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WHO Ebola Response Team, 2014, Ebola virus disease in West Africa — The first 9 months of the epidemic and forward projections, New England Journal of Medicine, Vol: 371, Pages: 1481-1495, ISSN: 0028-4793
BACKGROUNDOn March 23, 2014, the World Health Organization (WHO) was notified of an outbreak of Ebola virus disease (EVD) in Guinea. On August 8, the WHO declared the epidemic to be a “public health emergency of international concern.”METHODSBy September 14, 2014, a total of 4507 probable and confirmed cases, including 2296 deaths from EVD (Zaire species) had been reported from five countries in West Africa — Guinea, Liberia, Nigeria, Senegal, and Sierra Leone. We analyzed a detailed subset of data on 3343 confirmed and 667 probable Ebola cases collected in Guinea, Liberia, Nigeria, and Sierra Leone as of September 14.RESULTSThe majority of patients are 15 to 44 years of age (49.9% male), and we estimate that the case fatality rate is 70.8% (95% confidence interval [CI], 69 to 73) among persons with known clinical outcome of infection. The course of infection, including signs and symptoms, incubation period (11.4 days), and serial interval (15.3 days), is similar to that reported in previous outbreaks of EVD. On the basis of the initial periods of exponential growth, the estimated basic reproduction numbers (R0) are 1.71 (95% CI, 1.44 to 2.01) for Guinea, 1.83 (95% CI, 1.72 to 1.94) for Liberia, and 2.02 (95% CI, 1.79 to 2.26) for Sierra Leone. The estimated current reproduction numbers (R) are 1.81 (95% CI, 1.60 to 2.03) for Guinea, 1.51 (95% CI, 1.41 to 1.60) for Liberia, and 1.38 (95% CI, 1.27 to 1.51) for Sierra Leone; the corresponding doubling times are 15.7 days (95% CI, 12.9 to 20.3) for Guinea, 23.6 days (95% CI, 20.2 to 28.2) for Liberia, and 30.2 days (95% CI, 23.6 to 42.3) for Sierra Leone. Assuming no change in the control measures for this epidemic, by November 2, 2014, the cumulative reported numbers of confirmed and probable cases are predicted to be 5740 in Guinea, 9890 in Liberia, and 5000 in Sierra Leone, exceeding 20,000 in total.CONCLUSIONSThese data indicate that without drastic improvements in control measures, the numbers of
Bielby J, Donnelly CA, Pope LC, et al., 2014, Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis, Proceedings of the National Academy of Sciences of the United States of America, Vol: 111, Pages: 9193-9198, ISSN: 0027-8424
Where wildlife disease requires management, culling is frequently considered but not always effective. In the British Isles, control of cattle tuberculosis (TB) is hindered by infection in wild badger (Meles meles) populations. Large-scale badger culling can reduce the incidence of confirmed cattle TB, but these benefits are undermined by culling-induced changes in badger behavior (termed perturbation), which can increase transmission among badgers and from badgers to cattle. Test–vaccinate/remove (TVR) is a novel approach that entails testing individual badgers for infection, vaccinating test-negative animals, and killing test-positive animals. Imperfect capture success, diagnostic sensitivity, and vaccine effectiveness mean that TVR would be expected to leave some infected and some susceptible badgers in the population. Existing simulation models predict that TVR could reduce cattle TB if such small-scale culling causes no perturbation, but could increase cattle TB if considerable perturbation occurs. Using data from a long-term study, we show that past small-scale culling was significantly associated with four metrics of perturbation in badgers: expanded ranging, more frequent immigration, lower genetic relatedness, and elevated prevalence of Mycobacterium bovis, the causative agent of TB. Though we could not reject the hypothesis that culling up to three badgers per social group might avoid perturbation, we also could not reject the hypothesis that killing a single badger prompted detectable perturbation. When considered alongside existing model predictions, our findings suggest that implementation of TVR, scheduled for 2014, risks exacerbating the TB problem rather than controlling it. Ongoing illegal badger culling is likewise expected to increase cattle TB risks.
