases, Naval Medical Research Center, Silver Spring, MD (T.L.); the Roslin Institute, University of Edinburgh, and Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh (J.K.B.), the Health Protection and Influenza Research Group, Division of Epidemiology and Public Health, University of Nottingham, Nottingham (J.S.N.-V.-T.), and the Virus Reference Laboratory, Public Health England, London (A. Bermingham) - all in the United Kingdom; the Department of Pandemic and Epidemic Diseases, World Health Organization, Geneva (M.S., N.S., R.A.F.); the Department of Pediatrics, Vanderbilt University School of Medicine, Nashville (M.R.D., J.D.C.); the Center for Global Health, Institut Pasteur, Paris (M.D.V.K.); and the Institute of Health Policy Management and Evaluation, University of Toronto, and the Department of Critical Care Medicine and Department of Medicine, Sunnybrook Health Sciences Centre - both in Toronto (R.A.F.).

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http://dx.doi.org/10.1056/NEJMsr1408795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5362064PMC
February 2017

Natural T Cell-mediated Protection against Seasonal and Pandemic Influenza. Results of the Flu Watch Cohort Study.

Am J Respir Crit Care Med 2015 Jun;191(12):1422-31

2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.

Rationale: A high proportion of influenza infections are asymptomatic. Animal and human challenge studies and observational studies suggest T cells protect against disease among those infected, but the impact of T-cell immunity at the population level is unknown.

Objectives: To investigate whether naturally preexisting T-cell responses targeting highly conserved internal influenza proteins could provide cross-protective immunity against pandemic and seasonal influenza.

Methods: We quantified influenza A(H3N2) virus-specific T cells in a population cohort during seasonal and pandemic periods between 2006 and 2010. Follow-up included paired serology, symptom reporting, and polymerase chain reaction (PCR) investigation of symptomatic cases.

Measurements And Main Results: A total of 1,414 unvaccinated individuals had baseline T-cell measurements (1,703 participant observation sets). T-cell responses to A(H3N2) virus nucleoprotein (NP) dominated and strongly cross-reacted with A(H1N1)pdm09 NP (P < 0.001) in participants lacking antibody to A(H1N1)pdm09. Comparison of paired preseason and post-season sera (1,431 sets) showed 205 (14%) had evidence of infection based on fourfold influenza antibody titer rises. The presence of NP-specific T cells before exposure to virus correlated with less symptomatic, PCR-positive influenza A (overall adjusted odds ratio, 0.27; 95% confidence interval, 0.11-0.68; P = 0.005, during pandemic [P = 0.047] and seasonal [P = 0.049] periods). Protection was independent of baseline antibodies. Influenza-specific T-cell responses were detected in 43%, indicating a substantial population impact.

Conclusions: Naturally occurring cross-protective T-cell immunity protects against symptomatic PCR-confirmed disease in those with evidence of infection and helps to explain why many infections do not cause symptoms. Vaccines stimulating T cells may provide important cross-protective immunity.
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http://dx.doi.org/10.1164/rccm.201411-1988OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476562PMC
June 2015

Longevity and determinants of protective humoral immunity after pandemic influenza infection.

Am J Respir Crit Care Med 2015 Feb;191(3):325-32

1 Section of Respiratory Infections, National Heart and Lung Institute, and.

Rationale: Antibodies to influenza hemagglutinin are the primary correlate of protection against infection. The strength and persistence of this immune response influences viral evolution and consequently the nature of influenza epidemics. However, the durability and immune determinants of induction of humoral immunity after primary influenza infection remain unclear.

Objectives: The spread of a novel H1N1 (A[H1N1]pdm09) virus in 2009 through an unexposed population offered a natural experiment to assess the nature and longevity of humoral immunity after a single primary influenza infection.

Methods: We followed A(H1N1)pdm09-seronegative adults through two influenza seasons (2009-2011) as they developed A(H1N1)pdm09 influenza infection or were vaccinated. Antibodies to A(H1N1)pdm09 virus were measured by hemagglutination-inhibition assay in individuals with paired serum samples collected preinfection and postinfection or vaccination to assess durability of humoral immunity. Preexisting A(H1N1)pdm09-specific multicytokine-secreting CD4 and CD8 T cells were quantified by multiparameter flow cytometry to test the hypothesis that higher frequencies of CD4(+) T-cell responses predict stronger antibody induction after infection or vaccination.

