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Comparison of Reverse Transcription (RT)-Quantitative PCR and RT-Droplet Digital PCR for Detection of Genomic and Subgenomic SARS-CoV-2 RNA.
Morón-López, Sara; Riveira-Muñoz, Eva; Urrea, Victor; Gutiérrez-Chamorro, Lucia; Ávila-Nieto, Carlos; Noguera-Julian, Marc; Carrillo, Jorge; Mitjà, Oriol; Mateu, Lourdes; Massanella, Marta; Ballana, Ester; Martinez-Picado, Javier.
  • Morón-López S; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Riveira-Muñoz E; CIBER de Enfermedades Infecciosas, Madrid, Spain.
  • Urrea V; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Gutiérrez-Chamorro L; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Ávila-Nieto C; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Noguera-Julian M; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Carrillo J; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Mitjà O; CIBER de Enfermedades Infecciosas, Madrid, Spain.
  • Mateu L; IrsiCaixa AIDS Research Institute, Badalona, Spain.
  • Massanella M; CIBER de Enfermedades Infecciosas, Madrid, Spain.
  • Ballana E; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
  • Martinez-Picado J; Fight Infections Foundation, Badalona, Spain.
Microbiol Spectr ; : e0415922, 2023 Mar 21.
Article in English | MEDLINE | ID: covidwho-2272926
ABSTRACT
Most individuals acutely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibit mild symptoms. However, 10 to 20% of those infected develop long-term symptoms, referred to as post-coronavirus disease 2019 (COVID-19) condition (PCC). One hypothesis is that PCC might be exacerbated by viral persistence in tissue sanctuaries. Therefore, the accurate detection and quantification of SARS-CoV-2 are not only necessary for viral load monitoring but also crucial for detecting long-term viral persistence and determining whether viral replication is occurring in tissue reservoirs. In this study, the sensitivity and robustness of reverse transcription (RT)-droplet digital PCR (ddPCR) and RT-quantitative PCR (qPCR) techniques have been compared for the detection and quantification of SARS-CoV-2 genomic and subgenomic RNAs from oropharyngeal swabs taken from confirmed SARS-CoV-2-positive, SARS-CoV-2-exposed, and nonexposed individuals as well as from samples from mice infected with SARS-CoV-2. Our data demonstrated that both techniques presented equivalent results in the mid- and high-viral-load ranges. Additionally, RT-ddPCR was more sensitive than RT-qPCR in the low-viral-load range, allowing the accurate detection of positive results in individuals exposed to the virus. Overall, these data suggest that RT-ddPCR might be an alternative to RT-qPCR for detecting low viral loads in samples and for assessing viral persistence in samples from individuals with PCC. IMPORTANCE We developed one-step reverse transcription (RT)-droplet digital PCR (ddPCR) protocols to detect SARS-CoV-2 RNA and compared them to the gold-standard RT-quantitative PCR (RT-qPCR) method. RT-ddPCR was more sensitive than RT-qPCR in the low-viral-load range, while both techniques were equivalent in the mid- and high-viral-load ranges. Overall, these results suggest that RT-ddPCR might be a viable alternative to RT-qPCR when it comes to detecting low viral loads in samples, which is a highly relevant issue for determining viral persistence in as-yet-unknown tissue reservoirs in individuals suffering from post-COVID conditions or long COVID.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study Topics: Long Covid Language: English Journal: Microbiol Spectr Year: 2023 Document Type: Article Affiliation country: Spectrum.04159-22

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study Topics: Long Covid Language: English Journal: Microbiol Spectr Year: 2023 Document Type: Article Affiliation country: Spectrum.04159-22