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Article ; Online: Monitoring the reproductive number of COVID-19 in France: Comparative estimates from three datasets.

Bonaldi, Christophe / Fouillet, Anne / Sommen, Cécile / Lévy-Bruhl, Daniel / Paireau, Juliette

2023 Volume 18, Issue 10, Page(s) e0293585

Abstract: Background: The effective reproduction number (Rt) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of Rt during an outbreak is a major indicator used to monitor changes in ... ...

Abstract	Background: The effective reproduction number (Rt) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of Rt during an outbreak is a major indicator used to monitor changes in disease transmission and assess the effectiveness of interventions. The estimation of Rt usually requires the identification of infected cases in the population, which can prove challenging with the available data, especially when asymptomatic people or with mild symptoms are not usually screened. The purpose of this study was to perform sensitivity analysis of Rt estimates for COVID-19 surveillance in France based on three data sources with different sensitivities and specificities for identifying infected cases. Methods: We applied a statistical method developed by Cori et al. to estimate Rt using (1) confirmed cases identified from positive virological tests in the population, (2) suspected cases recorded by a national network of emergency departments, and (3) COVID-19 hospital admissions recorded by a national administrative system to manage hospital organization. Results: Rt estimates in France from May 27, 2020, to August 12, 2022, showed similar temporal trends regardless of the dataset. Estimates based on the daily number of confirmed cases provided an earlier signal than the two other sources, with an average lag of 3 and 6 days for estimates based on emergency department visits and hospital admissions, respectively. Conclusion: The COVID-19 experience confirmed that monitoring temporal changes in Rt was a key indicator to help the public health authorities control the outbreak in real time. However, gaining access to data on all infected people in the population in order to estimate Rt is not straightforward in practice. As this analysis has shown, the opportunity to use more readily available data to estimate Rt trends, provided that it is highly correlated with the spread of infection, provides a practical solution for monitoring the COVID-19 pandemic and indeed any other epidemic.
MeSH term(s)	Humans ; COVID-19/epidemiology ; Pandemics ; Basic Reproduction Number ; France/epidemiology ; Hospitalization
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0293585
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Two-dose measles vaccine effectiveness remains high over time: A French observational study, 2017-2019.

Franconeri, Léa / Antona, Denise / Cauchemez, Simon / Lévy-Bruhl, Daniel / Paireau, Juliette

Vaccine

2023 Volume 41, Issue 39, Page(s) 5797–5804

Abstract: Background: From 2008 to 2019, France has experienced a resurgence of measles epidemics. Surveillance data have shown that the proportion of cases vaccinated with two doses of measles-containing vaccine (MCV) increased with age, raising concerns about ... ...

Abstract	Background: From 2008 to 2019, France has experienced a resurgence of measles epidemics. Surveillance data have shown that the proportion of cases vaccinated with two doses of measles-containing vaccine (MCV) increased with age, raising concerns about the duration of vaccine protection. Our objectives were to investigate age-stratified vaccine effectiveness (VE) for the second dose of MCV (MCV2) and to quantify protection levels over time. Methods: We analyzed data on measles cases aged 2-31 years, reported via mandatory notification to the French measles surveillance system from October 2017 to September 2019. We estimated an age-stratified VE for MCV2 using the screening method, which compares the vaccination status of cases with that of the general population. We improved this method by accounting for natural immunity, exploring four scenarios with four possible levels of natural immunity in the population. In addition, we quantified the decay rate of protection over time, by fitting an exponential decay model among individuals vaccinated in early life. Results: In the baseline analysis (absence of natural immunity), VE estimates were high in all age groups and decreased with age, from 99.6 % (95 % confidence interval: 99.3-99.8) in 2-5 years old to 91.4 % (85.1-95.0) in 26-31 years old. Accounting for natural immunity increased VE in the older age group to 93.2-99.2 % depending on the scenario. We estimated that VE was slowly decreasing over time, with an exponential decay rate of 0.0022/year (0.0017-0.0028), leading to VE of 96.7 % (96.0-97.4) 16 years after MCV2 vaccination. This decline was most compatible with scenario 2, a scenario of 4.4 % naturally immunized, non-vaccinated individuals in the 26-31 years old. Conclusion: Our study confirms the continued high effectiveness of two doses of MCV with only slight degradation, decades after immunization. These findings support the importance of achieving a very high vaccination coverage with 2 doses of MCV.
MeSH term(s)	Humans ; Aged ; Child, Preschool ; Adult ; Measles Vaccine ; Vaccine Efficacy ; Measles/epidemiology ; Measles/prevention & control ; Epidemics ; France/epidemiology
Chemical Substances	Measles Vaccine
Language	English
Publishing date	2023-08-14
Publishing country	Netherlands
Document type	Observational Study ; 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.2023.08.018
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Article ; Online: Monitoring the reproductive number of COVID-19 in France

