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Article ; Online: Forecasting upper respiratory tract infection burden using high-dimensional time series data and forecast combinations.

Lim, Jue Tao / Tan, Kelvin Bryan / Abisheganaden, John / Dickens, Borame L

2023 Volume 19, Issue 2, Page(s) e1010892

Abstract: Upper respiratory tract infections (URTIs) represent a large strain on primary health resources. To mitigate URTI transmission and public health burdens, it is important to pre-empt and provide forward guidance on URTI burden, while taking into account ... ...

Abstract	Upper respiratory tract infections (URTIs) represent a large strain on primary health resources. To mitigate URTI transmission and public health burdens, it is important to pre-empt and provide forward guidance on URTI burden, while taking into account various facets which influence URTI transmission. This is so that appropriate public health measures can be taken to mitigate strain on primary care resources. This study describes a new approach to forecasting URTIs which can be used for national public health resource planning. Specifically, using environmental and disease data comprising more than 1000 dimensions, we developed sub-models which optimizes model explainability, in-sample model fit, predictive accuracy and combines many weaker predictors over a 2-month time horizon to generate direct, point forecasts over a 1-8 week ahead forecast horizon. Predictive performance was evaluated using rolling out-of-sample forecast assessment within both periods with/without structural breaks in transmission over the period of 2012-2022. We showed that forecast combinations of 5 other forecasting models had better and more consistent predictive performance than other modelling approaches, over periods with and without structural breaks in transmission dynamics. Furthermore, epidemiological analysis on high dimensional data was enabled using post-selection inference, to show the dynamic association between lower temperature, increases in past relative humidity and absolute humidity and increased URTIs attendance. The methods proposed can be used for outbreak preparedness and guide healthcare resource planning, in both stable periods of transmission and periods where structural breaks in data occur.
MeSH term(s)	Humans ; Time Factors ; Disease Outbreaks ; Public Health ; Temperature ; Respiratory Tract Infections ; Forecasting
Language	English
Publishing date	2023-02-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010892
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Feasibility of wastewater-based detection of emergent pandemics through a global network of airports.

Jin, Shihui / Dickens, Borame L / Toh, Kai Yee / Lye, David Chien Boon / Lee, Vernon J / Cook, Alex R

PLOS global public health

2024 Volume 4, Issue 3, Page(s) e0003010

Abstract: Wastewater-based surveillance has been put into practice during the pandemic. Persistence of SARS-CoV-2 in faeces of infected individuals, and high volume of passengers travelling by air, make it possible to detect virus from aircraft wastewater, lending ...

Abstract	Wastewater-based surveillance has been put into practice during the pandemic. Persistence of SARS-CoV-2 in faeces of infected individuals, and high volume of passengers travelling by air, make it possible to detect virus from aircraft wastewater, lending itself to the potential identification of a novel pathogen prior to clinical diagnosis. In this study, we estimated the likelihood of detecting the virus through aircraft wastewater from the probabilities of air travel, viral shedding, defecation, testing sensitivity, and sampling. We considered various hypothetical scenarios, with diverse sampling proportions of inbound flights, surveillance airports, and sources of outbreaks. Our calculations showed that the probability of detecting SARS-CoV-2 would increase exponentially against time in the early phase of the pandemic, and would be much higher if the 20 major airports in Asia, Europe, and North America cooperated to perform aircraft wastewater surveillance. We also found other contributors to early detection, including high sampling proportion of inbound flight at destination airports, small population size of the epicentre relative to the travel volume, and large volume of outbound travelers to major airports around the globe. We concluded that routine aircraft wastewater monitoring could be a feasible approach for early identification and tracking of an emerging pathogen with high faecal shedding rates, particularly when implemented through a global surveillance network of major airports.
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ISSN	2767-3375
ISSN (online)	2767-3375
DOI	10.1371/journal.pgph.0003010
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

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

Digital health

2023 Volume 9, Page(s) 20552076231178418

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.
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2819396-9
ISSN	2055-2076
ISSN	2055-2076
DOI	10.1177/20552076231178418
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Article ; Online: The need for pre-emptive control strategies for mpox in Asia and Oceania.

