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Rakover A, Galmiche S, Charmet T, Chény O, Omar F, David C, Martin S, Mailles A, Fontanet A. Source of SARS-CoV-2 infection: results from a series of 584,846 cases in France from October 2020 to August 2022. BMC Public Health 2024; 24:325. [PMID: 38287286 PMCID: PMC10826227 DOI: 10.1186/s12889-024-17772-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND We aimed to study the source of infection for recently SARS-CoV-2-infected individuals from October 2020 to August 2022 in France. METHODS Participants from the nationwide ComCor case-control study who reported recent SARS-CoV-2 infection were asked to document the source and circumstances of their infection through an online questionnaire. Multivariable logistic regression was used to identify the factors associated with not identifying any source of infection. RESULTS Among 584,846 adults with a recent SARS-CoV-2 infection in France, 46.9% identified the source of infection and an additional 22.6% suspected an event during which they might have become infected. Known and suspected sources of infection were household members (30.8%), extended family (15.6%), work colleagues (15.0%), friends (11.0%), and possibly multiple/other sources (27.6%). When the source of infection was known, was not a household member, and involved a unique contact (n = 69,788), characteristics associated with transmission events were indoors settings (91.6%), prolonged (> 15 min) encounters (50.5%), symptomatic source case (64.9%), and neither the source of infection nor the participant wearing a mask (82.2%). Male gender, older age, lower education, living alone, using public transportation, attending places of public recreation (bars, restaurants, nightclubs), public gatherings, and cultural events, and practicing indoor sports were all independently associated with not knowing the source of infection. CONCLUSION Two-thirds of infections were attributed to interactions with close relatives, friends, or work colleagues. Extra-household indoor encounters without masks were commonly reported and represented avoidable circumstances of infection. TRIAL REGISTRATION ClinicalTrials.gov registration number: NCT04607941.
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Affiliation(s)
- Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France.
| | - Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Centre for Translational Research, Paris, France
| | | | | | - Sophie Martin
- Caisse Nationale de L'Assurance Maladie, Paris, France
| | | | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 Rue du Docteur Roux, 75015, Paris, France
- Conservatoire National Des Arts Et Métiers, Unité PACRI, Paris, France
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Galmiche S, Charmet T, Rakover A, Schaeffer L, Chény O, von Platen C, Omar F, David C, Mailles A, Carrat F, Fontanet A. Risk of SARS-CoV-2 Infection Among Households With Children in France, 2020-2022. JAMA Netw Open 2023; 6:e2334084. [PMID: 37713194 PMCID: PMC10504612 DOI: 10.1001/jamanetworkopen.2023.34084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023] Open
Abstract
Importance Understanding the contribution of children to SARS-CoV-2 circulation in households is critical for designing public health policies and mitigation strategies. Objective To identify temporal changes in the risk of SARS-CoV-2 infection in people living with children. Design, Setting, and Participants This case-control study included online questionnaire responses from French adults between October 2020 and October 2022. Eligible cases were adults with ongoing SARS-CoV-2 infection with an email address on record with the national health insurance system, which centralized all new diagnoses in France. Eligible controls were adults who had never tested positive for SARS-CoV-2 until February 2021, when eligibility was extended to all adults without ongoing SARS-CoV-2 infection. Exposure Transmission of SARS-CoV-2 from a child (aged under 18 years) within the household in the descriptive analysis, as reported by the participating case. Sharing household with a child (of any age or broken down by school level) in the case-control analysis. Main Outcome and Measures Ongoing SARS-CoV-2 infection diagnosed by reverse transcription-polymerase chain reaction or supervised rapid antigen test (ie, not self-tests). Results A total of 682 952 cases were included for the descriptive analysis (68.8% female, median [IQR] age, 44 [34-55] years). Among those, 45 108 (6.6%) identified a household child as the source case; this proportion peaked at 10.4% during the Omicron BA.1 wave (December 20, 2021, to April 8, 2022). For the case-control analysis, we matched 175 688 cases (with a 4:1 ratio) for demographic characteristics with 43 922 controls. In multivariable logistic regression