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Molecular epidemiology of white spot syndrome virus

Molecular epidemiology of white spot syndrome virus [7A.3]

In 1992 a new disease agent was first noted in shrimp aquaculture: white spot syndrome virus (WSSV), a DNA virus belonging to the novel Nimaviridae virus family. WSSV infection results in massive mortality in cultured shrimp – causing enormous economic damage to the shrimp industry – and the virus spread world-wide within a decade. We previously showed that the WSSV genome became progressively smaller as the virus spread throughout Asia, and that viral virulence and competitive fitness increased concurrently. Here, we first determined what variable loci in the WSSV genome are suitable molecular markers for determining patterns of viral spread at different spatiotemporal scales.
Recorded Dec 4 2009 19 mins
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Presented by
B.T.M. Dieu, Wageningen University, The Netherlands
Presentation preview: Molecular epidemiology of white spot syndrome virus
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  • Climate Change and Vector Borne Disease: what to expect Recorded: Dec 4 2009 44 mins
    R.R. Colwell, Johns Hopkins University Bloomberg School of Public Health, USA
    Climate Change and Vector Borne Disease: what to expect [INV7]

    Vectorborne diseases have long been recognized to be climate driven, but it is now clear that many infectious diseases are intricately related to weather patterns, climate, and seasonality. Epidemics of cholera, a devastating disease occurring predominantly in third world countries, has been shown to be directly correlated with environmental parameters including sea surface temperature, sea surface height, and salinity, among others. Recent studies incorporating satellite sensing technology, ground truth measurements, and microbiological analyses have provided the basis for predictive modeling of cholera epidemics in Bangladesh, India, and East Africa. These findings will be discussed as a paradigm for global infectious diseases in this century.
  • Modelling H1N1 pandemic with InfluSim tells us to enforce(cont.) Recorded: Dec 4 2009 17 mins
    M. Schwehm, ExploSYS GmbH, Leinfelden, Germany
    Modelling H1N1 pandemic with InfluSim tells us to enforce social distancing among kids [7B.4]

    The current influenza pandemic is characterized by fast outbreaks with low final size. Modelling this with homogeneous mixing assumptions fails, as we have to use a large R0 to reconstruct the rise of the wave, but this produces high final sizes. To explain the pandemic, we have to assume heterogeneous mixing.
    InfluSim uses a contact matrix that controls the interaction of six age groups. The default values of this contact matrix are based on observed contact counts. Assuming that contacts among children are more of a nature which facilitates transmission than contacts among adults, we increase child-child entries by a factor four. This modification yet needs to be refined to, but it already allows to reconstruct outbreaks in the southern hemisphere with R0<1.5: outbreaks are quick and reach 10-20% of the population; attack rates are highest in children are (a fact which has been observed frequently); even without pre-existing immunity in the elderly, their attack rates are low. Our results are consistent with the breakdown of the first wave in Mexico city after closing schools and universities, with the rise of cases after re-opening schools in the US, and with the situation in Germany where the wave started in the only state without autumn holidays in October.
  • Vaccination against pandemic influenza A/H1N1v in England(cont.) Recorded: Dec 4 2009 24 mins
    Marc Baguelin, Health Protection Agency, UK
    Vaccination against pandemic influenza A/H1N1v in England: A real-time economic evaluation [7B.3]

    Background: Decisions on how to mitigate an evolving pandemic are technically challenging. We present a real time assessment of the effectiveness and cost-effectiveness of alternative influenza A/H1N1v vaccination strategies.
  • Molecular epidemiology of white spot syndrome virus Recorded: Dec 4 2009 19 mins
    B.T.M. Dieu, Wageningen University, The Netherlands
    Molecular epidemiology of white spot syndrome virus [7A.3]

    In 1992 a new disease agent was first noted in shrimp aquaculture: white spot syndrome virus (WSSV), a DNA virus belonging to the novel Nimaviridae virus family. WSSV infection results in massive mortality in cultured shrimp – causing enormous economic damage to the shrimp industry – and the virus spread world-wide within a decade. We previously showed that the WSSV genome became progressively smaller as the virus spread throughout Asia, and that viral virulence and competitive fitness increased concurrently. Here, we first determined what variable loci in the WSSV genome are suitable molecular markers for determining patterns of viral spread at different spatiotemporal scales.
  • Cattle movement network and the potential for transmission(cont.) Recorded: Dec 4 2009 17 mins
    V.V. Volkova, University of Edinburgh, UK
    Cattle movement network and the potential for transmission of endemic infections [7A.2]