Christophe Bonaldi / Anne Fouillet / Cécile Sommen / Daniel Lévy-Bruhl / Juliette Paireau

PLoS ONE, Vol 18, Iss

Comparative estimates from three datasets

2023 Volume 10

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
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: Monitoring the reproductive number of COVID-19 in France

Christophe Bonaldi / Anne Fouillet / Cécile Sommen / Daniel Lévy-Bruhl / Juliette Paireau

PLoS ONE, Vol 18, Iss 10, p e

Comparative estimates from three datasets.

2023 Volume 0293585

Abstract: Background The effective reproduction number (Rt) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of Rt during an outbreak is a major indicator used to monitor changes in disease ...

Abstract	Background The effective reproduction number (Rt) quantifies the average number of secondary cases caused by one person with an infectious disease. Near-real-time monitoring of Rt during an outbreak is a major indicator used to monitor changes in disease transmission and assess the effectiveness of interventions. The estimation of Rt usually requires the identification of infected cases in the population, which can prove challenging with the available data, especially when asymptomatic people or with mild symptoms are not usually screened. The purpose of this study was to perform sensitivity analysis of Rt estimates for COVID-19 surveillance in France based on three data sources with different sensitivities and specificities for identifying infected cases. Methods We applied a statistical method developed by Cori et al. to estimate Rt using (1) confirmed cases identified from positive virological tests in the population, (2) suspected cases recorded by a national network of emergency departments, and (3) COVID-19 hospital admissions recorded by a national administrative system to manage hospital organization. Results Rt estimates in France from May 27, 2020, to August 12, 2022, showed similar temporal trends regardless of the dataset. Estimates based on the daily number of confirmed cases provided an earlier signal than the two other sources, with an average lag of 3 and 6 days for estimates based on emergency department visits and hospital admissions, respectively. Conclusion The COVID-19 experience confirmed that monitoring temporal changes in Rt was a key indicator to help the public health authorities control the outbreak in real time. However, gaining access to data on all infected people in the population in order to estimate Rt is not straightforward in practice. As this analysis has shown, the opportunity to use more readily available data to estimate Rt trends, provided that it is highly correlated with the spread of infection, provides a practical solution for monitoring the COVID-19 pandemic and ...
Keywords	Medicine ; R ; Science ; Q
Subject code	333
Language	English
Publishing date	2023-01-01T00:00:00Z
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: Two-dose measles vaccine effectiveness remains high over time: a French observational study, 2017-2019

Franconeri, Léa / Antona, Denise / Cauchemez, Simon / Lévy-Bruhl, Daniel / Paireau, Juliette

Vaccine.

2023

Abstract: From 2008 to 2019, France has experienced a resurgence of measles epidemics. Surveillance data have shown that the proportion of cases vaccinated with two doses of measles-containing vaccine (MCV) increased with age, raising concerns about the duration ... ...