Kucharski A, Mills H, Pinsent A, et al., 2014, Distinguishing Between Reservoir Exposure and Human-to-Human Transmission for Emerging Pathogens Using Case Onset Data., PLoS Curr, Vol: 6
Pathogens such as MERS-CoV, influenza A/H5N1 and influenza A/H7N9 are currently generating sporadic clusters of spillover human cases from animal reservoirs. The lack of a clear human epidemic suggests that the basic reproductive number R0 is below or very close to one for all three infections. However, robust cluster-based estimates for low R0 values are still desirable so as to help prioritise scarce resources between different emerging infections and to detect significant changes between clusters and over time. We developed an inferential transmission model capable of distinguishing the signal of human-to-human transmission from the background noise of direct spillover transmission (e.g. from markets or farms). By simulation, we showed that our approach could obtain unbiased estimates of R0, even when the temporal trend in spillover exposure was not fully known, so long as the serial interval of the infection and the timing of a sudden drop in spillover exposure were known (e.g. day of market closure). Applying our method to data from the three largest outbreaks of influenza A/H7N9 outbreak in China in 2013, we found evidence that human-to-human transmission accounted for 13% (95% credible interval 1%-32%) of cases overall. We estimated R0 for the three clusters to be: 0.19 in Shanghai (0.01-0.49), 0.29 in Jiangsu (0.03-0.73); and 0.03 in Zhejiang (0.00-0.22). If a reliable temporal trend for the spillover hazard could be estimated, for example by implementing widespread routine sampling in sentinel markets, it should be possible to estimate sub-critical values of R0 even more accurately. Should a similar strain emerge with R0>1, these methods could give a real-time indication that sustained transmission is occurring with well-characterised uncertainty.
Winskill P, Harris AF, Morgan SA, et al., 2014, Genetic control of Aedes aegypti: data-driven modelling to assess the effect of releasing different life stages and the potential for long-term suppression, Parasites & Vectors, Vol: 7, ISSN: 1756-3305
Blake IM, Donnelly CA, 2014, A simple incidence-based method to avoid misinterpretation of bovine tuberculosis incidence trends in great britain., PLoS Curr, Vol: 6
The incidence of bovine tuberculosis (TB) in Great Britain has generally been increasing in recent decades. Routine ante-mortem testing of cattle herds is required for disease surveillance and control, due to the asymptomatic nature of the infection. The Department for Environment, Food and Rural Affairs (Defra) publishes TB incidence trends as the percentage of officially TB-free (OTF) herds tested per month with OTF status withdrawn due to post-mortem evidence of infection. This method can result in artefactual fluctuations. We have previously demonstrated an alternative method, that distributes incidents equally over the period of risk, provides a more accurate representation of underlying risk. However, this method is complex and it may not be sufficiently straightforward for use in the national statistics. Here we present a simple incidence-based method that adjusts for the time between tests and show it can provide a reasonable representation of the underlying risk without artefactual fluctuations.