Gan, Gregory / Janhavi, A / Tong, Guan / Lim, Jue Tao / Dickens, Borame L

Infectious Disease Modelling

2023 Volume 9, Issue 1, Page(s) 214–223

Abstract: Introduction: The transmission dynamics of the recent mpox outbreak highlights the lack of infrastructure available to rapidly respond to novel STI outbreaks, of which Asia and Oceania remains particularly susceptible. Here, we simulate outbreaks in ... ...

Abstract	Introduction: The transmission dynamics of the recent mpox outbreak highlights the lack of infrastructure available to rapidly respond to novel STI outbreaks, of which Asia and Oceania remains particularly susceptible. Here, we simulate outbreaks in this setting and propose the use of pre-emptive vaccination within the men who have sex with men (MSM) community before the arrival and establishment of the virus. Materials and methods: Using data driven heterogeneous sexual contact networks, we simulated outbreaks of mpox in Singapore, Hong Kong, and Sydney. An individual based SEIR compartmental model was used to simulate epidemic trajectories and the impact of different vaccination uptakes was assessed in their ability to avert or suppress outbreaks upon the arrival of mpox within the MSM populations. Results: The highly dense sexual networks of Singapore and Sydney experience rapid outbreaks, with infection peaks occurring at day 41 and 23 respectively, compared to Hong Kong which occurs at day 77. Across the simulations with no vaccination, 68.2%-89.7% of the MSM community will become infected with mpox across the different cities, over a simulation period of 1 year. By implementing vaccination strategies, the infection rate across the cities can be reduced to as low as 3.1% of the population (range: 3.1%-82.2%) depending on the implementation and uptake of the vaccine. Vaccination is also extremely effective in slowing the start of the epidemic, delaying the epidemic peak by 36-50 days in Hong Kong, or even preventing the outbreak of mpox. Discussion: With extremely dense and well-connected sexual contact networks, where 65.2%-83.2% of the population are connected to a super-spreader in the different contact networks, pre-emptive or immediate vaccination upon identification of the first case is strongly recommended to help better manage the outbreak of mpox and prevent potential straining of healthcare systems.
Language	English
Publishing date	2023-12-28
Publishing country	China
Document type	Journal Article
ZDB-ID	3015225-2
ISSN	2468-0427 ; 2468-2152
ISSN (online)	2468-0427
ISSN	2468-2152
DOI	10.1016/j.idm.2023.12.005
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimated Health Outcomes and Costs Associated With Use of Monoclonal Antibodies for Prevention or Mitigation of SARS-CoV-2 Infections.

Park, Minah / Tan, Kelvin Bryan / Vasoo, Shawn / Dickens, Borame L / Lye, David / Cook, Alex R

JAMA network open

2022 Volume 5, Issue 4, Page(s) e225750

MeSH term(s)	Antibodies, Monoclonal/therapeutic use ; Antibodies, Viral ; COVID-19 ; Humans ; Outcome Assessment, Health Care ; SARS-CoV-2
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Viral
Language	English
Publishing date	2022-04-01
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.5750
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Article ; Online: Differential Household Attack Rates Mirror the Ability to Control Coronavirus Disease 2019 (COVID-19).

Cook, Alex R / Dickens, Borame L / Wilder-Smith, Annelies

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2020 Volume 72, Issue 12, Page(s) e1166–e1167

MeSH term(s)	COVID-19 ; Contact Tracing ; Family Characteristics ; Humans ; Incidence ; SARS-CoV-2
Language	English
Publishing date	2020-12-10
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciaa1842
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Zs.A 1505: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 480: Show issues

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Article ; Online: Institutional versus home isolation to curb the COVID-19 outbreak - Authors' reply.

Wilder-Smith, Annelies / Cook, Alex R / Dickens, Borame L

Lancet (London, England)

2020 Volume 396, Issue 10263, Page(s) 1632–1633

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections/epidemiology ; Disease Outbreaks/prevention & control ; Humans ; Pandemics ; Pneumonia, Viral ; Quarantine ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-11-06
Publishing country	England
Document type	Letter ; Comment
ZDB-ID	3306-6
ISSN	1474-547X ; 0023-7507 ; 0140-6736
ISSN (online)	1474-547X
ISSN	0023-7507 ; 0140-6736
DOI	10.1016/S0140-6736(20)32171-1
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Ua VI Zs.5: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MG 94: Show issues

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Article ; Online: Association between ambient air pollutants and upper respiratory tract infection and pneumonia disease burden in Thailand from 2000 to 2022: a high frequency ecological analysis.

