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Article ; Online: Altered demographic profile of hospitalizations during the second COVID-19 wave in Amazonas, Brazil

Charles Whittaker / Oliver Ratmann / Christopher Dye / Ester C. Sabino / Nuno R. Faria

The Lancet Regional Health. Americas, Vol 2, Iss , Pp 100064- (2021)

2021

Keywords	SARS-CoV-2 ; Gamma VOC ; age-stratified severity ; Manaus ; Brazil ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chikungunya

William M. de Souza / Guilherme S. Ribeiro / Shirlene T.S. de Lima / Ronaldo de Jesus / Filipe R.R. Moreira / Charles Whittaker / Maria Anice M. Sallum / Christine V.F. Carrington / Ester C. Sabino / Uriel Kitron / Nuno R. Faria / Scott C. Weaver

The Lancet Regional Health. Americas, Vol 30, Iss , Pp 100673- (2024)

a decade of burden in the Americas

2024

Abstract: Summary: In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 ... ...

Abstract	Summary: In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 countries or territories in the Americas. Here, we outline the current status and epidemiological aspects of chikungunya in the Americas and discuss prospects for future research and public health strategies to combat CHIKV in the region.
Keywords	Chikungunya virus ; Arbovirus ; Mosquito-borne virus ; Alphavirus ; Americas ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2024-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Global variation in force-of-infection trends for human Taenia solium taeniasis/cysticercosis

Matthew A Dixon / Peter Winskill / Wendy E Harrison / Charles Whittaker / Veronika Schmidt / Astrid Carolina Flórez Sánchez / Zulma M Cucunuba / Agnes U Edia-Asuke / Martin Walker / María-Gloria Basáñez

eLife, Vol

2022 Volume 11

Abstract: Infection by Taenia solium poses a major burden across endemic countries. The World Health Organization (WHO) 2021–2030 Neglected Tropical Diseases roadmap has proposed that 30% of endemic countries achieve intensified T. solium control in hyperendemic ... ...

Abstract	Infection by Taenia solium poses a major burden across endemic countries. The World Health Organization (WHO) 2021–2030 Neglected Tropical Diseases roadmap has proposed that 30% of endemic countries achieve intensified T. solium control in hyperendemic areas by 2030. Understanding geographical variation in age-prevalence profiles and force-of-infection (FoI) estimates will inform intervention designs across settings. Human taeniasis (HTT) and human cysticercosis (HCC) age-prevalence data from 16 studies in Latin America, Africa, and Asia were extracted through a systematic review. Catalytic models, incorporating diagnostic performance uncertainty, were fitted to the data using Bayesian methods, to estimate rates of antibody (Ab)-seroconversion, infection acquisition and Ab-seroreversion or infection loss. HCC FoI and Ab-seroreversion rates were also estimated across 23 departments in Colombia from 28,100 individuals. Across settings, there was extensive variation in all-ages seroprevalence. Evidence for Ab-seroreversion or infection loss was found in most settings for both HTT and HCC and for HCC Ab-seroreversion in Colombia. The average duration until humans became Ab-seropositive/infected decreased as all-age (sero)prevalence increased. There was no clear relationship between the average duration humans remain Ab-seropositive and all-age seroprevalence. Marked geographical heterogeneity in T. solium transmission rates indicate the need for setting-specific intervention strategies to achieve the WHO goals.
Keywords	taenia solium ; one health ; modelling ; neglected tropical diseases ; statistics ; zoonotic infections ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Machine-learning aided in situ drug sensitivity screening predicts treatment outcomes in ovarian PDX tumors

Max J. Cotler / Khalil B. Ramadi / Xiaonan Hou / Elena Christodoulopoulos / Sebastian Ahn / Ashvin Bashyam / Huiming Ding / Melissa Larson / Ann L. Oberg / Charles Whittaker / Oliver Jonas / Scott H. Kaufmann / S. John Weroha / Michael J. Cima

Translational Oncology, Vol 21, Iss , Pp 101427- (2022)

2022

Abstract: Long-term treatment outcomes for patients with high grade ovarian cancers have not changed despite innovations in therapies. There is no recommended assay for predicting patient response to second-line therapy, thus clinicians must make treatment ... ...