Cauchemez S, Fraser C, Van Kerkhove MD, et al., 2014, Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility, LANCET INFECTIOUS DISEASES, Vol: 14, Pages: 50-56, ISSN: 1473-3099
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- Citations: 226
Koukounari A, Donnelly CA, Moustaki I, et al., 2013, A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda, PLOS Computational Biology, Vol: 9, ISSN: 1553-734X
Regular treatment with praziquantel (PZQ) is the strategy for human schistosomiasis control aiming to prevent morbidity in later life. With the recent resolution on schistosomiasis elimination by the 65th World Health Assembly, appropriate diagnostic tools to inform interventions are keys to their success. We present a discrete Markov chains modelling framework that deals with the longitudinal study design and the measurement error in the diagnostic methods under study. A longitudinal detailed dataset from Uganda, in which one or two doses of PZQ treatment were provided, was analyzed through Latent Markov Models (LMMs). The aim was to evaluate the diagnostic accuracy of Circulating Cathodic Antigen (CCA) and of double Kato-Katz (KK) faecal slides over three consecutive days for Schistosoma mansoni infection simultaneously by age group at baseline and at two follow-up times post treatment. Diagnostic test sensitivities and specificities and the true underlying infection prevalence over time as well as the probabilities of transitions between infected and uninfected states are provided. The estimated transition probability matrices provide parsimonious yet important insights into the re-infection and cure rates in the two age groups. We show that the CCA diagnostic performance remained constant after PZQ treatment and that this test was overall more sensitive but less specific than single-day double KK for the diagnosis of S. mansoni infection. The probability of clearing infection from baseline to 9 weeks was higher among those who received two PZQ doses compared to one PZQ dose for both age groups, with much higher re-infection rates among children compared to adolescents and adults. We recommend LMMs as a useful methodology for monitoring and evaluation and treatment decision research as well as CCA for mapping surveys of S. mansoni infection, although additional diagnostic tools should be incorporated in schistosomiasis elimination programs.
Winskill P, McKemey A, Alphey L, et al., 2013, OPTIMISING FIELD RELEASES OF ENGINEERED MALE MOSQUITOES, PATHOGENS AND GLOBAL HEALTH, Vol: 107, Pages: 421-421, ISSN: 2047-7724
Donnelly CA, Nouvellet P, 2013, The contribution of badgers to confirmed tuberculosis in cattle in high-incidence areas in England., PLoS Curr, Vol: 5
The role of badgers in the transmission and maintenance of bovine tuberculosis (TB) in British cattle is widely debated as part of the wider discussions on whether badger culling and/or badger vaccination should play a role in the government's strategy to eradicate cattle TB. The key source of information on the contribution from badgers within high-cattle-TB-incidence areas of England is the Randomised Badger Culling Trial (RBCT), with two analyses providing estimates of the average overall contribution of badgers to confirmed cattle TB in these areas. A dynamical model characterizing the association between the estimated prevalence of Mycobacterium bovis (the causative agent of bovine TB) among badgers culled in the initial RBCT proactive culls and the incidence among sympatric cattle herds prior to culling is used to estimate the average overall contribution of badgers to confirmed TB herd breakdowns among proactively culled areas. The resulting estimate based on all data (52%) has considerable uncertainty (bootstrap 95% confidence interval (CI): 9.1-100%). Separate analyses of experimental data indicated that the largest estimated reduction in confirmed cattle TB achieved inside the proactive culling areas was 54% (overdispersion-adjusted 95% CI: 38-66%), providing a lower bound for the average overall contribution of badgers to confirmed cattle TB. Thus, taking into account both results, the best estimate of the average overall contribution of badgers is roughly half, with 38% being a robustly estimated lower bound. However, the dynamical model also suggested that only 5.7% (bootstrap 95% CI: 0.9-25%) of the transmission to cattle herds is badger-to-cattle with the remainder of the average overall contribution from badgers being in the form of onward cattle-to-cattle transmission. These estimates, confirming that badgers do play a role in bovine TB transmission, inform debate even if they do not point to a single way forward.