Measurements And Main Results: Antibodies induced by natural infection persisted at constant high titer for a minimum of approximately 15 months. Contrary to our initial hypothesis, the fold increase in A(H1N1)pdm09-specific antibody titer after infection was inversely correlated to the frequency of preexisting circulating A(H1N1)pdm09-specific CD4(+)IL-2(+)IFN-γ(-)TNF-α(-) T cells (r = -0.4122; P = 0.03).

Conclusions: The longevity of protective humoral immunity after influenza infection has important implications for influenza transmission dynamics and vaccination policy, and identification of its predictive cellular immune correlate could guide vaccine development and evaluation.
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http://dx.doi.org/10.1164/rccm.201410-1798OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351579PMC
February 2015

Enhanced MERS coronavirus surveillance of travelers from the Middle East to England.

Emerg Infect Dis 2014 Sep;20(9):1562-4

During the first year of enhanced MERS coronavirus surveillance in England, 77 persons traveling from the Middle East had acute respiratory illness and were tested for the virus. Infection was confirmed in 2 travelers with acute respiratory distress syndrome and 2 of their contacts. Patients with less severe manifestations tested negative.
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http://dx.doi.org/10.3201/eid2009.140817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178421PMC
September 2014

Randomised controlled trial and health economic evaluation of the impact of diagnostic testing for influenza, respiratory syncytial virus and Streptococcus pneumoniae infection on the management of acute admissions in the elderly and high-risk 18- to 64-year-olds.

Health Technol Assess 2014 May;18(36):1-274, vii-viii

Health Protection Agency, Centre for Infections, London, UK.

Background: Western industrialised nations face a large increase in the number of older people. People over the age of 60 years account for almost half of the 16.8 million hospital admissions in England from 2009 to 2010. During 2009-10, respiratory infections accounted for approximately 1 in 30 hospital admissions and 1 in 20 of the 51.5 million bed-days.

Objective: To determine the diagnostic accuracy and clinical effectiveness and cost-effectiveness of rapid molecular and near-patient diagnostic tests for influenza, respiratory syncytial virus (RSV) and Streptococcus pneumoniae infections in comparison with traditional laboratory culture.

Methods: We carried out a randomised controlled trial (RCT) to evaluate impact on prescribing and clinical outcomes of point-of-care tests (POCTs) for influenza A and B and pneumococcal infection, reverse transcriptase-polymerase chain reaction (RT-PCR) tests for influenza A and B and RSV A and B, and conventional culture for these pathogens. We evaluated diagnostic accuracy of POCTs for influenza and pneumococcal infection, RT-PCR for influenza and sputum culture for S. pneumoniae using samples collected during the RCT. We did a systematic review and meta-analysis of POCTs for influenza A and B. We evaluated ease and speed of use of each test, process outcomes and cost-effectiveness.

Results: There was no evidence of association between diagnostic group and prescribing or clinical outcomes. Using PCR as 'gold standard', Quidel Influenza A + B POCT detected 24.4% [95% confidence interval (CI) 16.0% to 34.6%] of influenza infections (specificity 99.7%, 95% CI 99.2% to 99.9%); viral culture detected 21.6% (95% CI 13.5% to 31.6%; specificity 99.8%, 95% CI 99.4% to 100%). Using blood culture as 'gold standard', BinaxNOW pneumococcal POCT detected 57.1% (95% CI 18.4% to 90.1%) of pneumococcal infections (specificity 92.5%; 95% CI 90.6% to 94.1%); sputum culture detected 100% (95% CI 2.5% to 100%; specificity 97.2%, 95% CI 94.3% to 98.9%). Overall, pooled estimates of sensitivity and specificity of POCTs for influenza from the literature were 74% (95% CI 67% to 80%) and 99% (95% CI 98% to 99%), respectively. Median intervals from specimen collection to test result were 15 minutes [interquartile range (IQR) 10-23 minutes) for Quidel Influenza A + B POCT, 20 minutes (IQR 15-30 minutes) for BinaxNOW pneumococcal POCT, 50.8 hours (IQR 44.3-92.6 hours) for semi-nested conventional PCR, 29.2 hours (IQR 26-46.9 hours) for real-time PCR, 629.6 hours (IQR 262.5-846.7 hours) for culture of influenza and 84.4 hours (IQR 70.7-137.8 hours) and 71.4 hours (IQR 69.15-84.0 hours) for culture of S. pneumoniae in blood and sputum, respectively. Both POCTs were rated straightforward and undemanding; blood culture was moderately complex and all other tests were complex. Costs and quality-adjusted life-years (QALYs) of each diagnostic strategy were similar. Incrementally, PCR was most cost-effective (78.3% probability at a willingness to pay of £20,000/QALY). Few patients were admitted within a timescale conducive to treatment with a neuraminidase inhibitor according to National Institute for Health and Care Excellence guidance.

