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Article ; Online: Why development of outbreak analytics tools should be valued, supported, and funded.

Jombart, Thibaut

2021 Volume 21, Issue 4, Page(s) 458–459

MeSH term(s)	COVID-19/epidemiology ; Data Analysis ; Decision Making, Organizational ; Decision Support Techniques ; Disease Outbreaks/prevention & control ; Disease Outbreaks/statistics & numerical data ; Epidemiological Monitoring ; Humans ; Preventive Health Services/economics ; Preventive Health Services/organization & administration ; Software/economics
Language	English
Publishing date	2021-01-11
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(20)30996-8
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Book ; Online: Extended data for

Thibaut Jombart

Inferring the number of COVID-19 cases from recently reported deaths

2020

Abstract: Supplementary material for the paper: Inferring the number of COVID-19 cases from recently reported ... ...

Abstract	Supplementary material for the paper: Inferring the number of COVID-19 cases from recently reported deaths
Keywords	covid19
Language	English
Publishing date	2020-03-30
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic.

Evans, Beth / Jombart, Thibaut

Vaccine

2022 Volume 40, Issue 26, Page(s) 3531–3535

Abstract: Whilst COVID-19 vaccination strategies continue to receive considerable emphasis worldwide, the extent to which routine immunisation (RI) has been impacted during the first year of the pandemic remains unclear. Understanding the existence, extent, and ... ...

Abstract	Whilst COVID-19 vaccination strategies continue to receive considerable emphasis worldwide, the extent to which routine immunisation (RI) has been impacted during the first year of the pandemic remains unclear. Understanding the existence, extent, and variations in RI disruptions globally may help inform policy and resource prioritisation as the pandemic continues. We modelled historical, country-specific RI trends using publicly available vaccination coverage data for diphtheria, tetanus and pertussis-containing vaccine first-dose (DTP1) and third-dose (DTP3) from 2000 to 2019. We report a 2·9% (95 %
MeSH term(s)	COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Vaccines ; Diphtheria-Tetanus-Pertussis Vaccine ; Global Health ; Humans ; Infant ; Pandemics/prevention & control ; Vaccination ; Vaccination Coverage
Chemical Substances	COVID-19 Vaccines ; Diphtheria-Tetanus-Pertussis Vaccine
Language	English
Publishing date	2022-01-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2022.01.044
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Article ; Online: Assessing the feasibility of Phase 3 vaccine trials against Marburg Virus Disease: A modelling study.

Qian, George Y / Jombart, Thibaut / John Edmunds, W

Vaccine: X

2023 Volume 14, Page(s) 100321

Abstract: Background: Outbreaks of Marburg virus disease (MVD) are rare and small in size, with only 18 recorded outbreaks since 1967, only two of which involved more than 100 cases. It has been proposed, therefore, that Phase 3 trials for MVD vaccines should be ... ...

Abstract	Background: Outbreaks of Marburg virus disease (MVD) are rare and small in size, with only 18 recorded outbreaks since 1967, only two of which involved more than 100 cases. It has been proposed, therefore, that Phase 3 trials for MVD vaccines should be held open over multiple outbreaks until sufficient end points accrue to enable vaccine efficacy (VE) to be calculated. Here we estimate how many outbreaks might be needed for VE to be estimated. Methods: We adapt a mathematical model of MVD transmission to simulate a Phase 3 individually randomised placebo controlled vaccine trial. We assume in the base case that vaccine efficacy is 70% and that 50% of individuals in affected areas are enrolled into the trial (1:1 randomisation). We further assume that the vaccine trial starts two weeks after public health interventions are put in place and that cases occurring within 10 days of vaccination are not included in VE calculations. Results: The median size of simulated outbreaks was 2 cases. Only 0.3% of simulated outbreaks were predicted to have more than 100 MVD cases. 95% of simulated outbreaks terminated before cases accrued in the placebo and vaccine arms. Therefore the number of outbreaks required to estimate VE was large: after 100 outbreaks, the estimated VE was 69% but with considerable uncertainty (95% CIs: 0%-100%) while the estimated VE after 200 outbreaks was 67% (95% CIs: 42%-85%). Altering base-case assumptions made little difference to the findings. In a sensitivity analysis, increasing Conclusions: It is unlikely that the efficacy of any candidate vaccine can be calculated before more MVD outbreaks have occurred than have been recorded to date. This is because MVD outbreaks tend to be small, public health interventions have been historically effective at reducing transmission, and vaccine trials are only likely to start after these interventions are already in place. Hence, it is expected that outbreaks will terminate before, or shortly after, cases start to accrue in the vaccine and placebo arms.
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article
ISSN	2590-1362
ISSN (online)	2590-1362
DOI	10.1016/j.jvacx.2023.100321
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analysis of global routine immunisation coverage shows disruption and stagnation during the first two-years of the COVID-19 pandemic with tentative recovery in 2022.

