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Article ; Online: Mortality among populations affected by armed conflict in northeast Nigeria, 2016 to 2019.

Checchi, Francesco / Jarvis, Christopher I / van Zandvoort, Kevin / Warsame, Abdihamid

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 30, Page(s) e2217601120

Abstract: Armed conflict, displacement and food insecurity have affected Adamawa, Borno, and Yobe states of northeast Nigeria (population ≈ 12 million) since 2009. Insecurity escalated in 2013 to 2015, but the humanitarian response was delayed and the crisis' ... ...

Abstract	Armed conflict, displacement and food insecurity have affected Adamawa, Borno, and Yobe states of northeast Nigeria (population ≈ 12 million) since 2009. Insecurity escalated in 2013 to 2015, but the humanitarian response was delayed and the crisis' health impact was unquantified due to incomplete death registration and limited ground access. We estimated mortality attributable to this crisis using a small-area estimation approach that circumvented these challenges. We fitted a mixed effects model to household mortality data collected as part of 70 ground surveys implemented by humanitarian actors. Model predictors, drawn from existing data, included livelihood typology, staple cereal price, vaccination geocoverage, and humanitarian actor presence. To project accurate death tolls, we reconstructed population denominators based on forced displacement. We used the model and population estimates to project mortality under observed conditions and varying assumed counterfactual conditions, had there been no crisis, with the difference providing excess mortality. Death rates were highly elevated across most ground surveys, with net negative household migration. Between April 2016 and December 2019, we projected 490,000 excess deaths (230,000 children under 5 y) in the most likely counterfactual scenario, with a range from 90,000 (best-case) to 550,000 (worst-case). Death rates were two to three times higher than counterfactual levels, double the projected national rate, and highest in 2016 to 2017. Despite limited scope (we could not study the situation before 2016 or in neighboring affected countries), our findings suggest a staggering health impact of this crisis. Further studies to document mortality in this and other crises are needed to guide decision-making and memorialize their human toll.
MeSH term(s)	Child ; Humans ; Nigeria/epidemiology ; Seizures ; Vaccination ; Forecasting ; Armed Conflicts
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2217601120
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Article ; Online: The health needs of refugees from Ukraine.

Murphy, Adrianna / Fuhr, Daniela / Roberts, Bayard / Jarvis, Christopher I / Tarasenko, Anna / McKee, Martin

BMJ (Clinical research ed.)

2022 Volume 377, Page(s) o864

MeSH term(s)	Health Services Accessibility ; Health Services Needs and Demand ; Humans ; Refugees ; Socioeconomic Factors ; Ukraine
Language	English
Publishing date	2022-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	1362901-3
ISSN	1756-1833 ; 0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
ISSN (online)	1756-1833
ISSN	0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
DOI	10.1136/bmj.o864
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Article ; Online: Inference is bliss: Simulation for power estimation for an observational study of a cholera outbreak intervention.

Ratnayake, Ruwan / Checchi, Francesco / Jarvis, Christopher I / Edmunds, W John / Finger, Flavio

PLoS neglected tropical diseases

2022 Volume 16, Issue 2, Page(s) e0010163

Abstract: Background: The evaluation of ring vaccination and other outbreak-containment interventions during severe and rapidly-evolving epidemics presents a challenge for the choice of a feasible study design, and subsequently, for the estimation of statistical ... ...

