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bioRxiv. 2017 August 18; DOI:10.1101/177451
Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, et al.
bioRxiv. 2017 August 18; DOI:10.1101/177451
Real-time forecasts based on mathematical models can inform critical decision-making during infectious disease outbreaks. Yet, epidemic forecasts are rarely evaluated during or after the event, and there is little guidance on the best metrics for assessment. Here, we propose an evaluation approach that disentangles different components of forecasting ability using metrics that separately assess the calibration, sharpness and unbiasedness of forecasts. This makes it possible to assess not just how close a forecast was to reality but also how well uncertainty has been quantified. We used this approach to analyse the performance of weekly forecasts we generated in real time in Western Area, Sierra Leone, during the 2013–16 Ebola epidemic in West Africa. We investigated a range of forecast model variants based on the model fits generated at the time with a semi-mechanistic model, and found that good probabilistic calibration was achievable at short time horizons of one or two weeks ahead but models were increasingly inaccurate at longer forecasting horizons. This suggests that forecasts may have been of good enough quality to inform decision making requiring predictions a few weeks ahead of time but not longer, reflecting the high level of uncertainty in the processes driving the trajectory of the epidemic. Comparing forecasts based on the semi-mechanistic model to simpler null models showed that the best semi-mechanistic model variant performed better than the null models with respect to probabilistic calibration, and that this would have been identified from the earliest stages of the outbreak. As forecasts become a routine part of the toolkit in public health, standards for evaluation of performance will be important for assessing quality and improving credibility of mathematical models, and for elucidating difficulties and trade-offs when aiming to make the most useful and reliable forecasts.
Journal Article > ResearchFull Text
BMC Infect Dis. 2018 April 11; Volume 18 (Issue 1); 172.; DOI:10.1186/s12879-018-3073-1
le Polain de Waroux O, Cohuet S, Ndazima D, Kucharski AJ, Juan-Giner A, et al.
BMC Infect Dis. 2018 April 11; Volume 18 (Issue 1); 172.; DOI:10.1186/s12879-018-3073-1
BACKGROUND
Quantification of human interactions relevant to infectious disease transmission through social contact is central to predict disease dynamics, yet data from low-resource settings remain scarce.
METHODS
We undertook a social contact survey in rural Uganda, whereby participants were asked to recall details about the frequency, type, and socio-demographic characteristics of any conversational encounter that lasted for ≥5 min (henceforth defined as 'contacts') during the previous day. An estimate of the number of 'casual contacts' (i.e. < 5 min) was also obtained.
RESULTS
In total, 566 individuals were included in the study. On average participants reported having routine contact with 7.2 individuals (range 1-25). Children aged 5-14 years had the highest frequency of contacts and the elderly (≥65 years) the fewest (P < 0.001). A strong age-assortative pattern was seen, particularly outside the household and increasingly so for contacts occurring further away from home. Adults aged 25-64 years tended to travel more often and further than others, and males travelled more frequently than females.
CONCLUSION
Our study provides detailed information on contact patterns and their spatial characteristics in an African setting. It therefore fills an important knowledge gap that will help more accurately predict transmission dynamics and the impact of control strategies in such areas.
Quantification of human interactions relevant to infectious disease transmission through social contact is central to predict disease dynamics, yet data from low-resource settings remain scarce.
METHODS
We undertook a social contact survey in rural Uganda, whereby participants were asked to recall details about the frequency, type, and socio-demographic characteristics of any conversational encounter that lasted for ≥5 min (henceforth defined as 'contacts') during the previous day. An estimate of the number of 'casual contacts' (i.e. < 5 min) was also obtained.
RESULTS
In total, 566 individuals were included in the study. On average participants reported having routine contact with 7.2 individuals (range 1-25). Children aged 5-14 years had the highest frequency of contacts and the elderly (≥65 years) the fewest (P < 0.001). A strong age-assortative pattern was seen, particularly outside the household and increasingly so for contacts occurring further away from home. Adults aged 25-64 years tended to travel more often and further than others, and males travelled more frequently than females.
CONCLUSION
Our study provides detailed information on contact patterns and their spatial characteristics in an African setting. It therefore fills an important knowledge gap that will help more accurately predict transmission dynamics and the impact of control strategies in such areas.
Journal Article > Meta-AnalysisFull Text
Epidemics. 2019 March 2; Volume 27; DOI:10.1016/j.epidem.2019.03.001
Robert A, Camacho A, Edmunds WJ, Baguelin M, Muyembe JJT, et al.
