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Article ; Online: Inference of malaria reproduction numbers in three elimination settings by combining temporal data and distance metrics

Isobel Routledge / H. Juliette T. Unwin / Samir Bhatt

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

2021 Volume 21

Abstract: Abstract Individual-level geographic information about malaria cases, such as the GPS coordinates of residence or health facility, is often collected as part of surveillance in near-elimination settings, but could be more effectively utilised to infer ... ...

Abstract	Abstract Individual-level geographic information about malaria cases, such as the GPS coordinates of residence or health facility, is often collected as part of surveillance in near-elimination settings, but could be more effectively utilised to infer transmission dynamics, in conjunction with additional information such as symptom onset time and genetic distance. However, in the absence of data about the flow of parasites between populations, the spatial scale of malaria transmission is often not clear. As a result, it is important to understand the impact of varying assumptions about the spatial scale of transmission on key metrics of malaria transmission, such as reproduction numbers. We developed a method which allows the flexible integration of distance metrics (such as Euclidian distance, genetic distance or accessibility matrices) with temporal information into a single inference framework to infer malaria reproduction numbers. Twelve scenarios were defined, representing different assumptions about the likelihood of transmission occurring over different geographic distances and likelihood of missing infections (as well as high and low amounts of uncertainty in this estimate). These scenarios were applied to four individual level datasets from malaria eliminating contexts to estimate individual reproduction numbers and how they varied over space and time. Model comparison suggested that including spatial information improved models as measured by second order AIC (ΔAICc), compared to time only results. Across scenarios and across datasets, including spatial information tended to increase the seasonality of temporal patterns in reproduction numbers and reduced noise in the temporal distribution of reproduction numbers. The best performing parameterisations assumed long-range transmission (> 200 km) was possible. Our approach is flexible and provides the potential to incorporate other sources of information which can be converted into distance or adjacency matrices such as travel times or molecular ...
Keywords	Medicine ; R ; Science ; Q
Subject code	550
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantifying the direct and indirect protection provided by insecticide treated bed nets against malaria

H. Juliette T. Unwin / Ellie Sherrard-Smith / Thomas S. Churcher / Azra C. Ghani

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

2023 Volume 12

Abstract: Long lasting insecticide treated mosquito nets (LLINs) provide protection from malaria through both direct effects to the user and indirect community-level effects. Here, the authors use mathematical modelling to assess the relative contributions of ... ...

Abstract	Long lasting insecticide treated mosquito nets (LLINs) provide protection from malaria through both direct effects to the user and indirect community-level effects. Here, the authors use mathematical modelling to assess the relative contributions of these effects under different insecticide resistance and LLIN usage scenarios.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Analysis of the potential for a malaria vaccine to reduce gaps in malaria intervention coverage

H. Juliette T. Unwin / Lazaro Mwandigha / Peter Winskill / Azra C. Ghani / Alexandra B. Hogan

Malaria Journal, Vol 20, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Background The RTS,S/AS01 malaria vaccine is currently being evaluated in a cluster-randomized pilot implementation programme in three African countries. This study seeks to identify whether vaccination could reach additional children who are at ...