analysis, household exposure to children was associated with an increased risk of infection mainly at the end of summer 2021 (receding Delta wave) and during winter 2022 (Omicron BA.1 wave). In subgroup analysis by school level of the child, living with children under the age of 6 was associated with increased odds of infection throughout the study period, peaking at an odds ratio (OR) 1.8 (95% CI, 1.6-2.1) for children looked after by professional in-home caregivers, 1.7 (95% CI, 1.5-1.7) for children in day care facilities, and 1.6 (95% CI, 1.4-1.8) for children in preschool. The ORs associated with household exposure to children aged 6 to 14 years increased during the Delta (August 14, 2021, to December 19, 2021) and Omicron BA.1 waves, reaching 1.6 (95% CI, 1.5-1.7) for primary school children and 1.4 (95% CI, 1.3-1.5) for middle school children. Exposure to older children aged 15 to 17 years was associated with a moderate risk until April 2021, with an OR of 1.2 (95% CI, 1.2-1.3) during curfew in early 2021 (December 4, 2020, to April 8, 2021). Conclusions and Relevance The presence of children, notably very young ones, was associated with an increased risk of SARS-CoV-2 infection in other household members, especially during the Delta and Omicron BA.1 waves. These results should help to guide policies targeting children and immunocompromised members of their household.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Laura Schaeffer
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Olivia Chény
- Center for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Cassandre von Platen
- Center for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Faïza Omar
- Department of Public Affairs—Public Statistics, Institut Ipsos, Paris, France
| | - Christophe David
- Department of Public Affairs—Public Statistics, Institut Ipsos, Paris, France
| | | | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Unité PACRI, Conservatoire National des Arts et Métiers, Paris, France
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Galmiche S, Charmet T, Madec Y, Rakover A, Schaeffer L, Chény O, Omar F, Martin S, Mailles A, Carrat F, Fontanet A. Reduction of SARS-CoV-2 intra-household child-to-parent transmission associated with ventilation: results from a case-control study. BMC Public Health 2023; 23:1240. [PMID: 37365557 DOI: 10.1186/s12889-023-16144-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/18/2023] [Indexed: 06/28/2023] Open
Abstract
PURPOSE Our objective was to describe circumstances of SARS-CoV-2 household transmission and to identify factors associated with a lower risk of transmission in a nationwide case-control study in France. METHODS In a descriptive analysis, we analysed cases reporting transmission from someone in the household (source case). Index cases could invite a non-infected household member to participate as a related control. In such situations, we compared the exposures of the index case and related control to the source case by conditional logistic regression matched for household, restricted to households in which the source case was a child, and the index case and related control were the infected child's parents. RESULTS From October 27, 2020 to May 16, 2022, we included 104 373 cases for the descriptive analysis with a documented infection from another household member. The source case was mostly the index case's child (46.9%) or partner (45.7%). In total, 1026 index cases invited a related control to participate in the study. In the case-control analysis, we included 611 parental pairs of cases and controls exposed to the same infected child. COVID-19 vaccination with 3 + doses versus no vaccination (OR 0.1, 95%CI: 0.04-0.4), isolation from the source case (OR 0.6, 95%CI: 0.4-0.97) and the ventilation of indoor areas (OR 0.6, 95%CI: 0.4-0.9) were associated with lower risk of infection. CONCLUSION Household transmission was common during the SARS-CoV-2 pandemic in France. Mitigation strategies, including isolation and ventilation, decreased the risk of secondary transmission within the household. TRIAL REGISTRATION ClinicalTrials.gov registration number: NCT04607941.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
- Sorbonne Université, Ecole Doctorale Pierre Louis de Santé Publique, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Yoann Madec
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Arthur Rakover
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Laura Schaeffer
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Centre for Translational Research, Paris, France
| | | | - Sophie Martin
- Caisse Nationale de L'Assurance Maladie, Paris, France
| | | | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, 25 rue du Docteur Roux, Paris, 75015, France.
- Conservatoire National Des Arts Et Métiers, Unité PACRI, Paris, France.
