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Background Interventions to mitigate the COVID-19 pandemic may impact other respiratory diseases. Aims We aimed to study the course of pertussis in France over an 8-year period including the beginning of the COVID-19 pandemic and its association with COVID-19 mitigation strategies, using multiple nationwide data sources and regression models. Methods We analysed the number of French pertussis cases between 2013 and 2020, using PCR test results from nationwide outpatient laboratories (Source 1) and a network of the paediatric wards from 41 hospitals (Source 2). We also used reports of a national primary care paediatric network (Source 3). We conducted a quasi-experimental interrupted time series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles and secular trend, and included a binary variable for the first national lockdown (start 16 March 2020). Results We identified 19,039 pertussis cases from these data sources. Pertussis cases decreased significantly following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.10 (95% CI: 0.04–0.26) and 0.22 (95% CI: 0.07–0.66) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 with a median of, respectively, one (IQR: 0–2) and 0 cases (IQR: 0–0) per month before and after lockdown (p = 0.0048). Conclusions The strong reduction in outpatient and hospitalised pertussis cases suggests an impact of COVID-19 mitigation measures on pertussis epidemiology. Pertussis vaccination recommendations should be followed carefully, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.

Phylodynamic analyses generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce theCOVFlowpipeline, accessible athttps://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in theBeast2software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.

Since early 2021, SARS-CoV-2 variants of concern (VOCs) have been causing epidemic rebounds in many countries. Their properties are well characterized at the epidemiological level but the potential underlying within-host determinants remain poorly understood. We analyze a longitudinal cohort of 6944 individuals with 14 304 cycle threshold (Ct) values of reverse-transcription quantitative polymerase chain reaction (RT-qPCR) VOC screening tests performed in the general population and hospitals in France between February 6 and August 21, 2021. To convert Ct values into numbers of virus copies, we performed an additional analysis using droplet digital PCR (ddPCR). We find that the number of viral genome copies reaches a higher peak value and has a slower decay rate in infections caused by Alpha variant compared to that caused by historical lineages. Following the evidence that viral genome copies in upper respiratory tract swabs are informative on contagiousness, we show that the kinetics of the Alpha variant translate into significantly higher transmission potentials, especially in older populations. Finally, comparing infections caused by the Alpha and Delta variants, we find no significant difference in the peak viral copy number. These results highlight that some of the differences between variants may be detected in virus load variations.

We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.

International audience; We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.

Analysing 5,061 variant-specific tests performed on SARS-CoV-2 positive samples collected in France between 31 May and 8 June 2021 reveals a rapid growth of the δ variant in the Ile-de-France region. The next weeks will prove decisive but the magnitude of the estimated transmission advantage (with a 95% confidence interval between 67 and 120%) could represent a major challenge for public health authorities.

International audience; To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April–7 May 2021 in France. In this period, contrarily to January–March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5–16.2) and Hauts-de-France (17.3%; 95% CI: 15.9–18.7) regions. This is consistent with VOC β’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.

SARS-CoV-2 variants threaten our ability to control COVID-19 epidemics. We analyzed 36,590 variant-specific RT-PCR tests performed on samples collected between April 12 and May 7, 2021 in France to compare variant spread. Contrarily to January to March 2021, we found that the V2 variant had a significant transmission advantage over V1 in some regions (15.1 to 16.1% in Île-de-France and 16.1 to 18.8% in Hauts-de-France). This shift in transmission advantage is consistent with the immune evasion abilities of V2 and the high levels of immunization in these regions.

International audience; Variants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26–February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated.

SARS-CoV-2 variants raise major concerns regarding the control of COVID-19 epidemics. We analyse 40,000 specific RT-PCR tests performed on SARS-CoV-2-positive samples collected between Jan 26 and Feb 16, 2021. We find a high transmission advantage of variants and show that their spread in the country is more advanced than anticipated.