Abstract	Abstract Background The RTS,S/AS01 malaria vaccine is currently being evaluated in a cluster-randomized pilot implementation programme in three African countries. This study seeks to identify whether vaccination could reach additional children who are at risk from malaria but do not currently have access to, or use, core malaria interventions. Methods Using data from household surveys, the overlap between malaria intervention coverage and childhood vaccination (diphtheria-tetanus-pertussis dose 3, DTP3) uptake in 20 African countries with at least one first administrative level unit with Plasmodium falciparum parasite prevalence greater than 10% was calculated. Multilevel logistic regression was used to explore patterns of overlap by demographic and socioeconomic variables. The public health impact of delivering RTS,S/AS01 to those children who do not use an insecticide-treated net (ITN), but who received the DTP3 vaccine, was also estimated. Results Uptake of DTP3 was higher than malaria intervention coverage in most countries. Overall, 34% of children did not use ITNs and received DTP3, while 35% of children used ITNs and received DTP3, although this breakdown varied by country. It was estimated that there are 33 million children in these 20 countries who do not use an ITN. Of these, 23 million (70%) received the DTP3 vaccine. Vaccinating those 23 million children who receive DTP3 but do not use an ITN could avert up to an estimated 9.7 million (range 8.5–10.8 million) clinical malaria cases each year, assuming all children who receive DTP3 are administered all four RTS,S doses. An additional 10.8 million (9.5–12.0 million) cases could be averted by vaccinating those 24 million children who receive the DTP3 vaccine and use an ITN. Children who had access to or used an ITN were 9–13% more likely to reside in rural areas compared to those who had neither intervention regardless of vaccination status. Mothers’ education status was a strong predictor of intervention uptake and was positively associated with use of ...
Keywords	Malaria vaccine ; RTS,S/AS01 ; Expanded Programme on Immunization ; Demographic and Health Surveys ; DHS Program ; Arctic medicine. Tropical medicine ; RC955-962 ; Infectious and parasitic diseases ; RC109-216
Subject code	360
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using Hawkes Processes to model imported and local malaria cases in near-elimination settings.

H Juliette T Unwin / Isobel Routledge / Seth Flaxman / Marian-Andrei Rizoiu / Shengjie Lai / Justin Cohen / Daniel J Weiss / Swapnil Mishra / Samir Bhatt

PLoS Computational Biology, Vol 17, Iss 4, p e

2021 Volume 1008830

Abstract: Developing new methods for modelling infectious diseases outbreaks is important for monitoring transmission and developing policy. In this paper we propose using semi-mechanistic Hawkes Processes for modelling malaria transmission in near-elimination ... ...

Abstract	Developing new methods for modelling infectious diseases outbreaks is important for monitoring transmission and developing policy. In this paper we propose using semi-mechanistic Hawkes Processes for modelling malaria transmission in near-elimination settings. Hawkes Processes are well founded mathematical methods that enable us to combine the benefits of both statistical and mechanistic models to recreate and forecast disease transmission beyond just malaria outbreak scenarios. These methods have been successfully used in numerous applications such as social media and earthquake modelling, but are not yet widespread in epidemiology. By using domain-specific knowledge, we can both recreate transmission curves for malaria in China and Eswatini and disentangle the proportion of cases which are imported from those that are community based.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-04-01T00:00:00Z
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: Publisher Correction

Katy A. M. Gaythorpe / Sangeeta Bhatia / Tara Mangal / H. Juliette T. Unwin / Natsuko Imai / Gina Cuomo-Dannenburg / Caroline E. Walters / Elita Jauneikaite / Helena Bayley / Mara D. Kont / Andria Mousa / Lilith K. Whittles / Steven Riley / Neil M. Ferguson

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

Children’s role in the COVID-19 pandemic: a systematic review of early surveillance data on susceptibility, severity, and transmissibility

2021 Volume 2

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Children’s role in the COVID-19 pandemic

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

a systematic review of early surveillance data on susceptibility, severity, and transmissibility

2021 Volume 14

Abstract: Abstract SARS-CoV-2 infections have been reported in all age groups including infants, children, and adolescents. However, the role of children in the COVID-19 pandemic is still uncertain. This systematic review of early studies synthesises evidence on ... ...

