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2. Custom multi‑tumor next‑generation sequencing panel for routine molecular diagnosis of solid tumors: Validation and results from three‑year clinical use

Author

Chevrier, Sandy, primary, Brasselet, Astrid, additional, Carnet, Marion, additional, Chevriaux, Angélique, additional, Gibeaud, Anne, additional, Jourdain, Marine, additional, Mananet, Hugo, additional, Truntzer, Caroline, additional, Beltjens, Françoise, additional, Charon‑barra, Céline, additional, Arnould, Laurent, additional, Albuisson, Juliette, additional, Comte, Anthony, additional, Derangère, Valentin, additional, Goussot, Vincent, additional, and Boidot, Romain, additional

Published
2022
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3. Identifying the target population for primary Respiratory Syncytial Virus two-step prevention in infants: Normative Outcome of Hospitalisation Assessment for Newborns (NOHAN)

Author

Jourdain, Marine, primary, Benchaib, Mehdi, additional, Ploin, Dominique, additional, Gillet, Yves, additional, Javouhey, Etienne, additional, Horvat, Côme, additional, Massoud, Mona, additional, Butin, Marine, additional, Claris, Olivier, additional, Lina, Bruno, additional, and Casalegno, Jean-Sebastien, additional

Published
2022
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4. Real-time, portable genome sequencing for Ebola surveillance

Author

Quick, Joshua, Loman, Nicholas J., Duraffour, Sophie, Simpson, Jared T., Severi, Ettore, Cowley, Lauren, Bore, Joseph Akoi, Koundouno, Raymond, Dudas, Gytis, Mikhail, Amy, Ouédraogo, Nobila, Afrough, Babak, Bah, Amadou, Baum, Jonathan H. J., Becker-Ziaja, Beate, Boettcher, Jan Peter, Cabeza-Cabrerizo, Mar, Camino-Sánchez, Álvaro, Carter, Lisa L., Doerrbecker, Juliane, Enkirch, Theresa, Dorival, Isabel García-, Hetzelt, Nicole, Hinzmann, Julia, Holm, Tobias, Kafetzopoulou, Liana Eleni, Koropogui, Michel, Kosgey, Abigael, Kuisma, Eeva, Logue, Christopher H., Mazzarelli, Antonio, Meisel, Sarah, Mertens, Marc, Michel, Janine, Ngabo, Didier, Nitzsche, Katja, Pallasch, Elisa, Patrono, Livia Victoria, Portmann, Jasmine, Repits, Johanna Gabriella, Rickett, Natasha Y., Sachse, Andreas, Singethan, Katrin, Vitoriano, Inês, Yemanaberhan, Rahel L., Zekeng, Elsa G., Racine, Trina, Bello, Alexander, Sall, Amadou Alpha, Faye, Ousmane, Faye, Oumar, Magassouba, NʼFaly, Williams, Cecelia V., Amburgey, Victoria, Winona, Linda, Davis, Emily, Gerlach, Jon, Washington, Frank, Monteil, Vanessa, Jourdain, Marine, Bererd, Marion, Camara, Alimou, Somlare, Hermann, Camara, Abdoulaye, Gerard, Marianne, Bado, Guillaume, Baillet, Bernard, Delaune, Déborah, Nebie, Koumpingnin Yacouba, Diarra, Abdoulaye, Savane, Yacouba, Pallawo, Raymond Bernard, Gutierrez, Giovanna Jaramillo, Milhano, Natacha, Roger, Isabelle, Williams, Christopher J., Yattara, Facinet, Lewandowski, Kuiama, Taylor, James, Rachwal, Phillip, Turner, Daniel J., Pollakis, Georgios, Hiscox, Julian A., Matthews, David A., Shea, Matthew K. Oʼ, Johnston, Andrew McD., Wilson, Duncan, Hutley, Emma, Smit, Erasmus, Di Caro, Antonino, Wölfel, Roman, Stoecker, Kilian, Fleischmann, Erna, Gabriel, Martin, Weller, Simon A., Koivogui, Lamine, Diallo, Boubacar, Keïta, Sakoba, Rambaut, Andrew, Formenty, Pierre, Günther, Stephan, and Carroll, Miles W.

Published
2016
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5. Low levels of respiratory syncytial virus activity in Europe during the 2020/21 season: what can we expect in the coming summer and autumn/winter?