Evans, Beth / Keiser, Olivia / Kaiser, Laurent / Jombart, Thibaut

Vaccine: X

2023 Volume 15, Page(s) 100383

Abstract: Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020, and further so in 2021, the extent of continued interruptions in 2022 and/or rebounds to previous trends remains unclear. We modelled ... ...

Abstract	Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020, and further so in 2021, the extent of continued interruptions in 2022 and/or rebounds to previous trends remains unclear. We modelled country-specific RI trends using validated estimates of national coverage from the World Health Organisation and United Nation Children's Fund for 182 countries (accounting for > 97% of children globally), to project expected diphtheria, tetanus, and pertussis-containing vaccine first-dose (DTP1), third-dose (DTP3) and measles-containing vaccine first-dose (MCV1) coverage for 2020-2022 based on pre-pandemic trends (from 2000 to 2019). We provide further evidence of peak pandemic immunisation disruption in 2021, followed by tentative recovery in 2022. We report a 3.4% (95 %CI: [2.5%; 4.4%]) decline in global DTP3 coverage in 2021 compared to 2000-2019 trends, from an expected 89.8% to reported 86.4%. This coverage gap reduced to a 2.7% (95 %CI: [1.8%; 3.6%]) decline in 2022, with reported coverage rising to 87.2%. Similar results were seen for DTP1 and MCV1. Whilst partial rebounds are encouraging, global coverage decline translates to a 17-year setback in RI to 2005 levels, and the majority of countries retain coverage at or lower than pre-pandemic levels. The Americas, Africa, and Asia were the most impacted regions; and low- and middle-income countries the most affected income groups. The number of annual Zero Dose (ZD) children - indicating those receiving no immunisations - increased from 12.1 million (M) globally in 2019 to a peak of 16.7 M in 2021, then reduced to 13.1 M in 2022. Overall, we estimate an excess of 8.8 M ZD children cumulatively in 2020-2022 compared to pre-pandemic levels. This work can be used as an objective baseline to inform future interventions to prioritise and target interventions, and facilitate catch-up of growing populations of under- and un-immunised children.
Language	English
Publishing date	2023-09-06
Publishing country	England
Document type	Journal Article
ISSN	2590-1362
ISSN (online)	2590-1362
DOI	10.1016/j.jvacx.2023.100383
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A mathematical model of Marburg virus disease outbreaks and the potential role of vaccination in control.

Qian, George Y / Edmunds, W John / Bausch, Daniel G / Jombart, Thibaut

BMC medicine

2023 Volume 21, Issue 1, Page(s) 439

Abstract: Background: Marburg virus disease is an acute haemorrhagic fever caused by Marburg virus. Marburg virus is zoonotic, maintained in nature in Egyptian fruit bats, with occasional spillover infections into humans and nonhuman primates. Although rare, ... ...

