Sars cov 2 test

SARS-CoV-2 RNA levels in nasopharyngeal swabs were determined by quantitative RT-PCR using the cobas^® SARS-CoV-2 Test on the cobas^® 6800 system (Roche Diagnostic, Mannheim, Germany). For quantification of SARS-CoV-2-RNA in copies/mL, a standard curve derived from a dilution series of a SARS-CoV-2 cell culture isolate in VTM and adjusted to Ct values obtained from two samples with defined SARS-CoV-2-RNA copy numbers (10⁶ and 10⁵ copies/mL; INSTAND e.V., Duesseldorf, Germany) was used. For calibration purposes of quantitative assessments, reference samples were included with each PCR run. The dual-target RT-PCR independently targets the ORF1a/b and the sarbecovirus E genes, and assays were considered positive if at least one target returned a positive result (Ct values reflecting an inverse relationship with viral load). Of note, in vitro tests carried out prior to the current study did not indicate any interaction between the study products and the PCR reaction (see supplementary PCR data). For data analysis, negative PCR results were replaced with the Ct value 45 and the cp/mL value 1, respectively. Information on individual variants was obtained through the original laboratory reports, when available. Detection of the alpha (B.1.1.7) variant was based on single nucleotide polymorphism analysis for SARS-CoV-2 spike gene mutation N501Y and deletion H69/V70.

The following experimental approaches will be implemented (
Figure 3), including:
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Reverse transcription polymerase chain reaction (RT-PCR) of nasal swabs using Roche cobas® SARS-CoV-2 test
^{20 (link)}.

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Pathogen sequencing with results via the COVID-19 Genomics UK (COG-UK) consortium
²¹ .

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Host DNA extraction, quantification and SNP analysis via the Illumina Infinium® GlobalScreeningArray-24v1.0
^{22 (link)}.

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IgG antibodies assay to antigen S1, defining seroconversion (initially using the EUROIMMUN assay
^{23 (link)}).

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Blood RNA extraction focusing on host transcriptomics;

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Peripheral blood mononuclear cells (PBMCs) are a scarce resource and discussions are ongoing about maximising yield;

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Saliva will be diluted and aliquots are available. Further aliquoting will be dependent on demand;

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Other antibody, antigen tests may also be made available should they emerge;

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Serum and plasma will be aliquoted into 100µL samples and divided into packs for individual research teams. Excess RNA (swab and blood) and host DNA will potentially also be available.

As part of its public health strategy, Alberta offered SARS-CoV-2 molecular testing beginning in January 2020 for travel-related requests using a gel-based reverse transcriptase PCR (RT-PCR) assay (COVID-19-specific and pan-coronavirus) (4 (link)). From February 2020 onward, laboratory-developed real-time RT-PCR assays targeting the SARS-CoV-2 envelope (E) and/or RNA-dependent-RNA-polymerase (RdRp) were implemented, followed by a laboratory-developed E/RdRp/MS2 multiplex assay or Seegene (2019-nCoV assay, Seegene), Xpert (Xpress SARS-CoV-2, Cepheid), Aptima (SARS-CoV-2 assay, Hologic), BD Max (BioGX SARS-CoV-2, BD Molecular Diagnostics), Simplexa (COVID-19 direct test, DiaSorin), or cobas 6800 (SARS-CoV-2 test, Roche) testing (depending on laboratory testing location) for all symptomatic patients (27 (link), 28 (link)). Between 29 May 2020 and 4 November 2020, broad asymptomatic testing was made available to all Albertans.