Author

van Summeren, Jojanneke, Meijer, Adam, Aspelund, Guðrún, Casalegno, Jean Sebastien, Erna, Guðrún, Hoang, Uy, Lina, Bruno, de Lusignan, Simon, Teirlinck, Anne C., Thors, Valtýr, Paget, John, Ouziel, Antoine, Tardy, Jean-claude, Gaucherand, Pascal, Massardier, Jerome, Polazzi, Stephanie, Duclos, Antoine, Benchaib, Mehdi, Cartier, Regine, Jourdain, Marine, Ottmann, Michelle, Kramer, Rolf, Fiorini, Sylvie, Rivat, Nathalie, Mekki, Yahia, Fort-Jacquier, Julie, Barral, Maud-Catherine, Noelie, Vey, Haesebaert, Julie, Horvat, Come, Vidoni, Leo, Reynes, Jean-Marc, Eleouet, Jean-Francois, Josset, Laurence, Receveur, Matthieu, Javouhey, Etienne, Ploin, Dominique, Valette, Martine, Fanget, Remi, Targe, Sandrine Couray, Myar-Dury, Anne-Florence, Doret-Dion, Muriel, Massoud, Mona, Masson, Elsa, Bard, Emilie, Queromes, Gregory, Vanhems, Phillipe, Claris, Olivier, Butin, Marine, Ader, Florence, Bin, Sylvie, Gaymard, Alexandre, Morfin, Florence, Gillet, Yves, Netherlands Institute for Health Services Research [Utrecht] (NIVEL), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Directorate of Health [Reykjavík], Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Landspitali National University Hospital of Iceland, University of Oxford [Oxford], Children’s Hospital [Reykjavik, Iceland], University of Iceland [Reykjavik], This study is performed as a side project of the RSV ComNet study. The aim of the RSV ComNet project is to measure the disease burden of RSV in children aged ≤5 years in primary care, and is funded by Sanofi Pasteur and AstraZeneca., VRS study group in Lyon: Antoine Ouziel, Jean-claude Tardy, Pascal Gaucherand, Jerome Massardier, Stephanie Polazzi, Antoine Duclos, Mehdi Benchaib, Regine Cartier, Marine Jourdain, Michelle Ottmann, Rolf Kramer, Sylvie Fiorini, Nathalie Rivat, Yahia Mekki, Julie Fort-Jacquier, Maud-Catherine Barral, Vey Noelie, Julie Haesebaert, Come Horvat, Leo Vidoni, Jean-Marc Reynes, Jean-Francois Eleouet, Laurence Josset, Matthieu Receveur, Etienne Javouhey, Dominique Ploin, Martine Valette, Remi Fanget, Sandrine Couray Targe, Anne-Florence Myar-Dury, Muriel Doret-Dion, Mona Massoud, Elsa Masson, Emilie Bard, Gregory Queromes, Phillipe Vanhems, Olivier Claris, Marine Butin, Florence Ader, Sylvie Bin, Alexandre Gaymard, Florence Morfin, Yves Gillet, and Lyon, VRS study group in

Subjects
Author's Correction, 0301 basic medicine, Veterinary medicine, viruses, Iceland, surveillance data, MESH: Respiratory Syncytial Virus, Human, Respiratory syncytial virus, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, Epidemiology, MESH: COVID-19, 030212 general & internal medicine, Respiratory system, Child, virus diseases, RSV, respiratory system, MESH: Iceland, MESH: Infant, Europe, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, epidemiology, France, Seasons, Winter season, Rapid Communication, medicine.medical_specialty, 2019-20 coronavirus outbreak, Surveillance data, Coronavirus disease 2019 (COVID-19), COVID-19 pandemic, Respiratory Syncytial Virus Infections, Biology, Virus, 03 medical and health sciences, MESH: Respiratory Syncytial Virus Infections, Virology, medicine, Humans, MESH: SARS-CoV-2, MESH: Humans, SARS-CoV-2, Public Health, Environmental and Occupational Health, Small children, COVID-19, Infant, MESH: France, 030104 developmental biology, Respiratory Syncytial Virus, Human, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Europe, MESH: Seasons
Abstract

International audience; Since the introduction of non-pharmacological interventions to control COVID-19, respiratory syncytial virus (RSV) activity in Europe has been limited. Surveillance data for 17 countries showed delayed RSV epidemics in France (≥ 12 w) and Iceland (≥ 4 w) during the 2020/21 season. RSV cases (predominantly small children) in France and Iceland were older compared with previous seasons. We hypothesise that future RSV epidemic(s) could start outside the usual autumn/winter season and be larger than expected. Year-round surveillance of RSV is of critical importance.

