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1. Assessment of serological techniques for screening patients for COVID-19 (COVID-SER): a prospective, multicentric study

Author

Sophie Trouillet-Assant, Amélie Massardier-Pilonchery, Barbara Charbotel, Nicolas Guibert, Jean-Baptiste Fassier, Muriel Rabilloud, Chloe Albert Vega, Antonin Bal, Julie Anne Nazare, Pascal Fascia, Adèle Paul, Constance d Aubarede, Virginie Pitiot, Matthieu Lahousse, André Boibieux, Djamila Makhloufi, Chantal Simon, Mary Anne Trabaud, François Gueyffier, Jérôme Adnot, Dulce Alfaiate, Alain Bergeret, Florent Bonnet, Gaëlle Bourgeois, Florence Brunel-Dalmas, Eurydice Caire, Pierre Chiarello, Laurent Cotte, Constance d'Aubarede, François Durupt, Escuret Vanessa, Fascia Pascal, Fassier Jean-Baptiste, Fontaine Juliette, Gaillot-Durand Lucie, Gaymard Alexandre, Gillet Myriam, Godinot Matthieu, Gueyffier François, Guibert Nicolas, Josset Laurence, Lahousse Matthieu, Lina Bruno, Lozano Hélène, Makhloufi Djamila, Massardier-Pilonchéry Amélie, Milon Marie-Paule, Moll Frédéric, Morfin Florence, Narbey David, Nazare Julie-Anne, Oria Fatima, Paul Adèle, Perry Marielle, Pitiot Virginie, Prudent Mélanie, Rabilloud Muriel, Samperiz Audrey, Schlienger Isabelle, Simon Chantal, Trabaud Mary-Anne, and Trouillet-Assant Sophie

Subjects
Medicine
Abstract

Introduction The COVID-19 pandemic caused by SARS-CoV-2 threatens global public health, and there is an urgent public health need to assess acquired immunity to SARS-CoV-2. Serological tests might provide results that can be complementary to or confirm suspected COVID-19 cases and reveal previous infection. The performance of serological assays (sensitivity and specificity) has to be evaluated before their use in the general population. The neutralisation capacity of the produced antibodies also has to be evaluated.Methods and analysis We set up a prospective, multicentric clinical study to evaluate the performance of serological kits among a population of healthcare workers presenting mild symptoms suggestive of SARS-CoV-2 infection. Four hundred symptomatic healthcare workers will be included in the COVID-SER study. The values obtained from a control cohort included during the prepandemic time will be used as reference. A workflow was set up to study serological response to SARS-CoV-2 infection and to evaluate antibody neutralisation capacity in patients with a confirmed SARS-CoV-2 infection. The sensitivity and specificity of the tests will be assessed using molecular detection of the virus as a reference. The measurement of IgM and IgG antibodies will be performed once per week for 6 consecutive weeks and then at 6, 12, 18, 24 and 36 months after the diagnosis. The kinetics of IgM and IgG will determine the optimal period to perform serological testing. The proportion of false negative PCR tests in symptomatic subjects will be determined on the basis of subsequent seroconversions.Ethics and dissemination Ethical approval has been obtained from the national review board for biomedical research in April 2020 (Comité de Protection des Personnes Sud Méditerranée I, Marseille, France) (ID RCB 2020-A00932-37). Results will be disseminated through presentations at scientific meetings and publications in peer-reviewed journals.Trial registration number NCT04341142.

Published
2020
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2. Advancing respiratory virus diagnostics: integrating the nasal IFN-I score for improved viral detection

Author

Mommert-Tripon, Marine, Parraud, Delphine, Grosbois, Cloé, Gaymard, Alexandre, Cheynet, Valérie, Lina, Bruno, Oriol, Guy, Laurent, Frédéric, Dupré, Caroline, Semanas, Quentin, Bal, Antonin, Generenaz, Laurence, Pons, Sylvie, Brengel-Pesce, Karen, Guichard, Audrey, Mouton, William, Morfin, Florence, Fleurie, Aurore, and Trouillet-Assant, Sophie

Published
2024
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3. Heterogeneity of Clinical Phenotypes in Severe Acute Respiratory Infections Owing to Respiratory Syncytial Virus: A Need to Look Beyond Hospitalization

Author

Panetta, Luc, Javouhey, Etienne, Claris, Olivier, Gaucherand, Pascal, Massardier, Jerome, Vanhems, Philippe, Bin, Sylvie, Polazzi, Stephanie, Cartier, Regine, Morfin, Florence, Jourdain, Marine, Valette, Martine, Ottmann, Michelle, Terrier, Olivier, Fiorini, Sylvie, Rivat, Nathalie, Renard, Florent, Roy-Cordero, Alvaro, Jaakkola, Kaisa, Portefaix, Aurélie, Nunes, Marta, Chauvel, Cecile, Mekki, Yahia, Wallet, Florent, Touzet, Sandrine, Ader, Florence, Conrad, Anne, Horvat, Côme, Duclaux-Loras, Lélia, Ouziel, Antoine, Butin, Marine, Couray-Targe, Sandrine, Myard-Dury, Anne-Florence, Haesebaert, Julie, Massoud, Mona, Benchaib, Mehdi, Ploin, Anne, Gillet, Yves, Lina, Bruno, Casalegno, Jean-Sebastien, and Ploin, Dominique

Published
2025
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11. Determinants of protection against SARS-CoV-2 Omicron BA.1 and Delta infections in fully vaccinated outpatients

Author

Roy, Alvaro, primary, Saade, Carla, additional, Josset, Laurence, additional, Clément, Bénédicte, additional, Morfin, Florence, additional, Destras, Grégory, additional, Valette, Martine, additional, Icard, Vinca, additional, Oblette, Antoine, additional, Debombourg, Marion, additional, Garrigou, Christine, additional, Brengel-Pesce, Karen, additional, Generenaz, Laurence, additional, Saker, Kahina, additional, Hernu, Romain, additional, Pozzetto, Bruno, additional, Lina, Bruno, additional, Trabaud, Mary-Anne, additional, Trouillet-Assant, Sophie, additional, and Bal, Antonin, additional