Limitations: The accuracy study was limited by inadequate gold standards.

Conclusions: All tests had limitations. We found no evidence that POCTs for influenza or S. pneumoniae, or PCR for influenza or RSV influenced antimicrobial prescribing or clinical outcomes. The total costs and QALYs of each diagnostic strategy were similar, although, incrementally, PCR was the most cost-effective strategy. The analysis does not support routine use of POCTs for either influenza or pneumococcal antigen for adults presenting with acute cardiopulmonary conditions, but suggests that conventional viral culture for clinical diagnosis should be replaced by PCR.

Trial Registration: Current Controlled Trials ISRCTN21521552.

Funding: This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 18, No. 36. See the NIHR Journals Library website for further project information.
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http://dx.doi.org/10.3310/hta18360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781605PMC
May 2014

Comparative community burden and severity of seasonal and pandemic influenza: results of the Flu Watch cohort study.

Lancet Respir Med 2014 Jun 17;2(6):445-54. Epub 2014 Mar 17.

Respiratory Virus Unit, Public Health England, Colindale, UK.

Background: Assessment of the effect of influenza on populations, including risk of infection, illness if infected, illness severity, and consultation rates, is essential to inform future control and prevention. We aimed to compare the community burden and severity of seasonal and pandemic influenza across different age groups and study years and gain insight into the extent to which traditional surveillance underestimates this burden.

Methods: Using preseason and postseason serology, weekly illness reporting, and RT-PCR identification of influenza from nasal swabs, we tracked the course of seasonal and pandemic influenza over five successive cohorts (England 2006-11; 5448 person-seasons' follow-up). We compared burden and severity of seasonal and pandemic strains. We weighted analyses to the age and regional structure of England to give nationally representative estimates. We compared symptom profiles over the first week of illness for different strains of PCR-confirmed influenza and non-influenza viruses using ordinal logistic regression with symptom severity grade as the outcome variable.

Findings: Based on four-fold titre rises in strain-specific serology, on average influenza infected 18% (95% CI 16-22) of unvaccinated people each winter. Of those infected there were 69 respiratory illnesses per 100 person-influenza-seasons compared with 44 per 100 in those not infected with influenza. The age-adjusted attributable rate of illness if infected was 23 illnesses per 100 person-seasons (13-34), suggesting most influenza infections are asymptomatic. 25% (18-35) of all people with serologically confirmed infections had PCR-confirmed disease. 17% (10-26) of people with PCR-confirmed influenza had medically attended illness. These figures did not differ significantly when comparing pandemic with seasonal influenza. Of PCR-confirmed cases, people infected with the 2009 pandemic strain had markedly less severe symptoms than those infected with seasonal H3N2.

Interpretation: Seasonal influenza and the 2009 pandemic strain were characterised by similar high rates of mainly asymptomatic infection with most symptomatic cases self-managing without medical consultation. In the community the 2009 pandemic strain caused milder symptoms than seasonal H3N2.

Funding: Medical Research Council and the Wellcome Trust.
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http://dx.doi.org/10.1016/S2213-2600(14)70034-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164821PMC
June 2014

Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation.

Lancet Infect Dis 2014 Feb 17;14(2):140-5. Epub 2013 Dec 17.

Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands; Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands. Electronic address:

Background: Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013.

Methods: We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nucleocapsid (N) gene, and open reading frame (ORF) 1a. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay.

Findings: We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nucleotide sequence of an ORF1a fragment (940 nucleotides) and a 4·2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV.

Interpretation: Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot conclude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible.

Funding: European Union projects EMPERIE (contract number 223498), ANTIGONE (contract number 278976), and the VIRGO consortium.
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http://dx.doi.org/10.1016/S1473-3099(13)70690-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106553PMC
February 2014

Incidence of influenza A(H1N1)pdm09 infection, United Kingdom, 2009-2011.