Epidemics. 2019 March 2; Volume 27; DOI:10.1016/j.epidem.2019.03.001
Health care workers (HCW) are at risk of infection during Ebola virus disease outbreaks and therefore may be targeted for vaccination before or during outbreaks. The effect of these strategies depends on the role of HCW in transmission which is understudied. To evaluate the effect of HCW-targeted or community vaccination strategies, we used a transmission model to explore the relative contribution of HCW and the community to transmission. We calibrated the model to data from multiple Ebola outbreaks. We quantified the impact of ahead-of-time HCW-targeted strategies, and reactive HCW and community vaccination. We found that for some outbreaks (we call "type 1″) HCW amplified transmission both to other HCW and the community, and in these outbreaks prophylactic vaccination of HCW decreased outbreak size. Reactive vaccination strategies had little effect because type 1 outbreaks ended quickly. However, in outbreaks with longer time courses ("type 2 outbreaks"), reactive community vaccination decreased the number of cases, with or without prophylactic HCW-targeted vaccination. For both outbreak types, we found that ahead-of-time HCW-targeted strategies had an impact at coverage of 30%. The vaccine strategies tested had a different impact depending on the transmission dynamics and previous control measures. Although we will not know the characteristics of a new outbreak, ahead-of-time HCW-targeted vaccination can decrease the total outbreak size, even at low vaccine coverage.
Journal Article > ResearchFull Text
Epidemics. 2018 December 1; Volume 25; 72-79.; DOI:10.1016/j.epidem.2018.05.008
le Polain de Waroux O, Flasche S, Kucharski AJ, Langendorf C, Ndazima D, et al.
Epidemics. 2018 December 1; Volume 25; 72-79.; DOI:10.1016/j.epidem.2018.05.008
Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, it remains unclear how the frequency and nature of human interactions shape an individual's risk of infection. We analysed data on daily social encounters individually matched to data on S. pneumoniae carriage and acute respiratory symptoms (ARS), from 566 individuals who took part in a survey in South-West Uganda. We found that the frequency of physical (i.e. skin-to-skin), long (≥1 h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact - was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 7% (2-13%) respectively. In contrast, the number of casual contacts (<5 min long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people suffering from ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models, and more studies should be undertaken to further validate our results.
Journal Article > ResearchFull Text
medRxiv. 2019 August 17; DOI:10.1101/19003434
Funk S, Takahashi S, Hellewell J, Gadroen K, Carrion Martin AI, et al.
medRxiv. 2019 August 17; DOI:10.1101/19003434
The Katanga region in the Democratic Republic of Congo (DRC) has been struck by repeated epidemics of measles, with large outbreaks occurring in 2010–13 and 2015. In many of the affected health zones, reactive mass vaccination campaigns were conducted in response to the outbreaks. Here, we attempted to determine how effective the vaccination campaigns in 2015 were in curtailing the ongoing outbreak. We further sought to establish whether the risk of large measles outbreaks in different health zones could have been determined in advance to help prioritise areas for vaccination campaign and speed up the response. In doing so, we first attempted to identify factors that could have been used in 2015 to predict in which health zones the greatest outbreaks would occur. Administrative vaccination coverage was not a good predictor of the size of outbreaks in different health zones. Vaccination coverage derived from surveys, on the other hand, appeared to give more reliable estimates of health zones of low vaccination coverage and, consequently, large outbreaks. On a coarser geographical scale, the provinces most affected in 2015 could be predicted from the outbreak sizes in 2010–13. This, combined with the fact that the vast majority of reported cases were in under-5 year olds, would suggest that there are systematic issues of undervaccination. If this was to continue, outbreaks would be expected to continue to occur in the affected health zones at regular intervals, mostly concentrated in under-5 year olds. We further used a model of measles transmission to estimate the impact of the vaccination campaigns, by first fitting a model to the data including the campaigns and then re-running this without vaccination. We estimated the reactive campaigns to have reduced the size of the overall outbreak by approximately 21,000 (IQR: 16,000–27,000; 95% CI: 8300–38,000) cases. There was considerable heterogeneity in the impact of campaigns, with campaigns started earlier after the start of an outbreak being more impactful. Taken together, these findings suggest that while a strong routine vaccination regime remains the most effective means of measles control, it might be possible to improve the effectiveness of reactive campaigns by considering predictive factors to trigger a more targeted vaccination response.
Journal Article > ReviewFull Text
Lancet Infect Dis. 2021 March 1; Volume 21 (Issue 3); e37-e48.; DOI:10.1016/S1473-3099(20)30479-5
Ratnayake R, Finger F, Azman AS, Lantagne D, Funk S, et al.
Lancet Infect Dis. 2021 March 1; Volume 21 (Issue 3); e37-e48.; DOI:10.1016/S1473-3099(20)30479-5
Globally, cholera epidemics continue to challenge disease control. Although mass campaigns covering large populations are commonly used to control cholera, spatial targeting of case households and their radius is emerging as a potentially efficient strategy. We did a Scoping Review to investigate the effectiveness of interventions delivered through case-area targeted intervention, its optimal spatiotemporal scale, and its effectiveness in reducing transmission. 53 articles were retrieved. We found that antibiotic chemoprophylaxis, point-of-use water treatment, and hygiene promotion can rapidly reduce household transmission, and single-dose vaccination can extend the duration of protection within the radius of households. Evidence supports a high-risk spatiotemporal zone of 100 m around case households, for 7 days. Two evaluations separately showed reductions in household transmission when targeting case households, and in size and duration of case clusters when targeting radii. Although case-area targeted intervention shows promise for outbreak control, it is critically dependent on early detection capacity and requires prospective evaluation of intervention packages.