Published
2021
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6. Characteristics of the delayed respiratory syncytial virus epidemic, 2020/2021, Rhône Loire, France

Author

Casalegno, Jean-Sebastien, Ploin, Dominique, Cantais, Aymeric, Masson, Elsa, Bard, Emilie, Valette, Martine, Fanget, Remi, Targe, Sandrine Couray, Myar-Dury, Anne-Florence, Doret-Dion, Muriel, Massoud, Mona, Queromes, Gregory, Vanhems, Philippe, Claris, Olivier, Butin, Marine, Pillet, Sylvie, Ader, Florence, Bin, Sylvie, Gaymard, Alexandre, Lina, Bruno, Morfin, Florence, Javouhey, Etienne, Gillet, Yves, Ouziel, Antoine, Tardy, Jean-claude, Gaucherand, Pascal, Panetta, Luc, Massardier, Jerome, Polazzi, Stephanie, Duclos, Antoine, Benchaib, Mehdi, Cartier, Regine, Jourdain, Marine, Ottmann, Michelle, Kramer, Rolf, Fiorini, Sylvie, Rivat, Nathalie, Mekki, Yahia, Fort-Jacquier, Julie, Barral, Maud-Catherine, Noelie, Vey, Haesebaert, Julie, Horvat, Come, Vidoni, Leo, Reynes, Jean-Marc, Eleouet, Jean-Francois, Josset, Laurence, Receveur, Matthieu, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), Université Jean Monnet - Saint-Étienne (UJM), Hôpital Edouard Herriot [CHU - HCL], Santé publique, épidémiologie et écologie évolutive des maladies infectieuses (PHE3ID), Pôle Information Médicale Evaluation Recherche (IMER), Hôpital de la Croix-Rousse [CHU - HCL], VRS study group in Lyon: Antoine Ouziel, Jean-claude Tardy, Pascal Gaucherand, Luc Panetta, Jerome Massardier, Stephanie Polazzi, Antoine Duclos, Mehdi Benchaib, Regine Cartier, Marine Jourdain, Michelle Ottmann, Rolf Kramer, Sylvie Fiorini, Nathalie Rivat, Yahia Mekki, Julie Fort-Jacquier, Maud-Catherine Barral, Vey Noelie, Julie Haesebaert, Come Horvat, Leo Vidoni, Jean-Marc Reynes, Jean-Francois Eleouet, Laurence Josset, Matthieu Receveur, Reynes, Jean-Marc, Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne)

Subjects
0301 basic medicine, Pediatrics, Epidemiology, pharmacological interventions, MESH: Hospitalization, MESH: Respiratory Syncytial Virus, Human, disease burden, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, 030212 general & internal medicine, Respiratory system, Child, Respiratory Tract Infections, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Respiratory tract infections, Incidence (epidemiology), RSV, MESH: Infant, Hospitalization, non-pharmacological interventions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, bronchiolitis, France, Rapid Communication, Adult, medicine.medical_specialty, Respiratory Syncytial Virus Infections, Virus, MESH: Respiratory Syncytial Virus Infections, 03 medical and health sciences, Virology, Lower respiratory tract infection, medicine, Humans, Epidemics, MESH: Epidemics, Disease burden, MESH: Humans, business.industry, SARS-CoV-2, Public Health, Environmental and Occupational Health, Outbreak, COVID-19, Infant, MESH: Adult, medicine.disease, MESH: France, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Bronchiolitis, Respiratory Syncytial Virus, Human, MESH: Respiratory Tract Infections, SARI, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract

International audience; The Rhône-Loire metropolitan areas’ 2020/21 respiratory syncytial virus (RSV) epidemic was delayed following the implementation of non-pharmaceutical interventions (NPI), compared with previous seasons. Very severe lower respiratory tract infection incidence among infants ≤ 3 months decreased twofold, the proportion of cases among children aged > 3 months to 5 years increased, and cases among adults > 65 years were markedly reduced. NPI appeared to reduce the RSV burden among at-risk groups, and should be promoted to minimise impact of future RSV outbreaks.