Emerg Infect Dis 2013 Nov;19(11):1866-9

We conducted a longitudinal community cohort study of healthy adults in the UK. We found significantly higher incidence of influenza A(H1N1)pdm09 infection in 2010-11 than in 2009-10, a substantial proportion of subclinical infection, and higher risk for infection during 2010-11 among persons with lower preinfection antibody titers.
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http://dx.doi.org/10.3201/eid1911.130295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837661PMC
November 2013

Cellular immune correlates of protection against symptomatic pandemic influenza.

Nat Med 2013 Oct 22;19(10):1305-12. Epub 2013 Sep 22.

Respiratory Infections Section, National Heart and Lung Institute, Imperial College London, London, UK.

The role of T cells in mediating heterosubtypic protection against natural influenza illness in humans is uncertain. The 2009 H1N1 pandemic (pH1N1) provided a unique natural experiment to determine whether crossreactive cellular immunity limits symptomatic illness in antibody-naive individuals. We followed 342 healthy adults through the UK pandemic waves and correlated the responses of pre-existing T cells to the pH1N1 virus and conserved core protein epitopes with clinical outcomes after incident pH1N1 infection. Higher frequencies of pre-existing T cells to conserved CD8 epitopes were found in individuals who developed less severe illness, with total symptom score having the strongest inverse correlation with the frequency of interferon-γ (IFN-γ)(+) interleukin-2 (IL-2)(-) CD8(+) T cells (r = -0.6, P = 0.004). Within this functional CD8(+)IFN-γ(+)IL-2(-) population, cells with the CD45RA(+) chemokine (C-C) receptor 7 (CCR7)(-) phenotype inversely correlated with symptom score and had lung-homing and cytotoxic potential. In the absence of crossreactive neutralizing antibodies, CD8(+) T cells specific to conserved viral epitopes correlated with crossprotection against symptomatic influenza. This protective immune correlate could guide universal influenza vaccine development.
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http://dx.doi.org/10.1038/nm.3350DOI Listing
October 2013

Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort.

J Antimicrob Chemother 2013 Oct 12;68(10):2324-31. Epub 2013 Jun 12.

Microbiology Services Colindale, Public Health England, London, UK.

Objective: To perform antiviral susceptibility monitoring of treated individuals in the community during the 2009 influenza A(H1N1) pandemic in England.

Patients And Methods: Between 200 and 400 patients were enrolled daily through the National Pandemic Flu Service (NPFS) and issued with a self-sampling kit. Initially, only persons aged 16 and over were eligible, but from 12 November (week 45), self-sampling was extended to include school-age children (5 years and older). All samples received were screened for influenza A(H1N1)pdm09 as well as seasonal influenza [A(H1N1), A(H3N2) and influenza B] by a combination of RT-PCR and virus isolation methods. Influenza A(H1N1)pdm09 RT-PCR-positive samples were screened for the oseltamivir resistance-inducing H275Y substitution, and a subset of samples also underwent phenotypic antiviral susceptibility testing by enzyme inhibition assay.

Results: We were able to detect virus by RT-PCR in self-taken samples and recovered infectious virus enabling further virological characterization. The majority of influenza A(H1N1)pdm09 RT-PCR-positive NPFS samples (n = 1273) were taken after oseltamivir treatment had begun. No reduction in phenotypic susceptibility to neuraminidase inhibitors was detected, but five cases with minority quasi-species of oseltamivir-resistant virus (an H275Y amino acid substitution in neuraminidase) were detected.

Conclusions: Self-sampling is a useful tool for community surveillance, particularly for the follow-up of drug-treated patients. The virological study of self-taken samples from the NPFS provided a unique opportunity to evaluate the emergence of oseltamivir resistance in treated individuals with mild illness in the community, a target population that may not be captured by traditional sentinel surveillance schemes.
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http://dx.doi.org/10.1093/jac/dkt203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313964PMC
October 2013

Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection.

J Clin Virol 2013 Mar 14;56(3):260-70. Epub 2012 Dec 14.

HPA Microbiology Services Division, London NW9 5HT, UK.