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Supplisson O, Charmet T, Galmiche S, Schaeffer L, Chény O, Lévy A, Jeandet N, Omar F, David C, Mailles A, Fontanet A. SARS-CoV-2 self-test uptake and factors associated with self-testing during Omicron BA.1 and BA.2 waves in France, January to May 2022. Euro Surveill 2023; 28:2200781. [PMID: 37140451 PMCID: PMC10161682 DOI: 10.2807/1560-7917.es.2023.28.18.2200781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/03/2023] [Indexed: 05/05/2023] Open
Abstract
BackgroundFollowing the SARS-CoV-2 Omicron variant spread, the use of unsupervised antigenic rapid diagnostic tests (self-tests) increased.AimThis study aimed to measure self-test uptake and factors associated with self-testing.MethodsIn this cross-sectional study from 20 January to 2 May 2022, the case series from a case-control study on factors associated with SARS-CoV-2 infection were used to analyse self-testing habits in France. A multivariable quasi-Poisson regression was used to explore the variables associated with self-testing among symptomatic cases who were not contacts of another infected individual. The control series from the same study was used as a proxy for the self-test background rate in the non-infected population of France.ResultsDuring the study period, 179,165 cases who tested positive through supervised tests were recruited. Of these, 64.7% had performed a self-test in the 3 days preceding this supervised test, of which 79,038 (68.2%) were positive. The most frequently reported reason for self-testing was the presence of symptoms (64.6%). Among symptomatic cases who were not aware of being contacts of another case, self-testing was positively associated with being female, higher education, household size, being a teacher and negatively associated with older age, not French by birth, healthcare-related work and immunosuppression. Among the control series, 12% self-tested during the 8 days preceding questionnaire filling, with temporal heterogeneity.ConclusionThe analysis showed high self-test uptake in France with some inequalities which must be addressed through education and facilitated access (cost and availability) for making it a more efficient epidemic control tool.
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Affiliation(s)
- Olivier Supplisson
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Center for Interdisciplinary Research in Biology, Ecology and Evolution of Health team (Collège de France, CNRS/UMR 7241, Inserm U1050), Paris, France
- Sorbonne Université, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Simon Galmiche
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Sorbonne Université, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
| | - Olivia Chény
- Institut Pasteur, Université Paris Cité, Clinical Operation Coordination Office, Paris, France
| | - Anne Lévy
- Caisse Nationale d'Assurance Maladie, Paris, France
| | | | | | | | | | - Arnaud Fontanet
- Institut Pasteur, Université Paris Cité, Emerging Diseases Epidemiology Unit, Paris, France
- Conservatoire National des Arts et Métiers, unité PACRI, Paris, France
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Galmiche S, Cortier T, Charmet T, Schaeffer L, Chény O, von Platen C, Lévy A, Martin S, Omar F, David C, Mailles A, Carrat F, Cauchemez S, Fontanet A. SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study. Lancet Microbe 2023:S2666-5247(23)00005-8. [PMID: 37084751 PMCID: PMC10112864 DOI: 10.1016/s2666-5247(23)00005-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/08/2022] [Accepted: 12/23/2022] [Indexed: 04/23/2023]
Abstract
BACKGROUND The incubation period of SARS-CoV-2 has been estimated for the known variants of concern. However, differences in study designs and settings make comparing variants difficult. We aimed to estimate the incubation period for each variant of concern compared with the historical strain within a unique and large study to identify individual factors and circumstances associated with its duration. METHODS In this case series analysis, we included participants (aged ≥18 years) of the ComCor case-control study in France who had a SARS-CoV-2 diagnosis between Oct 27, 2020, and Feb 4, 2022. Eligible participants were those who had the historical strain or a variant of concern during a single encounter with a known index case who was symptomatic and for whom the incubation period could be established, those who reported doing a reverse-transcription-PCR (RT-PCR) test, and those who were symptomatic by study completion. Sociodemographic and clinical characteristics, exposure information, circumstances of infection, and COVID-19 vaccination details were obtained via an online questionnaire, and variants were established through variant typing after RT-PCR testing or by matching the time that a positive test was reported with the predominance of a specific variant. We used multivariable linear regression to identify factors associated with the duration of the incubation period (defined as the number of days from contact with the index case to symptom onset). FINDINGS 20 413 participants were eligible for inclusion in this study. Mean incubation period varied across variants: 4·96 days (95% CI 4·90-5·02) for alpha (B.1.1.7), 5·18 days (4·93-5·43) for beta (B.1.351) and gamma (P.1), 4·43 days (4·36-4·49) for delta (B.1.617.2), and 3·61 days (3·55-3·68) for omicron (B.1.1.529) compared with 4·61 days (4·56-4·66) for the historical strain. Participants with omicron had a shorter incubation period than participants with the historical strain (-0·9 days, 95% CI -1·0 to -0·7). The incubation period increased with age (participants aged ≥70 years had an incubation period 0·4 days [0·2 to 0·6] longer than participants aged 18-29 years), in female participants (by 0·1 days, 0·0 to 0·2), and in those who wore a mask during contact with the index case (by 0·2 days, 0·1 to 0·4), and was reduced in those for whom the index case was symptomatic (-0·1 days, -0·2 to -0·1). These data were robust to sensitivity analyses correcting for an over-reporting of incubation periods of 7 days. INTERPRETATION SARS-CoV-2 incubation period is notably reduced in omicron cases compared with all other variants of concern, in young people, after transmission from a symptomatic index case, after transmission to a maskless secondary case, and (to a lesser extent) in men. These findings can inform future COVID-19 contact-tracing strategies and modelling. FUNDING Institut Pasteur, the French National Agency for AIDS Research-Emerging Infectious Diseases, Fondation de France, the INCEPTION project, and the Integrative Biology of Emerging Infectious Diseases project.