Published
2021
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7. BURDEN OF HOSPITALIZATION DUE TO RESPIRATORY SYNCYTIAL VIRUS (RSV)-VERY SEVERE ASSOCIATED LOWER RESPIRATORY TRACT INFECTION (VS-ALRI) IN THE FIRST YEAR OF LIFE IN A MAJOR URBAN CITY, LYON, FRANCE. On behalf the VRS Study group in Lyon

Author

C Horvat, L Duclaux-Loras, A Myard-Dury, B Lina, E Javouhey, Y Gillet, J S Casalegno, Ottmann, Michele, Ploin, Dominique, Gaymard, Alexandre, Kramer, Rolf, Benchaib, Mehdi, Yahia Mekki, Javouhey, Etienne, Duclos, Antoine, Gillet, Yves, Polazzi, Stephanie, Lina, Bruno, Vanhems, Philippe, Claris, Olivier, Valette, Martine, Couray-Targe, Sandrine, Massoud, Mona, Cartier, Régine, Josset, Laurence, Butin, Marine, Bin, Sylvie, Horvat, Côme, Jean-Sebastien Casalegno, Jourdain, Marine, Ouziel, Antoine, Anne-Florence Myard-Dury, Doret-Dion, Muriel, Fiorini, Sylvie, Morfin-Sherpa, Florence, Gaucherand, Pascal, Ader, Florence, Rivat, Nathalie, and Lyon, The VRS Study Group In

Published
2020
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8. Very severe RSV-associated respiratory tract infection in children living in a French urban city: Incidence and risk factors (ESPID 2020)

Author

L Duclos-Lauras, L Alexandre, A Paul, T Guichard, E Rault, S Fiorini, N Rivat, Ploin, Dominique, Benchaib, Mehdi, Kramer, Rolf, Yahia Mekki, Duclos, Antoine, Javouhey, Etienne, Gillet, Yves, Lina, Bruno, Vanhems, Philippe, Claris, Olivier, Valette, Martine, Couray-Targe, Sandrine, Massoud, Mona, Cartier, Régine, Lyon, The VRS Study Group In, Morfin-Sherpa, Florence, Ottmann, Michele, Bin, Sylvie, Butin, Marine, Horvat, Côme, Jourdain, Marine, Biot, Blandine, Ouziel, Antoine, Doret-Dion, Muriel, Gaucherand, Pascal, Massardier, Jerome, Anne-Florence Myard-Dury, Polazzi, Stephanie, and Jean-Sebastien Casalegno

Published
2020
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9. Identifying the Target Population for Primary Respiratory Syncytial Virus Two-Step Prevention in Infants: Normative Outcome of Hospitalisation Assessment for Newborns (NOHAN).

Author

Jourdain, Marine, Benchaib, Mehdi, Ploin, Dominique, Gillet, Yves, Javouhey, Etienne, Horvat, Come, Massoud, Mona, Butin, Marine, Claris, Olivier, Lina, Bruno, and Casalegno, Jean-Sebastien

Subjects
RESPIRATORY syncytial virus, NEWBORN screening, INFANTS, MOTHER-infant relationship, BIRTH weight, HUMAN metapneumovirus infection
Abstract

Background: Respiratory syncytial virus (RSV) is the leading cause of acute respiratory infection- related hospitalisations in infants (RSVh). Most of these infants are younger than 6 months old with no known risk factors. An efficient RSVh prevention program should address both mothers and infants, relying on Non-Pharmaceutical (NPI) and Pharmaceutical Interventions (PI). This study aimed at identifying the target population for these two interventions. Methods: Laboratory-confirmed RSV-infected infants hospitalised during the first 6 months of life were enrolled from the Hospices Civils de Lyon birth cohort (2014 to 2018). Clinical variables related to pregnancy and birth (sex, month of birth, birth weight, gestational age, parity) were used for descriptive epidemiology, multivariate logistic regression, and predictive score development. Results: Overall, 616 cases of RSVh in 45,648 infants were identified. Being born before the epidemic season, prematurity, and multiparity were independent predictors of RSVh. Infants born in January or June to August with prematurity and multiparity, and those born in September or December with only one other risk factor (prematurity or multiparity) were identified as moderate-risk, identifying the mothers as candidates for a first-level NPI prevention program. Infants born in September or December with prematurity and multiparity, and those born in October or November were identified as high-risk, identifying the mothers and infants as candidates for a second-level (NPI and PI) intervention. Conclusions: It is possible to determine predictors of RSVh at birth, allowing early enrollment of the target population in a two-level RSV prevention intervention. [ABSTRACT FROM AUTHOR]