Published
2023
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12. Outcomes of post-exposure vaccination by modified vaccinia Ankara to prevent mpox (formerly monkeypox): a retrospective observational study in Lyon, France, June to August 2022

Author

Merad, Yanis, primary, Gaymard, Alexandre, additional, Cotte, Laurent, additional, Perpoint, Thomas, additional, Alfaiate, Dulce, additional, Godinot, Matthieu, additional, Becker, Agathe, additional, Cannesson, Olivier, additional, Batalla, Anne-Sophie, additional, Oria-Yassir, Fatima, additional, Landré, Sophie, additional, Morfin, Florence, additional, Bouscambert, Maude, additional, Valour, Florent, additional, Ader, Florence, additional, and Conrad, Anne, additional

Published
2022
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14. Live virus neutralization testing in convalescent patients and subjects vaccinated against 19A, 20B, 20I/501Y.V1 and 20H/501Y.V2 isolates of SARS-CoV-2

Author

Saade, Carla, Gonzalez, Claudia, Bal, Antonin, Valette, Martine, Saker, Kahina, Lina, Bruno, Josset, Laurence, Trabaud, Mary-Anne, Thiery, Guillaume, Botelho-Nevers, Elisabeth, Paul, Stéphane, Verhoeven, Paul, Bourlet, Thomas, Pillet, Sylvie, Morfin, Florence, Trouillet-Assant, Sophie, Pozzetto, Bruno, and on behalf of COVID-SER study group

Subjects
Letter, COVID-19 Vaccines, SARS-CoV-2, COVID-19, Antibodies, Viral, Antibodies, Neutralizing, 20H/501Y.V2, Neutralization Tests, 20I/501Y.V1, Humans, live virus neutralization test, variant of concern, humoral response, 20B
Abstract

SARS-CoV-2 mutations appeared recently and can lead to conformational changes in the spike protein and probably induce modifications in antigenicity. We assessed the neutralizing capacity of antibodies to prevent cell infection, using a live virus neutralization test with different strains [19A (initial one), 20B (B.1.1.241 lineage), 20I/501Y.V1 (B.1.1.7 lineage), and 20H/501Y.V2 (B.1.351 lineage)] in serum samples collected from different populations: two-dose vaccinated COVID-19-naive healthcare workers (HCWs; Pfizer-BioNTech BNT161b2), 6-months post mild COVID-19 HCWs, and critical COVID-19 patients. No significant difference was observed between the 20B and 19A isolates for HCWs with mild COVID-19 and critical patients. However, a significant decrease in neutralization ability was found for 20I/501Y.V1 in comparison with 19A isolate for critical patients and HCWs 6-months post infection. Concerning 20H/501Y.V2, all populations had a significant reduction in neutralizing antibody titers in comparison with the 19A isolate. Interestingly, a significant difference in neutralization capacity was observed for vaccinated HCWs between the two variants but not in the convalescent groups.

Published
2021

15. Determinants of protection against SARS‐CoV‐2 Omicron BA.1 and Delta infections in fully vaccinated outpatients.

Author

Roy, Alvaro, Saade, Carla, Josset, Laurence, Clément, Bénédicte, Morfin, Florence, Destras, Grégory, Valette, Martine, Icard, Vinca, Billaud, Geneviéve, Oblette, Antoine, Debombourg, Marion, Garrigou, Christine, Brengel‐Pesce, Karen, Generenaz, Laurence, Saker, Kahina, Hernu, Romain, Pozzetto, Bruno, Lina, Bruno, Trabaud, Mary‐Anne, and Trouillet‐Assant, Sophie

Subjects
SARS-CoV-2 Omicron variant, SARS-CoV-2, PEPTIDES, VACCINATION, OUTPATIENTS
Abstract

We aimed to evaluate the association between the humoral and cellular immune responses and symptomatic SARS‐CoV‐2 infection with Delta or Omicron BA.1 variants in fully vaccinated outpatients. Anti‐receptor binding domain (RBD) IgG levels and interferon‐gamma (IFN‐γ) release were evaluated at PCR‐diagnosis of SARS‐CoV‐2 in 636 samples from negative and positive patients during Delta and Omicron BA.1 periods. Median levels of anti‐RBD IgG in positive patients were significantly lower than in negative patients for both variants (p < 0.05). The frequency of Omicron BA.1 infection in patients with anti‐RBD IgG concentrations ≥1000 binding antibody units (BAU)/mL was 51.0% and decreased to 34.4% in patients with concentrations ≥3000 BAU/mL. For Delta infection, the frequency of infection was significantly lower when applying the same anti‐RBD IgG thresholds (13.3% and 5.3% respectively, p < 0.05). In addition, individuals in the hybrid immunity group had a 4.5 times lower risk of Delta infection compared to the homologous vaccination group (aOR = 0.22, 95% CI: [0.05−0.64]. No significant decrease in the risk of Omicron BA.1 infection was observed in the hybrid group compared to the homologous group, but the risk decreased within the hybrid group as anti‐RBD IgG titers increased (aOR = 0.08, 95% CI: [0.01−0.41], p = 0.008). IFN‐γ release post‐SARS‐CoV‐2 peptide stimulation was not different between samples from patients infected (either with Delta or Omicron BA.1 variant) or not (p > 0.05). Our results show that high circulating levels of anti‐RBD IgG and hybrid immunity were independently associated with a lower risk of symptomatic SARS‐CoV‐2 infection in outpatients with differences according to the infecting variant (www.clinicaltrials.gov; ID NCT05060939). [ABSTRACT FROM AUTHOR]

Published
2023
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16. Dynamics of viral shedding during ancestral or Omicron BA.1 SARS-CoV-2 infection and enhancement of pre-existing immunity during breakthrough infections