Summary Background In April–May, 2013, France modified its pertussis vaccination schedule, which uses the acellular pertussis vaccine, from three primary doses at 2, 3, and 4 months of age and a first booster at 16–18 months of age (former schedule) to two primary doses at 2 and 4 months of age and a first booster at 11 months of age (new schedule). We aimed to assess the subsequent effect of the vaccine schedule change on pertussis epidemiology in France. Methods In this modelling study, using data collected between Jan 1, 2012, and Dec 31, 2019, from French national surveillance sources, we analysed the PCR test results of nasopharyngeal swabs collected from symptomatic outpatients aged 2–20 years with suspected pertussis. We developed a negative binomial regression model for the number of confirmed pertussis cases by year and age to assess the relative risks of pertussis depending on vaccine schedule. The linear predictor included the year, the age group, the population size, and a proxy of waning immunity. We tested different models in which waning immunity could vary with vaccine schedule and type of primary vaccine. The models were fitted to the 2012–18 data via Bayesian Markov chain Monte Carlo sampling, and the 2019 data were left out for external model validation. We also compared the anti-pertussis toxin (PT) antibody concentrations in leftover sera from children not tested for pertussis or recent respiratory tract infection aged 2–5 years born before and after the vaccine schedule change. Findings We collected data on 7493 confirmed cases of pertussis. The model that best fitted the 2012–18 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. 3 years after vaccination, the risk of developing pertussis was 1·7 (95% CI 1·4–2·0) times higher for children vaccinated according to the new schedule than those vaccinated according to the former schedule. The model correctly predicted the age distribution of cases in 2019. Geometric mean concentrations (GMC) of anti-PT IgG were 50% lower in children aged 2 years vaccinated with the new schedule (GMC=5·85 IU/mL [95% CI 4·08–8·39]) than in children of the same age vaccinated with the former schedule (GMC=11·62 IU/mL [95% CI 9·05–14·92]; p=0·0016), and 43% lower in children aged 3 years vaccinated with the new schedule (GMC=3·88 IU/mL [95% CI 2·82–5·34]) than those with the former schedule (GMC=6·80 IU/mL [95% CI 4·77–9·70]; p=0·026). Interpretation A shorter-lived protection induced by the new vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in children aged 2–5 years. If similar findings are observed in other countries and clinical trials, these findings should be considered in future pertussis vaccination policies. Funding INCEPTION, Labex-IBEID, Institut Pasteur, and Sante Publique France.

Background: In 2013, France modified its pertussis vaccination schedule to remove one dose at 3 months of age and change the age of the booster dose from 16 to 11 months. We aimed to assess the subsequent impact on pertussis epidemiology in France. Methods: We analysed the PCR test results of nasopharyngeal swabs (N=7493) collected from symptomatic outpatients aged 2-20 years old between 2012 and 2019 in France. We developed a Poisson regression model in which the number of positive cases by year and age depended on the year, age group, population size of each age group and a proxy of waning immunity that could vary with vaccine schedule. We also compared the anti-pertussis toxin (PT) antibody levels of 315 children born before and after the vaccine schedule change. Findings: The model that best fitted the 2012-2018 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. Four years after vaccination, the risk of developing pertussis was 2.1 (95% CI, 1.7-2.2) times higher for children vaccinated according to the new schedule than those vaccinated according to the previous schedule. The model correctly predicted the age distribution of cases in 2019. Anti-PT IgG levels were significantly lower in children born after implementation of the new schedule, compared to children born before. Interpretation: A shorter-lived protection induced by the 2/4+11 vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in 2-5-year olds. Funding Statement: This project was funded by the INCEPTION interdisciplinary project at Institut Pasteur, “Understanding whooping cough resurgence in Europe by combining genomic, epidemiological and sociological approaches” (French Government Investissements d’Avenir grant ANR-16-CONV-0005). This work received financial support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant n_ANR-10-LABX-62-IBEID). Institutional support was provided by Institut Pasteur and Sante publique France. Declaration of Interests: None to declare. Ethics Approval Statement: The data collection received approval by French supervisory ethics authority (CNIL, n°1474593), and was approved by the local Institutional Review board (N° 2020 1028160733). All data processing and storage comply with the General Data Protection Regulation (GDPR) and ethical standards of the National Research Committee. This study was conducted in accordance with the Helsinki Declaration, with informed consent obtained from each patient’s guardians.