Van Kerkhove MD, Hirve S, Koukounari A, et al., 2013, Estimating age-specific cumulative incidence for the 2009 influenza pandemic: a meta-analysis of A(H1N1)pdm09 serological studies from 19 countries, Influenza and Other Respiratory Viruses, Vol: 7, Pages: 872-886, ISSN: 1750-2640
BACKGROUND: The global impact of the 2009 influenza A(H1N1) pandemic (H1N1pdm) is not well understood. OBJECTIVES: We estimate overall and age-specific prevalence of cross-reactive antibodies to H1N1pdm virus and rates of H1N1pdm infection during the first year of the pandemic using data from published and unpublished H1N1pdm seroepidemiological studies. METHODS: Primary aggregate H1N1pdm serologic data from each study were stratified in standardized age groups and evaluated based on when sera were collected in relation to national or subnational peak H1N1pdm activity. Seropositivity was assessed using well-described and standardized hemagglutination inhibition (HI titers >/=32 or >/=40) and microneutralization (MN >/= 40) laboratory assays. The prevalence of cross-reactive antibodies to the H1N1pdm virus was estimated for studies using sera collected prior to the start of the pandemic (between 2004 and April 2009); H1N1pdm cumulative incidence was estimated for studies in which collected both pre- and post-pandemic sera; and H1N1pdm seropositivity was calculated from studies with post-pandemic sera only (collected between December 2009-June 2010). RESULTS: Data from 27 published/unpublished studies from 19 countries/administrative regions - Australia, Canada, China, Finland, France, Germany, Hong Kong SAR, India, Iran, Italy, Japan, Netherlands, New Zealand, Norway, Reunion Island, Singapore, United Kingdom, United States, and Vietnam - were eligible for inclusion. The overall age-standardized pre-pandemic prevalence of cross-reactive antibodies was 5% (95%CI 3-7%) and varied significantly by age with the highest rates among persons >/=65 years old (14% 95%CI 8-24%). Overall age-standardized H1N1pdm cumulative incidence was 24% (95%CI 20-27%) and varied significantly by age with the highest in children 5-19 (47% 95%CI 39-55%) and 0-4 years old (36% 95%CI 30-43%). CONCLUSIONS: Our results offer unique insight into the global impact of the H1N1 pandemic a
Godfray HCJ, Donnelly CA, Kao RR, et al., 2013, A restatement of the natural science evidence base relevant to the control of bovine tuberculosis in Great Britain, Proceedings of the Royal Society B: Biological Sciences, Vol: 280, ISSN: 0962-8452
Bovine tuberculosis (bTB) is a very important disease of cattle in Great Britain, where it has been increasing in incidence and geographical distribution. In addition to cattle, it infects other species of domestic and wild animals, in particular the European badger (Meles meles). Policy to control bTB is vigorously debated and contentious because of its implications for the livestock industry and because some policy options involve culling badgers, the most important wildlife reservoir. This paper describes a project to provide a succinct summary of the natural science evidence base relevant to the control of bTB, couched in terms that are as policy-neutral as possible. Each evidence statement is placed into one of four categories describing the nature of the underlying information. The evidence summary forms the appendix to this paper and an annotated bibliography is provided in the electronic supplementary material.
Donnelly C, 2013, Badger-cull statistics carry uncertainty, NATURE, Vol: 499, Pages: 154-154, ISSN: 0028-0836
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- Citations: 3
Cauchemez S, Van Kerkhove MD, Riley S, et al., 2013, Transmission scenarios for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and how to tell them apart, EUROSURVEILLANCE, Vol: 18, Pages: 7-13, ISSN: 1560-7917
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- Citations: 8
Nouvellet P, Donnelly CA, Nardi MD, et al., 2013, Rabies and Canine Distemper Virus Epidemics in the Red Fox Population of Northern Italy (2006-2010), PLOS One, Vol: 8, ISSN: 1932-6203
Since 2006 the red fox (Vulpes vulpes) population in north-eastern Italy has experienced an epidemic of canine distemper virus (CDV). Additionally, in 2008, after a thirteen-year absence from Italy, fox rabies was re-introduced in the Udine province at the national border with Slovenia. Disease intervention strategies are being developed and implemented to control rabies in this area and minimise risk to human health. Here we present empirical data and the epidemiological picture relating to these epidemics in the period 2006–2010. Of important significance for epidemiological studies of wild animals, basic mathematical models are developed to exploit information collected from the surveillance program on dead and/or living animals in order to assess the incidence of infection. These models are also used to estimate the rate of transmission of both diseases and the rate of vaccination, while correcting for a bias in early collection of CDV samples. We found that the rate of rabies transmission was roughly twice that of CDV, with an estimated effective contact between infected and susceptible fox leading to a new infection occurring once every 3 days for rabies, and once a week for CDV. We also inferred that during the early stage of the CDV epidemic, a bias in the monitoring protocol resulted in a positive sample being almost 10 times more likely to be collected than a negative sample. We estimated the rate of intake of oral vaccine at 0.006 per day, allowing us to estimate that roughly 68% of the foxes would be immunised. This was confirmed by field observations. Finally we discuss the implications for the eco-epidemiological dynamics of both epidemics in relation to control measures.