Author

Saade, Carla, primary, Brengel-Pesce, Karen, additional, Gaymard, Alexandre, additional, Trabaud, Mary-Anne, additional, Destras, Gregory, additional, Oriol, Guy, additional, Cheynet, Valérie, additional, Debombourg, Marion, additional, Mokdad, Bouchra, additional, Billaud, Geneviève, additional, Oblette, Antoine, additional, Créhalet, Hervé, additional, Giannoli, Jean-Marc, additional, Garrigou, Christine, additional, Generenaz, Laurence, additional, Compagnon, Christelle, additional, Boibieux, André, additional, Lina, Bruno, additional, Morfin, Florence, additional, Pozzetto, Bruno, additional, Josset, Laurence, additional, Trouillet Assant, Sophie, additional, and Bal, Antonin, additional

Published
2022
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17. Rapid and reliable inactivation protocols for the diagnostics of emerging viruses: The example of SARS‐CoV‐2 and monkeypox virus

Author

Quéromès, Grégory, primary, Frobert, Emilie, additional, Bouscambert‐Duchamp, Maude, additional, Oblette, Antoine, additional, Valette, Martine, additional, Billaud, Geneviève, additional, Escuret, Vanessa, additional, Lina, Bruno, additional, Morfin, Florence, additional, and Gaymard, Alexandre, additional

Published
2022
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19. SARS-CoV-2 N-Antigen Quantification in Respiratory Tract, Plasma and Urine: Kinetics and Association with RT-qPCR Results.

Author

Parraud, Delphine, Maucotel, Anne-Lise, Bouscambert, Maude, Morfin, Florence, Bitker, Laurent, Chidiac, Christian, De Castro, Nathalie, Frobert, Emilie, and Gaymard, Alexandre

Subjects
SARS-CoV-2, DELAYED diagnosis, COVID-19 testing, ANTIGENS, URINE, EXCRETION
Abstract

Qualitative SARS-CoV-2 antigen assays based on immunochromatography are useful for mass diagnosis of COVID-19, even though their sensitivity is poor in comparison with RT-PCR assays. In addition, quantitative assays could improve antigenic test performance and allow testing with different specimens. Using quantitative assays, we tested 26 patients for viral RNA and N-antigen in respiratory samples, plasma and urine. This allowed us to compare the kinetics between the three compartments and to compare RNA and antigen concentrations in each. Our results showed the presence of N-antigen in respiratory (15/15, 100%), plasma (26/59, 44%) and urine (14/54, 28.9%) samples, whereas RNA was only detected in respiratory (15/15, 100%) and plasma (12/60, 20%) samples. We detected N-antigen in urine and plasma samples until the day 9 and day 13 post-inclusion, respectively. The antigen concentration was found to correlate with RNA levels in respiratory (p < 0.001) and plasma samples (p < 0.001). Finally, urinary antigen levels correlated with plasma levels (p < 0.001). Urine N-antigen detection could be part of the strategy for the late diagnosis and prognostic evaluation of COVID-19, given the ease and painlessness of sampling and the duration of antigen excretion in this biological compartment. [ABSTRACT FROM AUTHOR]

Published
2023
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21. SARS-CoV-2 rapid test versus RT-qPCR on noninvasive respiratory self-samples during a city mass testing campaign.

Author

Gagnaire, Julie, Bonjean, Paul, Verot, Elise, Boulamail, Billal, Labetoulle, Remi, Gonzalo, Sylvie, Hilliquin, Delphine, Pillet, Sylvie, Michaud, Patrick, Brebion, Amélie, Morfin, Florence, Goff, Jérôme Le, Pelissier, Carole, Bourlet, Thomas, group, AutoCov study, Chauvin, Franck, Berthelot, Philippe, Botelho-Nevers, Elisabeth, and Pozzetto, Bruno

Published
2022
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23. Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness

Author

Bal, Antonin, primary, Destras, Gregory, additional, Sabatier, Marina, additional, Pichon, Maxime, additional, Regue, Hadrien, additional, Oriol, Guy, additional, Gillet, Yves, additional, Lina, Bruno, additional, Brengel-Pesce, Karen, additional, Josset, Laurence, additional, and Morfin, Florence, additional

Published
2022
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24. Six-month antibody response to SARS-CoV-2 in healthcare workers assessed by virus neutralization and commercial assays

Author

Fascia Pascal, Adnot Jérôme, Fontaine Juliette, Massardier-Pilonchéry Amélie, Boibieux André, Josset Laurence, Nicolas Guibert, Oria Fatima, Nazare Julie-Anne, Chiarello Pierre, Samperiz Audrey, Antonin Bal, Prudent Mélanie, Simon Chantal, Dulce Alfaiate, Fassier Jean-Baptiste, Florence Morfin-Sherpa, Constance d'Aubarede, Brunel-Dalmas Florence, Lahousse Matthieu, Pitiot Virginie, Trabaud Mary-Anne, Gaillot-Durand Lucie, Bal Antonin, Lina Bruno, Trouillet-Assant Sophie, Gueyffier François, Perry Marielle, Gillet Myriam, Adèle Paul, Jean-Baptiste Fassier, Valette Martine, Bourgeois Gaëlle, Lozano Hélène, Kahina Saker, Alfaiate Dulce, Morfin Florence, Mary-Anne Trabaud, Rabilloud Muriel, Schlienger Isabelle, Narbey David, Durupt François, Makhloufi Djamila, Bruno Pozzetto, Paul Adèle, Caire Eurydice, Bergeret Alain, Godinot Matthieu, Escuret Vanessa, Bonnet Florent, Moll Frédéric, Guibert Nicolas, Gaymard Alexandre, Cotte Laurent, Sophie Trouillet-Assant, Muriel Rabilloud, Virginie Pitiot, Amélie Massardier-Pilonchery, Milon Marie-Paule, Charbotel Barbara, Carole Langlois-Jacques, Bruno Lina, Hospices Civils de Lyon (HCL), Unité Mixte de Recherche Epidémiologique et de Surveillance Transport Travail Environnement (UMRESTTE UMR_T9405), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Gustave Eiffel, Université de Lyon, Institut des Agents Infectieux [Lyon] (IAI), Service de médecine et santé au travail, hospices civils de Lyon, Laboratoire de virologie, Physiopathologie et biothérapies des infections muqueuses (GIMAP), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM), 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), 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), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)