Abstract	Abstract SARS-CoV-2 infections have been reported in all age groups including infants, children, and adolescents. However, the role of children in the COVID-19 pandemic is still uncertain. This systematic review of early studies synthesises evidence on the susceptibility of children to SARS-CoV-2 infection, the severity and clinical outcomes in children with SARS-CoV-2 infection, and the transmissibility of SARS-CoV-2 by children in the initial phases of the COVID-19 pandemic. A systematic literature review was conducted in PubMed. Reviewers extracted data from relevant, peer-reviewed studies published up to July 4th 2020 during the first wave of the SARS-CoV-2 outbreak using a standardised form and assessed quality using the NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. For studies included in the meta-analysis, we used a random effects model to calculate pooled estimates of the proportion of children considered asymptomatic or in a severe or critical state. We identified 2775 potential studies of which 128 studies met our inclusion criteria; data were extracted from 99, which were then quality assessed. Finally, 29 studies were considered for the meta-analysis that included information of symptoms and/or severity, these were further assessed based on patient recruitment. Our pooled estimate of the proportion of test positive children who were asymptomatic was 21.1% (95% CI: 14.0–28.1%), based on 13 included studies, and the proportion of children with severe or critical symptoms was 3.8% (95% CI: 1.5–6.0%), based on 14 included studies. We did not identify any studies designed to assess transmissibility in children and found that susceptibility to infection in children was highly variable across studies. Children’s susceptibility to infection and onward transmissibility relative to adults is still unclear and varied widely between studies. However, it is evident that most children experience clinically mild disease or remain asymptomatically infected. More comprehensive ...
Keywords	Medicine ; R ; Science ; Q
Subject code	360
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 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: 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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Article ; Online: Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

Swapnil Mishra / Sören Mindermann / Mrinank Sharma / Charles Whittaker / Thomas A Mellan / Thomas Wilton / Dimitra Klapsa / Ryan Mate / Martin Fritzsche / Maria Zambon / Janvi Ahuja / Adam Howes / Xenia Miscouridou / Guy P Nason / Oliver Ratmann / Elizaveta Semenova / Gavin Leech / Julia Fabienne Sandkühler / Charlie Rogers-Smith /

Michaela Vollmer / H Juliette T Unwin / Yarin Gal / Meera Chand / Axel Gandy / Javier Martin / Erik Volz / Neil M Ferguson / Samir Bhatt / Jan M Brauner / Seth Flaxman

EClinicalMedicine, Vol 39, Iss , Pp 101064- (2021)

2021

Abstract: Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some ...

Abstract	Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences ...
Keywords	SARS-CoV-2 ; Variants of concern ; Epidemiology ; Waste water monitoring ; Genomic surveillance ; Public health ; Medicine (General) ; R5-920
Subject code	360
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo’

Ilaria Dorigatti / Enrico Lavezzo / Laura Manuto / Constanze Ciavarella / Monia Pacenti / Caterina Boldrin / Margherita Cattai / Francesca Saluzzo / Elisa Franchin / Claudia Del Vecchio / Federico Caldart / Gioele Castelli / Michele Nicoletti / Eleonora Nieddu / Elisa Salvadoretti / Beatrice Labella / Ludovico Fava / Simone Guglielmo / Mariateresa Fascina /

Marco Grazioli / Gualtiero Alvisi / Maria Cristina Vanuzzo / Tiziano Zupo / Reginetta Calandrin / Vittoria Lisi / Lucia Rossi / Ignazio Castagliuolo / Stefano Merigliano / H. Juliette T. Unwin / Mario Plebani / Andrea Padoan / Alessandra R. Brazzale / Stefano Toppo / Neil M. Ferguson / Christl A. Donnelly / Andrea Crisanti

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 11

Abstract: Vo’, Italy, is a unique setting for studying SARS-CoV-2 antibody dynamics because mass testing was conducted there early in the pandemic. Here, the authors perform two follow-up serological surveys and estimate seroprevalence, the extent of within- ... ...

Abstract	Vo’, Italy, is a unique setting for studying SARS-CoV-2 antibody dynamics because mass testing was conducted there early in the pandemic. Here, the authors perform two follow-up serological surveys and estimate seroprevalence, the extent of within-household transmission, and the impact of contact tracing.
Keywords	Science ; Q
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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