Koukounari A, Moustaki I, Grassly NC, et al., 2013, Using a Nonparametric Multilevel Latent Markov Model to Evaluate Diagnostics for Trachoma, American Journal of Epidemiology, Vol: 177, Pages: 913-922, ISSN: 0002-9262
In disease control or elimination programs, diagnostics are essential for assessing the impact of interventions, refining treatment strategies, and minimizing the waste of scarce resources. Although high-performance tests are desirable, increased accuracy is frequently accompanied by a requirement for more elaborate infrastructure, which is often not feasible in the developing world. These challenges are pertinent to mapping, impact monitoring, and surveillance in trachoma elimination programs. To help inform rational design of diagnostics for trachoma elimination, we outline a nonparametric multilevel latent Markov modeling approach and apply it to 2 longitudinal cohort studies of trachoma-endemic communities in Tanzania (2000–2002) and The Gambia (2001–2002) to provide simultaneous inferences about the true population prevalence of Chlamydia trachomatis infection and disease and the sensitivity, specificity, and predictive values of 3 diagnostic tests for C. trachomatis infection. Estimates were obtained by using data collected before and after mass azithromycin administration. Such estimates are particularly important for trachoma because of the absence of a true “gold standard” diagnostic test for C. trachomatis. Estimated transition probabilities provide useful insights into key epidemiologic questions about the persistence of disease and the clearance of infection as well as the required frequency of surveillance in the postelimination setting.
Bhatt S, Lam TT, Lycett SJ, et al., 2013, The evolutionary dynamics of influenza A virus adaptation to mammalian hosts, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 368, ISSN: 0962-8436
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- Citations: 37
Karolemeas K, Donnelly CA, Conlan AJK, et al., 2012, The Effect of Badger Culling on Breakdown Prolongation and Recurrence of Bovine Tuberculosis in Cattle Herds in Great Britain, PLOS One, Vol: 7, ISSN: 1932-6203
Bovine tuberculosis is endemic in cattle herds in Great Britain, with a substantial economic impact. A reservoir of Mycobacterium bovis within the Eurasian badger (Meles meles) population is thought to have hindered disease control. Cattle herd incidents, termed breakdowns, that are either ‘prolonged’ (lasting ≥240 days) or ‘recurrent’ (with another breakdown within a specified time period) may be important foci for onward spread of infection. They drain veterinary resources and can be demoralising for farmers. Randomised Badger Culling Trial (RBCT) data were re-analysed to examine the effects of two culling strategies on breakdown prolongation and recurrence, during and after culling, using a Bayesian hierarchical model. Separate effect estimates were obtained for the ‘core’ trial areas (where culling occurred) and the ‘buffer’ zones (up to 2 km outside of the core areas). For breakdowns that started during the culling period, ‘reactive’ (localised) culling was associated with marginally increased odds of prolongation, with an odds ratio (OR) of 1.7 (95% credible interval [CI] 1.1–2.4) within the core areas. This effect was not present after the culling ceased. There was no notable effect of ‘proactive’ culling on prolongation. In contrast, reactive culling had no effect on breakdown recurrence, though there was evidence of a reduced risk of