Publications
307 results found
Tang J, Hanage WP, Fraser C, et al., 2009, Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach, PLOS COMPUTATIONAL BIOLOGY, Vol: 5, ISSN: 1553-734X
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- Citations: 75
Garske T, Legrand J, Donnelly CA, et al., 2009, Assessing the severity of the novel influenza A/H1N1 pandemic, BRITISH MEDICAL JOURNAL, Vol: 339, ISSN: 0959-8146
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- Citations: 164
Fraser C, Donnelly CA, Cauchemez S, et al., 2009, Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings, SCIENCE, Vol: 324, Pages: 1557-1561, ISSN: 0036-8075
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- Citations: 1393
Hanage WP, Fraser C, Tang J, et al., 2009, Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus, SCIENCE, Vol: 324, Pages: 1454-1457, ISSN: 0036-8075
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- Citations: 132
Baggaley RF, Griffin JT, Chapman R, et al., 2009, Estimating the public health impact of the effect of herpes simplex virus suppressive therapy on plasma HIV-1 viral load, AIDS, Vol: 23, Pages: 1005-1013, ISSN: 0269-9370
Objective: Trials of herpes simplex virus (HSV) suppressive therapy among HSV-2/HIV-1-infected individuals have reported an impacton plasma HIV-1 viral loads(PVLs). Our aim was to estimate the population-level impact of suppressive therapy on female-to-male HIV-1 sexual transmission.Design and methods: By comparing prerandomization and postrandomization individual-level PVL data from the first two HSV suppressive therapy randomized controlled trials in sub-Saharan Africa, we estimated the effect of treatment on duration of asymptomatic infection and number of HIV-1 transmission events for each trial.Results: Assuming that a reduction in PVL is accompanied by an increased duration of HIV-1 asymptomatic infection, 4-6 years of HSV suppressive therapy produce a 1-year increase in the duration of this stage. To avert one HIV-1 transmission requires 8.8 [95% confidence interval (CI), 5.9-14.9] and 11.4 (95% Cl, 7.8-27.5) women to be treated from halfway through their HIV-1 asymptomatic period, using results from Burkina Faso and South African trials, respectively. Regardless of the timing of treatment initiation, 51.6 (95% Cl, 30.4-137.0) and 66.5 (95% Cl, 36.7-222.6) treatment-years are required to avert one HIV-1 infection. Distributions of set-point PVL values from sub-Saharan African populations suggest that unintended adverse consequences of therapy at the population level (i.e. increased HIV-1 transmission due to increased duration of infection) are unlikely to occur in these settings.Conclusion: HSV suppressive therapy may avert relatively few HIV-1 transmission events per person-year of treatment. Its use as a prevention intervention may be limited; however, further research into its effect on rate of CD4 cell count decline and the impact of higher dosing schedules is warranted. (C) 2009 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins
Lipsitch M, Colijn C, Cohen T, et al., 2009, No coexistence for free: Neutral null models for multistrain pathogens, EPIDEMICS, Vol: 1, Pages: 2-13, ISSN: 1755-4365
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- Citations: 96
Fraser C, Alm EJ, Polz MF, et al., 2009, The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity, SCIENCE, Vol: 323, Pages: 741-746, ISSN: 0036-8075
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- Citations: 287
Ghani A, Baguelin M, Griffin J, et al., 2009, The early transmission dynamics of H1N1pdm influenza in the United Kingdom, PLoS currents, Vol: 1
Pellis L, Ferguson NM, Fraser C, 2008, The relationship between real-time and discrete-generation models of epidemic spread, Mathematical Biosciences, Vol: 216, Pages: 63-70, ISSN: 0025-5564
Grassly NC, Fraser C, 2008, Mathematical models of infectious disease transmission, NATURE REVIEWS MICROBIOLOGY, Vol: 6, Pages: 477-487, ISSN: 1740-1526
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- Citations: 351
Bezemer D, de WF, Boerlijst MC, et al., 2008, A resurgent HIV-1 epidemic among men who have sex with men in the era of potent antiretroviral therapy., AIDS, Vol: 22, Pages: 1071-1077, ISSN: 1473-5571
Reducing viral load, highly active antiretroviral therapy has the potential to limit onwards transmission of HIV-1 and thus help contain epidemic spread. However, increases in risk behaviour and resurgent epidemics have been widely reported post-highly active antiretroviral therapy. The aim of this study was to quantify the impact that highly active antiretroviral therapy had on the epidemic.