    A livestock farm population can be considered as a network connected by movements of animals. We reconstruct the Scottish cattle farm network in four one-year intervals from July 2003 to June 2007. We score each directed contact between a pair of farms in a particular year in three ways: 1) present or absent (unweighted); 2) weighted by the number of batches moved; 3) weighted by the total number of cattle moved. (1) is most appropriate for a highly transmissible infection with high on-farm prevalence (likely to be transmitted by any contact); (3) is most appropriate for a rare infection with low on-farm prevalence (the probability of transmission is low and linearly dependent on the number of animals moved); and (2) refers to an intermediate epidemiological scenario. We quantify the basic reproduction number, R0, for an infectious disease in this network for all three contact definitions. Since we are considering a one-year interval, our results are most relevant to endemic chronic infections. We find that, depending on how the contact between farms is defined, properties of the farm contact matrix have substantial impact on R0. We have previously developed means of identifying a 20% subset of farms contributing the most to R0 in a livestock network based on contributions to the dominant eigenvalue of the contact matrix. Applying this methodology, we show that removal of the contacts made by this subset of farms in Scottish cattle network in a given year results in at least 91% reduction in the magnitude of R0 for unweighted contact, at least 96% reduction for contact weighted by number of batches, and at least 98% reduction for contact weighted by total number of cattle moved. In practice, the pattern of infectious contacts between farms can be altered through livestock movement restrictions or pre-movement testing.
  • Analysis of cost-effectiveness of school closure (cont.) Recorded: Dec 4 2009 18 mins
    L. Pellis, N.M. Ferguson, Imperial College London, UK
    Analysis of cost-effectiveness of school closure strategies in the novel H1N1 2009 influenza pandemic [7B.1]

    School closure is a form of non-pharmaceutical intervention often adopted on an ad hoc basis in influenza outbreaks, but the effectiveness of which remains controversial. Here we examine the extent to which the benefits of long-term school closure for mitigating influenza pandemics can be preserved while reducing the time for which schools need to be closed. Two main implementation strategies are investigated, both based on monitoring local levels of absenteeism in schools: a purely reactive policy, in which each school closes when it experiences an outbreak, and an area-based policy, where outbreaks in a certain number of schools in an area trigger closure of all schools in that area. We found that the optimal strategy for the purely reactive policy requires such a low threshold level of absenteeism that closure risks being triggered by normal background levels of influenza-like-illness related absenteeism in schools. However, we find that an area-based policy could overcome this problem. Our analysis reinforces earlier work showing that school closure is predicted to have a more pronounced effect on reducing peak epidemic incidence than final attack rate. In addition, we show that if the duration of closure is limited, the policy should not be implemented too early. Overall, we find that with the right triggers, even short durations of closure can have a considerable impact on peak incidence.
  • Determining the kernel of an animal epidemic using limited(cont.) Recorded: Dec 4 2009 20 mins
    C. Rorres, University of Pennsylvania, USA
    Determining the kernel of an animal epidemic using limited, incomplete, or ongoing data [7A.1]

    Powerful computing platforms and new global positioning systems have greatly expanded the development and implementation of spatial, discrete-time, stochastic, SEIR models of animal epidemics. The kernels of these models, however, contain parameters whose numerical values must be known to implement them for the purpose of preventing, predicting, and controlling epidemics.

    The infrequency of many animal epidemics and the incomplete nature of data from past or ongoing epidemics restricts our ability to determine these epidemic parameters. To address this problem we introduce three techniques for making good estimations of the parameters based on the types of data being collected.
  • What I wish modelling could do for global health Recorded: Dec 4 2009 40 mins
    P. Piot, Institute for Global Health, Imperial College London, UK
    What I wish modelling could do for global health [INV6]

    Mathematical models have contributed greatly to our understanding of the spread and control of infectious diseases worldwide. In global health they have mainly been used for developing theoretical frameworks for the spread of human and animal infections, advocacy, evaluating cost-effectiveness, and for guiding intervention implementation.
  • Identifying natural reservoir hosts in a multi-host (cont.) Recorded: Dec 3 2009 12 mins
    H. Nishiura, University of Utrecht, The Netherlands
    Identifying natural reservoir hosts in a multi-host population: A case study of influenza in waterfowl [3B.6]