In order to comply with national and international clinical laboratory accreditation standards (e.g. the ISO 15189, Clinical Pathology Accreditation standards) and with the joint code of practice for research, there must be a method of assessing that test methods are "fit for purpose". This document gives guidance on development and describes how a validation file is produced. A test method may be a commercial kit, an in-house assay or reagent or a set of reagents bought separately and used to prepare an in house assay. A validation file is needed for both current and new test procedures. The file may refer to data recorded in workbooks, papers and reports. Modifications to assays (including commercially available assays) necessitate either an update to the validation file or creation of a new file. This paper is intended to provide a generic framework for in-house assay development and validation of new nucleic acid amplification assays including real-time polymerase chain reaction (PCR).
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http://dx.doi.org/10.1016/j.jcv.2012.11.013DOI Listing
March 2013

Predominance of heterosubtypic IFN-γ-only-secreting effector memory T cells in pandemic H1N1 naive adults.

Eur J Immunol 2012 Nov 15;42(11):2913-24. Epub 2012 Aug 15.

Department of Respiratory Medicine, National Heart and Lung Institute, Imperial College London, Paddington, London, UK.

The 2009/10 pandemic (pH1N1) highlighted the need for vaccines conferring heterosubtypic immunity against antigenically shifted influenza strains. Although cross-reactive T cells are strong candidates for mediating heterosubtypic immunity, little is known about the population-level prevalence, frequency, and cytokine-secretion profile of heterosubtypic T cells to pH1N1. To assess this, pH1N1 sero-negative adults were recruited. Single-cell IFN-γ and IL-2 cytokine-secretion profiles to internal proteins of pH1N1 or live virus were enumerated and characterised. Heterosubtypic T cells recognising pH1N1 core proteins were widely prevalent, being detected in 90% (30 of 33) of pH1N1-naïve individuals. Although the last exposure to influenza was greater than 6 months ago, the frequency and proportion of the IFN-γ-only-secreting T-cell subset was significantly higher than the IL-2-only-secreting subset. CD8(+) IFN-γ-only-secreting heterosubtypic T cells were predominantly CCR7(-) CD45RA(-) effector-memory phenotype, expressing the tissue-homing receptor CXCR3 and degranulation marker CD107. Receipt of the 2008-09 influenza vaccine did not alter the frequency of these heterosubtypic T cells, highlighting the inability of current vaccines to maintain this heterosubtypic T-cell pool. The surprisingly high prevalence of pre-existing circulating pH1N1-specific CD8(+) IFN-γ-only-secreting effector memory T cells with cytotoxic and lung-homing potential in pH1N1-seronegative adults may partly explain the low case fatality rate despite high rates of infection of the pandemic in young adults.
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http://dx.doi.org/10.1002/eji.201242504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310933PMC
November 2012

Seroepidemiologic study of pandemic (H1N1) 2009 during outbreak in boarding school, England.

Emerg Infect Dis 2011 Sep;17(9):1670-7

Health Protection Agency, London, UK.

We conducted a seroepidemiologic study during an outbreak of pandemic (H1N1) 2009 in a boarding school in England. Overall, 353 (17%) of students and staff completed a questionnaire and provided a serum sample. The attack rate was 40.5% and 34.1% for self-reported acute respiratory infection (ARI). Staff were less likely to be seropositive than students 13-15 years of age (staff 20-49 years, adjusted odds ratio [AOR] 0.30; >50 years AOR 0.20). Teachers were more likely to be seropositive than other staff (AOR 7.47, 95% confidence interval [CI] 2.31-24.2). Of seropositive persons, 44.6% (95% CI 36.2%-53.3%) did not report ARI. Conversely, of 141 with ARI and 63 with influenza-like illness, 45.8% (95% CI 37.0%-54.0%) and 30.2% (95% CI 19.2%-43.0%) had negative test results, respectively. A weak association was found between seropositivity and a prophylactic dose of antiviral agents (AOR 0.55, 95% CI 0.30-0.99); prophylactic antiviral agents lowered the odds of ARI by 50%.
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http://dx.doi.org/10.3201/eid1709.100761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322048PMC
September 2011

Mycoplasma pneumoniae and respiratory virus infections in children with persistent cough in England: a retrospective analysis.

Pediatr Infect Dis J 2011 Dec;30(12):1047-51

Department of Primary Health Care, University of Oxford, Oxford, United Kingdom.

Background: Persistent cough following an acute respiratory tract infection is common in children, but clinicians may find it difficult to give accurate prognostic information on likely duration of cough without a microbiologic diagnosis. This study estimates the prevalence of Mycoplasma pneumoniae (Mp) and assesses the prognostic value of detecting Mp and respiratory viruses in children with persistent cough.