recurrence in proactive core areas during the culling period (ORs and 95% CIs: 0.82 (0.64–1.0) and 0.69 (0.54–0.86) for 24- and 36-month recurrence respectively). Again these effects were not present after the culling ceased. There seemed to be no effect of culling on breakdown prolongation or recurrence in the buffer zones. These results suggest that the RBCT badger culling strategies are unlikely to reduce either the prolongation or recurrence of breakdowns in the long term, and that reactive strategies (such as employed during the RB
Blake IM, Donnelly CA, 2012, Estimating risk over time using data from targeted surveillance systems: Application to bovine tuberculosis in Great Britain, EPIDEMICS, Vol: 4, Pages: 179-186, ISSN: 1755-4365
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- Citations: 2
Wolbers M, Kleinschmidt I, Simmons CP, et al., 2012, Considerations in the Design of Clinical Trials to Test Novel Entomological Approaches to Dengue Control, PLOS Neglected Tropical Diseases, Vol: 6, ISSN: 1935-2727
Williamson SM, Tucker AW, McCrone IS, et al., 2012, Descriptive clinical and epidemiological characteristics of influenza A H1N1 2009 virus infections in pigs in England, VETERINARY RECORD, Vol: 171, Pages: 271-U47, ISSN: 0042-4900
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- Citations: 20
Harris AF, McKemey AR, Nimmo D, et al., 2012, Successful suppression of a field mosquito population by sustained release of engineered male mosquitoes, NATURE BIOTECHNOLOGY, Vol: 30, Pages: 828-830, ISSN: 1087-0156
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- Citations: 264
Karolemeas K, de la Rua-Domenech R, Cooper R, et al., 2012, Estimation of the Relative Sensitivity of the Comparative Tuberculin Skin Test in Tuberculous Cattle Herds Subjected to Depopulation, PLOS One, Vol: 7, ISSN: 1932-6203
Bovine tuberculosis (bTB) is one of the most serious economic animal health problems affecting the cattle industry in Great Britain (GB), with incidence in cattle herds increasing since the mid-1980s. The single intradermal comparative cervical tuberculin (SICCT) test is the primary screening test in the bTB surveillance and control programme in GB and Ireland. The sensitivity (ability to detect infected cattle) of this test is central to the efficacy of the current testing regime, but most previous studies that have estimated test sensitivity (relative to the number of slaughtered cattle with visible lesions [VL] and/or positive culture results) lacked post-mortem data for SICCT test-negative cattle. The slaughter of entire herds (“whole herd slaughters” or “depopulations”) that are infected by bTB are occasionally conducted in GB as a last-resort control measure to resolve intractable bTB herd breakdowns. These provide additional post-mortem data for SICCT test-negative cattle, allowing a rare opportunity to calculate the animal-level sensitivity of the test relative to the total number of SICCT test-positive and negative VL animals identified post-mortem (rSe). In this study, data were analysed from 16 whole herd slaughters (748 SICCT test-positive and 1031 SICCT test-negative cattle) conducted in GB between 1988 and 2010, using a Bayesian hierarchical model. The overall rSe estimate of the SICCT test at the severe interpretation was 85% (95% credible interval [CI]: 78–91%), and at standard interpretation was 81% (95% CI: 70–89%). These estimates are more robust than those previously reported in GB due to inclusion of post-mortem data from SICCT test-negative cattle.