    Introduction: Whereas wild waterfowl are considered as the natural reservoir host of all influenza A viruses, the role of migratory birds in the spread of avian influenza is not fully understood. Previous ecological observations suggested that Arctic breeding migratory waterfowl, notably Anseriformes and Charadriiformes (including ducks, geese and swans), are potential reservoirs of influenza virus, but we have yet to know which bird species play a predominant role as a reservoir host of influenza virus.
  • Little-italy: An agent-based approach to the estimation of(cont.) Recorded: Dec 3 2009 14 mins
    F. Iozzi, Università Bocconi, Italy
    Little-italy: An agent-based approach to the estimation of contact data [3A.6]

    Introduction. Social contact patterns still represents the most critical issue underlying the modelling of directly transmitted infectious diseases. For example their knowledge is crucial to design appropriate pandemics containment measures.
    Methods. We compute synthetic “contacts” and “time in contact” matrices by age through agent based simulation of a simple individual based model (IBM) of socio-demographic dynamics. The model integrates Italian data on time use with routine socio-demographic data (e.g. school and workplace attendance, household structures, etc), and it is called “Little Italy” because each artificial agent is a clone of a real one, i.e. his/her daily diaries is the daily diary observed in a corresponding real individual sampled in the Italian time use-survey. This allows to incorporate random variation in individual behaviour from time-use data. Little Italy matrices are then validated against recently collected Italian serological data on Varicella and ParvoVirus, and their performances compared with other available matrices, such as the “Polymod” matrix, the “Time-Use” matrix, and the matrices used in the Italian IBM for pandemic containment.
  • Early detection of dengue outbreaks in Thailand using a (cont.) Recorded: Dec 3 2009 19 mins
    N.G. Reich, Johns Hopkins School of Public Health, USA
    Early detection of dengue outbreaks in Thailand using a spatial-temporal hidden Markov surveillance model [6A.6]

    Dengue is a major cause of morbidity in Thailand. Large increases in incidence provide a particular challenge to the public health system because treatment of severe cases requires significant resources. Advanced warning of increases in incidence could help public health authorities allocate resources more effectively and mitigate the impact of epidemics. In collaboration with the Thai Ministry of Public Health, we have developed a statistical model for infectious disease surveillance that uses data from across Thailand to give early warning of developing epidemics. We extended existing hidden Markov model methodologies for early outbreak detection by defining the unobserved states of the model relative to the reproductive rate Rt. Defining the model in this way provides an intuitive and epidemiologically meaningful state-space. Using dengue data from the Thai national notifiable disease surveillance system between 1999 and 2005 we estimated the posterior probability of being in an epidemic state (Rt >> 1) given the observed case reports for each province and information from nearby provinces on previous weeks. This model can be prospectively applied in order to provide an early indication of when a province is at risk of a major outbreak. We evaluated the theoretical performance of this model by examining the timeliness of outbreak detection of simulated epidemics. We compared the performance of this model in early detection of outbreaks with other detection models on both simulated and Thai surveillance data. Our model can be used to monitor disease activity and promptly respond to an emerging epidemic.
  • Fighting disease-driven extinction: in situ removal of (cont.) Recorded: Dec 3 2009 17 mins
    B.J. Doddington, Imperial College London, UK
    Fighting disease-driven extinction: in situ removal of infectious disease threats to wildlife [6B.5]

    Infectious disease is increasingly being recognised as a driving force in species extinction in taxa as diverse as bats and amphibians. Amphibian chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is now known to be one of the most potent emerging threats to biodiversity yet discovered. In recent decades, over 43% of amphibian species have gone into steep decline and the fungus has been found to be a principal driver in many of these declines as it spreads across the planet. Extinction in the wild is often cited as a possible outcome of chytridiomycosis, with captive breeding viewed as necessary to ensuring the survival of species.
  • Micro and macro population effects in disease transmission(cont.) Recorded: Dec 3 2009 15 mins
    R. Silhol, Université Pierre et Marie Curie, France
    Micro and macro population effects in disease transmission: The case of varicella [6A.3]

    The profiles of VZV (varicella-zoster virus) seroprevalence show large variability in European countries where vaccination is not implemented. For example, the median age at infection ranges between 2 years-olds (y.o.) in the The Netherlands and 6 y.o. in Italy. Micro population structure (e.g. households) as well as macro population structure (e.g. municipality) may explain such differences.