Abstract	Long-term treatment outcomes for patients with high grade ovarian cancers have not changed despite innovations in therapies. There is no recommended assay for predicting patient response to second-line therapy, thus clinicians must make treatment decisions based on each individual patient. Patient-derived xenograft (PDX) tumors have been shown to predict drug sensitivity in ovarian cancer patients, but the time frame for intraperitoneal (IP) tumor generation, expansion, and drug screening is beyond that for tumor recurrence and platinum resistance to occur, thus results do not have clinical utility. We describe a drug sensitivity screening assay using a drug delivery microdevice implanted for 24 h in subcutaneous (SQ) ovarian PDX tumors to predict treatment outcomes in matched IP PDX tumors in a clinically relevant time frame. The SQ tumor response to local microdose drug exposure was found to be predictive of the growth of matched IP tumors after multi-week systemic therapy using significantly fewer animals (10 SQ vs 206 IP). Multiplexed immunofluorescence image analysis of phenotypic tumor response combined with a machine learning classifier could predict IP treatment outcomes against three second-line cytotoxic therapies with an average AUC of 0.91.
Keywords	Drug delivery ; Ovarian cancer ; Personalized medicine ; Patient derived xenograft ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Force-of-infection of Taenia solium porcine cysticercosis

Matthew A. Dixon / Peter Winskill / Wendy E. Harrison / Charles Whittaker / Veronika Schmidt / Elsa Sarti / Saw Bawm / Michel M. Dione / Lian F. Thomas / Martin Walker / Maria-Gloria Basáñez

Scientific Reports, Vol 10, Iss 1, Pp 1-

a modelling analysis to assess global incidence and prevalence trends

2020 Volume 14

Abstract: Abstract The World Health Organization (WHO) called, in 2012, for a validated strategy towards Taenia solium taeniasis/cysticercosis control and elimination. Estimating pig force-of-infection (FoI, the average rate at which susceptible pigs become ... ...

Abstract	Abstract The World Health Organization (WHO) called, in 2012, for a validated strategy towards Taenia solium taeniasis/cysticercosis control and elimination. Estimating pig force-of-infection (FoI, the average rate at which susceptible pigs become infected) across geographical settings will help understand local epidemiology and inform effective intervention design. Porcine cysticercosis (PCC) age-prevalence data (from 15 studies in Latin America, Africa and Asia) were identified through systematic review. Catalytic models were fitted to the data using Bayesian methods, incorporating uncertainty in diagnostic performance, to estimate rates of antibody seroconversion, viable metacestode acquisition, and seroreversion/infection loss. There was evidence of antibody seroreversion across 5 studies, and of infection loss in 6 studies measured by antigen or necropsy, indicating transient serological responses and natural resolution of infection. Concerted efforts should be made to collect robust data using improved diagnostics to better understand geographical heterogeneities in T. solium transmission to support post-2020 WHO targets.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate [version 2; peer review

Richard G. FitzJohn / Edward S. Knock / Lilith K. Whittles / Pablo N. Perez-Guzman / Sangeeta Bhatia / Fernando Guntoro / Oliver J. Watson / Charles Whittaker / Neil M. Ferguson / Anne Cori / Marc Baguelin / John A. Lees

Wellcome Open Research, Vol

2 approved]

2021 Volume 5

Abstract: State space models, including compartmental models, are used to model physical, biological and social phenomena in a broad range of scientific fields. A common way of representing the underlying processes in these models is as a system of stochastic ... ...

