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Article ; Online: Short-term and long-term epidemiological impacts of sustained vector control in various dengue endemic settings

Haoyang Sun / Joel Koo / Borame L Dickens / Hannah E Clapham / Alex R Cook

PLoS Computational Biology, Vol 18, Iss 4, p e

A modelling study.

2022 Volume 1009979

Abstract: As the most widespread viral infection transmitted by the Aedes mosquitoes, dengue has been estimated to cause 51 million febrile disease cases globally each year. Although sustained vector control remains key to reducing the burden of dengue, current ... ...

Abstract	As the most widespread viral infection transmitted by the Aedes mosquitoes, dengue has been estimated to cause 51 million febrile disease cases globally each year. Although sustained vector control remains key to reducing the burden of dengue, current understanding of the key factors that explain the observed variation in the short- and long-term vector control effectiveness across different transmission settings remains limited. We used a detailed individual-based model to simulate dengue transmission with and without sustained vector control over a 30-year time frame, under different transmission scenarios. Vector control effectiveness was derived for different time windows within the 30-year intervention period. We then used the extreme gradient boosting algorithm to predict the effectiveness of vector control given the simulation parameters, and the resulting machine learning model was interpreted using Shapley Additive Explanations. According to our simulation outputs, dengue transmission would be nearly eliminated during the early stage of sustained and intensive vector control, but over time incidence would gradually bounce back to the pre-intervention level unless the intervention is implemented at a very high level of intensity. The time point at which intervention ceases to be effective is strongly influenced not only by the intensity of vector control, but also by the pre-intervention transmission intensity and the individual-level heterogeneity in biting risk. Moreover, the impact of many transmission model parameters on the intervention effectiveness is shown to be modified by the intensity of vector control, as well as to vary over time. Our study has identified some of the critical drivers for the difference in the time-varying effectiveness of sustained vector control across different dengue endemic settings, and the insights obtained will be useful to inform future model-based studies that seek to predict the impact of dengue vector control in their local contexts.
Keywords	Biology (General) ; QH301-705.5
Subject code	330
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Features of the urban environment associated with Aedes aegypti abundance in high-rise public apartments in Singapore

Stephanie A Fernandez / Haoyang Sun / Borame L Dickens / Lee Ching Ng / Alex R Cook / Jue Tao Lim

PLoS Neglected Tropical Diseases, Vol 17, Iss 2, p e

An environmental case-control study.

2023 Volume 0011075

Abstract: Aedes aegypti abundance in residential estates is hypothesized to contribute to localised outbreaks of dengue in Singapore. Knowing the factors in the urban environment underlying high Ae. aegypti abundance could guide intervention efforts to reduce Ae. ... ...

Abstract	Aedes aegypti abundance in residential estates is hypothesized to contribute to localised outbreaks of dengue in Singapore. Knowing the factors in the urban environment underlying high Ae. aegypti abundance could guide intervention efforts to reduce Ae. aegypti breeding and the incidence of dengue. In this study, objective data on Ae. aegypti abundance in public apartment blocks estimated by Singapore's nationally representative Gravitrap surveillance system was obtained from the National Environmental Agency. Low and high abundance status public apartment blocks were classified based on the Gravitrap Aegypti Index, corresponding to the lowest and highest quartiles respectively. An environmental case-control study was conducted, wherein a blinded assessment of urban features hypothesised to form breeding habitats was conducted in 50 randomly sampled public apartment blocks with low and high abundance statuses each. Logistic regression was performed to identify features that correlated with abundance status. A multivariable logistic model was created to determine key urban features found in corridors and void decks which were predictive of the Ae. aegypti abundance status of the public apartment block. At a statistical level of significance of 0.20, the presence of gully traps [Odds Ratio (OR): 1.34, 95% Confidence Interval (CI): 1.10, 1.66], age of the public apartment block [OR: 2.23, 95% CI: 1.48, 3.60], housing price [OR: 0.33, 95% CI: 0.16, 0.61] and corridor cleanliness [OR: 0.67, 95% CI: 0.40, 1.07] were identified as important predictors of abundance status. To reduce Ae. aegypti abundance around public apartment blocks and potential onward dengue transmission, gully traps could be remodelled or replaced by other drainage types. Routine inspections of Ae. aegypti breeding should be targeted at older and low-income neighbourhoods. Campaigns for cleaner corridors should be promoted.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	720
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Use of Bluetooth contact tracing technology to model COVID-19 quarantine policies in high-risk closed populations