Abstract	Background: The evaluation of ring vaccination and other outbreak-containment interventions during severe and rapidly-evolving epidemics presents a challenge for the choice of a feasible study design, and subsequently, for the estimation of statistical power. To support a future evaluation of a case-area targeted intervention against cholera, we have proposed a prospective observational study design to estimate the association between the strength of implementation of this intervention across several small outbreaks (occurring within geographically delineated clusters around primary and secondary cases named 'rings') and its effectiveness (defined as a reduction in cholera incidence). We describe here a strategy combining mathematical modelling and simulation to estimate power for a prospective observational study. Methodology and principal findings: The strategy combines stochastic modelling of transmission and the direct and indirect effects of the intervention in a set of rings, with a simulation of the study analysis on the model results. We found that targeting 80 to 100 rings was required to achieve power ≥80%, using a basic reproduction number of 2.0 and a dispersion coefficient of 1.0-1.5. Conclusions: This power estimation strategy is feasible to implement for observational study designs which aim to evaluate outbreak containment for other pathogens in geographically or socially defined rings.
MeSH term(s)	Basic Reproduction Number ; Cholera/epidemiology ; Computer Simulation ; Disease Outbreaks ; Humans ; Models, Theoretical ; Prospective Studies
Language	English
Publishing date	2022-02-16
Publishing country	United States
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0010163
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Article ; Online: Inference is bliss

Ruwan Ratnayake / Francesco Checchi / Christopher I Jarvis / W John Edmunds / Flavio Finger

PLoS Neglected Tropical Diseases, Vol 16, Iss 2, p e

Simulation for power estimation for an observational study of a cholera outbreak intervention.

2022 Volume 0010163

Abstract: Background The evaluation of ring vaccination and other outbreak-containment interventions during severe and rapidly-evolving epidemics presents a challenge for the choice of a feasible study design, and subsequently, for the estimation of statistical ... ...

Abstract	Background The evaluation of ring vaccination and other outbreak-containment interventions during severe and rapidly-evolving epidemics presents a challenge for the choice of a feasible study design, and subsequently, for the estimation of statistical power. To support a future evaluation of a case-area targeted intervention against cholera, we have proposed a prospective observational study design to estimate the association between the strength of implementation of this intervention across several small outbreaks (occurring within geographically delineated clusters around primary and secondary cases named 'rings') and its effectiveness (defined as a reduction in cholera incidence). We describe here a strategy combining mathematical modelling and simulation to estimate power for a prospective observational study. Methodology and principal findings The strategy combines stochastic modelling of transmission and the direct and indirect effects of the intervention in a set of rings, with a simulation of the study analysis on the model results. We found that targeting 80 to 100 rings was required to achieve power ≥80%, using a basic reproduction number of 2.0 and a dispersion coefficient of 1.0-1.5. Conclusions This power estimation strategy is feasible to implement for observational study designs which aim to evaluate outbreak containment for other pathogens in geographically or socially defined rings.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Subject code	310
Language	English
Publishing date	2022-02-01T00:00:00Z
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: Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys

Prestige, Em / Coletti, Pietro / Backer, Jantien A. / Davies, Nicholas J. / Edmunds, W. John / Jarvis, Christopher I.

medRxiv

Abstract: During the COVID-19 pandemic, aggregated mobility data was frequently used to estimate changing social contact rates. By taking contact matrices estimated pre-pandemic, and transforming these using pandemic–era mobility data, epidemiologists attempted to ...

Abstract	During the COVID-19 pandemic, aggregated mobility data was frequently used to estimate changing social contact rates. By taking contact matrices estimated pre-pandemic, and transforming these using pandemic–era mobility data, epidemiologists attempted to predict the number of contacts individuals were expected to have during large-scale restrictions. This study explores the most effective method for this transformation, comparing it to the accuracy of pandemic–era contact surveys. We compared four methods for scaling synthetic contact matrices: two using fitted regression models and two using ″na&iumlve″ mobility or mobility squared models. The regression models were fitted using CoMix contact survey and Google mobility data from the UK over March 2020 – March 2021. The four models were then used to scale synthetic contact matrices—a representation of pre–pandemic behaviour—using mobility data from the UK, Belgium and the Netherlands to predict the number of contacts expected in ″work″ and ″other″ settings for a given mobility level. We then compared partial reproduction numbers estimated from the four models with those calculated directly from CoMix contact matrices across the three countries. The accuracy of each model was assessed using root mean squared error. The fitted regression models had substantially more accurate predictions than the na&iumlve models, even when the regression models were applied to Belgium and the Netherlands. Across all countries investigated, the na&iumlve model using mobility alone was the least accurate, followed by the na&iumlve model using mobility squared. When attempting to estimate social contact rates during a pandemic without the resources available to conduct contact surveys, using a model fitted to data from another pandemic context is likely to be an improvement over using a ″na&iumlve″ model based on raw mobility data. If a na&iumlve model is to be used, mobility squared may be a better predictor of contact rates than mobility per se.
Keywords	covid19
Language	English
Publishing date	2023-12-19
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.12.19.23300209
Database	COVID19