Published
2022
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10. Définition d’épitopes CTL dans l’ADN VIH-1 archivé et présentables par le HLA-B : perspective vaccinale

Author

Jourdain, Marine and UB -, BU Carreire

Subjects
Vaccination thérapeutique, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Épitopes CTL, HLA de classe I, HIV - 1, Immunogénétique, V iral cure, Immunogenetics, Guérison, CTL epitopes, Therapeutic vaccines, VIH-1, HLA alleles
Abstract

Due to advances in antiretroviral therapy (ART), HIV-1 replication can nowadays be controlled among treated patients. Now, the objective is to find new therapeutic strategies to either eradicate the virus or achieve a “functional cure”. Therapeutic vaccines inducing cytotoxic T lymphocytes (CTL) are one of the most promising approaches. An effective vaccine must take into account the CTL epitopes variability in viral reservoirs and the human leukocytes antigen (HLA)-class I- allele-specific restriction. Using data from archived virus in HIV-1-infected patients from the Bordeaux University Hospital, we provide confirmation of important CTL epitope variability in HIV-1 proviral DNA, a major source contributing to viral rebound after stopping ART. We also found that mutations leading to this variability can affect the predicting MHC-I-epitope binding affinity and prevent their recognition. Moreover, we have identified highly conserved epitopes and epitopes carrying mutations with no significant effect on binding affinity, which are restricted by the most common HLA-B alleles in Caucasians and Africans. These epitopes could be used for the development of a multi-epitope-based peptide vaccine according to the genetics of patients., Grâce aux antirétroviraux, il est désormais possible de contrôler durablement la réplication du VIH-1 chez les patients sous traitement. L’objectif est maintenant de trouver de nouvelles stratégies thérapeutiques visant soit une éradication du virus soit une guérison « fonctionnelle ». L’une d’entre elles consiste en l’élaboration d’un vaccin thérapeutique impliquant les lymphocytes T cytotoxiques (CTL). La mise au point d’un vaccin efficace doit inévitablement tenir compte de la variabilité des épitopes CTL dans les réservoirs viraux et de leur présentation par les molécules HLA de classe I. Dans cette étude réalisée sur des virus archivés chez des patients infectés par le VIH-1 suivis au CHU de Bordeaux, nous confirmons l’importante variabilité des épitopes CTL au sein de l’ADN proviral à partir duquel la réplication virale sera généralement réinitiée lors d’un arrêt thérapeutique. Nos résultats montrent que les mutations à l’origine de cette variabilité peuvent diminuer l’affinité théorique de ces épitopes pour les molécules HLA et empêcher leur présentation. Par ailleurs, nous avons identifié des épitopes présentables par les allèles HLA-B les plus fréquents dans la population caucasienne et africaine, épitopes hautement conservés ou dont la variabilité n’affecte pas l’affinité pour les molécules HLA. Ces épitopes pourraient être utilisés pour l’élaboration d’un vaccin lipopeptidique qui tiendra compte de la génétique immunitaire de l’hôte.

Published
2018

11. Provir/Latitude 45 study: A step towards a multi-epitopic CTL vaccine designed on archived HIV-1 DNA and according to dominant HLA I alleles

Author

Tumiotto, Camille, primary, Alves, Bruna M., additional, Recordon-Pinson, Patricia, additional, Jourdain, Marine, additional, Bellecave, Pantxika, additional, Guidicelli, Gwenda-Line, additional, Visentin, Jonathan, additional, Bonnet, Fabrice, additional, Hessamfar, Mojdan, additional, Neau, Didier, additional, Sanchez, Jorge, additional, Brander, Christian, additional, Sajadi, Mohammad, additional, Eyzaguirre, Lindsay, additional, Soares, Esmeralda A., additional, Routy, Jean-Pierre, additional, Soares, Marcelo A., additional, and Fleury, Hervé, additional

Published
2019
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