Yinxiaohe Sun / Joel Ruihan Koo / Minah Park / Huso Yi / Borame L Dickens / Alex R Cook

Digital Health, Vol

2023 Volume 9

Abstract: Containment measures in high-risk closed settings, like migrant worker (MW) dormitories, are critical for mitigating emerging infectious disease outbreaks and protecting potentially vulnerable populations in outbreaks such as coronavirus disease 2019 ( ... ...

Abstract	Containment measures in high-risk closed settings, like migrant worker (MW) dormitories, are critical for mitigating emerging infectious disease outbreaks and protecting potentially vulnerable populations in outbreaks such as coronavirus disease 2019 (COVID-19). The direct impact of social distancing measures can be assessed through wearable contact tracing devices. Here, we developed an individual-based model using data collected through a Bluetooth wearable device that collected 33.6M and 52.8M contact events in two dormitories in Singapore, one apartment style and the other a barrack style, to assess the impact of measures to reduce the social contact of cases and their contacts. The simulation of highly detailed contact networks accounts for different infrastructural levels, including room, floor, block, and dormitory, and intensity in terms of being regular or transient. Via a branching process model, we then simulated outbreaks that matched the prevalence during the COVID-19 outbreak in the two dormitories and explored alternative scenarios for control. We found that strict isolation of all cases and quarantine of all contacts would lead to very low prevalence but that quarantining only regular contacts would lead to only marginally higher prevalence but substantially fewer total man-hours lost in quarantine. Reducing the density of contacts by 30% through the construction of additional dormitories was modelled to reduce the prevalence by 14 and 9% under smaller and larger outbreaks, respectively. Wearable contact tracing devices may be used not just for contact tracing efforts but also to inform alternative containment measures in high-risk closed settings.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	600
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Urban-Rural Disparities for COVID-19

Minah Park / Jue Tao Lim / Lin Wang / Alex R. Cook / Borame L. Dickens

Health Data Science, Vol

Evidence from 10 Countries and Areas in the Western Pacific

2021 Volume 2021

Abstract: Background. Limited evidence on the effectiveness of various types of social distancing measures, from voluntary physical distancing to a community-wide quarantine, exists for the Western Pacific Region (WPR) which has large urban and rural populations. ... ...

Abstract	Background. Limited evidence on the effectiveness of various types of social distancing measures, from voluntary physical distancing to a community-wide quarantine, exists for the Western Pacific Region (WPR) which has large urban and rural populations. Methods. We estimated the time-varying reproduction number (Rt) in a Bayesian framework using district-level mobility data provided by Facebook (i) to assess how various social distancing policies have contributed to the reduction in transmissibility of SARS-COV-2 and (ii) to examine within-country variations in behavioural responses, quantified by reductions in mobility, for urban and rural areas. Results. Social distancing measures were largely effective in reducing transmissibility, with Rt estimates decreased to around the threshold of 1. Within-country analysis showed substantial variation in public compliance across regions. Reductions in mobility were significantly lower in rural and remote areas than in urban areas and metropolitan cities (p<0.001) which had the same scale of social distancing orders in place. Conclusions. Our findings provide empirical evidence that public compliance and consequent intervention effectiveness differ between urban and rural areas in the WPR. Further work is required to ascertain the factors affecting these differing behavioural responses, which can assist in policy-making efforts and increase public compliance in rural areas where populations are older and have poorer access to healthcare.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	910
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	American Association for the Advancement of Science (AAAS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Testing strategies to contain COVID-19 in migrant worker dormitories

Joel R Koo / Borame L Dickens / Shihui Jin / Jue Tao Lim / Yinxiaohe Sun / Ken Wei Tan / Alex R Cook

Journal of Migration and Health, Vol 5, Iss , Pp 100079- (2022)

2022

Abstract: Introduction: COVID-19 transmission within overcrowded migrant worker dormitories is an ongoing global issue. Many countries have implemented extensive control measures to prevent the entire migrant worker population from becoming infected. Here, we ... ...