    This variability was investigated in a population based study of varicella in about 12000 children of 7800 French households residing in Corsica island. We first estimated varicella force of infection and cumulative incidence according to sibship rank. Time-dependant Cox proportional hazards models using demographical data were estimated in order to evaluate the impact of several micro (e.g. sibship size), macro configurations (e.g. school or municipality size) on varicella hazard. Varicella Attack Rates and Secondary Attack rate were also estimated. We investigated the spatial variability and autocorrelation of varicella age at infection using the frailties of a multilevel Cox model.
  • Dissecting the influences of climate and demography on the(cont.) Recorded: Dec 3 2009 19 mins
    J.O. Lloyd-Smith, University of California at Los Angeles, USA
    Dissecting the influences of climate and demography on the dynamics of leptospirosis in California sea lions [6B.2]

    Available soon.
  • Association between highly pathogenic avian influenza (cont.) Recorded: Dec 3 2009 17 mins
    L.A. Reperant, Princeton University, USA
    Association between highly pathogenic avian influenza H5N1 virus outbreaks in wild birds in Europe and the 0°C isotherm [6B.1]

    Movements of wild birds following a cold spell may have resulted in the introduction of highly pathogenic avian influenza virus (HPAIV) H5N1 in Europe during winter 2005-2006. However, the role of wild birds in the spread of HPAIV H5N1 is highly debated, and the association between the occurrence of HPAIV H5N1 outbreaks in Europe and cold-weather movements of wild birds remains conjectural. Wild waterbirds winter in areas where water-bodies are unfrozen in order to feed, yet winter as close as possible to their breeding grounds in order to optimize their reproductive success. Wild waterbirds thus are expected to congregate in suitable habitats close to the freezing front in winter, which may favour the transmission of HPAIV H5N1 and result in detectable outbreaks in wild birds.
  • Estimation of epidemiological parameters in real time (cont.) Recorded: Dec 3 2009 20 mins
    M.J.M. Baguelin, Health Protection Agency, UK
    Estimation of epidemiological parameters in real time during the early UK swine flu epidemic [5B.4]

    Introduction: Following the emergence of H1N1swl swine flu in Mexico in spring 2009, the UK was one of the first countries affected outside of the north American continent. The Health Protection Agency took on the task of monitoring, in real time, the patterns of spreading in the country and estimating key epidemiological parameters (serial interval, basic reproduction numbers, relative susceptibility and infectivity by classes of age) to determine the prospects for future spreading and inform policy-making.

    Methods: A rich data set of cases and their contacts was collected following the First Few Hundred protocol, developed by the Health Protection Agency specifically for swine flu. To estimate the reproduction number, R, we developed a method that uses individual-level information, such as known contacts or clusters (where specific individual contacts were not known they were imputed probabilistically). Differences in susceptibility and infectivity of children and adults were determined by comparison of patterns of transmission with contact patterns from the POLYMOD study. Projections of scenarios consistent with evolving current knowledge were used to inform policy-making.
  • Understanding the dynamics of seasonal influenza in Italy:(cont.) Recorded: Dec 3 2009 17 mins
    A. Lunelli, University of Trento, Italy
    Understanding the dynamics of seasonal influenza in Italy: An analysis of disease incidence and population susceptibility [2B.2]

    We analyze the dynamics of influenza in Italy during the last eight epidemic seasons, from 2000-2001 to 2008-2009, in order to investigate the factors that determine the remarkable differences in subsequent epidemics and regulate transmission.
    The analysis is based on data from the surveillance system, combined with virological and serological information: weekly case notifications have been collected each year from November till April through a sentinel network; moreover, virological data are available on the fraction of cases ascribed to each subtype (H1N1, H3N2 and B) and on the circulating strains; finally, a sample of adult patients have been tested at the beginning of each epidemic season for protection against the strains used for vaccination in that season.