Abstract	State space models, including compartmental models, are used to model physical, biological and social phenomena in a broad range of scientific fields. A common way of representing the underlying processes in these models is as a system of stochastic processes which can be simulated forwards in time. Inference of model parameters based on observed time-series data can then be performed using sequential Monte Carlo techniques. However, using these methods for routine inference problems can be made difficult due to various engineering considerations: allowing model design to change in response to new data and ideas, writing model code which is highly performant, and incorporating all of this with up-to-date statistical techniques. Here, we describe a suite of packages in the R programming language designed to streamline the design and deployment of state space models, targeted at infectious disease modellers but suitable for other domains. Users describe their model in a familiar domain-specific language, which is converted into parallelised C++ code. A fast, parallel, reproducible random number generator is then used to run large numbers of model simulations in an efficient manner. We also provide standard inference and prediction routines, though the model simulator can be used directly if these do not meet the user’s needs. These packages provide guarantees on reproducibility and performance, allowing the user to focus on the model itself, rather than the underlying computation. The ability to automatically generate high-performance code that would be tedious and time-consuming to write and verify manually, particularly when adding further structure to compartments, is crucial for infectious disease modellers. Our packages have been critical to the development cycle of our ongoing real-time modelling efforts in the COVID-19 pandemic, and have the potential to do the same for models used in a number of different domains.
Keywords	Medicine ; R ; Science ; Q
Subject code	006
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Wellcome
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling

Communications Medicine, Vol 2, Iss 1, Pp 1-

2022 Volume 13

Abstract: Brazeau et al. use a statistical modelling approach to estimate COVID-19 infection fatality ratios from seroprevalence data. The authors’ model accounts for seroreversion over the course of the pandemic, as well as other important uncertainties such as ... ...

Abstract	Brazeau et al. use a statistical modelling approach to estimate COVID-19 infection fatality ratios from seroprevalence data. The authors’ model accounts for seroreversion over the course of the pandemic, as well as other important uncertainties such as serologic test characteristics.
Keywords	Medicine ; R
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using mortuary and burial data to place COVID-19 in Lusaka, Zambia within a global context

Richard J. Sheppard / Oliver J. Watson / Rachel Pieciak / James Lungu / Geoffrey Kwenda / Crispin Moyo / Stephen Longa Chanda / Gregory Barnsley / Nicholas F. Brazeau / Ines C. G. Gerard-Ursin / Daniela Olivera Mesa / Charles Whittaker / Simon Gregson / Lucy C. Okell / Azra C. Ghani / William B. MacLeod / Emanuele Del Fava / Alessia Melegaro / Jonas Z. Hines /

Lloyd B. Mulenga / Patrick G. T. Walker / Lawrence Mwananyanda / Christopher J. Gill

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 15

Abstract: Abstract Reported COVID-19 cases and associated mortality remain low in many sub-Saharan countries relative to global averages, but true impact is difficult to estimate given limitations around surveillance and mortality registration. In Lusaka, Zambia, ... ...

Abstract	Abstract Reported COVID-19 cases and associated mortality remain low in many sub-Saharan countries relative to global averages, but true impact is difficult to estimate given limitations around surveillance and mortality registration. In Lusaka, Zambia, burial registration and SARS-CoV-2 prevalence data during 2020 allow estimation of excess mortality and transmission. Relative to pre-pandemic patterns, we estimate age-dependent mortality increases, totalling 3212 excess deaths (95% CrI: 2104–4591), representing an 18.5% (95% CrI: 13.0–25.2%) increase relative to pre-pandemic levels. Using a dynamical model-based inferential framework, we find that these mortality patterns and SARS-CoV-2 prevalence data are in agreement with established COVID-19 severity estimates. Our results support hypotheses that COVID-19 impact in Lusaka during 2020 was consistent with COVID-19 epidemics elsewhere, without requiring exceptional explanations for low reported figures. For more equitable decision-making during future pandemics, barriers to ascertaining attributable mortality in low-income settings must be addressed and factored into discourse around reported impact differences.
Keywords	Science ; Q
Subject code	310
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Field performance of the malaria highly sensitive rapid diagnostic test in a setting of varying malaria transmission

Julia Mwesigwa / Hannah Slater / John Bradley / Binta Saidy / Fatima Ceesay / Charles Whittaker / Ballah Kandeh / Davis Nkwakamna / Chris Drakeley / Jean-Pierre Van Geertruyden / Teun Bousema / Jane Achan / Umberto D’Alessandro

Malaria Journal, Vol 18, Iss 1, Pp 1-

2019 Volume 13

Abstract: Abstract Background The Gambia has successfully reduced malaria transmission. The human reservoir of infection could further decrease if malaria-infected individuals could be identified by highly sensitive, field-based, diagnostic tools and then treated. ...

