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Article ; Online: Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences.

Tran-Kiem, Cécile / Bedford, Trevor

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

2024 Volume 121, Issue 15, Page(s) e2305299121

Abstract: Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction ... ...

Abstract	Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction number
MeSH term(s)	Humans ; Phylogeny ; Communicable Diseases ; Contact Tracing
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2305299121
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Book ; Online: Code and data for

Salje, Henrik / Tran Kiem, Cécile

Estimating the burden of SARS-CoV-2 in France

2020

Abstract: Code used for the inference of the probability of hospitalization and death by age and sex and the implementation and calibration of the transmission model of COVID-19 in the french population (Salje et al., Science, 2020). Aggregated hospitalization ... ...

Abstract	Code used for the inference of the probability of hospitalization and death by age and sex and the implementation and calibration of the transmission model of COVID-19 in the french population (Salje et al., Science, 2020). Aggregated hospitalization data for France used for the calibration of those models are also made available.
Keywords	covid19
Language	English
Publishing date	2020-05-13
Publishing country	eu
Document type	Book ; Online
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Book ; Online: Code and data for

Salje, Henrik / Tran Kiem, Cécile

Estimating the burden of SARS-CoV-2 in France

2020

Abstract	Code used for the inference of the probability of hospitalization and death by age and sex and the implementation and calibration of the transmission model of COVID-19 in the french population (Salje et al., Science, 2020). Aggregated hospitalization data for France used for the calibration of those models are also made available. Update to account for patients outcome on the Diamond Princess cruise ship.
Keywords	covid19
Language	English
Publishing date	2020-05-13
Publishing country	eu
Document type	Book ; Online
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Article ; Online: Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic.

Paredes, Miguel I / Ahmed, Nashwa / Figgins, Marlin / Colizza, Vittoria / Lemey, Philippe / McCrone, John T / Müller, Nicola / Tran-Kiem, Cécile / Bedford, Trevor

Cell

2024 Volume 187, Issue 6, Page(s) 1374–1386.e13

Abstract: The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and ... ...

Abstract	The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
MeSH term(s)	Humans ; Communicable Diseases, Emerging ; Disease Outbreaks ; Epidemics ; Mpox (monkeypox)/epidemiology ; Mpox (monkeypox)/transmission ; Mpox (monkeypox)/virology ; Public Health ; Monkeypox virus/physiology
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2024.02.003
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Zs.A 1167: 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)
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Article ; Online: Epidemiology and control of SARS-CoV-2 epidemics in partially vaccinated populations: a modeling study applied to France.

Bosetti, Paolo / Tran Kiem, Cécile / Andronico, Alessio / Colizza, Vittoria / Yazdanpanah, Yazdan / Fontanet, Arnaud / Benamouzig, Daniel / Cauchemez, Simon

BMC medicine

2022 Volume 20, Issue 1, Page(s) 33

Abstract: Background: Vaccination is expected to change the epidemiology and management of SARS-CoV-2 epidemics.: Methods: We used an age-stratified compartmental model calibrated to French data to anticipate these changes and determine implications for the ... ...

Abstract	Background: Vaccination is expected to change the epidemiology and management of SARS-CoV-2 epidemics. Methods: We used an age-stratified compartmental model calibrated to French data to anticipate these changes and determine implications for the control of an autumn epidemic. We assumed vaccines reduce the risk of hospitalization, infection, and transmission if infected by 95%, 60%, and 50%, respectively. Results: In our baseline scenario characterized by basic reproduction number R Conclusions: With the Delta variant, vaccinated individuals are well protected against hospitalization but remain at risk of infection and should therefore apply protective behaviors (e.g., mask-wearing). Targeting non-vaccinated individuals may maximize epidemic control while minimizing costs for society. Vaccinating children protects them from the deleterious effects of non-pharmaceutical measures. Control strategies should account for the changing SARS-CoV-2 epidemiology.
MeSH term(s)	Adolescent ; Adult ; COVID-19 ; COVID-19 Vaccines ; Child ; Child, Preschool ; Epidemics ; Epidemiological Models ; France/epidemiology ; Humans ; Infant ; Infant, Newborn ; Middle Aged ; SARS-CoV-2
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-01-26
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/s12916-022-02235-1
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Article ; Online: Impact of booster vaccination on the control of COVID-19 Delta wave in the context of waning immunity: application to France in the winter 2021/22.