    We used an SEIR age-structured epidemic model to simulate the dynamics of the infection (weighting the contribution of each circulating strain), coupled with a statistical model that takes into account the sampling process in case notification and seroprotection tests. Through a likelihood-based approach, we perform parameter inference, comparing the observed number of cases and the tested level of immunity (for the years of good concordance between vaccine and circulating strains) with the corresponding values predicted by the model.
  • Vaccination strategies to mitigate pandemic influenza: (cont.) Recorded: Dec 3 2009 14 mins
    G. Chowell, Arizona State University, USA
    Vaccination strategies to mitigate pandemic influenza: Mexico as a case study [5B.2]

    We explore vaccination strategies against influenza in Mexico using an age-structured transmission model and local epidemiological data based on past experience with influenza pandemics and the novel H1N1 influenza virus. Depending on the timing of implementation, we assess preemptive vaccination strategies that are conducted before the epidemic strikes and concurrent strategies that start after the epidemic onset. In the context of limited vaccine supplies, we evaluate vaccination strategies that either conform to a seasonal influenza vaccination strategy which targets the youngest children and persons over 65 years of age or an adaptive vaccination strategy that allocates vaccines to age groups based on age-specific rates of hospitalization or mortality monitored in the early stages of the pandemic. Preemptive vaccination had little impact on transmission at coverage levels modeled up to 20%. Overall the adaptive vaccination strategy outperformed the seasonal influenza vaccination allocation strategy for the majority of scenarios considered including that based on the 2009 novel A/H1N1 influenza virus outbreak. These simulations could inform policies for Mexico and other countries with similar demographic features with regard to the specific epidemiology of the novel swine influenza strain. We discuss also logistical issues associated with the implementation of adaptive vaccination strategies in the context of past and future influenza pandemics.
  • Influenza A and B transmission and control in public (cont.) Recorded: Dec 3 2009 17 mins
    S. Stebbins, University of Pittsburgh Graduate School of Public Health, USA
    Influenza A and B transmission and control in public schools in Pittsburgh, PA [2B.1]

    Introduction: The spread of the novel 2009 H1N1 (“swine”) influenza pandemic highlights both the successes and failures of our understanding of influenza transmission and epidemiology. Definitive parameters of transmission (contact, droplet, airborne, other routes) remain significantly in question, as does the effectiveness of typical non-pharmaceutical interventions (NPIs) such as “cover your cough”, hand hygiene, alcohol-based hand sanitizers and hand washing. The current phase six pandemic of H1N1 influenza underscores the importance of collecting and evaluating data on the effectiveness of NPIs.
  • Transmission and within-host dynamics of the foot-and (cont.) Recorded: Dec 3 2009 19 mins
    R. Howey, University of Edinburgh, UK
    Transmission and within-host dynamics of the foot-and-mouth disease virus [2A.1]

    In this paper we investigate the within-host dynamics of the foot-and-mouth disease virus (FMDV) and its relation to host-host transmission. A differential equation model is fitted to experiential data from infected cattle: (i) the concentration of FMDV genomes in the blood (ii) concentration of infectious virus in the blood (iii) antibody levels, and (iv) interferon levels. In the experiment eight cattle were infected after being in contact with inoculated cattle for eight hours. Samples were taken over a time course of approximately fourteen days, initially daily and then bi-daily. The infectiousness of the cattle was tested by challenging a different susceptible cow for 24 hours at 2 day intervals. Statistical analysis of the data using repeated measure analysis with a mixed covariance pattern model showed that successful transmission was significantly associated with the presence of virus in the air (p=0.015), in nasal swab samples (p=0.0127) and with high levels in the oesophageal-pharyngeal fluid (OPF) (p=0.021). Model parameters were estimated using maximum-likelihood methods, assuming log-normal errors in the data and left-censoring observations below a minimum detection threshold. The likelihood surface was sampled using Markov chain Monte Carlo giving credible intervals for each parameter. Our results show there is considerable variation of the within-host dynamics of FMDV between cattle. We consider the relationship between the within-host dynamics of the fitted model and transmission. In particular, our results suggest a high probability of infection when virus levels in the blood are high and low otherwise. An understanding of the within-host dynamics of FMDV and how it relates to transmission provides insights into the next level of virus transmission within a herd, and ultimately on control and prevention strategies of FMDV.
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  • Title: Molecular epidemiology of white spot syndrome virus
  • Live at: Dec 4 2009 11:30 am
  • Presented by: B.T.M. Dieu, Wageningen University, The Netherlands
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