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Affiliation(s)
- Simon Galmiche
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Ecole Doctorale Pierre Louis de Santé Publique, Sorbonne Université, Paris, France
| | - Thomas Cortier
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, Paris, France; Ecole Doctorale Pierre Louis de Santé Publique, Sorbonne Université, Paris, France
| | - Tiffany Charmet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Laura Schaeffer
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Olivia Chény
- Centre for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Cassandre von Platen
- Centre for Translational Research, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anne Lévy
- Caisse Nationale de l'Assurance Maladie, Paris, France
| | - Sophie Martin
- Caisse Nationale de l'Assurance Maladie, Paris, France
| | | | | | | | - Fabrice Carrat
- The National Institute of Health and Medical Research, Sorbonne Université, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris Cité, Paris, France; Conservatoire National des Arts et Métiers, Unité Pasteur-Cnam Risques Infectieux et Émergents, Paris, France.
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Grant R, Charmet T, Schaeffer L, Galmiche S, Madec Y, Von Platen C, Chény O, Omar F, David C, Rogoff A, Paireau J, Cauchemez S, Carrat F, Septfons A, Levy-Bruhl D, Mailles A, Fontanet A. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France. Lancet Reg Health Eur 2022; 13:100278. [PMID: 34849500 PMCID: PMC8616730 DOI: 10.1016/j.lanepe.2021.100278] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND We aimed to assess the settings and activities associated with SARS-CoV-2 infection in the context of B.1.617.2 (Delta) variant circulation in France, as well as the protection against symptomatic Delta infection. METHODS In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 23 May and 13 August 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire and multivariable logistic regression analysis was used to determine the association between acute SARS-CoV-2 infection and recent activity-related exposures, past history of SARS-CoV-2 infection, and COVID-19 vaccination. FINDINGS We did not find any differences in the settings and activities associated with Delta versus non-Delta infections and grouped them for subsequent analyses. In multivariable analysis involving 12634 cases (8644 Delta and 3990 non-Delta) and 5560 controls, we found individuals under 40 years and attending bars (aOR:1.9; 95%CI:1.6-2.2) or parties (aOR:3.4; 95%CI:2.8-4.2) to be at increased risk of infection. In those aged 40 years and older, having children attend daycare (aOR:1.9; 95%CI:1.1-3.3), kindergarten (aOR:1.6; 95%CI:1.2-2.1), primary school (aOR:1.4; 95%CI:1.2-1.6) or middle school (aOR:1.3; 95%CI:1.2-1.6) were associated with increased risk of infection. We found strong protection against symptomatic Delta infection for those with prior infection whether it was recent (2-6 months) (95%; 95%CI:90-97) or associated with one dose (85%; 95%CI:78-90) or two doses of mRNA vaccine (96%; 95%CI:87-99). For those without past infection, protection was lower with two doses of mRNA vaccine (67%; 95%CI:63-71). INTERPRETATION In line with other observational studies, we find reduced vaccine effectiveness against symptomatic Delta infections. The settings and activities at increased risk of infection indicate where efforts to reinforce individual and public health measures need to be concentrated.