Subjects
Male, Time Factors, Antibodies, Viral, Neutralization, MEDECINE, Health personnel, 0302 clinical medicine, SANTE, SARS-COV2, Medicine, 030212 general & internal medicine, Letter to the Editor, 0303 health sciences, biology, PERSONNEL DE SANTE, virus diseases, General Medicine, Middle Aged, University hospital, TRAVAIL, 3. Good health, Titer, Infectious Diseases, Female, Antibody, Serological assays, ANTICORPS, Adult, Microbiology (medical), 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Health Personnel, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), education, GESTION DU PERSONNEL, Virus Neutralization, Virus, 03 medical and health sciences, Neutralization Tests, Seroprevalence, Humans, Healthcare workers, Virus neutralisation assay, 030304 developmental biology, SARS-CoV-2, business.industry, COVID-19, Antibodies, Neutralizing, Virology, Antibody response, biology.protein, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract

We conducted a prospective study in healthcare workers (n=296) of the University Hospital of Lyon, France. Serum samples (n=296) collected six months after disease onset were tested using three commercial assays: the Wantai Ab assay detecting total antibodies against the receptor binding domain (RBD) of the S protein, the bioMerieux Vidas assay detecting IgG to the RBD and the Abbott Architect assay detecting IgG to the N protein. The neutralising antibody (NAb) titre was also determined for all samples with a virus neutralisation assay (VNA) using live virus. The positivity rate was 100% with the Wantai assay, 84.8% with the bioMerieux assay and 55.4% with the Abbott assay. Only 51% of HCWs were positive for the presence of NAb. Less than 10 % of HCWs had a NAb titre greater than 80. At a neutralising titre of 80, the area under the curves [IC 95%] was 0.71 [0.62-0.81], 0.75 [0.65-0.85] and 0.95 [0.92-0.97] for Wantai, Abbott and Vidas respectively. The data presented herein suggest that commercial assays detecting antibodies against the N protein must not be used in long-term seroprevalence surveys while the Wantai assay could be useful for this purpose. VNA should remain the gold standard to assess the protective antibody response, but some commercial assays could be used as first-line screening of long-term presence of NAb.

Published
2021
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25. Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation, France, December 2021 - February 2022

Author

Bal, Antonin, primary, Simon, Bruno, additional, Destras, Gregory, additional, Chalvignac, Richard, additional, Semanas, Quentin, additional, Oblette, Antoine, additional, Queromes, Gregory, additional, Fanget, Remi, additional, Regue, Hadrien, additional, Morfin, Florence, additional, Valette, Martine, additional, Lina, Bruno, additional, and Josset, Laurence, additional

Published
2022
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28. Application of a forecasting model to mitigate the consequences of unexpected RSV surge: Experience from the post-COVID-19 2021/22 winter season in a major metropolitan centre, Lyon, France.

Author

Casalegno, Jean-Sebastien, Bents, Samantha, Paget, John, Gillet, Yves, Ploin, Dominique, Javouhey, Etienne, Lina, Bruno, Morfin, Florence, Grenfell, Bryan T., and Baker, Rachel E.

Subjects
RISK assessment, PUBLIC health surveillance, PREDICTION models, SEASONS, RESPIRATORY syncytial virus infections, TIME series analysis, DESCRIPTIVE statistics, PEDIATRICS, SIMULATION methods in education, METROPOLITAN areas, DISEASE susceptibility, DATA analysis software, FORECASTING, COVID-19 pandemic, DISEASE risk factors
Abstract

Background The emergence of COVID-19 triggered the massive implementation of non-pharmaceutical interventions (NPI) which impacted the circulation of respiratory syncytial virus (RSV) during the 2020/2021 season. Methods A time-series susceptible-infected-recovered (TSIR) model was used early September 2021 to forecast the implications of this disruption on the future 2021/2022 RSV epidemic in Lyon urban population. Results When compared to observed hospital-confirmed cases, the model successfully captured the early start, peak timing, and end of the 2021/2022 RSV epidemic. These simulations, added to other streams of surveillance data, shared and discussed among the local field experts were of great value to mitigate the consequences of this atypical RSV outbreak on our hospital paediatric department. Conclusions TSIR model, fitted to local hospital data covering large urban areas, can produce plausible post-COVID-19 RSV simulations. Collaborations between modellers and hospital management (who are both model users and data providers) should be encouraged in order to validate the use of dynamical models to timely allocate hospital resources to the future RSV epidemics. [ABSTRACT FROM AUTHOR]

Published
2023
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29. Rapid and reliable inactivation protocols for the diagnostics of emerging viruses: The example of SARS‐CoV‐2 and monkeypox virus.

