"Sample pooling of RNA extracts to speed up SARS-CoV-2 diagnosis using CDC FDA EUA RT-qPCR kit"

• Published in: Virus research 2020-12, Vol.290, p.198173-198173, Article 198173
• Main Authors: Freire-Paspuel, Byron, Vega-Mariño, Patricio, Velez, Alberto, Cruz, Marilyn, Garcia-Bereguiain, Miguel Angel
• Format: Article
• Language: English
• Subjects: CDC; COVID-19 - diagnosis; COVID-19 Nucleic Acid Testing - economics; Diagnostic Tests, Routine; Humans; Nasopharynx - virology; Pools; Reagent Kits, Diagnostic; Real-Time Polymerase Chain Reaction; RNA, Viral - genetics; RT-qPCR; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Short Communication; Specimen Handling - methods; Specimen Handling - standards; Time Factors
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2020.198173

•2019-nCoV CDC kit used 3 different FAM probes for SARS-CoV-2 so 3 PCR reactions per sample are needed.•Pooling 3 RNA extractions into a single PCR reaction speed up diagnosis.•Pooling 3 RNA extractions into a single PCR reaction keeps 100% sensitivity. The CDC protocol for SARS-CoV2 RT-PCR diagnosis (2019-nCoV CDC kit) is considered a gold standard worldwide; based on three different FAM probes (N1 and N2 for viral detection; RP for RNA extraction quality control), three reactions per sample are needed for SARS-CoV-2 diagnosis. We herein describe a sample pooling protocol: pooling 3 RNA extractions into a single PCR reaction; we tested this protocol with 114 specimens grouped in 38 pools and found no significant differences for N1 and N2 Ct values between pool and single sample PCR reaction. This pool of three protocol has a sensitivity of 100 % compared to the standard single sample protocol. For a typical 96-well plate, this pool assay allows 96 samples processing, speeding up diagnosis and reducing cost while maintaining clinical performance, particularly useful for SARS-CoV-2 diagnosis at developing countries.