Abstract	Abstract Background The Gambia has successfully reduced malaria transmission. The human reservoir of infection could further decrease if malaria-infected individuals could be identified by highly sensitive, field-based, diagnostic tools and then treated. Methods A cross-sectional survey was done at the peak of the 2017 malaria season in 47 Gambian villages. From each village, 100 residents were randomly selected for finger-prick blood samples to detect Plasmodium falciparum infections using highly sensitive rapid diagnostic tests (HS-RDT) and PCR. The sensitivity and specificity of the HS-RDT were estimated (assuming PCR as the gold standard) across varying transmission intensities and in different age groups. A deterministic, age-structured, dynamic model of malaria transmission was used to estimate the impact of mass testing and treatment (MTAT) with HS-RDT in four different scenarios of malaria prevalence by PCR: 5, 15, 30, and 60%, and with seasonal transmission. The impact was compared both to MTAT with conventional RDT and mass drug administration (MDA). Results Malaria prevalence by HS-RDT was 15% (570/3798; 95% CI 13.9–16.1). The HS-RDT sensitivity and specificity were 38.4% (191/497, 95% CI 34.2–42.71) and 88.5% (2922/3301; 95% CI 87.4–89.6), respectively. Sensitivity was the highest (50.9%, 95% CI 43.3–58.5%) in high prevalence villages (20–50% by PCR). The model predicted that in very low transmission areas (≤ 5%), three monthly rounds of MTAT with HS-RDT, starting towards the end of the dry season and testing 65 or 85% of the population for 2 consecutive years, would avert 62 or 78% of malaria cases (over 2 years), respectively. The effect of the intervention would be lower in a moderate transmission setting. In all settings, MDA would be superior to MTAT with HS-RDT which would be superior to MTAT with conventional RDT. Conclusion The HS-RDT’s field sensitivity was modest and varied by transmission intensity. In low to very low transmission areas, three monthly rounds per year of MTAT with HS-RDT at 85% coverage for 2 consecutive years would reduce malaria prevalence to such low levels that additional strategies may achieve elimination. The model prediction would need to be confirmed by cluster-randomized trials.
Keywords	Highly sensitive rapid diagnostic test ; Malaria ; Mass testing and treatment ; Plasmodium falciparum ; Transmission areas ; Arctic medicine. Tropical medicine ; RC955-962 ; Infectious and parasitic diseases ; RC109-216
Subject code	616
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling

Swapnil Mishra / James A. Scott / Daniel J. Laydon / Seth Flaxman / Axel Gandy / Thomas A. Mellan / H. Juliette T. Unwin / Michaela Vollmer / Helen Coupland / Oliver Ratmann / Melodie Monod / Harrison H. Zhu / Anne Cori / Katy A. M. Gaythorpe / Lilith K. Whittles / Charles Whittaker / Christl A. Donnelly / Neil M. Ferguson / Samir Bhatt

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 9

Abstract: Abstract The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in ... ...

Abstract	Abstract The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in the UK, Sweden and Denmark shaped COVID-19 mortality in each country, using a counterfactual assessment: what would the impact have been, had each country adopted the others’ policies? Using a Bayesian semi-mechanistic model without prior assumptions on the mechanism or effectiveness of interventions, we estimate the time-varying reproduction number for the UK, Sweden and Denmark from daily mortality data. We use two approaches to evaluate counterfactuals which transpose the transmission profile from one country onto another, in each country’s first wave from 13th March (when stringent interventions began) until 1st July 2020. UK mortality would have approximately doubled had Swedish policy been adopted, while Swedish mortality would have more than halved had Sweden adopted UK or Danish strategies. Danish policies were most effective, although differences between the UK and Denmark were significant for one counterfactual approach only. Our analysis shows that small changes in the timing or effectiveness of interventions have disproportionately large effects on total mortality within a rapidly growing epidemic.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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