Abstract	Introduction: COVID-19 transmission within overcrowded migrant worker dormitories is an ongoing global issue. Many countries have implemented extensive control measures to prevent the entire migrant worker population from becoming infected. Here, we explore case count outcomes when utilizing lockdown and testing under different testing measures and transmissibility settings. Methods: We built a mathematical model which estimates transmission across 10 different blocks with 1000 individuals per block under different parameter combinations and testing conditions over the period of 1 month. We vary parameters including differences in block connectivity, underlying recovered proportions at the time of intervention, case importation rates and testing protocols using either PCR or rapid antigen testing. Results: We estimate that a relatively transmissible environment with fortnightly PCR testing at a relatively low initial recovered proportion of 40%, low connectivity where 10% of contacts occurred outside of the infected individuals’ block and a high importation rate of 1100000 per day, results in an average of 39 (95%Interval: 9–121) new COVID-19 cases after one month of observation. Similar results were observed for weekly rapid antigen testing at 33 (9–95) cases. Interpretation: Our findings support the need for either fortnightly PCR testing or weekly rapid antigen testing in high population density environments such as migrant worker dormitories. Repeated mass testing is highly effective, preventing localized site outbreaks and reducing the need for site wide lockdowns or other extensive social distancing measures within and outside of dormitories.
Keywords	Public aspects of medicine ; RA1-1270 ; Colonies and colonization. Emigration and immigration. International migration ; JV1-9480
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Importations of COVID-19 into African countries and risk of onward spread

Haoyang Sun / Borame L. Dickens / Alex R. Cook / Hannah E. Clapham

BMC Infectious Diseases, Vol 20, Iss 1, Pp 1-

2020 Volume 13

Abstract: Abstract Background The emergence of a novel coronavirus (SARS-CoV-2) in Wuhan, China, at the end of 2019 has caused widespread transmission around the world. As new epicentres in Europe and America have arisen, of particular concern is the increased ... ...

Abstract	Abstract Background The emergence of a novel coronavirus (SARS-CoV-2) in Wuhan, China, at the end of 2019 has caused widespread transmission around the world. As new epicentres in Europe and America have arisen, of particular concern is the increased number of imported coronavirus disease 2019 (COVID-19) cases in Africa, where the impact of the pandemic could be more severe. We aim to estimate the number of COVID-19 cases imported from 12 major epicentres in Europe and America to each African country, as well as the probability of reaching 10,000 cases in total by the end of March, April, May, and June following viral introduction. Methods We used the reported number of cases imported from the 12 major epicentres in Europe and America to Singapore, as well as flight data, to estimate the number of imported cases in each African country. Under the assumption that Singapore has detected all the imported cases, the estimates for Africa were thus conservative. We then propagated the uncertainty in the imported case count estimates to simulate the onward spread of the virus, until 10,000 cases are reached or the end of June, whichever is earlier. Specifically, 1,000 simulations were run separately under four different combinations of parameter values to test the sensitivity of our results. Results We estimated Morocco, Algeria, South Africa, Egypt, Tunisia, and Nigeria as having the largest number of COVID-19 cases imported from the 12 major epicentres. Based on our 1,000 simulation runs, Morocco and Algeria’s estimated probability of reaching 10,000 cases by end of March was close to 100% under all scenarios. In particular, we identified countries with less than 1,000 cases in total reported by end of June whilst the estimated probability of reaching 10,000 cases by then was higher than 50% even under the most optimistic scenario. Conclusions Our study highlights particular countries that are likely to reach (or have reached) 10,000 cases far earlier than the reported data suggest, calling for the prioritization of resources to mitigate the further spread of the epidemic.
Keywords	Coronavirus ; COVID-19 ; SARS-CoV-2 ; Africa ; Mathematical modelling ; Infectious and parasitic diseases ; RC109-216 ; covid19
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: A Systematic Review of COVID-19 Epidemiology Based on Current Evidence