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Affiliation(s)
- Rebecca Grant
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
- Sorbonne University, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Simon Galmiche
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Yoann Madec
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
| | - Cassandre Von Platen
- Institut Pasteur, Université de Paris, Centre for Translational Research, F-75015 Paris, France
| | - Olivia Chény
- Institut Pasteur, Université de Paris, Centre for Translational Research, F-75015 Paris, France
| | | | | | | | - Juliette Paireau
- Institut Pasteur, Université de Paris, CNRS UMR2000, Mathematical Modelling of Infectious Diseases Unit, F-75015 Paris, France
| | - Simon Cauchemez
- Institut Pasteur, Université de Paris, CNRS UMR2000, Mathematical Modelling of Infectious Diseases Unit, F-75015 Paris, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, hôpital Saint-Antoine, APHP, 27 rue Chaligny, Paris F75571
| | | | | | | | - Arnaud Fontanet
- Institut Pasteur, Université de Paris, Emerging Diseases Epidemiology Unit, F-75015 Paris, France
- Conservatoire National des Arts et Métiers, Unité PACRI, Paris, France
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Galmiche S, Charmet T, Schaeffer L, Paireau J, Grant R, Chény O, Von Platen C, Maurizot A, Blanc C, Dinis A, Martin S, Omar F, David C, Septfons A, Cauchemez S, Carrat F, Mailles A, Levy-Bruhl D, Fontanet A. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study. Lancet Reg Health Eur 2021; 7:100148. [PMID: 34124709 PMCID: PMC8183123 DOI: 10.1016/j.lanepe.2021.100148] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. METHODS In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. FINDINGS Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). INTERPRETATION Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. FUNDING Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance" Tous unis contre le virus").
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Affiliation(s)
- Simon Galmiche
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Juliette Paireau
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit; UMR2000; CNRS, Paris, France
- Santé Publique France, Saint-Maurice, France
| | - Rebecca Grant
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
- Sorbonne University, Paris, France
| | - Olivia Chény
- Institut Pasteur, Centre for Translational Research, Paris, France
| | | | | | - Carole Blanc
- Caisse Nationale d'Assurance Maladie, Paris, France
| | - Annika Dinis
- Caisse Nationale d'Assurance Maladie, Paris, France
| | | | | | | | | | - Simon Cauchemez
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit; UMR2000; CNRS, Paris, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, hôpital Saint-Antoine, APHP, 27 rue Chaligny, Paris, France F75571
| | | | | | - Arnaud Fontanet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
- Conservatoire national des arts et métiers, Unité PACRI, Paris, France
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Galmiche S, Charmet T, Schaeffer L, Paireau J, Grant R, Chény O, Von Platen C, Maurizot A, Blanc C, Dinis A, Martin S, Omar F, David C, Septfons A, Cauchemez S, Carrat F, Mailles A, Levy-Bruhl D, Fontanet A. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study. Lancet Reg Health Eur 2021; 7:100148. [PMID: 34124709 DOI: 10.1016/j.lanepe.2021.10014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
BACKGROUND We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. METHODS In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. FINDINGS Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). INTERPRETATION Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. FUNDING Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance" Tous unis contre le virus").
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Affiliation(s)
- Simon Galmiche
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Tiffany Charmet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Juliette Paireau
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit; UMR2000; CNRS, Paris, France
- Santé Publique France, Saint-Maurice, France
| | - Rebecca Grant
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
- Santé Publique France, Saint-Maurice, France
| | - Olivia Chény
- Sorbonne University, Paris, France
- Institut Pasteur, Centre for Translational Research, Paris, France
| | | | | | - Carole Blanc
- Caisse Nationale d'Assurance Maladie, Paris, France
| | - Annika Dinis
- Caisse Nationale d'Assurance Maladie, Paris, France
| | | | | | | | | | - Simon Cauchemez
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit; UMR2000; CNRS, Paris, France
| | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, hôpital Saint-Antoine, APHP, 27 rue Chaligny, Paris, France F75571
| | | | | | - Arnaud Fontanet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
- Conservatoire national des arts et métiers, Unité PACRI, Paris, France
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Charmet T, Schaeffer L, Grant R, Galmiche S, Chény O, Von Platen C, Maurizot A, Rogoff A, Omar F, David C, Septfons A, Cauchemez S, Gaymard A, Lina B, Lefrancois LH, Enouf V, van der Werf S, Mailles A, Levy-Bruhl D, Carrat F, Fontanet A. Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France. Lancet Reg Health Eur 2021; 8:100171. [PMID: 34278372 PMCID: PMC8277121 DOI: 10.1016/j.lanepe.2021.100171] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background We aimed to assess the effectiveness of two doses of mRNA COVID-19 vaccines against COVID-19 with the original virus and other lineages circulating in France. Methods In this nationwide case-control study, cases were SARS-CoV-2 infected adults with onset of symptoms between 14 February and 3 May 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire on recent activity-related exposures and vaccination history. Information about the infecting virus was based on a screening RT-PCR for either B.1.1.7 or B.1.351/P.1 variants. Findings Included in our analysis were 7 288 adults infected with the original SARS-CoV-2 virus, 31 313 with the B.1.1.7 lineage, 2 550 with B.1.351/P1 lineages, and 3 644 controls. In multivariable analysis, the vaccine effectiveness (95% confidence interval) seven days after the second dose of mRNA vaccine was estimated at 88% (81-92), 86% (81-90) and 77% (63-86) against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Recent (2 to 6 months) history of virologically confirmed SARS-CoV-2 infection was found to be 83% (76-88), 88% (85-91) and 83% (71-90) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively; and more distant (> 6 months) infections were 76% (54-87), 84% (75-90), and 74% (41-89) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Interpretation In real-life settings, two doses of mRNA vaccines proved to be effective against COVID-19 with the original virus, B.1.1.7 lineage and B.1.351/P.1 lineages. Funding Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance “Tous unis contre le virus”).
