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      Efficient Simulation of the Spatial Transmission Dynamics of Influenza

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          Abstract

          Early data from the 2009 H1N1 pandemic (H1N1pdm) suggest that previous studies over-estimated the within-country rate of spatial spread of pandemic influenza. As large spatially resolved data sets are constructed, the need for efficient simulation code with which to investigate the spatial patterns of the pandemic becomes clear. Here, we present a significant improvement to the efficiency of an individual-based stochastic disease simulation framework commonly used in multiple previous studies. We quantify the efficiency of the revised algorithm and present an alternative parameterization of the model in terms of the basic reproductive number. We apply the model to the population of Taiwan and demonstrate how the location of the initial seed can influence spatial incidence profiles and the overall spread of the epidemic. Differences in incidence are driven by the relative connectivity of alternate seed locations. The ability to perform efficient simulation allows us to run a batch of simulations and take account of their average in real time. The averaged data are stable and can be used to differentiate spreading patterns that are not readily seen by only conducting a few runs.

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          Most cited references 17

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          Pandemic potential of a strain of influenza A (H1N1): early findings.

          A novel influenza A (H1N1) virus has spread rapidly across the globe. Judging its pandemic potential is difficult with limited data, but nevertheless essential to inform appropriate health responses. By analyzing the outbreak in Mexico, early data on international spread, and viral genetic diversity, we make an early assessment of transmissibility and severity. Our estimates suggest that 23,000 (range 6000 to 32,000) individuals had been infected in Mexico by late April, giving an estimated case fatality ratio (CFR) of 0.4% (range: 0.3 to 1.8%) based on confirmed and suspected deaths reported to that time. In a community outbreak in the small community of La Gloria, Veracruz, no deaths were attributed to infection, giving an upper 95% bound on CFR of 0.6%. Thus, although substantial uncertainty remains, clinical severity appears less than that seen in the 1918 influenza pandemic but comparable with that seen in the 1957 pandemic. Clinical attack rates in children in La Gloria were twice that in adults ( /=15 years: 29%). Three different epidemiological analyses gave basic reproduction number (R0) estimates in the range of 1.4 to 1.6, whereas a genetic analysis gave a central estimate of 1.2. This range of values is consistent with 14 to 73 generations of human-to-human transmission having occurred in Mexico to late April. Transmissibility is therefore substantially higher than that of seasonal flu, and comparable with lower estimates of R0 obtained from previous influenza pandemics.
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            Strategies for mitigating an influenza pandemic

            Pandemic flu: talking tactics Numerical models of the epidemiology of a potential flu pandemic show there is no single magic bullet which can control the outbreak, but that a combination of approaches could reduce transmission and save many lives. Border restrictions are unlikely to have much effect and travel restrictions within one country would make very little difference to the spread of a pandemic within that country. The models predict that a pandemic in the United Kingdom would peak within two to three months of the first case, and be over within 4 months. It also shows that vaccines need to be available within two months of the start of a pandemic to have a big effect in reducing infection rates. That means that vaccines would need to be stockpiled in advance to be effective. Supplementary information The online version of this article (doi:10.1038/nature04795) contains supplementary material, which is available to authorized users.
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              Strategies for containing an emerging influenza pandemic in Southeast Asia.

              Highly pathogenic H5N1 influenza A viruses are now endemic in avian populations in Southeast Asia, and human cases continue to accumulate. Although currently incapable of sustained human-to-human transmission, H5N1 represents a serious pandemic threat owing to the risk of a mutation or reassortment generating a virus with increased transmissibility. Identifying public health interventions that might be able to halt a pandemic in its earliest stages is therefore a priority. Here we use a simulation model of influenza transmission in Southeast Asia to evaluate the potential effectiveness of targeted mass prophylactic use of antiviral drugs as a containment strategy. Other interventions aimed at reducing population contact rates are also examined as reinforcements to an antiviral-based containment policy. We show that elimination of a nascent pandemic may be feasible using a combination of geographically targeted prophylaxis and social distancing measures, if the basic reproduction number of the new virus is below 1.8. We predict that a stockpile of 3 million courses of antiviral drugs should be sufficient for elimination. Policy effectiveness depends critically on how quickly clinical cases are diagnosed and the speed with which antiviral drugs can be distributed.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2010
                4 November 2010
                : 5
                : 11
                Affiliations
                [1 ]Institute of Information Science, Academia Sinica, Taipei, Taiwan
                [2 ]Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
                [3 ]Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
                [4 ]Centers for Disease Control, Taipei, Taiwan
                [5 ]Department of Infectious Disease Epidemiology, University of Hong Kong, Hong Kong
                [6 ]Department of Radiation Oncology, Far Eastern Memorial Hospital, Taipei, Taiwan
                [7 ]Department of Computer Science, University of Virginia, Charlottesville, Virginia, United States of America
                Dana-Farber Cancer Institute, United States of America
                Author notes

                Conceived and designed the experiments: MTT TCMC JHC HSK CJL SR BJS CHS DWW TSH. Performed the experiments: MTT TCMC JHC CWH HSK CJL SR BJS CHS DWW TSH. Analyzed the data: MTT TCMC JHC CWH HSK CJL SR BJS CHS DWW TSH. Contributed reagents/materials/analysis tools: MTT TCMC JHC CWH HSK CJL SR BJS CHS DWW TSH. Wrote the paper: MTT TCMC SR BJS CHS DWW TSH.

                Article
                10-PONE-RA-18947R1
                10.1371/journal.pone.0013292
                2973967
                21079810
                Tsai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Counts
                Pages: 8
                Categories
                Research Article
                Computer Science/Information Technology
                Infectious Diseases/Epidemiology and Control of Infectious Diseases
                Public Health and Epidemiology/Epidemiology
                Public Health and Epidemiology/Infectious Diseases

                Uncategorized

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