Bosetti, Paolo / Tran Kiem, Cécile / Andronico, Alessio / Paireau, Juliette / Levy-Bruhl, Daniel / Alter, Lise / Fontanet, Arnaud / Cauchemez, Simon

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2022 Volume 27, Issue 1

Abstract: Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak ... ...

Abstract	Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak by 25%, 36% and 43% respectively, with a delay of 5 months between second and third dose. A 10% reduction in transmission rates might further reduce it by 41%, indicating that even small increases in protective behaviours may be critical to mitigate the wave.
MeSH term(s)	COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; France/epidemiology ; Humans ; Immunization, Secondary ; SARS-CoV-2 ; Seasons ; Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-01-06
Publishing country	Sweden
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2022.27.1.2101125
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Article ; Online: How do i bite thee? let me count the ways: Exploring the implications of individual biting habits of Aedes aegypti for dengue transmission.

Christofferson, Rebecca C / Wearing, Helen J / Turner, Erik A / Walsh, Christine S / Salje, Henrik / Tran-Kiem, Cécile / Cauchemez, Simon

PLoS neglected tropical diseases

2022 Volume 16, Issue 10, Page(s) e0010818

Abstract: In models of mosquito-borne transmission, the mosquito biting rate is an influential parameter, and understanding the heterogeneity of the process of biting is important, as biting is usually assumed to be relatively homogeneous across individuals, with ... ...

Abstract	In models of mosquito-borne transmission, the mosquito biting rate is an influential parameter, and understanding the heterogeneity of the process of biting is important, as biting is usually assumed to be relatively homogeneous across individuals, with time-between-bites described by an exponentially distributed process. However, these assumptions have not been addressed through laboratory experimentation. We experimentally investigated the daily biting habits of Ae. aegypti at three temperatures (24°C, 28°C, and 32°C) and determined that there was individual heterogeneity in biting habits (number of bites, timing of bites, etc.). We further explored the consequences of biting heterogeneity using an individual-based model designed to examine whether a particular biting profile determines whether a mosquito is more or less likely to 1) become exposed given a single index case of dengue (DENV) and 2) transmit to a susceptible human individual. Our experimental results indicate that there is heterogeneity among individuals and among temperature treatments. We further show that this results in altered probabilities of transmission of DENV to and from individual mosquitoes based on biting profiles. While current model representation of biting may work under some conditions, it might not uniformly be the best fit for this process. Our data also confirm that biting is a non-monotonic process with temperatures around 28°C being optimum.
MeSH term(s)	Aedes ; Animals ; Dengue ; Dengue Virus ; Habits ; Humans ; Mosquito Vectors
Language	English
Publishing date	2022-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0010818
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Article: Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic.

Paredes, Miguel I / Ahmed, Nashwa / Figgins, Marlin / Colizza, Vittoria / Lemey, Philippe / McCrone, John T / Müller, Nicola / Tran-Kiem, Cécile / Bedford, Trevor

medRxiv : the preprint server for health sciences

2023

Abstract	The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case-reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
Language	English
Publishing date	2023-12-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.27.23293266
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Article ; Online: Lockdown as a last resort option in case of COVID-19 epidemic rebound: a modelling study.

Tran Kiem, Cécile / Crépey, Pascal / Bosetti, Paolo / Levy Bruhl, Daniel / Yazdanpanah, Yazdan / Salje, Henrik / Boëlle, Pierre-Yves / Cauchemez, Simon

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2021 Volume 26, Issue 22

Abstract: BackgroundGiven its high economic and societal cost, policymakers might be reluctant to implement a large-scale lockdown in case of coronavirus disease (COVID-19) epidemic rebound. They may consider it as a last resort option if alternative control ... ...