Journal Article > Short ReportFull Text
Emerg Infect Dis. 2024 August 1; Volume 30 (Issue 8); 1677-1682.; DOI:10.3201/eid3008.231137
Ratnayake R, Knee J, Cumming O, Saidi JM, Rumedeka BB, et al.
Emerg Infect Dis. 2024 August 1; Volume 30 (Issue 8); 1677-1682.; DOI:10.3201/eid3008.231137
We evaluated the spatiotemporal clustering of rapid diagnostic test−positive cholera cases in Uvira, eastern Democratic Republic of the Congo. We detected spatiotemporal clusters that consistently overlapped with major rivers, and we outlined the extent of zones of increased risk that are compatible with the radii currently used for targeted interventions.
Journal Article > ResearchFull Text
PLoS Comput Biol. 2022 May 23; Volume 18 (Issue 5); e1008800.; DOI: 10.1371/journal.pcbi.1008800
Jarvis CI, Gimma A, Finger F, Morris TP, Thompson JA, et al.
PLoS Comput Biol. 2022 May 23; Volume 18 (Issue 5); e1008800.; DOI: 10.1371/journal.pcbi.1008800
The fraction of cases reported, known as 'reporting', is a key performance indicator in an outbreak response, and an essential factor to consider when modelling epidemics and assessing their impact on populations. Unfortunately, its estimation is inherently difficult, as it relates to the part of an epidemic which is, by definition, not observed. We introduce a simple statistical method for estimating reporting, initially developed for the response to Ebola in Eastern Democratic Republic of the Congo (DRC), 2018-2020. This approach uses transmission chain data typically gathered through case investigation and contact tracing, and uses the proportion of investigated cases with a known, reported infector as a proxy for reporting. Using simulated epidemics, we study how this method performs for different outbreak sizes and reporting levels. Results suggest that our method has low bias, reasonable precision, and despite sub-optimal coverage, usually provides estimates within close range (5-10%) of the true value. Being fast and simple, this method could be useful for estimating reporting in real-time in settings where person-to-person transmission is the main driver of the epidemic, and where case investigation is routinely performed as part of surveillance and contact tracing activities.
Journal Article > ResearchFull Text
PLoS Negl Trop Dis. 2017 July 21; Volume 11 (Issue 7); DOI:10.1371/journal.pntd.0005767
Métras R, Fournié G, Dommerques L, Camacho A, Cavalerie L, et al.
PLoS Negl Trop Dis. 2017 July 21; Volume 11 (Issue 7); DOI:10.1371/journal.pntd.0005767
Rift Valley fever (RVF) is a major zoonotic and arboviral hemorrhagic fever. The conditions leading to RVF epidemics are still unclear, and the relative role of climatic and anthropogenic factors may vary between ecosystems. Here, we estimate the most likely scenario that led to RVF emergence on the island of Mayotte, following the 2006-2007 African epidemic. We developed the first mathematical model for RVF that accounts for climate, animal imports and livestock susceptibility, which is fitted to a 12-years dataset. RVF emergence was found to be triggered by the import of infectious animals, whilst transmissibility was approximated as a linear or exponential function of vegetation density. Model forecasts indicated a very low probability of virus endemicity in 2017, and therefore of re-emergence in a closed system (i.e. without import of infected animals). However, the very high proportion of naive animals reached in 2016 implies that the island remains vulnerable to the import of infectious animals. We recommend reinforcing surveillance in livestock, should RVF be reported is neighbouring territories. Our model should be tested elsewhere, with ecosystem-specific data.
Journal Article > ResearchFull Text
Emerg Infect Dis. 2015 March 1; Volume 21 (Issue 3); 393-399.; DOI:10.3201/eid2103.141892
Kucharski AJ, Camacho A, Checchi F, Waldman RJ, Grais RF, et al.
Emerg Infect Dis. 2015 March 1; Volume 21 (Issue 3); 393-399.; DOI:10.3201/eid2103.141892
In some parts of western Africa, Ebola treatment centers (ETCs) have reached capacity. Unless capacity is rapidly scaled up, the chance to avoid a generalized Ebola epidemic will soon diminish. The World Health Organization and partners are considering additional Ebola patient care options, including community care centers (CCCs), small, lightly staffed units that could be used to isolate patients outside the home and get them into care sooner than otherwise possible. Using a transmission model, we evaluated the benefits and risks of introducing CCCs into Sierra Leone's Western Area, where most ETCs are at capacity. We found that use of CCCs could lead to a decline in cases, even if virus transmission occurs between CCC patients and the community. However, to prevent CCC amplification of the epidemic, the risk of Ebola virus-negative persons being exposed to virus within CCCs would have to be offset by a reduction in community transmission resulting from CCC use.