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Article ; Online: Spatial connectivity in mosquito-borne disease models: a systematic review of methods and assumptions.

Lee, Sophie A / Jarvis, Christopher I / Edmunds, W John / Economou, Theodoros / Lowe, Rachel

Journal of the Royal Society, Interface

2021 Volume 18, Issue 178, Page(s) 20210096

Abstract: Spatial connectivity plays an important role in mosquito-borne disease transmission. Connectivity can arise for many reasons, including shared environments, vector ecology and human movement. This systematic review synthesizes the spatial methods used to ...

Abstract	Spatial connectivity plays an important role in mosquito-borne disease transmission. Connectivity can arise for many reasons, including shared environments, vector ecology and human movement. This systematic review synthesizes the spatial methods used to model mosquito-borne diseases, their spatial connectivity assumptions and the data used to inform spatial model components. We identified 248 papers eligible for inclusion. Most used statistical models (84.2%), although mechanistic are increasingly used. We identified 17 spatial models which used one of four methods (spatial covariates, local regression, random effects/fields and movement matrices). Over 80% of studies assumed that connectivity was distance-based despite this approach ignoring distant connections and potentially oversimplifying the process of transmission. Studies were more likely to assume connectivity was driven by human movement if the disease was transmitted by an
MeSH term(s)	Aedes ; Animals ; Dengue ; Humans ; Models, Statistical ; Mosquito Vectors ; Vector Borne Diseases
Language	English
Publishing date	2021-05-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0096
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Article ; Online: The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment.

Jarvis, Christopher I / Gimma, Amy / van Zandvoort, Kevin / Wong, Kerry L M / Edmunds, W John

BMC medicine

2021 Volume 19, Issue 1, Page(s) 52

Abstract: Background: England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10 pm closing for bars and ... ...

Abstract	Background: England's COVID-19 response transitioned from a national lockdown to localised interventions. In response to rising cases, these were supplemented by national restrictions on contacts (the Rule of Six), then 10 pm closing for bars and restaurants, and encouragement to work from home. These were quickly followed by a 3-tier system applying different restrictions in different localities. As cases continued to rise, a second national lockdown was declared. We used a national survey to quantify the impact of these restrictions on epidemiologically relevant contacts. Methods: We compared paired measures on setting-specific contacts before and after each restriction started and tested for differences using paired permutation tests on the mean change in contacts and the proportion of individuals decreasing their contacts. Results: Following the imposition of each measure, individuals tended to report fewer contacts than they had before. However, the magnitude of the changes was relatively small and variable. For instance, although early closure of bars and restaurants appeared to have no measurable effect on contacts, the work from home directive reduced mean daily work contacts by 0.99 (95% confidence interval CI] 0.03-1.94), and the Rule of Six reduced non-work and school contacts by a mean of 0.25 (0.01-0.5) per day. Whilst Tier 3 appeared to also reduce non-work and school contacts, the evidence for an effect of the lesser restrictions (Tiers 1 and 2) was much weaker. There may also have been some evidence of saturation of effects, with those who were in Tier 1 (least restrictive) reducing their contacts markedly when they entered lockdown, which was not reflected in similar changes in those who were already under tighter restrictions (Tiers 2 and 3). Conclusions: The imposition of various local and national measures in England during the summer and autumn of 2020 has gradually reduced contacts. However, these changes are smaller than the initial lockdown in March. This may partly be because many individuals were already starting from a lower number of contacts.
MeSH term(s)	Adolescent ; Adult ; Aged ; COVID-19/epidemiology ; COVID-19/prevention & control ; Child ; Child, Preschool ; England/epidemiology ; Female ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; Middle Aged ; Physical Distancing ; Quarantine/trends ; Schools/trends ; Workplace ; Young Adult
Language	English
Publishing date	2021-02-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2131669-7
ISSN	1741-7015 ; 1741-7015
ISSN (online)	1741-7015
ISSN	1741-7015
DOI	10.1186/s12916-021-01924-7
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Article ; Online: Pregnancy during COVID-19: social contact patterns and vaccine coverage of pregnant women from CoMix in 19 European countries.