Author

Quéromès, Grégory, Frobert, Emilie, Bouscambert‐Duchamp, Maude, Oblette, Antoine, Valette, Martine, Billaud, Geneviève, Escuret, Vanessa, Lina, Bruno, Morfin, Florence, and Gaymard, Alexandre

Subjects
SARS-CoV-2, CORONAVIRUS diseases, SODIUM dodecyl sulfate, POLYMERASE chain reaction, MONKEYPOX, PUBLIC health
Abstract

The emergence and sustained transmission of novel pathogens are exerting an increasing demand on the diagnostics sector worldwide, as seen with the ongoing severe acute respiratory coronavirus 2 (SARS‐CoV‐2) pandemic and the more recent public health concern of monkeypox virus (MPXV) since May 2022. Appropriate and reliable viral inactivation measures are needed to ensure the safety of personnel handling these infectious samples. In the present study, seven commercialized diagnosis buffers, heat (56°C and 60°C), and sodium dodecyl sulfate detergent (2.0%, 1.0%, and 0.5% final concentrations) were tested against infectious SARS‐CoV‐2 and MPXV culture isolates on Vero cell culture. Cytopathic effects were observed up to 7 days postinoculation and viral load evolution was measured by semiquantitative polymerase chain reaction. The World Health Organization recommends an infectious titer reduction of at least 4 log10. As such, the data show efficacious SARS‐CoV‐2 inactivation by all investigated methods, with >6.0 log10 reduction. MPXV inactivation was also validated with all investigated methods with 6.9 log10 reductions, although some commercial buffers required a longer incubation period to yield complete inactivation. These results are valuable for facilities, notably those without biosafety level‐3 capabilities, that need to implement rapid and reliable protocols common against both SARS‐CoV‐2 and MPXV. [ABSTRACT FROM AUTHOR]

Published
2023
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30. 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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31. Correction: Early nasal type I IFN immunity against SARS-CoV-2 is compromised in patients with autoantibodies against type I IFNs

Author

Lopez, Jonathan, primary, Mommert, Marine, additional, Mouton, William, additional, Pizzorno, Andrés, additional, Brengel-Pesce, Karen, additional, Mezidi, Mehdi, additional, Villard, Marine, additional, Lina, Bruno, additional, Richard, Jean-Christophe, additional, Fassier, Jean-Baptiste, additional, Cheynet, Valérie, additional, Padey, Blandine, additional, Duliere, Victoria, additional, Julien, Thomas, additional, Paul, Stéphane, additional, Bastard, Paul, additional, Belot, Alexandre, additional, Bal, Antonin, additional, Casanova, Jean-Laurent, additional, Rosa-Calatrava, Manuel, additional, Morfin, Florence, additional, Walzer, Thierry, additional, and Trouillet-Assant, Sophie, additional

Published
2021
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32. Early nasal type I IFN immunity against SARS-CoV-2 is compromised in patients with autoantibodies against type I IFNs

Author

Lopez, Jonathan, primary, Mommert, Marine, additional, Mouton, William, additional, Pizzorno, Andrés, additional, Brengel-Pesce, Karen, additional, Mezidi, Mehdi, additional, Villard, Marine, additional, Lina, Bruno, additional, Richard, Jean-Christophe, additional, Fassier, Jean-Baptiste, additional, Cheynet, Valérie, additional, Padey, Blandine, additional, Duliere, Victoria, additional, Julien, Thomas, additional, Paul, Stéphane, additional, Bastard, Paul, additional, Belot, Alexandre, additional, Bal, Antonin, additional, Casanova, Jean-Laurent, additional, Rosa-Calatrava, Manuel, additional, Morfin, Florence, additional, Walzer, Thierry, additional, and Trouillet-Assant, Sophie, additional

Published
2021
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33. Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

Author

Gaymard, Alexandre, Bosetti, Paolo, Feri, Adeline, Destras, Gregory, Enouf, Vincent, Andronico, Alessio, Burrel, Sonia, Behillil, Sylvie, Sauvage, Claire, Bal, Antonin, Morfin, Florence, Van Der Werf, Sylvie, Josset, Laurence, Blanquart, François, Coignard, Bruno, Cauchemez, Simon, Lina, Bruno, Gault, Elyanne, Moreau, Frédérique, Brichler, Ségolène, Delagrèverie, Héloïse, Descamps, Diane, Charpentier, Charlotte, Rozenberg, Flore, L'Honneur, Anne-Sophie, Veyer, David, Bélec, Laurent, Fourati, Slim, Rodriguez, Christophe, Pawlotsky, Jean-Michel, Fourgeaud, Jacques, Abid, Hanène, Roque-Afonso, Anne-Marie, Fenaux, Honorine, Jary, Aude, Marot, Stéphane, Salmona, Maud, Chaix, Marie-Laure, Morand-Joubert, Laurence, Schnuriger, Aurélie, Juillet, Stéphanie Marque, Bargain, Pauline, Poggi, Cécile, Chollet, Lionel, Guillaume, Clémence, Guinard, Jérôme, Vallet, Sophie, Pilorgé, Léa, Schvoerer, Evelyne, Hartard, Cédric, Castelain, Sandrine, François, Catherine, Ducancelle, Alexandra, Lefeuvre, Caroline, Lepiller, Quentin, Marty-Quinternet, Solène, Bellecave, Pantxika, Tumiotto, Camille, Dina, Julia, Le Gouil, Meriadeg, Henquell, Cécile, Mirand, Audrey, Césaire, Raymond, de Rougemont, Alexis, Auvray, Christelle, Larrat, Sylvie, Némoz, Benjamin, Tinez, Claire, Guigon, Aurélie, Hantz, Sébastien, Rogez, Sylvie, Dos Santos, Georges, Perez, Pascale, Jost, Christelle, Montes, Brigitte, Foulongne, Vincent, Imbert, Berthe-Marie, Bressollette, Céline, Giordanengo, Valérie, Gonfrier, Géraldine, Garcia, Magali, Lévêque, Nicolas, Brodard, Véronique, Moret, Hélène, Thibault, Vincent, Maillard, Anne, Jaffar-Bandjee, Marie-Christine, Gueudin, Marie, Plantier, Jean-Christophe, Pozzetto, Bruno, Pillet, Sylvie, Fafi-Kremer, Samira, Solis, Morgane, Izopet, Jacques, Trémeaux, Pauline, Stefic, Karl, Handala, Lynda, Billaud, Geneviève, Frobert, Emilie, Mérens, Audrey, Bigaillon, Christine, Desroches, Marine, Thepenier, Cédric, Janvier, Frédéric, Otto, Marie-Pierre, Roquebert, Bénédicte, Haïm-Boukobza, Stéphanie, Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Hospices Civils de Lyon (HCL), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (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), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Laboratoire de Virologie [CHU Amiens], CHU Amiens-Picardie, ANRS - Maladies infectieuses émergentes (ANRS - MIE), Institut National de la Santé et de la Recherche Médicale (INSERM), We acknowledge financial support from Santé publique France (the French national public health agency), the French Ministry of health (Grant COVIDseq), the Consortium for the surveillance and research on emerging pathogens via microbial genomics (EMERGEN) coordinated by Santé publique France and ANRS Maladies Infectieuses Emergentes, the Investissement d’Avenir programme, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases programme (grant ANR-10-LABX-62-IBEID), the European Union’s Horizon 2020 research and in-novation programme under grants 101003589 (RECOVER). This work has been supported by the laboratories belonging to the ColVHB network*., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), 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), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Gestionnaire, Hal Sorbonne Université, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)