Methods: We retrospectively analyzed blood samples, nasopharyngeal aspirates (NPAs), and cough duration data from 179 children with persistent cough lasting 14 days or longer. Of these children, 37% had serologically confirmed Bordetella pertussis (pertussis). We detected Mp by polymerase chain reaction of NPAs and IgM serology, and respiratory viruses (human rhinoviruses, influenza viruses, respiratory syncytial viruses, and human metapneumovirus) by polymerase chain reaction of NPAs. We used Kaplan-Meier analyses to calculate median cough durations with 95% confidence intervals (CIs).

Results: We detected Mp in 22 of 170 children with sufficient blood and/or NPAs (12.9%, 95% CI: 8.7-18.8). Cough duration in children with positive Mp serology (median: 39 days, 95% CI: 24-54) was significantly shorter than in children with positive pertussis serology (median: 118 days, 95% CI: 82-154, P < 0.001). The presence of respiratory viruses did not significantly lengthen cough duration in children with pertussis (median: 154 days, 95% CI: 74-234, P = 0.810). Only 3 children had both Mp and respiratory virus infections.

Conclusions: Mp is an important infection in children with persistent cough and is associated with a significantly shorter duration of cough than pertussis. However, detecting respiratory viruses does not add prognostic value in children with pertussis.
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http://dx.doi.org/10.1097/INF.0b013e31822db5e2DOI Listing
December 2011

Has estimation of numbers of cases of pandemic influenza H1N1 in England in 2009 provided a useful measure of the occurrence of disease?

Influenza Other Respir Viruses 2011 Nov 9;5(6):e504-12. Epub 2011 May 9.

Health Protection Agency, Centre for Infections, London, UK.

Background: Surveillance indicators of influenza activity have generally provided robust comparative trend data for England. These indicators became less reliable, however, for monitoring trends in activity, or comparisons with previous years, during the influenza pandemic in 2009 because of changes in the perception of risk and changes in the systems of healthcare delivery. An approach was developed to estimate the number of cases of influenza-like illness (ILI) occurring because of infection with pandemic influenza virus.

Methods And Findings: The number of cases was estimated each week in England on the basis of total number of patients consulting healthcare services with ILI; estimates of the proportion of individuals in the community experiencing an ILI-seeking health care; and the proportion of these positive on laboratory testing. Almost 800,000 cases (range 375,000-1·6 million) of symptomatic ILI cases were estimated to have occurred over the course of the two waves of pandemic activity in England. More cases were estimated to have occurred in the second wave than in the first.

Conclusions: These results underestimate the total number of infections as they do not include asymptomatic infections nor those with mild illness not meeting the definition of a case of ILI. Nevertheless, the case number estimates provide a useful indicator of the trend in influenza activity and weekly data were extensively used in media reports. Although surveillance methods differ between countries, the approach of synthesising available data sources to produce an overall estimate of case numbers could be applied more widely to provide comparative data.
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http://dx.doi.org/10.1111/j.1750-2659.2011.00259.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855140PMC
November 2011

Monitoring the emergence of community transmission of influenza A/H1N1 2009 in England: a cross sectional opportunistic survey of self sampled telephone callers to NHS Direct.

BMJ 2009 Aug 27;339:b3403. Epub 2009 Aug 27.

Health Protection Agency Real-time Syndromic Surveillance Team, Birmingham B3 2PW.

Objective: To evaluate ascertainment of the onset of community transmission of influenza A/H1N1 2009 (swine flu) in England during the earliest phase of the epidemic through comparing data from two surveillance systems.

Design: Cross sectional opportunistic survey.

Study Samples: Results from self samples by consenting patients who had called the NHS Direct telephone health line with cold or flu symptoms, or both, and results from Health Protection Agency (HPA) regional microbiology laboratories on patients tested according to the clinical algorithm for the management of suspected cases of swine flu.

Setting: Six regions of England between 24 May and 30 June 2009.

Main Outcome Measure: Proportion of specimens with laboratory evidence of influenza A/H1N1 2009.