Abstract	Background: Marburg virus disease is an acute haemorrhagic fever caused by Marburg virus. Marburg virus is zoonotic, maintained in nature in Egyptian fruit bats, with occasional spillover infections into humans and nonhuman primates. Although rare, sporadic cases and outbreaks occur in Africa, usually associated with exposure to bats in mines or caves, and sometimes with secondary human-to-human transmission. Outbreaks outside of Africa have also occurred due to importation of infected monkeys. Although all previous Marburg virus disease outbreaks have been brought under control without vaccination, there is nevertheless the potential for large outbreaks when implementation of public health measures is not possible or breaks down. Vaccines could thus be an important additional tool, and development of several candidate vaccines is under way. Methods: We developed a branching process model of Marburg virus transmission and investigated the potential effects of several prophylactic and reactive vaccination strategies in settings driven primarily by multiple spillover events as well as human-to-human transmission. Linelist data from the 15 outbreaks up until 2022, as well as an Approximate Bayesian Computational framework, were used to inform the model parameters. Results: Our results show a low basic reproduction number which varied across outbreaks, from 0.5 [95% CI 0.05-1.8] to 1.2 [95% CI 1.0-1.9] but a high case fatality ratio. Of six vaccination strategies explored, the two prophylactic strategies (mass and targeted vaccination of high-risk groups), as well as a combination of ring and targeted vaccination, were generally most effective, with a probability of potential outbreaks being terminated within 1 year of 0.90 (95% CI 0.90-0.91), 0.89 (95% CI 0.88-0.90), and 0.88 (95% CI 0.87-0.89) compared with 0.68 (0.67-0.69) for no vaccination, especially if the outbreak is driven by zoonotic spillovers and the vaccination campaign initiated as soon as possible after onset of the first case. Conclusions: Our study shows that various vaccination strategies can be effective in helping to control outbreaks of MVD, with the best approach varying with the particular epidemiologic circumstances of each outbreak.
MeSH term(s)	Animals ; Humans ; Marburg Virus Disease/epidemiology ; Marburg Virus Disease/prevention & control ; Chiroptera ; Bayes Theorem ; Disease Outbreaks/prevention & control ; Vaccination ; Marburgvirus ; Models, Theoretical ; Vaccines
Chemical Substances	Vaccines
Language	English
Publishing date	2023-11-14
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/s12916-023-03108-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic

Evans, Beth / Jombart, Thibaut

Vaccine. 2022 Jan. 20,

2022

Abstract	Whilst COVID-19 vaccination strategies continue to receive considerable emphasis worldwide, the extent to which routine immunisation (RI) has been impacted during the first year of the pandemic remains unclear. Understanding the existence, extent, and variations in RI disruptions globally may help inform policy and resource prioritisation as the pandemic continues. We modelled historical, country-specific RI trends using publicly available vaccination coverage data for diphtheria, tetanus and pertussis-containing vaccine first-dose (DTP1) and third-dose (DTP3) from 2000 to 2019. We report a 2·9% (95 %CI: [2·2%; 3·6%]) global decline in DTP3 coverage from an expected 89·2% to a reported 86·3%; and a 2·2% decline in DTP1 coverage (95 %CI: [1·6%; 2·8%]). These declines translate to levels of coverage last observed in 2005, thus suggesting a potential 15-years setback in RI improvements. Further research is required to understand which factors – e.g., health seeking behaviours or non-pharmaceutical interventions – linked to the COVID-19 crisis impacted vaccination coverage.
Keywords	COVID-19 infection ; diphtheria ; issues and policy ; pandemic ; prioritization ; tetanus ; vaccination ; vaccines
Language	English
Dates of publication	2022-0120
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2022.01.044
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Time series analysis of routine immunisation coverage during the COVID-19 pandemic in 2021 shows continued global decline and increases in Zero Dose children

Evans, Beth / Keiser, Olivia / Kaiser, Laurent / Jombart, Thibaut

medRxiv

Abstract: Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020 compared to previous immunisation performance, the extent of continued interruptions in 2021 and/or rebounds to previous trends remains ... ...

