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cobas® SARS-CoV-2 Qualitative for use on the cobas® 5800/6800/8800 Systems is a real-time RT-PCR test intended for the qualitative detection of nucleic acids from SARS-CoV-2 in nasal and nasopharyngeal specimens collected from symptomatic individuals suspected of COVID-19 by their healthcare provider.

Results are for the detection of SARS-CoV-2 RNA. Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. Positive results do not rule out bacterial infection or co-infection with other pathogens.

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions. Results are meant to be used in conjunction with clinical observations, patient history, recent exposures and epidemiological information, and laboratory data, in accordance with the guidelines provided by the relevant public health authorities. cobas® SARS-CoV-2 Qualitative is intended for use by qualified clinical laboratory personnel specifically instructed and trained in the techniques of real-time PCR and on the use of the cobas® 5800/6800/8800 Systems.

cobas® SARS-CoV-2 Qualitative is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection. The cobas® 5800 System is designed as one integrated instrument. The cobas® 6800/8800 Systems consist of the sample supply module, the transfer module, the processing module, and the analytic module. Automated data management is performed by the cobas® 5800 or cobas® 6800/8800 Systems software(s), which assigns test results for all tests. Results can be reviewed directly on the system screen, and printed as a report.

Nucleic acid from patient samples and added internal control RNA (RNA IC) molecules are simultaneously extracted. Nucleic acid is released by addition of proteinase and lysis reagent to the sample. The released nucleic acid binds to the silica surface of the added magnetic glass particles. Unbound substances and impurities, such as denatured protein, cellular debris and potential PCR inhibitors, are removed with subsequent wash steps and purified nucleic acid is eluted from the magnetic glass particles with elution buffer at elevated temperature. External controls (positive and negative) are processed in the same way.

Selective amplification of target nucleic acid from the sample is achieved by the use of targetspecific forward and reverse primers for ORF1 a/b non-structural region that is unique to SARS-CoV-2. Additionally, a conserved region in the structural protein envelope E-gene were chosen for pan-Sarbecovirus detection. The pan-Sarbecovirus detection sets will also detect SARS-CoV-2 virus.

Selective amplification of RNA Internal Control is achieved by the use of non-competitive sequence specific forward and reverse primers which have no homology with the coronavirus genome. A thermostable DNA polymerase enzyme is used for amplification.

The cobas® SARS-CoV-2 Qualitative master mix contains detection probes which are specific for the coronavirus type SARS-CoV-2, members of the Sarbecovirus subgenus, and the RNA Internal Control nucleic acid. The coronavirus and RNA Internal Control detection probes are each labeled with unique fluorescent dyes that act as a reporter. Each probe also has a second dye which acts as a quencher. When not bound to the target sequence, the fluorescent signals of the intact probes are suppressed by the quencher dye. During the PCR amplification step, hybridization of the probes to the specific single-stranded DNA template results in cleavage of the probe by the 5' to 3' exonuclease activity of the DNA polymerase resulting in separation of the reporter and quencher dyes and the generation of a fluorescent signal. With each PCR cycle, increasing amounts of cleaved probes are generated and the cumulative signal of the reporter dye increases concomitantly. Each reporter dye is measured at defined wavelengths, which enables simultaneous detection and discrimination of the amplified coronavirus target and the RNA Internal Control. The master mix includes deoxyuridine triphosphate (dUTP), instead of deoxythimidine triphosphate (dTTP), which is incorporated into the newly synthesized DNA (amplicon). Any contaminating amplicons from previous PCR runs are destroyed by the AmpErase enzyme [uracil-N-glycosylase], which is included in the PCR mix, when heated in the first thermal cycling step. However, newly formed amplicons are not destroyed since the AmpErase enzyme is inactivated once exposed to temperatures above 55°C.

The provided text is a 510(k) Summary for the cobas SARS-CoV-2 Qualitative test. It primarily focuses on demonstrating substantial equivalence to a predicate device after software updates (ASAPs) and does not contain detailed acceptance criteria and performance data in the format typically required for a full clinical study report. The document states that the overall assay performance claims were not impacted by the changes implemented in the software updates.

Therefore, I cannot provide a detailed answer to all parts of your request based on the information given. However, I can extract the following:

1. A table of acceptance criteria and the reported device performance:

The document explicitly states that the "overall cobas® SARS-CoV-2 Qualitative assay performance claims were not impacted by changes implemented in SW cobas® SCoV2-QL ASAP 12.4.1 and SW cobas® 5800 SCoV2-QL ASAP 1.3.1, when compared to the current commercially available version of the ASAPs SW cobas® SCoV2-QL ASAP 12.1.0 and SW cobas® 5800 SCoV2-QL ASAP 1.1.1." This implies that the performance of the updated device is considered equivalent to the predicate device, which had already met its own set of acceptance criteria. However, the specific numerical acceptance criteria or the reported performance data for parameters like sensitivity, specificity, or LOD are not provided in this summary. The summary only asserts that the performance has not changed.

2. Sample size used for the test set and the data provenance (e.g. country of origin of the data, retrospective or prospective):

This information is not provided in the given 510(k) summary. The document focuses on changes to the Assay Specific Analysis Packages (ASAPs) and states that performance claims were not impacted. It does not describe a new clinical or analytical study with specific sample sizes or data provenance for the test set.

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts (e.g. radiologist with 10 years of experience):

This information is not provided in the given 510(k) summary. As an in-vitro diagnostic (IVD) PCR test, ground truth for such devices is typically established through a composite reference method, often including another highly sensitive and specific RT-PCR assay, rather than expert consensus on images.

4. Adjudication method (e.g. 2+1, 3+1, none) for the test set:

This information is not provided in the given 510(k) summary.

5. If a multi reader multi case (MRMC) comparative effectiveness study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance:

This is not applicable to this device. The cobas SARS-CoV-2 Qualitative test is an in-vitro diagnostic (IVD) RT-PCR assay for qualitative detection of viral nucleic acids, not an imaging device that requires human reader interpretation, nor does it incorporate AI for decision support.

6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done:

The device described is an automated RT-PCR test system. Its performance, by nature, is "standalone" in terms of the algorithm generating a result based on the sample processing. The results are then interpreted by qualified laboratory personnel. The summary indicates "Automated data management is performed by the cobas® 5800 or cobas® 6800/8800 Systems software(s), which assigns test results for all tests." This suggests algorithm-only processing for the primary result.

7. The type of ground truth used (expert consensus, pathology, outcomes data, etc.):

While not explicitly stated in this summary, for a SARS-CoV-2 qualitative RT-PCR test, the ground truth in performance studies (especially for the original clearance of K213804) would typically be established using a reference molecular method (e.g., another FDA-authorized RT-PCR test or a validated in-house RT-PCR assay), often combined with clinical data in some cases. The document does not describe the specific ground truth method used for the studies that established the initial performance claims of the predicate device (K213804), which are referenced as unchanged.

8. The sample size for the training set:

This information is not provided in the given 510(k) summary. This document describes software updates to an already cleared device, focusing on ensuring that the updates did not negatively impact its previously established performance. It's unlikely that new "training sets" in the machine learning sense were used for these specific software updates, which appear to refine interpretation logic rather than train a new model.

9. How the ground truth for the training set was established:

This information is not provided in the given 510(k) summary. See point 8.

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