Results: Influenza A/H1N1 2009 infections were detected in 91 (7%) of the 1385 self sampled specimens tested. In addition, eight instances of influenza A/H3 infection and two cases of influenza B infection were detected. The weekly rate of change in the proportions of infected individuals according to self obtained samples closely matched the rate of increase in the proportions of infected people reported by HPA regional laboratories. Comparing the data from both systems showed that local community transmission was occurring in London and the West Midlands once HPA regional laboratories began detecting 100 or more influenza A/H1N1 2009 infections, or a proportion positive of over 20% of those tested, each week.

Conclusions: Trends in the proportion of patients with influenza A/H1N1 2009 across regions detected through clinical management were mirrored by the proportion of NHS Direct callers with laboratory confirmed infection. The initial concern that information from HPA regional laboratory reports would be too limited because it was based on testing patients with either travel associated risk or who were contacts of other influenza cases was unfounded. Reports from HPA regional laboratories could be used to recognise the extent to which local community transmission was occurring.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733951PMC
http://dx.doi.org/10.1136/bmj.b3403DOI Listing
August 2009

Neuraminidase inhibitor resistance after oseltamivir treatment of acute influenza A and B in children.

Clin Infect Dis 2009 Feb;48(4):389-96

Infectious Diseases Unit, Leicester Royal Infirmary, Leicester, UK.

Background: Oseltamivir, a specific influenza neuraminidase inhibitor, is an effective treatment for seasonal influenza. Emergence of drug-resistant influenza viruses after treatment has been reported, particularly in children in Japan, where the dosing schedule is different from that used throughout the rest of the world. We investigated the emergence of drug-resistant infection in children treated with a tiered weight-based dosing regimen.

Methods: We analyzed sequential clinical nasopharyngeal samples, obtained before and after tiered weight-based oseltamivir therapy, from children with acute influenza during 2005-2007. We isolated viruses, tested for drug resistance with use of a fluorescence-based neuraminidase inhibition assay, performed neuraminidase gene sequencing, and determined quantitative viral loads.

Results: Sixty-four children (34 with influenza A subtype H3N2, 11 with influenza A subtype H1N1, and 19 with influenza B virus) aged 1-12 years (median age, 3 years, 1 month) were enrolled. By days 4-7 after initiation of treatment, of 64 samples tested, 47 (73.4%) and 26 (40.6%) had virus detectable by reverse-transcriptase polymerase chain reaction and culture, respectively. By days 8-12 after initiation of treatment, of 53 samples tested, 18 (33.9%) and 1 (1.8%) had virus detectable by reverse-transcriptase polymerase chain reaction and culture, respectively. We found no statistically significant differences in the reduction of viral shedding or time to clearance of virus between viral subtypes. Antiviral-resistant viruses were recovered from 3 (27.3%) of 11 children with influenza A subtype H1N1, 1 (2.9%) of 34 children with influenza A subtype H3N2, and 0 (0%) of 19 children with influenza B virus, all of whom were treated with oseltamivir (P = .004). There was no evidence of prolonged illness in children infected with drug-resistant virus.

Conclusions: Drug resistance emerges at a higher rate in influenza A subtype H1N1 virus than in influenza A subtype H3N2 or influenza B virus after tiered weight-based oseltamivir therapy. Virological surveillance for patterns of drug resistance is essential for determination of antiviral treatment strategies and for composition of pandemic preparedness stockpiles.
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http://dx.doi.org/10.1086/596311DOI Listing
February 2009

VII International Symposium on Respiratory Viral Infections.

Antivir Ther 2007 ;12(4 Pt B):671-93

Health Protection Agency, London, UK.

The VII International Symposium on Respiratory Viral Infections was a multidisciplinary forum for the presentation of recent advances in respiratory virus research with special emphasis on antiviral therapies and vaccine strategies. Topics covered in invited lectures included detection of novel respiratory viral pathogens and viral evolution, characterization of the 1918 pandemic virus, human metapneumovirus infections, human respiratory epithelial cultures for studying viral pathogenesis, the role of respiratory viruses in the pathogenesis of asthma, influenza-bacterial interactions, advances in generating vaccine candidates against global respiratory threats like avian influenza and SARS, antiviral resistance surveillance in influenza viruses, and a mini-symposium on advances in viral diagnostics. Other talks covered the live, attenuated intranasal influenza vaccine, monoclonals for respiratory syncytial virus (RSV), mechanisms of antiviral resistance in influenza B, and novel inhibitors for influenza, RSV and rhinovirus infections.
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November 2007