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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values
Samuel Alizon; Christian Selinger; Mircea T Sofonea; Stephanie Haim-Boukobza; Jean-Marc Giannoli; Laetitia Ninove; Sylvie Pillet; Thibault Vincent; Alexis de Rougemont; Camille Tumiotto; Morgane Solis; Robin Stephan; Celine Bressollette-Bodin; Maud Salmona; Anne-Sophie L'Honneur; Sylvie Behillil; Caroline Lefeuvre; Julia Dina; Sebastien Hantz; Cedric Hartard; David Veyer; HeloIse M Delagreverie; Slim Fourati; Benoit Visseaux; Cecile Henquell; Bruno Lina; Vincent Foulougne; Sonia Burrel.
Afiliação
  • Samuel Alizon; MIVEGEC, CNRS, IRD, University of Montpellier
  • Christian Selinger; MIVEGEC, CNRS, IRD, University of Montpellier
  • Mircea T Sofonea; MIVEGEC, CNRS, IRD, University of Montpellier
  • Stephanie Haim-Boukobza; Laboratoire CERBA, Saint-Ouen-L'Aumone, France
  • Jean-Marc Giannoli; BIOGROUP, Scientific Direction, France
  • Laetitia Ninove; Unite des Virus emergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Mediterranee Infection), Marseille, France
  • Sylvie Pillet; Laboratoire des agents infectieux et d'hygiene, CHU de Saint-Etienne, France
  • Thibault Vincent; Laboratoire de Virologie, CHU Rennes, France
  • Alexis de Rougemont; Laboratory of Virology, University Hospital of Dijon, F-21000, Dijon, France
  • Camille Tumiotto; Univ. Bordeaux, CNRS-UMR 5234, CHU Bordeaux, Virology Department, F-33000, Bordeaux, France
  • Morgane Solis; CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France / Universite de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
  • Robin Stephan; Laboratoire de Microbiologie, CHU Nimes, France
  • Celine Bressollette-Bodin; Nantes Universite, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN ; CHU Nantes, Service de Virologie ; CHU Nantes, C
  • Maud Salmona; Laboratoire de Virologie, Hopital Saint Louis, APHP, INSERM U976, equipe INSIGHT, Universite de Paris, France
  • Anne-Sophie L'Honneur; Assistance Publique-Hopitaux de Paris, Hopital Cochin, Service de Virologie, France
  • Sylvie Behillil; National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France.
  • Caroline Lefeuvre; Departement des Agents Infectieux, Laboratoire de Virologie, CHU d'Angers, Angers, France et Laboratoire HIFIH, UPRES EA 3859, Universite d'Angers, Angers, Fra
  • Julia Dina; Normandie Univ, UNICAEN, UNIROUEN, GRAM 2.0, 14000 Caen, France, Caen University Hospital, Department of Virology, F 14000 Caen, France
  • Sebastien Hantz; CHU Limoges, Laboratoire de Bacteriologie-Virologie-Hygiene, F-87000 Limoges, France et Univ. Limoges, RESINFIT, U 1092, F-87000 Limoges, France
  • Cedric Hartard; Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-les-Nancy, France ; Universite de Lorraine, CNRS, LCPME, F-54000, Nancy, France
  • David Veyer; Laboratoire de Virologie, Service de Microbiologie, hopital europeen Georges Pompidou, Assistance Publique-Hopitaux de Paris et Unite de Genomique Fonctionnelle
  • HeloIse M Delagreverie; AP-HP, Hopital Avicenne, Laboratoire de microbiologie clinique, Bobigny, France
  • Slim Fourati; Henri Mondor Hospital, virology department, France
  • Benoit Visseaux; Universite de Paris, Inserm, UMR 1137 IAME et Laboratoire de Virologie, Hopital Bichat Claude Bernard, AP-HP, Paris, France
  • Cecile Henquell; Service de Virologie medicale, 3IHP, CHU Clermont-Ferrand, France
  • Bruno Lina; CNR des virus des infections respiratoires (dont la Grippe), Institut des Agents Infectieux, Hopital de la Croix Rousse, HCL, Lyon, France
  • Vincent Foulougne; Laboratoire de Virologie, CHU de Montpellier, France
  • Sonia Burrel; Sorbonne Universite, INSERM U1136, Institut Pierre Louis d'Epidemiologie et de Sante Publique (IPLESP), AP-HP, Hopital Pitie-Salpetriere, Service de Virologie,
Preprint em Inglês | medRxiv | ID: ppmedrxiv-21253653
ABSTRACT
The SARS-CoV-2 pandemic has led to an unprecedented daily use of molecular RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of amplification cycles (Ct), is debated because of strong potential biases. We analyze a national database of tests performed on more than 2 million individuals between January and November 2020. Although we find Ct values to vary depending on the testing laboratory or the assay used, we detect strong significant trends with patient age, number of days after symptoms onset, or the state of the epidemic (the temporal reproduction number) at the time of the test. These results suggest that Ct values can be used to improve short-term predictions for epidemic surveillance.
Licença
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Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Estudo observacional / Estudo prognóstico / Pesquisa qualitativa Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Estudo observacional / Estudo prognóstico / Pesquisa qualitativa Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
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