Halloran ME, Ferguson NM, Eubank S, et al., 2008, Modeling targeted layered containment of an influenza pandemic in the United States, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 4639-4644, ISSN: 0027-8424
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- Citations: 423
Fraser C, 2007, Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic, PLOS ONE, Vol: 2, ISSN: 1932-6203
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- Citations: 267
Fraser C, 2007, Influenza pandemic vaccines: Spread them thin?, PLOS MEDICINE, Vol: 4, Pages: 977-979, ISSN: 1549-1277
Fraser C, Tomassini JE, Xi L, et al., 2007, Modeling the long-term antibody response of a human papillomavirus (HPV) virus-like particle (VLP) type 16 prophylactic vaccine, VACCINE, Vol: 25, Pages: 4324-4333, ISSN: 0264-410X
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- Citations: 119
Turner KME, Hanage WP, Fraser C, et al., 2007, Assessing the reliability of eBURST using simulated populations with known ancestry, BMC Microbiology, Vol: 7, ISSN: 1471-2180
Background: The program eBURST uses multilocus sequence typing data to divide bacterialpopulations into groups of closely related strains (clonal complexes), predicts the founding genotype of each group, and displays the patterns of recent evolutionary descent of all other strains in the group from the founder. The reliability of eBURST was evaluated using populations simulated with different levels of recombination in which the ancestry of all strains was known.Results: For strictly clonal simulations, where all allelic change is due to point mutation, the groups of related strains identified by eBURST were very similar to those expected from the true ancestry and most of the true ancestor-descendant relationships (90–98%) were identified by eBURST. Populations simulated with low or moderate levels of recombination showed similarly high performance but the reliability of eBURST declined with increasing recombination to mutationratio. Populations simulated under a high recombination to mutation ratio were dominated by a single large straggly eBURST group, which resulted from the incorrect linking of unrelated groups of strains into the same eBURST group. The reliability of the ancestor-descendant links in eBURST diagrams was related to the proportion of strains in the largest eBURST group, which provides auseful guide to when eBURST is likely to be unreliable.Conclusion: Examination of eBURST groups within populations of a range of bacterial speciesshowed that most were within the range in which eBURST is reliable, and only a small number (e.g. Burkholderia pseudomallei and Enterococcus faecium) appeared to have such high rates of recombination that eBURST is likely to be unrel iable. The study also demonstrates how three simple tests in eBURST v3 can be used to detect unreliable eBURST performance and recognisepopulations in which there appears to be a high rate of recombination relative to mutation.
Fraser C, Hanage WP, Spratt BG, 2007, Recombination and the nature of bacterial speciation, Science, Vol: 315, Pages: 476-480, ISSN: 0036-8075
Fraser C, Hollingsworth D, Chapman D, et al., 2007, Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis., Proc Natl Acad Sci USA, Vol: In press
Fraser C, Hollingsworth TD, Chapman R, et al., 2007, Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis, Proc Natl Acad Sci USA, Vol: in press
Spratt BG, Fraser C, Hanage WP, 2007, Exploring genetic relatedness, patterns of evolutionary descent, and the population genetics of bacterial pathogens using multilocus sequence typing, Encyclopedia of Infectious Diseases: Modern Methodologies, Editors: Tibayrenc, Publisher: Wiley, ISBN: 978-0-471-65732-3
Klinkenberg D, Fraser C, Heesterbeek H, 2006, The Effectiveness of Contact Tracing in Emerging Epidemics, PLOS ONE, Vol: 1, ISSN: 1932-6203
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- Citations: 141
Hanage WP, Spratt BG, Turner KME, et al., 2006, Modelling bacterial speciation, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 361, Pages: 2039-2044, ISSN: 1471-2970
A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we observe a transition between clonal structure and sexual structure as the rate of recombination increases. In the clonal situation, clearly resolved clusters are regularly formed, break up or go extinct. In the sexual situation, the formation of distinct clusters is prevented by the cohesive force of recombination. Where the rate of recombination is a declining log-linear function of the genetic distance between the donor and recipient strain, distinct clusters emerge even with high rates of recombination. These clusters arise in the absence of selection, and have many of the properties of species, with high recombination rates and thus sexual cohesion within clusters and low rates between clusters. Distance-scaled recombination can thus lead to a population splitting into distinct genotypic clusters, a process that mimics sympatric speciation. However, empirical estimates of the relationship between sequence divergence and recombination rate indicate that the decline in recombination is an insufficiently steep function of genetic distance to generate species in nature under neutral drift, and thus that other mechanisms should be invoked to explain speciation in the presence of recombination.
Hanage WP, Fraser C, Spratt BG, 2006, Sequences, sequence clusters and bacterial species, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 361, Pages: 1917-1927, ISSN: 0962-8436
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- Citations: 132
Grassly NC, Fraser C, Wenger J, et al., 2006, New strategies for the elimination of polio from India, SCIENCE, Vol: 314, Pages: 1150-1153, ISSN: 0036-8075
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- Citations: 196
Wu JT, Riley S, Fraser C, et al., 2006, Reducing the impact of the next influenza pandemic using household-based public health interventions., PLoS Med, Vol: 3, Pages: e361-e361
Ferguson NM, Cummings DAT, Fraser C, et al., 2006, Strategies for mitigating an influenza pandemic, NATURE, Vol: 442, Pages: 448-452, ISSN: 0028-0836
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- Citations: 1454
Grassly NC, Fraser C, 2006, Seasonal Infectious Disease Epidemiology, Proceedings of the Royal Society of London B, Vol: FirstCite Early Online Publish
Griffin JT, Fraser C, Gras L, et al., 2006, The effect on treatment comparisons of different measurement frequencies in human immunodeficiency virus observational databases, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 163, Pages: 676-683, ISSN: 0002-9262
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- Citations: 11
Hanage WP, Fraser C, Spratt BG, 2006, The impact of homologous recombination on the generation of diversity in bacteria, JOURNAL OF THEORETICAL BIOLOGY, Vol: 239, Pages: 210-219, ISSN: 0022-5193
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- Citations: 85
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