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3 protocols using abi 7500 fast

1

SARS-CoV-2 Antibody and PCR Testing

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An electrochemiluminescence immunoassay, Roche Elecsys® Anti-SARS-CoV-2 (99.5% sensitivity,7 (link) 99.8% specificity;7 (link),8 Roche, Switzerland, was used to identify antibodies in the serological samples. Reactive for optical density (a proxy for antibody titer) cutoff index 1.0 and non-reactive for cutoff index 1.0, according to manufacturer instructions.8 PCR testing of aliquots of Universal Transport Medium UTM) used for nasopharyngeal and oropharyngeal swab collection was utilized to assess current infection (Huachenyang Technology, China).
Aliquots were extracted using the QIAsymphony platform (QIAGEN, USA) and evaluated using the TaqPathTM COVID-19 Combo Kit (100% sensitivity and specificity;9 Thermo Fisher Scientific, USA) on an ABI 7500 FAST (Thermo Fisher, USA). On a Hamilton Microlab STAR (Hamilton, USA), samples were extracted using a custom protocol10 (link) and tested using the AccuPower SARS-CoV-2 Real-Time RT-PCR Kit (100% sensitivity and specificity)11 (link) on an ABI 7500 FAST, or directly loaded into a Roche cobas® 6800 system to be assayed. All laboratory testing was done at the HMC Central Laboratory according to defined procedures.12–15 (link) The laboratory is accredited by the College of American Pathologists.
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2

RNA Extraction and qRT-PCR Analysis

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RNA was extracted using the Promega Maxwell 16 with the LEV simplyRNA tissue kit (Promega AS1270), the Roche MagNAPure with the Cellular Total RNA Large Volume kit (Roche 05467535001), or the DirectZol RNA Mini kit (Zymo R2051). cDNA was prepared using dNTPs (Thermo Fisher R0181), random hexamers (Jena Bioscience PM-301) and M-MuLV reverse transcriptase (NEB M0253). For quantitative RT–PCR, specific Taqman probes and primers (Thermo Fisher 4331182) were used with TaqMan Universal PCR Master Mix (Applied Biosystems 4305719) or LightCycler© 480 Probes Master (Roche 04887301001). PCRs were performed on the Applied Biosystems ABI 7500 Fast or the Roche LightCycler 480 in technical triplicates.
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3

SARS-CoV-2 Detection Protocols and Platforms

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Nasopharyngeal and/or oropharyngeal swabs (Huachenyang Technology, China) were collected for PCR testing and placed in Universal Transport Medium (UTM). Aliquots of UTM were: extracted on a QIAsymphony platform (QIAGEN, USA) and tested with RT-qPCR using TaqPath COVID-19 Combo Kits (100% sensitivity and specificity [25 ]; Thermo Fisher Scientific, USA) on an ABI 7500 FAST (ThermoFisher, USA); extracted using a custom protocol [26 (link)] on a Hamilton Microlab STAR (Hamilton, USA) and tested using AccuPower SARS-CoV-2 Real-Time RT-PCR Kits (100% sensitivity and specificity [27 (link)]; Bioneer, Korea) on an ABI 7500 FAST; or loaded directly into a Roche cobas® 6800 system and assayed with a cobas® SARS-CoV-2 Test (95% sensitivity, 100% specificity [28 ]; Roche, Switzerland). The first assay targets the viral S, N, and ORF1ab regions. The second targets the viral RdRp and E-gene regions, and the third targets the ORF1ab and E-gene regions.
All tests were conducted at the HMC Central Laboratory or Sidra Medicine Laboratory, following standardized protocols.
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