Subjects
Author's Correction, Paris, medicine.medical_specialty, 2019-20 coronavirus outbreak, Lineage (genetic), Coronavirus disease 2019 (COVID-19), Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viral infections, [SDV]Life Sciences [q-bio], Context (language use), Biology, 03 medical and health sciences, 0302 clinical medicine, Virology, medicine, Humans, MESH: COVID-19, MESH: SARS-CoV-2, 030212 general & internal medicine, 030304 developmental biology, COVID, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, SARS-CoV-2, MESH: Paris, Public Health, Environmental and Occupational Health, COVID-19, [SDV] Life Sciences [q-bio], MESH: France, 20I/501Y.V1, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, surveillance, France, mutation, Rapid Communication, Demography
Abstract

International audience; The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% of all positive tests) performed on 7-8 January 2021 in France. The prevalence of 20I/501Y.V1 was 3.3% among positive tests nationwide and 6.9% in the Paris region. Analysing the recent rise in the prevalence of 20I/501Y.V1, we estimate that, in the French context, 20I/501Y.V1 is 52-69% more transmissible than the previously circulating lineages, depending on modelling assumptions.

Published
2021
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36. Type I IFN immunoprofiling in COVID-19 patients

Author

Mouton, William, Oriol, Guy, Compagnon, Christelle, Generenaz, Laurence, Cheynet, Valérie, Ader, Florence, Becker, Agathe, Benech, Nicholas, Chauvelot, Pierre, Chidiac, Christian, Conrad, Anne, Ferry, Tristan, Miailhes, Patrick, Perpoint, Thomas, Perry, Marielle, Pouderoux, Cécile, Roux, Sandrine, Triffault-Fillit, Claire, Valour, Florent, Hodane, Yonis, Chauvelot, Louis, Chabert, Paul, Provoost, Judith, David, Guillaume, Folliet, Laure, Lecam, Pierre, Billaud, Geneviève, Bouscambert, Maude, Escuret, Vanessa, Frobert, Emilie, Bal, Antonin, Destras, Grégory, Josset, Laurence, Morfin, Florence, Munier, Clément, Valette, Martine, Venet, Fabienne, Garnier, Lorna, Pescarmona, Rémi, Lombard, Christine, Walzer, Thierry, Trouillet-Assant, Sophie, Viel, Sebastien, Gaymard, Alexandre, Pons, Sylvie, Richard, Jean-Christophe, Perret, Magali, Villard, Marine, Brengel-Pesce, Karen, Lina, Bruno, Mezidi, Mehdi, Bitker, Laurent, and Belot, Alexandre

Published
2020
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37. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

Author

Bal, Antonin, Destras, Gregory, Gaymard, Alexandre, Stefic, Karl, Marlet, Julien, Eymieux, Sébastien, Regue, Hadrien, Semanas, Quentin, d’Aubarede, Constance, Billaud, Geneviève, Laurent, Frédéric, Gonzalez, Claudia, Mekki, Yahia, Valette, Martine, Bouscambert, Maude, Gaudy-Graffin, Catherine, Lina, Bruno, Morfin, Florence, Josset, Laurence, Casalegno, Jean-Sébastien, Frobert, Emilie, Escuret, Vanessa, Icard, Vinca, Jeannoel, Marion, Milon, Marie-Paule, Ramière, Christophe, Scholtès, Caroline, Tardy, Jean-Claude, Trabaud, Mary-Anne, Schuffenecker, Isabelle, Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), 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), Hospices Civils de Lyon (HCL), Morphogénèse et antigénicité du VIH et du virus des Hépatites (MAVIVH - U1259 Inserm - CHRU Tours ), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), The members of the COVID-Diagnosis HCL Study Group : Jean-Sébastien Casalegno, Emilie Frobert, Vanessa Escuret, Vinca Icard, Marion Jeannoel, Marie-Paule Milon, Christophe Ramière, Caroline Scholtès, Jean-Claude Tardy, Mary-Anne Trabaud, Isabelle Schuffenecker, 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), Marlet, Julien, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Tours, and Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS)

Subjects
0301 basic medicine, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Two step, spike protein, variants, deletion, Genome, Viral, Biology, spike protein, Genome, 03 medical and health sciences, COVID-19, whole genome sequencing, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Humans, Spike (database), Base sequence, Sequence Deletion, whole genome sequencing, variants, Base Sequence, deletion, SARS-CoV-2, Public Health, Environmental and Occupational Health, COVID-19, 030104 developmental biology, Spike Glycoprotein, Coronavirus, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Identification (biology), France, Rapid Communication
Abstract

International audience; We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69-V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

Published
2021
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38. 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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39. Live virus neutralisation testing in convalescent patients and subjects vaccinated against 19A, 20B, 20I/501Y.V1 and 20H/501Y.V2 isolates of SARS-CoV-2

Author

Gonzalez, Claudia, primary, Saade, Carla, additional, Bal, Antonin, additional, Valette, Martine, additional, Saker, Kahina, additional, Lina, Bruno, additional, Josset, Laurence, additional, Trabaud, Mary-Anne, additional, Thiery, Guillaume, additional, Botelho-Nevers, Elisabeth, additional, Paul, Stéphane, additional, Verhoeven, Paul, additional, Bourlet, Thomas, additional, Pillet, Sylvie, additional, Morfin, Florence, additional, Trouillet-Assant, Sophie, additional, and Pozzetto, Bruno, additional