Introduction Le diagnostic de la borreliose de Lyme repose sur un faisceau d’arguments cliniques, epidemiologiques et biologiques. Les tests biologiques realises sont essentiellement des serologies avec un depistage en ELISA suivi d’une immunoempreinte en cas de depistage positif ou douteux. Les performances minimales recommandees par l’EUCALB sont de plus de 90 % de specificite pour un reactif de depistage. La sensibilite requise, selon l’ANSM, est de 40 % a 60 % au stade de l’erytheme migrant, de 70 % a 90 % au stade secondaire de la neuroborreliose aigue et de 100 % au stade tertiaire. Le but de cette etude a ete de comparer les performances de 4 trousses de depistage des IgG. Materiels et methodes Les serums de 4 patients presentant un erytheme migrant, de 5 patients presentant une seroconversion des IgG en immunoempreinte Euroline RN-AT anti-Borrelia Bioadvance et de respectivement 34 et 22 patients avec immunoempreinte negative et positive pour au moins 3 bandes ont ete testes ainsi qu’un controle externe de la qualite. Une etude de repetabilite sur deux niveaux de controles internes de la qualite a ete realisee. Les trousses evaluees sont B. afzelii + VlsE IgG Europe ELISA de Virotech, Serion ELISA classic Borrelia burgdorferi IgG, Liaison Borrelia IgG de Diasorin et Enzygnost Lyme link Vlse/IgG de Siemens. Resultats Les 5 cas de seroconversion sont correctement detectes avec les 4 reactifs. En cas d’immunoempreinte positive, le depistage est positif ou douteux dans tous les cas excepte a une reprise avec le reactif Virotech (debut de seroconversion) et a 2 reprises avec le reactif Virion. Au stade de l’erytheme migrant les IgG sont absentes dans 2 a 4 cas sur 4 avec cependant la presence d’IgM pour tous les reactifs excepte un. Le controle externe de la qualite donne les resultats attendus avec les 4 reactifs. L’immunoempreinte negative est associee a un depistage positif ou douteux dans respectivement 1/34, 3/34, 6/34 et 7/34 cas soit a une specificite de 97 %, 91 %, 82 % et 80 % avec les reactifs Siemens, Virion, Virotech et Diasorin. La repetabilite niveau bas et haut est de 8,4 % et 9,9 % en Siemens, de 4,9 % et 12 % en Virion, de 3,3 % et 3,6 % en Virotech et de 2,0 % et 2,4 % en Diasorin. Conclusion Ces resultats soulignent l’importance de proceder a une evaluation interne des performances avant le choix d’une trousse et de suivre les recommandations de la SPILF.

International audience; IntroductionL’épidémiologie des infections causées par les mycobactéries non tuberculeuses d’expression respiratoire (MBNTER) est mal connue en Amérique latine, et en Guyane française en particulier. L’objectif principal de cette étude était de déterminer les caractéristiques de ces infections en Guyane. Les objectifs secondaires étaient de déterminer l’incidence des maladies pulmonaires liées aux MBNTER (MBNT-MP), et les caractéristiques spécifiques des malades infectés à Mycobacterium avium complexe (MAC) ou M. abscessus et de ceux infectés par le VIH.MéthodesIl s’agit d’une étude rétrospective observationnelle multicentrique entre 2008 et 2018, réalisée sur tous les hôpitaux de Guyane. Étaient inclus les patients ayant eu au moins une culture positive à MBNTER sur prélèvement respiratoire. Les cas étaient classés en 2 catégories : porteurs non malades et malades dues à une atteinte pulmonaire liée à MBNTER selon les critères définis par l’American Thoracic Society/Infectious Disease Society of America (ATS/IDSA) en 2007.RésultatsSur la période d’étude, 178 cas ont été inclus, parmi lesquels 147 étaient porteurs non malades et 31 malades. Les patients étaient plutôt des hommes (61 %), jeunes (âge médian 49 ans), vivant dans la précarité (64 %) avec des comorbidités respiratoires (33 %) ou une immunodépression avec des CD4 ≤ 50/mm3 dans 39 % des 46 % de patients séropositifs pour le VIH. Les MAC suivies de M. fortuitum puis M. abscessus étaient les plus fréquentes (38 %, 19 % et 6 % respectivement). Le taux d’incidence annuel moyen de MBNT-MP était à 1,07/100 000 habitants par an. La MBNT-MP était significativement associée à l’infection par le VIH, à la dénutrition, et aux espèces MAC et M. abscessus qui représentaient respectivement 81 % et 16 % des maladies pulmonaires à MBNT. La mortalité à un an toutes causes confondues était de 29 % chez les malades.ConclusionIl s’agit de la première étude réalisée sur les infections à MBNTER en Guyane. L’épidémiologie des MBNTER y est spécifique avec une population différente de celle de France métropolitaine. MAC et M. abscessus sont les espèces responsables de maladies respiratoires favorisées par une infection par le VIH, ou par des comorbidités respiratoires et la dénutrition, respectivement. Les caractéristiques chez le séropositif pour le VIH sont différentes et les critères ATS/IDSA n’y sont pas extrapolables rendant le diagnostic difficile. La mortalité est plus élevée en Guyane qu’en France métropolitaine.