Minah Park / Alex R. Cook / Jue Tao Lim / Yinxiaohe Sun / Borame L. Dickens

Journal of Clinical Medicine ; Volume 9 ; Issue 4

2020

Abstract: As the novel coronavirus (SARS-CoV-2) continues to spread rapidly across the globe, we aimed to identify and summarize the existing evidence on epidemiological characteristics of SARS-CoV-2 and the effectiveness of control measures to inform policymakers ...

Abstract	As the novel coronavirus (SARS-CoV-2) continues to spread rapidly across the globe, we aimed to identify and summarize the existing evidence on epidemiological characteristics of SARS-CoV-2 and the effectiveness of control measures to inform policymakers and leaders in formulating management guidelines, and to provide directions for future research. We conducted a systematic review of the published literature and preprints on the coronavirus disease (COVID-19) outbreak following predefined eligibility criteria. Of 317 research articles generated from our initial search on PubMed and preprint archives on 21 February 2020, 41 met our inclusion criteria and were included in the review. Current evidence suggests that it takes about 3-7 days for the epidemic to double in size. Of 21 estimates for the basic reproduction number ranging from 1.9 to 6.5, 13 were between 2.0 and 3.0. The incubation period was estimated to be 4-6 days, whereas the serial interval was estimated to be 4-8 days. Though the true case fatality risk is yet unknown, current model-based estimates ranged from 0.3% to 1.4% for outside China. There is an urgent need for rigorous research focusing on the mitigation efforts to minimize the impact on society.
Keywords	COVID-19 ; SARS-CoV-2 ; epidemiology ; basic reproduction number ; incubation period ; serial interval ; severity ; covid19
Subject code	306
Language	English
Publishing date	2020-03-31
Publisher	Multidisciplinary Digital Publishing Institute
Publishing country	ch
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Systematic Review of COVID-19 Epidemiology Based on Current Evidence

Minah Park / Alex R. Cook / Jue Tao Lim / Yinxiaohe Sun / Borame L. Dickens

Journal of Clinical Medicine, Vol 9, Iss 967, p

2020 Volume 967

Abstract	As the novel coronavirus (SARS-CoV-2) continues to spread rapidly across the globe, we aimed to identify and summarize the existing evidence on epidemiological characteristics of SARS-CoV-2 and the effectiveness of control measures to inform policymakers and leaders in formulating management guidelines, and to provide directions for future research. We conducted a systematic review of the published literature and preprints on the coronavirus disease (COVID-19) outbreak following predefined eligibility criteria. Of 317 research articles generated from our initial search on PubMed and preprint archives on 21 February 2020, 41 met our inclusion criteria and were included in the review. Current evidence suggests that it takes about 3-7 days for the epidemic to double in size. Of 21 estimates for the basic reproduction number ranging from 1.9 to 6.5, 13 were between 2.0 and 3.0. The incubation period was estimated to be 4-6 days, whereas the serial interval was estimated to be 4-8 days. Though the true case fatality risk is yet unknown, current model-based estimates ranged from 0.3% to 1.4% for outside China. There is an urgent need for rigorous research focusing on the mitigation efforts to minimize the impact on society.
Keywords	COVID-19 ; SARS-CoV-2 ; epidemiology ; basic reproduction number ; incubation period ; serial interval ; Medicine ; R ; covid19
Subject code	306
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

Haoyang Sun / Borame L. Dickens / Mark Jit / Alex R. Cook / L. Roman Carrasco

BMC Medicine, Vol 18, Iss 1, Pp 1-

2020 Volume 17

Abstract: Abstract Background Zika virus (ZIKV) emerged as a global epidemic in 2015–2016 from Latin America with its true geographical extent remaining unclear due to widely presumed underreporting. The identification of locations with potential and unknown ... ...