Published
2021
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40. Cluster of Coronavirus Disease 2019 (COVID-19) in the French Alps, February 2020

Author

Danis, Kostas, Epaulard, Olivier, Bénet, Thomas, Gaymard, Alexandre, Campoy, Séphora, Botelho-Nevers, Elisabeth, Bouscambert-Duchamp, Maude, Spaccaferri, Guillaume, Ader, Florence, Mailles, Alexandra, Boudalaa, Zoubida, Tolsma, Violaine, Berra, Julien, Vaux, Sophie, Forestier, Emmanuel, Landelle, Caroline, Fougere, Erica, Thabuis, Alexandra, Berthelot, Philippe, Veil, Raphael, Levy-Bruhl, Daniel, Chidiac, Christian, Lina, Bruno, Coignard, Bruno, Saura, Christine, Brottet, Elise, Casamatta, Delphine, Gallien, Yves, George, Scarlett, Viriot, Delphine, Ait Belghiti, Fatima, Bernard-Stoecklin, Sibylle, Desenclos, Jean-Claude, Giese, Coralie, Ghislain, Didier, Gounon, Magali, Grangeret, Nathalie, Marie, Cécile, Morel, Bruno, Deher, Muriel, Ronnaux Baron, Anne-Sophie, Courbis, Geneviève, Ragozin, Nathalie, Wolska, Monika, Serange, Eric, Mercatello, Delphine, Aiouaz, Soraya, Valette, Martine, Frobert, Emilie, Josset, Laurence, Escuret, Vanessa, Morfin, Florence, Billaud, Geneviève, Blanc, Myriam, Arata-Bardet, Julie, Froidure, Marie, Le Maréchal, Marion, Pavese, Patricia, Pierre, Isabelle, Becker, Agathe, Chauvelot, Pierre, Conrad, Anne, Ferry, Tristan, Miailhes, Patrick, Perpoint, Thomas, Pouderoux, Cécile, Roux, Sandrine, Valour, Florent, Lutz, Marie-France, Pouvaret, Anne, Vitrat, Virginie, Maillet, Mylène, Janssen, Cécile, Piet, Emilie, Bosch, Alexie, Destrem, Anne-Laure, Isnard, Margaux, Challan-Belval, Thibault, Wackenheim, Chloe, Couturier, Alice, Gheno, Gael, Roupioz, Thierry, Lucet, Nicolas, Ayouni, Stéphane, Vincent, Mireille, de Epidemiología, Servicio, General de Salud Pública del Gover Balear, Dirección, Masserey Spicher, Virginie, Bourquin, Catherine, Stoll, Jeanine, Chaud, Pascal, and Mounayar, Anne-Laure

Subjects
Microbiology (medical), Pediatrics, medicine.medical_specialty, Attack rate, Pneumonia, Viral, coronavirus, Disease cluster, Asymptomatic, 03 medical and health sciences, Betacoronavirus, 0302 clinical medicine, 030225 pediatrics, medicine, Major Article, Cluster Analysis, Humans, Serologic Tests, 030212 general & internal medicine, cluster, Index case, Pandemics, Aged, Retrospective Studies, Aged, 80 and over, Transmission (medicine), business.industry, SARS-CoV-2, COVID-19, Retrospective cohort study, Middle Aged, medicine.disease, infection, AcademicSubjects/MED00290, Infectious Diseases, Coinfection, Female, France, medicine.symptom, business, Coronavirus Infections, Viral load
Abstract

BackgroundOn 7 February 2020, French Health authorities were informed of a confirmed case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in an Englishman infected in Singapore who had recently stayed in a chalet in the French Alps. We conducted an investigation to identify secondary cases and interrupt transmission.MethodsWe defined as a confirmed case a person linked to the chalet with a positive reverse-transcription polymerase chain reaction sample for SARS-CoV-2.ResultsThe index case stayed 4 days in the chalet with 10 English tourists and a family of 5 French residents; SARS-CoV-2 was detected in 5 individuals in France, 6 in England (including the index case), and 1 in Spain (overall attack rate in the chalet: 75%). One pediatric case, with picornavirus and influenza A coinfection, visited 3 different schools while symptomatic. One case was asymptomatic, with similar viral load as that of a symptomatic case. Seven days after the first cases were diagnosed, 1 tertiary case was detected in a symptomatic patient with from the chalet a positive endotracheal aspirate; all previous and concurrent nasopharyngeal specimens were negative. Additionally, 172 contacts were monitored; all contacts tested for SARS-CoV-2 (N = 73) were negative.ConclusionsThe occurrence in this cluster of 1 asymptomatic case with similar viral load as a symptomatic patient suggests transmission potential of asymptomatic individuals. The fact that an infected child did not transmit the disease despite close interactions within schools suggests potential different transmission dynamics in children. Finally, the dissociation between upper and lower respiratory tract results underscores the need for close monitoring of the clinical evolution of suspected cases of coronavirus disease 2019.

Published
2020
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41. SARS-CoV-2 Omicron Variant, Lineage BA.1, Is Associated with Lower Viral Load in Nasopharyngeal Samples Compared to Delta Variant.

