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ddPCR increases detection of SARS-CoV-2 RNA in patients with low viral loads.
Marchio, Agnès; Batejat, Christophe; Vanhomwegen, Jessica; Feher, Maxence; Grassin, Quentin; Chazal, Maxime; Raulin, Olivia; Farges-Berth, Anne; Reibel, Florence; Estève, Vincent; Dejean, Anne; Jouvenet, Nolwenn; Manuguerra, Jean-Claude; Pineau, Pascal.
  • Marchio A; Unité "Organisation nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 28, rue du Docteur Roux, 75724, Paris, Cedex 15, France. agnes.marchio@pasteur.fr.
  • Batejat C; Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
  • Vanhomwegen J; Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
  • Feher M; Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
  • Grassin Q; Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
  • Chazal M; Département de Virologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Institut Pasteur, Paris, France.
  • Raulin O; Laboratoire de Biologie Médicale, Centre Hospitalier Compiègne-Noyon, Compiègne, France.
  • Farges-Berth A; Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site de Longjumeau, Longjumeau, France.
  • Reibel F; Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site d'Orsay, Orsay, France.
  • Estève V; Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site de Longjumeau, Longjumeau, France.
  • Dejean A; Laboratoire de Biologie Médicale, Groupe Hospitalier Nord-Essonne, Site d'Orsay, Orsay, France.
  • Jouvenet N; Unité "Organisation nucléaire et Oncogenèse", INSERM U993, Institut Pasteur, 28, rue du Docteur Roux, 75724, Paris, Cedex 15, France.
  • Manuguerra JC; Département de Virologie, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Institut Pasteur, Paris, France.
  • Pineau P; Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
Arch Virol ; 166(9): 2529-2540, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1305156
ABSTRACT
RT-qPCR detection of SARS-CoV-2 RNA still represents the method of reference to diagnose and monitor COVID-19. From the onset of the pandemic, however, doubts have been expressed concerning the sensitivity of this molecular diagnosis method. Droplet digital PCR (ddPCR) is a third-generation PCR technique that is particularly adapted to detecting low-abundance targets. We developed two-color ddPCR assays for the detection of four different regions of SARS-CoV-2 RNA, including non-structural (IP4-RdRP, helicase) and structural (E, N) protein-encoding sequences. We observed that N or E subgenomic RNAs are generally more abundant than IP4 and helicase RNA sequences in cells infected in vitro, suggesting that detection of the N gene, coding for the most abundant subgenomic RNA of SARS-CoV-2, increases the sensitivity of detection during the highly replicative phase of infection. We investigated 208 nasopharyngeal swabs sampled in March-April 2020 in different hospitals of Greater Paris. We found that 8.6% of informative samples (n = 16/185, P < 0.0001) initially scored as "non-positive" (undetermined or negative) by RT-qPCR were positive for SARS-CoV-2 RNA by ddPCR. Our work confirms that the use of ddPCR modestly, but significantly, increases the proportion of upper airway samples testing positive in the framework of first-line diagnosis of a French population.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / RNA, Viral / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Limits: Humans Country/Region as subject: Europa Language: English Journal: Arch Virol Year: 2021 Document Type: Article Affiliation country: S00705-021-05149-0

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / RNA, Viral / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Limits: Humans Country/Region as subject: Europa Language: English Journal: Arch Virol Year: 2021 Document Type: Article Affiliation country: S00705-021-05149-0