Abstract	From 2008 to 2019, France has experienced a resurgence of measles epidemics. Surveillance data have shown that the proportion of cases vaccinated with two doses of measles-containing vaccine (MCV) increased with age, raising concerns about the duration of vaccine protection. Our objectives were to investigate age-stratified vaccine effectiveness (VE) for the second dose of MCV (MCV2) and to quantify protection levels over time. We analyzed data on measles cases aged 2-31 years, reported via mandatory notification to the French measles surveillance system from October 2017 to September 2019. We estimated an age-stratified VE for MCV2 using the screening method, which compares the vaccination status of cases with that of the general population. We improved this method by accounting for natural immunity, exploring four scenarios with four possible levels of natural immunity in the population. In addition, we quantified the decay rate of protection over time, by fitting an exponential decay model among individuals vaccinated in early life. In the baseline analysis (absence of natural immunity), VE estimates were high in all age groups and decreased with age, from 99.6% (95% confidence interval: 99.3-99.8) in 2-5 years old to 91.4% (85.1-95.0) in 26-31 years old. Accounting for natural immunity increased VE in the older age group to 93.2-99.2% depending on the scenario. We estimated that VE was slowly decreasing over time, with an exponential decay rate of 0.0022/year (0.0017-0.0028), leading to VE of 96.7% (96.0-97.4) 16 years after MCV2 vaccination. This decline was most compatible with scenario 2, a scenario of 4.4% naturally immunized, non-vaccinated individuals in the 26-31 years old. Our study confirms the continued high effectiveness of two doses of MCV with only slight degradation, decades after immunization. These findings support the importance of achieving a very high vaccination coverage with 2 doses of MCV.
Keywords	confidence interval ; innate immunity ; measles ; models ; monitoring ; observational studies ; vaccination ; vaccines ; France ; Vaccine effectiveness ; Screening method ; Disease notification ; waning protection
Language	English
Publishing place	Elsevier Ltd
Document type	Article ; Online
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.2023.08.018
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France.

Paireau, Juliette / Charpignon, Marie-Laure / Larrieu, Sophie / Calba, Clémentine / Hozé, Nathanaël / Boëlle, Pierre-Yves / Thiebaut, Rodolphe / Prague, Mélanie / Cauchemez, Simon

BMC infectious diseases

2023 Volume 23, Issue 1, Page(s) 190

Abstract: Background: Multiple factors shape the temporal dynamics of the COVID-19 pandemic. Quantifying their relative contributions is key to guide future control strategies. Our objective was to disentangle the individual effects of non-pharmaceutical ... ...

Abstract	Background: Multiple factors shape the temporal dynamics of the COVID-19 pandemic. Quantifying their relative contributions is key to guide future control strategies. Our objective was to disentangle the individual effects of non-pharmaceutical interventions (NPIs), weather, vaccination, and variants of concern (VOC) on local SARS-CoV-2 transmission. Methods: We developed a log-linear model for the weekly reproduction number (R) of hospital admissions in 92 French metropolitan departments. We leveraged (i) the homogeneity in data collection and NPI definitions across departments, (ii) the spatial heterogeneity in the timing of NPIs, and (iii) an extensive observation period (14 months) covering different weather conditions, VOC proportions, and vaccine coverage levels. Findings: Three lockdowns reduced R by 72.7% (95% CI 71.3-74.1), 70.4% (69.2-71.6) and 60.7% (56.4-64.5), respectively. Curfews implemented at 6/7 pm and 8/9 pm reduced R by 34.3% (27.9-40.2) and 18.9% (12.04-25.3), respectively. School closures reduced R by only 4.9% (2.0-7.8). We estimated that vaccination of the entire population would have reduced R by 71.7% (56.4-81.6), whereas the emergence of VOC (mainly Alpha during the study period) increased transmission by 44.6% (36.1-53.6) compared with the historical variant. Winter weather conditions (lower temperature and absolute humidity) increased R by 42.2% (37.3-47.3) compared to summer weather conditions. Additionally, we explored counterfactual scenarios (absence of VOC or vaccination) to assess their impact on hospital admissions. Interpretation: Our study demonstrates the strong effectiveness of NPIs and vaccination and quantifies the role of weather while adjusting for other confounders. It highlights the importance of retrospective evaluation of interventions to inform future decision-making.
MeSH term(s)	Humans ; COVID-19/epidemiology ; COVID-19/prevention & control ; SARS-CoV-2 ; Pandemics/prevention & control ; Retrospective Studies ; Communicable Disease Control ; Vaccination ; Weather ; France/epidemiology
Language	English
Publishing date	2023-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2041550-3
ISSN	1471-2334 ; 1471-2334
ISSN (online)	1471-2334
ISSN	1471-2334
DOI	10.1186/s12879-023-08106-1
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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: An ensemble model based on early predictors to forecast COVID-19 health care demand in France.