Wong, Kerry L M / Gimma, Amy / Paixao, Enny S / Faes, Christel / Beutels, Philippe / Hens, Niel / Jarvis, Christopher I / Edmunds, W John

BMC pregnancy and childbirth

2022 Volume 22, Issue 1, Page(s) 757

Abstract: Background: Evidence and advice for pregnant women evolved during the COVID-19 pandemic. We studied social contact behaviour and vaccine uptake in pregnant women between March 2020 and September 2021 in 19 European countries.: Methods: In each ... ...

Abstract	Background: Evidence and advice for pregnant women evolved during the COVID-19 pandemic. We studied social contact behaviour and vaccine uptake in pregnant women between March 2020 and September 2021 in 19 European countries. Methods: In each country, repeated online survey data were collected from a panel of nationally-representative participants. We calculated the adjusted mean number of contacts reported with an individual-level generalized additive mixed model, modelled using the negative binomial distribution and a log link function. Mean proportion of people in isolation or quarantine, and vaccination coverage by pregnancy status and gender were calculated using a clustered bootstrap. Findings: We recorded 4,129 observations from 1,041 pregnant women, and 115,359 observations from 29,860 non-pregnant individuals aged 18-49. Pregnant women made slightly fewer contacts (3.6, 95%CI = 3.5-3.7) than non-pregnant women (4.0, 95%CI = 3.9-4.0), driven by fewer work contacts but marginally more contacts in non-essential social settings. Approximately 15-20% pregnant and 5% of non-pregnant individuals reported to be in isolation and quarantine for large parts of the study period. COVID-19 vaccine coverage was higher in pregnant women than in non-pregnant women between January and April 2021. Since May 2021, vaccination in non-pregnant women began to increase and surpassed that in pregnant women. Interpretation: Limited social contact to avoid pathogen exposure during the COVID-19 pandemic has been a challenge to many, especially women going through pregnancy. More recognition of maternal social support desire is needed in the ongoing pandemic. As COVID-19 vaccination continues to remain an important pillar of outbreak response, strategies to promote correct information can provide reassurance and facilitate informed pregnancy vaccine decisions in this vulnerable group.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Vaccines/therapeutic use ; Female ; Humans ; Pandemics/prevention & control ; Pregnancy ; Pregnant Women ; Vaccination ; Vaccines
Chemical Substances	COVID-19 Vaccines ; Vaccines
Language	English
Publishing date	2022-10-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2059869-5
ISSN	1471-2393 ; 1471-2393
ISSN (online)	1471-2393
ISSN	1471-2393
DOI	10.1186/s12884-022-05076-1
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Article ; Online: COVID-19: a need for real-time monitoring of weekly excess deaths.