Abstract	Abstract Background Zika virus (ZIKV) emerged as a global epidemic in 2015–2016 from Latin America with its true geographical extent remaining unclear due to widely presumed underreporting. The identification of locations with potential and unknown spread of ZIKV is a key yet understudied component for outbreak preparedness. Here, we aim to identify locations at a high risk of cryptic ZIKV spread during 2015–2016 to further the understanding of the global ZIKV epidemiology, which is critical for the mitigation of the risk of future epidemics. Methods We developed an importation simulation model to estimate the weekly number of ZIKV infections imported in each susceptible spatial unit (i.e. location that did not report any autochthonous Zika cases during 2015–2016), integrating epidemiological, demographic, and travel data as model inputs. Thereafter, a global risk model was applied to estimate the weekly ZIKV transmissibility during 2015–2016 for each location. Finally, we assessed the risk of onward ZIKV spread following importation in each susceptible spatial unit to identify locations with a high potential for cryptic ZIKV spread during 2015–2016. Results We have found 24 susceptible spatial units that were likely to have experienced cryptic ZIKV spread during 2015–2016, of which 10 continue to have a high risk estimate within a highly conservative scenario, namely, Luanda in Angola, Banten in Indonesia, Maharashtra in India, Lagos in Nigeria, Taiwan and Guangdong in China, Dakar in Senegal, Maputo in Mozambique, Kinshasa in Congo DRC, and Pool in Congo. Notably, among the 24 susceptible spatial units identified, some have reported their first ZIKV outbreaks since 2017, thus adding to the credibility of our results (derived using 2015–2016 data only). Conclusion Our study has provided valuable insights into the potentially high-risk locations for cryptic ZIKV circulation during the 2015–2016 pandemic and has also laid a foundation for future studies that attempt to further narrow this key knowledge gap. Our ...
Keywords	Zika virus ; Epidemic preparedness ; Global health ; Surveillance capacity ; Risk assessment ; Undetected transmission ; Medicine ; R
Subject code	910
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Importance of Geospatial Heterogeneity in Chronic Disease Burden for Policy Planning in an Urban Setting Using a Case Study of Singapore

Ken Wei Tan / Joel R. Koo / Jue Tao Lim / Alex R. Cook / Borame L. Dickens

International Journal of Environmental Research and Public Health, Vol 18, Iss 4406, p

2021 Volume 4406

Abstract: Chronic disease burdens continue to rise in highly dense urban environments where clustering of type II diabetes mellitus, acute myocardial infarction, stroke, or any combination of these three conditions is occurring. Many individuals suffering from ... ...

Abstract	Chronic disease burdens continue to rise in highly dense urban environments where clustering of type II diabetes mellitus, acute myocardial infarction, stroke, or any combination of these three conditions is occurring. Many individuals suffering from these conditions will require longer-term care and access to clinics which specialize in managing their illness. With Singapore as a case study, we utilized census data in an agent-modeling approach at an individual level to estimate prevalence in 2020 and found high-risk clusters with >14,000 type II diabetes mellitus cases and 2000–2500 estimated stroke cases. For comorbidities, 10% of those with type II diabetes mellitus had a past acute myocardial infarction episode, while 6% had a past stroke. The western region of Singapore had the highest number of high-risk individuals at 173,000 with at least one chronic condition, followed by the east at 169,000 and the north with the least at 137,000. Such estimates can assist in healthcare resource planning, which requires these spatial distributions for evidence-based policymaking and to investigate why such heterogeneities exist. The methodologies presented can be utilized within any urban setting where census data exists.
Keywords	statistical modeling ; chronic disease ; spatial epidemiology ; urbanization ; environmental health ; Medicine ; R
Subject code	360
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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