Abstract	Whilst it is now widely recognised that routine immunisation (RI) was disrupted by the COVID-19 pandemic in 2020 compared to previous immunisation performance, the extent of continued interruptions in 2021 and/or rebounds to previous trends remains unclear, with sporadic surveys reporting signs of immunisation system recovery at the end of 2020. We modelled country-specific RI trends using validated estimates of national coverage from the World Health Organisation and United Nation Children9s Fund for over 160 countries, to project expected diphtheria, tetanus, and pertussis-containing vaccine first-dose (DTP1), third-dose (DTP3) and measles-containing vaccine first-dose (MCV1) coverage for 2021 based on pre-pandemic trends (from 2000-2019). We estimated a 3.6% (95%CI: [2.6%; 4.6%]) decline in global DTP3 coverage in 2021 compared to 2000-2019 trends, from an expected 90.1% to a reported 86.5% across 164 reporting countries, and similar results for DTP1 (2.8% decline; 95%CI: [2.0%; 3.6%]), and for MCV1 (3.8% decline; 95%CI: [4.8%; 2.7%]). 86.5% global coverage in 2021 represents a further decrease from that reported in 2020 and 2019, and translates to a 16-year setback in RI coverage, i.e., 2005 levels. Hypothesised and early signals of rebounds to pre-pandemic coverage were not seen in most countries. The Americas, Africa, and Asia were the most impacted regions, with low- and middle-income countries the most affected income groups. The number of Zero Dose children also continued to increase in 2021. DTP1 coverage declined worldwide from an expected 93.7% to a reported 90.9% (2.8% decline; 95%CI: [2.0%; 3.6%]) which translates into an additional 3.4 million Zero Dose children on top of an expected 11.0 million (30.9% increase) at the global level. We hope this work will provide an objective baseline to inform future interventions and prioritisation aiming to facilitate rebounds in coverage to previous levels and catch-up of growing populations of under- and un-immunised children.
Keywords	covid19
Language	English
Publishing date	2023-02-08
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2023.02.06.23285411
Database	COVID19

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Article ; Online: Modelling that shaped the early COVID-19 pandemic response in the UK.

Brooks-Pollock, Ellen / Danon, Leon / Jombart, Thibaut / Pellis, Lorenzo

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2021 Volume 376, Issue 1829, Page(s) 20210001

Abstract: Infectious disease modelling has played an integral part of the scientific evidence used to guide the response to the COVID-19 pandemic. In the UK, modelling evidence used for policy is reported to the Scientific Advisory Group for Emergencies (SAGE) ... ...

Abstract	Infectious disease modelling has played an integral part of the scientific evidence used to guide the response to the COVID-19 pandemic. In the UK, modelling evidence used for policy is reported to the Scientific Advisory Group for Emergencies (SAGE) modelling subgroup, SPI-M-O (Scientific Pandemic Influenza Group on Modelling-Operational). This Special Issue contains 20 articles detailing evidence that underpinned advice to the UK government during the SARS-CoV-2 pandemic in the UK between January 2020 and July 2020. Here, we introduce the UK scientific advisory system and how it operates in practice, and discuss how infectious disease modelling can be useful in policy making. We examine the drawbacks of current publishing practices and academic credit and highlight the importance of transparency and reproducibility during an epidemic emergency. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Humans ; Pandemics ; SARS-CoV-2/pathogenicity ; United Kingdom/epidemiology
Language	English
Publishing date	2021-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2021.0001
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Book ; Online: Inferring COVID-19 cases from recent death.

Thibaut Jombart / Sam Abbott / Amy Gimma / kevinvzandvoort / Chris

2020

Abstract: This release contains the first stable version of the app and the associated reportfactory describing the model. ...

Abstract	This release contains the first stable version of the app and the associated reportfactory describing the model.
Keywords	shiny ; R ; app ; COVID-19 ; covid19
Language	English
Publishing date	2020-03-30
Publishing country	eu
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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