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Affiliation(s)
- Tiffany Charmet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Rebecca Grant
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France.,Sorbonne University, Paris, France
| | - Simon Galmiche
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France
| | - Olivia Chény
- Institut Pasteur, Centre for Translational Research, Paris, France
| | | | | | | | | | | | | | - Simon Cauchemez
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit; UMR2000; CNRS, Paris, France
| | - Alexandre Gaymard
- CNR des Virus des Infections Respiratoires, Institut des Agents Infectieux, Hospices Civils de Lyon.,Virpath, Centre International de Recherche En Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, UCBL, Lyon, France
| | - Bruno Lina
- CNR des Virus des Infections Respiratoires, Institut des Agents Infectieux, Hospices Civils de Lyon.,Virpath, Centre International de Recherche En Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, UCBL, Lyon, France
| | - Louise H Lefrancois
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569; Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569; Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France.,Mutualized Platform of Microbiology, Pasteur International Bioresources Network, Institut Pasteur, Paris, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur CNRS UMR 3569; Université de Paris, Paris, France.,National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | | | | | - Fabrice Carrat
- Sorbonne Université, Inserm, IPLESP, hôpital Saint-Antoine, APHP, 27 rue Chaligny, Paris F75571, France
| | - Arnaud Fontanet
- Institut Pasteur, Emerging Diseases Epidemiology Unit, Paris, France.,Conservatoire national des arts et métiers, Unité PACRI, Paris, France
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Blischak JD, Tailleux L, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann JL, Brosch R, Barreiro LB, Gilad Y. Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. Sci Rep 2017; 7:5702. [PMID: 28720766 PMCID: PMC5516010 DOI: 10.1038/s41598-017-05878-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/05/2017] [Indexed: 01/11/2023] Open
Abstract
Tuberculosis (TB) is a deadly infectious disease, which kills millions of people every year. The causative pathogen, Mycobacterium tuberculosis (MTB), is estimated to have infected up to a third of the world's population; however, only approximately 10% of infected healthy individuals progress to active TB. Despite evidence for heritability, it is not currently possible to predict who may develop TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from active TB. We measured gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms nearby the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated reasonable performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.
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Affiliation(s)
- John D Blischak
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Ludovic Tailleux
- Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France.
| | - Marsha Myrthil
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Cécile Charlois
- Centre de Lutte Antituberculeuse de Paris, DASES Mairie de Paris, 75013, Paris, France
| | - Emmanuel Bergot
- Service de pneumologie et oncologie thoracique, CHU Côte de Nacre, 14033, Caen, France
| | - Aurélien Dinh
- Maladies Infectieuses, AP-HP, Hôpital Universitaire Raymond-Poincaré, Garches, 92380, France
| | - Gloria Morizot
- Clinical Investigation & Access Biological Resources (ICAReB), Institut Pasteur, Paris, France
| | - Olivia Chény
- Clinical Core, Centre for Translational Science, Institut Pasteur, Paris, France
| | - Cassandre Von Platen
- Clinical Core, Centre for Translational Science, Institut Pasteur, Paris, France
| | - Jean-Louis Herrmann
- INSERM, U1173, UFR Simone Veil, Université de Versailles Saint Quentin, Saint Quentin en Yvelines, France
- APHP, Groupe Hospitalo-Universitaire Paris Île-de-France Ouest, Garches et Boulogne-Billancourt, France
| | - Roland Brosch
- Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Québec, Canada.
- Department of Pediatrics, University of Montreal, Montreal, Québec, Canada.
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.
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