Protocol detail

SARS-CoV-2 Detection via Real-Time RT-PCR

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The CDPH/VRDL performed real-time reverse transcription-polymerase chain reaction (RT-qPCR) on the 203 samples described above for SARS-CoV-2. Prior to May 21, 2020 [15 (link)], samples were extracted using Qiagen DSP Viral RNA Mini Kit with carrier RNA added (Qiagen) with extracts tested for SARS-CoV-2 using the FDA EUA approved 2019-nCoV CDC Real-Time RT-PCR Diagnostic Panel assay, which targets two regions of the nucleoprotein gene (N1 and N2). After May 21, 2020 [16 (link)], samples were extracted using the KingFisher Flex (Thermo Fisher Scientific) instrument according to the manufacturer’s instructions. These later samples were tested using the FDA EUA approved the Taqpath™ Multiplex Real-time RT-PCR test, which includes nucleoprotein (N) gene, spike (S) gene, and ORF1ab gene targets.

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Thissen J.B., Morrison M.D., Mulakken N., Nelson W.C., Daum C., Messenger S., Wadford D.A, & Jaing C. (2022). Evaluation of co-circulating pathogens and microbiome from COVID-19 infections. PLOS ONE, 17(12), e0278543.

Publication 2022

DSP Viral RNA Mini Kit KingFisher Flex

2019 ncov rt pcr diagnostic panel Assay Gene Nucleoprotein Real time pcr Reverse transcription Sars cov 2 Viral rna

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Variable analysis

independent variables

Sample extraction method: 1) Qiagen DSP Viral RNA Mini Kit with carrier RNA added (Qiagen) before May 21, 2020, and 2) KingFisher Flex (Thermo Fisher Scientific) instrument after May 21, 2020

dependent variables

SARS-CoV-2 detection using RT-qPCR: 1) FDA EUA approved 2019-nCoV CDC Real-Time RT-PCR Diagnostic Panel assay (targets N1 and N2 genes) before May 21, 2020, and 2) FDA EUA approved Taqpath™ Multiplex Real-time RT-PCR test (targets N gene, S gene, and ORF1ab gene) after May 21, 2020

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned

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