Author

Sentis, Célia, Billaud, Geneviève, Bal, Antonin, Frobert, Emilie, Bouscambert, Maude, Destras, Gregory, Josset, Laurence, Lina, Bruno, Morfin, Florence, and Gaymard, Alexandre

Subjects
SARS-CoV-2 Omicron variant, SARS-CoV-2 Delta variant, VIRAL load, MEDICAL personnel, WHOLE genome sequencing
Abstract

Objectives: High viral load in upper respiratory tract specimens observed for Delta cases might contribute to its increased infectivity compared to the other variant. However, it is not yet documented if the Omicron variant's enhanced infectivity is also related to a higher viral load. Our aim was to determine if the Omicron variant's spread is also related to higher viral loads compared to the Delta variant. Methods: Nasopharyngeal swabs, 129 (Omicron) and 85 (Delta), from Health Care Workers were collected during December 2021 at the University Hospital of Lyon, France. Cycle threshold (Ct) for the RdRp target of cobas® 6800 SARS-CoV-2 assay was used as a proxy to evaluate SARS-CoV-2 viral load. Variant identification was performed using a screening panel and confirmed by whole genome sequencing. Results: Herein, we showed that the RT-PCR Ct values in Health Care Workers sampled within 5 days after symptom onset were significantly higher for Omicron cases than Delta cases (21.7 for Delta variant and 23.8 for Omicron variant, p = 0.008). This difference was also observed regarding patient with complete vaccination. Conclusions: This result supports the studies showing that the increased transmissibility of Omicron is related to other mechanisms than higher virus excretion. [ABSTRACT FROM AUTHOR]

Published
2022
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43. Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

Author

Quéromès, Grégory, primary, Destras, Grégory, additional, Bal, Antonin, additional, Regue, Hadrien, additional, Burfin, Gwendolyne, additional, Brun, Solenne, additional, Fanget, Rémi, additional, Morfin, Florence, additional, Valette, Martine, additional, Trouillet-Assant, Sophie, additional, Lina, Bruno, additional, Frobert, Emilie, additional, and Josset, Laurence, additional

Published
2021
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44. Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

Author

Quéromès, Grégory, primary, Destras, Grégory, additional, Bal, Antonin, additional, Regue, Hadrien, additional, Burfin, Gwendolyne, additional, Brun, Solenne, additional, Fanget, Rémi, additional, Morfin, Florence, additional, Valette, Martine, additional, Lina, Bruno, additional, Frobert, Emilie, additional, and Josset, Laurence, additional

Published
2020
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46. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Author

Charre, Caroline, primary, Ginevra, Christophe, additional, Sabatier, Marina, additional, Regue, Hadrien, additional, Destras, Grégory, additional, Brun, Solenne, additional, Burfin, Gwendolyne, additional, Scholtes, Caroline, additional, Morfin, Florence, additional, Valette, Martine, additional, Lina, Bruno, additional, Bal, Antonin, additional, and Josset, Laurence, additional

Published
2020
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47. Type I IFN immunoprofiling in COVID-19 patients

Author

Trouillet-Assant, Sophie, primary, Viel, Sebastien, additional, Gaymard, Alexandre, additional, Pons, Sylvie, additional, Richard, Jean-Christophe, additional, Perret, Magali, additional, Villard, Marine, additional, Brengel-Pesce, Karen, additional, Lina, Bruno, additional, Mezidi, Mehdi, additional, Bitker, Laurent, additional, Belot, Alexandre, additional, Mouton, William, additional, Oriol, Guy, additional, Compagnon, Christelle, additional, Generenaz, Laurence, additional, Cheynet, Valérie, additional, Ader, Florence, additional, Becker, Agathe, additional, Benech, Nicholas, additional, Chauvelot, Pierre, additional, Chidiac, Christian, additional, Conrad, Anne, additional, Ferry, Tristan, additional, Miailhes, Patrick, additional, Perpoint, Thomas, additional, Perry, Marielle, additional, Pouderoux, Cécile, additional, Roux, Sandrine, additional, Triffault-Fillit, Claire, additional, Valour, Florent, additional, Hodane, Yonis, additional, Chauvelot, Louis, additional, Chabert, Paul, additional, Provoost, Judith, additional, David, Guillaume, additional, Folliet, Laure, additional, Lecam, Pierre, additional, Billaud, Geneviève, additional, Bouscambert, Maude, additional, Escuret, Vanessa, additional, Frobert, Emilie, additional, Bal, Antonin, additional, Destras, Grégory, additional, Josset, Laurence, additional, Morfin, Florence, additional, Munier, Clément, additional, Valette, Martine, additional, Venet, Fabienne, additional, Garnier, Lorna, additional, Pescarmona, Rémi, additional, Lombard, Christine, additional, and Walzer, Thierry, additional

Published
2020
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48. Performance Assessment of SARS-CoV-2 PCR Assays Developed by WHO Referral Laboratories

Author

Etievant, Sibyle, primary, Bal, Antonin, additional, Escuret, Vanessa, additional, Brengel-Pesce, Karen, additional, Bouscambert, Maude, additional, Cheynet, Valérie, additional, Generenaz, Laurence, additional, Oriol, Guy, additional, Destras, Gregory, additional, Billaud, Geneviève, additional, Josset, Laurence, additional, Frobert, Emilie, additional, Morfin, Florence, additional, and Gaymard, Alexandre, additional

Published
2020
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49. Sensitivity assessment of SARS-CoV-2 PCR assays developed by WHO referral laboratories

Author

Etievant, Sibyle, primary, Bal, Antonin, additional, Escuret, Vanessa, additional, Brengel–Pesce, Karen, additional, Bouscambert, Maude, additional, Cheynet, Valérie, additional, Generenaz, Laurence, additional, Oriol, Guy, additional, Destras, Gregory, additional, Billaud, Geneviève, additional, Josset, Laurence, additional, Frobert, Emilie, additional, Morfin, Florence, additional, and Gaymard, Alexandre, additional

Published
2020
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50. Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)

Author

Bal, Antonin, primary, Destras, Grégory, additional, Gaymard, Alexandre, additional, Bouscambert-Duchamp, Maude, additional, Valette, Martine, additional, Escuret, Vanessa, additional, Frobert, Emilie, additional, Billaud, Geneviève, additional, Trouillet-Assant, Sophie, additional, Cheynet, Valérie, additional, Brengel-Pesce, Karen, additional, Morfin, Florence, additional, Lina, Bruno, additional, and Josset, Laurence, additional

Published
2020
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