Abstract	BackgroundGiven its high economic and societal cost, policymakers might be reluctant to implement a large-scale lockdown in case of coronavirus disease (COVID-19) epidemic rebound. They may consider it as a last resort option if alternative control measures fail to reduce transmission.AimWe developed a modelling framework to ascertain the use of lockdown to ensure intensive care unit (ICU) capacity does not exceed a peak target defined by policymakers.MethodsWe used a deterministic compartmental model describing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the trajectories of COVID-19 patients in healthcare settings, accounting for age-specific mixing patterns and an increasing probability of severe outcomes with age. The framework is illustrated in the context of metropolitan France.ResultsThe daily incidence of ICU admissions and the number of occupied ICU beds are the most robust indicators to decide when a lockdown should be triggered. When the doubling time of hospitalisations estimated before lockdown is between 8 and 20 days, lockdown should be enforced when ICU admissions reach 3.0-3.7 and 7.8-9.5 per million for peak targets of 62 and 154 ICU beds per million (4,000 and 10,000 beds for metropolitan France), respectively. When implemented earlier, the lockdown duration required to get back below a desired level is also shorter.ConclusionsWe provide simple indicators and triggers to decide if and when a last-resort lockdown should be implemented to avoid saturation of ICU. These metrics can support the planning and real-time management of successive COVID-19 pandemic waves.
MeSH term(s)	COVID-19 ; Communicable Disease Control ; France/epidemiology ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2021-06-03
Publishing country	Sweden
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2021.26.22.2001536
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Article ; Online: Modelling the end of a Zero-COVID strategy using nirmatrelvir/ritonavir, vaccination and NPIs in Wallis and Futuna.

Brault, Antoine / Tran-Kiem, Cécile / Couteaux, Clément / Olié, Valérie / Paireau, Juliette / Yazdanpanah, Yazdan / Ghosn, Jade / Martin-Blondel, Guillaume / Bosetti, Paolo / Cauchemez, Simon

The Lancet regional health. Western Pacific

2022 Volume 30, Page(s) 100634

Abstract: Background: Ending Zero-COVID is challenging, particularly when vaccine coverage is low. Considering Wallis and Futuna, a French Zero-COVID territory affected by reluctance to vaccination, low immunity and high levels of comorbidities, we investigate ... ...

Abstract	Background: Ending Zero-COVID is challenging, particularly when vaccine coverage is low. Considering Wallis and Futuna, a French Zero-COVID territory affected by reluctance to vaccination, low immunity and high levels of comorbidities, we investigate how targeted use of nirmatrelvir/ritonavir (brand name Paxlovid) can complement vaccination and non-pharmaceutical interventions (NPIs), and mitigate the epidemic rebound expected when Zero-COVID ends. Methods: We developed a discrete age-stratified compartmental model describing SARS-CoV-2 spread and healthcare impact once Wallis and Futuna reopens. It accounts for comorbidity risk groups (CRG), vaccine coverage (2 doses, 3 doses), the effectiveness of vaccines (recent or old injection), treatments and NPIs. In our baseline scenario, cases aged 65+ in intermediate/high CRG and 40+ in high CRG are eligible for treatment. Findings: The epidemic is expected to start 13-20 days after reopening with a doubling time of 1.6-3.7 days. For medium transmission intensity (R Interpretation: Modelling suggests that test and treat may contribute to the mitigation of epidemic rebounds at the end of Zero-COVID, particularly in populations with low immunity and high levels of comorbidities. Funding: RECOVER, VEO, AXA, Groupama, SpF, IBEID, INCEPTION, EMERGEN.
Language	English
Publishing date	2022-11-14
Publishing country	England
Document type	Journal Article
ISSN	2666-6065
ISSN (online)	2666-6065
DOI	10.1016/j.lanwpc.2022.100634
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