Prager KC, Mazet JAK, Munson L, et al., 2012, The effect of protected areas on pathogen exposure in endangered African wild dog (<i>Lycaon pictus</i>) populations, BIOLOGICAL CONSERVATION, Vol: 150, Pages: 15-22, ISSN: 0006-3207
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- Citations: 24
Donnelly CA, Woodroffe R, 2012, Reduce uncertainty in UK badger culling, NATURE, Vol: 485, Pages: 582-582, ISSN: 0028-0836
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Yu H, Cauchemez S, Donnelly CA, et al., 2012, Transmission Dynamics, Border Entry Screening, and School Holidays during the 2009 Influenza A (H1N1) Pandemic, China, EMERGING INFECTIOUS DISEASES, Vol: 18, Pages: 758-766, ISSN: 1080-6040
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Lefevre EA, Carr BV, Inman CF, et al., 2012, Immune Responses in Pigs Vaccinated with Adjuvanted and Non-Adjuvanted A(H1N1)pdm/09 Influenza Vaccines Used in Human Immunization Programmes, PLOS One, Vol: 7, ISSN: 1932-6203
Following the emergence and global spread of a novel H1N1 influenza virus in 2009, two A(H1N1)pdm/09 influenza vaccines produced from the A/California/07/09 H1N1 strain were selected and used for the national immunisation programme in the United Kingdom: an adjuvanted split virion vaccine and a non-adjuvanted whole virion vaccine. In this study, we assessed the immune responses generated in inbred large white pigs (Babraham line) following vaccination with these vaccines and after challenge with A(H1N1)pdm/09 virus three months post-vaccination. Both vaccines elicited strong antibody responses, which included high levels of influenza-specific IgG1 and haemagglutination inhibition titres to H1 virus. Immunisation with the adjuvanted split vaccine induced significantly higher interferon gamma production, increased frequency of interferon gamma-producing cells and proliferation of CD4−CD8+ (cytotoxic) and CD4+CD8+ (helper) T cells, after in vitro re-stimulation. Despite significant differences in the magnitude and breadth of immune responses in the two vaccinated and mock treated groups, similar quantities of viral RNA were detected from the nasal cavity in all pigs after live virus challenge. The present study provides support for the use of the pig as a valid experimental model for influenza infections in humans, including the assessment of protective efficacy of therapeutic interventions.
Vial F, Donnelly CA, 2012, Localized reactive badger culling increases risk of bovine tuberculosis in nearby cattle herds, BIOLOGY LETTERS, Vol: 8, Pages: 50-53, ISSN: 1744-9561
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- Citations: 33
Cauchemez S, Boelle PY, Donnelly CA, et al., 2012, Real-time estimates in early detection of SARS, Emerging Infectious Diseases, Vol: 12, Pages: 110-113, ISSN: 1080-6040
We propose a Bayesian statistical framework for estimating the reproduction number R early in an epidemic. This method allows for the yet-unrecorded secondary cases if the estimate is obtained before the epidemic has ended. We applied our approach to the severe acute respiratory syndrome (SARS) epidemic that started in February 2003 in Hong Kong. Temporal patterns of R estimated after 5, 10, and 20 days were similar. Ninety-five percent credible intervals narrowed when more data were available but stabilized after 10 days. Using simulation studies of SARS-like outbreaks, we have shown that the method may be used for early monitoring of the effect of control measures.
Truscott J, Fraser C, Cauchemez S, et al., 2012, Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza, Journal of the Royal Society Interface, Vol: 9, Pages: 304-312, ISSN: 1742-5662
Seasonal influenza has considerable impact around the world, both economically and in mortality among risk groups, but there is considerable uncertainty as to the essential mechanisms and their parametrization. In this paper, we identify a number of characteristic features of influenza incidence time series in temperate regions, including ranges of annual attack rates and outbreak durations. By constraining the output of simple models to match these characteristic features, we investigate the role played by population heterogeneity, multiple strains, cross-immunity and the rate of strain evolution in the generation of incidence time series. Results indicate that an age-structured model with non-random mixing and co-circulating strains are both required to match observed time-series data. Our work gives estimates of the seasonal peak basic reproduction number, R0, in the range 1.6–3. Estimates of R0 are strongly correlated with the timescale for waning of immunity to current circulating seasonal influenza strain, which we estimate is between 3 and 8 years. Seasonal variation in transmissibility is largely confined to 15–30% of its mean value. While population heterogeneity and cross-immunity are required mechanisms, the degree of heterogeneity and cross-immunity is not tightly constrained. We discuss our findings in the context of other work fitting to seasonal influenza data.
Woodroffe R, Donnelly CA, 2011, Risk of contact between endangered African wild dogs <i>Lycaon pictus</i> and domestic dogs: opportunities for pathogen transmission, JOURNAL OF APPLIED ECOLOGY, Vol: 48, Pages: 1345-1354, ISSN: 0021-8901
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- Citations: 45
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