Choo, Esther Li Wen / Janhavi, A / Koo, Joel Ruihan / Yim, Steve H L / Dickens, Borame L / Lim, Jue Tao

BMC infectious diseases

2023 Volume 23, Issue 1, Page(s) 379

Abstract: Background: A pertinent risk factor of upper respiratory tract infections (URTIs) and pneumonia is the exposure to major ambient air pollutants, with short term exposures to different air pollutants being shown to exacerbate several respiratory ... ...

Abstract	Background: A pertinent risk factor of upper respiratory tract infections (URTIs) and pneumonia is the exposure to major ambient air pollutants, with short term exposures to different air pollutants being shown to exacerbate several respiratory conditions. Methods: Here, using disease surveillance data comprising of reported disease case counts at the province level, high frequency ambient air pollutant and climate data in Thailand, we delineated the association between ambient air pollution and URTI/Pneumonia burden in Thailand from 2000 - 2022. We developed mixed-data sampling methods and estimation strategies to account for the high frequency nature of ambient air pollutant concentration data. This was used to evaluate the effects past concentrations of fine particulate matter (PM Results: Across provinces, we found that past increases in CO, SO Conclusions: By developing a novel statistical methodology, we prevented subjective variable selection and discretization bias to detect associations, and provided a robust estimate on the effect of ambient air pollutants on URTI and pneumonia burden over a large spatial scale.
MeSH term(s)	Humans ; Air Pollutants/adverse effects ; Air Pollutants/analysis ; Environmental Pollutants/analysis ; Thailand/epidemiology ; Particulate Matter/adverse effects ; Particulate Matter/analysis ; Pneumonia/epidemiology ; Pneumonia/etiology ; Respiratory Tract Infections/epidemiology ; Environmental Exposure/adverse effects ; Environmental Exposure/analysis
Chemical Substances	Air Pollutants ; Environmental Pollutants ; Particulate Matter
Language	English
Publishing date	2023-06-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-023-08185-0
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Article ; Online: Modelling the Impact of Mass Testing to Transition from Pandemic Mitigation to Endemic COVID-19.

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

Viruses

2022 Volume 14, Issue 5

Abstract: As countries transition from pandemic mitigation to endemic COVID-19, mass testing may blunt the impact on the healthcare system of the liminal wave. We used GeoDEMOS-R, an agent-based model of Singapore's population with demographic distributions and ... ...

Abstract	As countries transition from pandemic mitigation to endemic COVID-19, mass testing may blunt the impact on the healthcare system of the liminal wave. We used GeoDEMOS-R, an agent-based model of Singapore's population with demographic distributions and vaccination status. A 250-day COVID-19 Delta variant model was run at varying maximal rapid antigen test sensitivities and frequencies. Without testing, the number of infections reached 1,021,000 (899,400-1,147,000) at 250 days. When conducting fortnightly and weekly mass routine rapid antigen testing 30 days into the outbreak at a maximal test sensitivity of 0.6, this was reduced by 12.8% (11.3-14.5%) and 25.2% (22.5-28.5%). An increase in maximal test sensitivity of 0.2 results a corresponding reduction of 17.5% (15.5-20.2%) and 34.4% (30.5-39.1%). Within the maximal test sensitivity range of 0.6-0.8, test frequency has a greater impact than maximal test sensitivity with an average reduction of 2.2% in infections for each day removed between tests in comparison to a 0.43% average reduction per 1% increase in test frequency. Our findings highlight that mass testing using rapid diagnostic tests can be used as an effective intervention for countries transitioning from pandemic mitigation to endemic COVID-19.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; Disease Outbreaks ; Humans ; Pandemics/prevention & control ; SARS-CoV-2
Language	English
Publishing date	2022-05-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14050967
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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 (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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