Leon, David A / Shkolnikov, Vladimir M / Smeeth, Liam / Magnus, Per / Pechholdová, Markéta / Jarvis, Christopher I

Lancet (London, England)

2020 Volume 395, Issue 10234, Page(s) e81

MeSH term(s)	Betacoronavirus ; COVID-19 ; Computer Systems ; Coronavirus Infections/mortality ; Data Collection ; Humans ; Information Dissemination ; Mortality/trends ; Pandemics ; Pneumonia, Viral/mortality ; Population Surveillance ; Public Health ; Publishing ; SARS-CoV-2 ; Time Factors
Keywords	covid19
Language	English
Publishing date	2020-04-22
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
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)30933-8
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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)
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Article ; Online: Characterising social contacts under COVID-19 control measures in Africa.

Dobreva, Zlatina / Gimma, Amy / Rohan, Hana / Djoudalbaye, Benjamin / Tshangela, Akhona / Jarvis, Christopher I / van Zandvoort, Kevin / Quaife, Matthew

BMC medicine

2022 Volume 20, Issue 1, Page(s) 344

Abstract: Background: Early in the COVID-19 pandemic, countries adopted non-pharmaceutical interventions (NPIs) such as lockdowns to limit SARS-CoV-2 transmission. Social contact studies help measure the effectiveness of NPIs and estimate parameters for modelling ...

Abstract	Background: Early in the COVID-19 pandemic, countries adopted non-pharmaceutical interventions (NPIs) such as lockdowns to limit SARS-CoV-2 transmission. Social contact studies help measure the effectiveness of NPIs and estimate parameters for modelling SARS-CoV-2 transmission. However, few contact studies have been conducted in Africa. Methods: We analysed nationally representative cross-sectional survey data from 19 African Union Member States, collected by the Partnership for Evidence-based Responses to COVID-19 (PERC) via telephone interviews at two time points (August 2020 and February 2021). Adult respondents reported contacts made in the previous day by age group, demographic characteristics, and their attitudes towards COVID-19. We described mean and median contacts across these characteristics and related contacts to Google Mobility reports and the Oxford Government Response Stringency Index for each country at the two time points. Results: Mean reported contacts varied across countries with the lowest reported in Ethiopia (9, SD=16, median = 4, IQR = 8) in August 2020 and the highest in Sudan (50, SD=53, median = 33, IQR = 40) in February 2021. Contacts of people aged 18-55 represented 50% of total contacts, with most contacts in household and work or study settings for both surveys. Mean contacts increased for Ethiopia, Ghana, Liberia, Nigeria, Sudan, and Uganda and decreased for Cameroon, the Democratic Republic of Congo (DRC), and Tunisia between the two time points. Men had more contacts than women and contacts were consistent across urban or rural settings (except in Cameroon and Kenya, where urban respondents had more contacts than rural ones, and in Senegal and Zambia, where the opposite was the case). There were no strong and consistent variations in the number of mean or median contacts by education level, self-reported health, perceived self-reported risk of infection, vaccine acceptance, mask ownership, and perceived risk of COVID-19 to health. Mean contacts were correlated with Google mobility (coefficient 0.57, p=0.051 and coefficient 0.28, p=0.291 in August 2020 and February 2021, respectively) and Stringency Index (coefficient -0.12, p = 0.304 and coefficient -0.33, p=0.005 in August 2020 and February 2021, respectively). Conclusions: These are the first COVID-19 social contact data collected for 16 of the 19 countries surveyed. We find a high reported number of daily contacts in all countries and substantial variations in mean contacts across countries and by gender. Increased stringency and decreased mobility were associated with a reduction in the number of contacts. These data may be useful to understand transmission patterns, model infection transmission, and for pandemic planning.
MeSH term(s)	Adult ; COVID-19/epidemiology ; COVID-19/prevention & control ; Communicable Disease Control ; Cross-Sectional Studies ; Female ; Humans ; Male ; Nigeria ; Pandemics/prevention & control ; SARS-CoV-2
Language	English
Publishing date	2022-10-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2131669-7
ISSN	1741-7015 ; 1741-7015
ISSN (online)	1741-7015
ISSN	1741-7015
DOI	10.1186/s12916-022-02543-6
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