Paireau, Juliette / Andronico, Alessio / Hozé, Nathanaël / Layan, Maylis / Crépey, Pascal / Roumagnac, Alix / Lavielle, Marc / Boëlle, Pierre-Yves / Cauchemez, Simon

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

2022 Volume 119, Issue 18, Page(s) e2103302119

Abstract: Short-term forecasting of the COVID-19 pandemic is required to facilitate the planning of COVID-19 health care demand in hospitals. Here, we evaluate the performance of 12 individual models and 19 predictors to anticipate French COVID-19-related health ... ...

Abstract	Short-term forecasting of the COVID-19 pandemic is required to facilitate the planning of COVID-19 health care demand in hospitals. Here, we evaluate the performance of 12 individual models and 19 predictors to anticipate French COVID-19-related health care needs from September 7, 2020, to March 6, 2021. We then build an ensemble model by combining the individual forecasts and retrospectively test this model from March 7, 2021, to July 6, 2021. We find that the inclusion of early predictors (epidemiological, mobility, and meteorological predictors) can halve the rms error for 14-d–ahead forecasts, with epidemiological and mobility predictors contributing the most to the improvement. On average, the ensemble model is the best or second-best model, depending on the evaluation metric. Our approach facilitates the comparison and benchmarking of competing models through their integration in a coherent analytical framework, ensuring that avenues for future improvements can be identified.
MeSH term(s)	COVID-19/epidemiology ; Delivery of Health Care ; France/epidemiology ; Health Services Needs and Demand ; Humans ; Pandemics/prevention & control ; Retrospective Studies
Language	English
Publishing date	2022-04-27
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.2103302119
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Article ; Online: Early chains of transmission of COVID-19 in France, January to March 2020.

Paireau, Juliette / Mailles, Alexandra / Eisenhauer, Catherine / de Laval, Franck / Delon, François / Bosetti, Paolo / Salje, Henrik / Pontiès, Valérie / Cauchemez, Simon

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

2022 Volume 27, Issue 6

Abstract: IntroductionSARS-CoV-2, the virus that causes COVID-19, has spread rapidly worldwide. In January 2020, a surveillance system was implemented in France for early detection of cases and their contacts to help limit secondary transmissions.AimTo use contact- ...

Abstract	IntroductionSARS-CoV-2, the virus that causes COVID-19, has spread rapidly worldwide. In January 2020, a surveillance system was implemented in France for early detection of cases and their contacts to help limit secondary transmissions.AimTo use contact-tracing data collected during the initial phase of the COVID-19 pandemic to better characterise SARS-CoV-2 transmission.MethodsWe analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterised the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.ResultsDuring the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95% confidence interval (CI): 3.6-4.6), increasing with age of index case and contact. Compared with co-workers/friends, family contacts were at higher risk of becoming cases (adjusted odds ratio (AOR): 2.1, 95% CI: 1.4-3.0) and nosocomial contacts were at lower risk (AOR: 0.3, 95% CI: 0.1-0.7). Of 328 infector/infectee pairs, 49% were family members. The distribution of secondary cases was highly over-dispersed: 80% of secondary cases were caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range (IQR): 2-8 days) in contact tracing pairs, where late transmission events may be censored, and 6.8 (3-8) days in pairs investigated retrospectively.ConclusionThis study increases knowledge of SARS-CoV-2 transmission, including the importance of superspreading events during the onset of the pandemic.
MeSH term(s)	COVID-19 ; Contact Tracing ; Humans ; Pandemics ; Retrospective Studies ; SARS-CoV-2
Language	English
Publishing date	2022-02-08
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.2022.27.6.2001953
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Article ; Online: Lockdown impact on COVID-19 epidemics in regions across metropolitan France.

Cauchemez, Simon / Kiem, Cécile Tran / Paireau, Juliette / Rolland, Patrick / Fontanet, Arnaud

Lancet (London, England)

2020 Volume 396, Issue 10257, Page(s) 1068–1069

MeSH term(s)	Betacoronavirus ; COVID-19 ; Communicable Disease Control ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; France ; Humans ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Social Isolation/psychology
Keywords	covid19
Language	English
Publishing date	2020-09-29
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)32034-1
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