(353 days)
The cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® SARS-CoV-2) is an automated, realtime reverse transcriptase polymerase chain reaction (RT-PCR) test intended for the rapid in vitro qualitative detection of nucleic acid from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in anterior nasal (nasal) and nasopharyngeal swab specimens collected from individuals with signs and symptoms of respiratory tract infection (i.e., symptomatic). Additionally, this test is intended to be used with nasal and necimens collected from individuals without signs and symptoms suspected of COVID-19 (i.e., asymptomatic).
The cobas® SARS-CoV-2 performed on the cobas® Liat® System is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiologic, and laboratory findings. SARS-CoV-2 RNA is generally detectable in nasal and nasopharyngeal swab specimens during the acute phase of infection.
Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out co-infection with other microorganisms.
A negative result from an asymptomatic individual is presumptive. Additionally, a negative result obtained with a nasal swab collected from an asymptomatic patient should be followed up by testing at least twice over three days with at least 48 hours between tests.
Negative results do not preclude SARS-CoV-2 infection.
The results of this test should not be used as the sole basis for diagnosis, treatment management decisions.
This test is intended for prescription use only and can be used in Point-of-Care settings.
The cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System (cobas® SARS-CoV-2) uses real-time reverse transcriptase polymerase chain reaction (RT-PCR) technology to rapidly (approximately 20 minutes) detect SARS-CoV-2 virus from nasopharyngeal and nasal swabs. The automation, small footprint, and easy-to-use interface of the cobas® Liat® System enable performance of this test to occur at the POC or in a clinical laboratory setting.
The cobas® SARS-CoV-2 assay is performed on the cobas® Liat® Analyzer which automates and integrates sample purification, nucleic acid amplification, and detection of the target sequence in biological samples using real-time RT-PCR assays. The assay targets both the ORF1 a/b nonstructural region and nucleocapsid protein gene that are unique to SARS-CoV-2. An Internal Process Control (IPC) is also included. The IPC is present to control for adequate processing of the target virus through steps of sample purification, nucleic acid amplification, and to monitor the presence of inhibitors in the RT-PCR processes.
Here's an analysis of the acceptance criteria and study findings for the "cobas SARS-CoV-2 Nucleic acid test for use on the cobas Liat System" based on the provided text:
Acceptance Criteria and Reported Device Performance
The acceptance criteria are implied by the clinical performance evaluation results, specifically the Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) with a composite comparator method. While explicit acceptance criteria values are not stated (e.g., "PPA must be >X%"), the device's performance is presented to demonstrate its effectiveness.
| Performance Metric | Acceptance Criteria (Implied) | Reported Device Performance (NPS - Symptomatic) | Reported Device Performance (NPS - Asymptomatic) | Reported Device Performance (NS - Symptomatic) | Reported Device Performance (NS - Asymptomatic) |
|---|---|---|---|---|---|
| Positive Percent Agreement (PPA) | High PPA (e.g., >90%) | 95.4% (95% CI: 90.4% - 97.9%) | 96.3% (95% CI: 87.5% - 99.0%) | 96.3% (95% CI: 91.6% - 98.4%) | 90.0% (95% CI: 78.6% - 95.7%) |
| Negative Percent Agreement (NPA) | High NPA (e.g., >95%) | 99.5% (95% CI: 98.4% - 99.8%) | 99.6% (95% CI: 99.0% - 99.8%) | 99.8% (95% CI: 99.0% - 100.0%) | 99.9% (95% CI: 99.5% - 100.0%) |
Study Information
-
Sample sizes used for the test set and data provenance:
- Clinical Performance Evaluation (Test Set):
- Evaluable NPS samples: 1874 (fresh and frozen)
- Symptomatic: 673 NPS
- Asymptomatic: 1201 NPS (413 suspected, 788 no suspicion)
- Evaluable NS samples: 1872 (fresh and frozen, including 1 indeterminate result)
- Symptomatic: 674 NS
- Asymptomatic: 1198 NS (411 suspected, 787 no suspicion)
- Frozen Samples (included in above totals): 23 positive and 23 negative NPS specimens, and 23 positive and 23 negative NS specimens.
- Data Provenance: Prospectively collected clinical specimens from February-June 2022 (fresh samples) and earlier during the COVID-19 pandemic (March-June 2021) for frozen samples. The document does not specify the country of origin, but it implies collection within "10 point-of-care healthcare facilities" without further geographic detail.
- Evaluable NPS samples: 1874 (fresh and frozen)
- Clinical Performance Evaluation (Test Set):
-
Number of experts used to establish the ground truth for the test set and the qualifications of those experts:
- The ground truth for the test set was established using a composite comparator method consisting of "three highly sensitive FDA-EUA-authorized laboratory-based RT-PCR assays."
- The document does not specify the number or qualifications of human experts involved in establishing this ground truth. The ground truth relies on the performance of these reference RT-PCR assays.
-
Adjudication method for the test set:
- The text describes a "composite comparator method" using "three highly sensitive FDA-EUA-authorized laboratory-based RT-PCR assays." This implies a form of consensus or a predefined algorithm for combining the results of these three assays to establish the definitive positive or negative status. However, the specific adjudication rules (e.g., "2 out of 3 positive for overall positive") are not explicitly described.
-
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:
- No MRMC comparative effectiveness study involving human readers or AI assistance is described. This study focuses on the standalone performance of the cobas SARS-CoV-2 test.
-
If a standalone (i.e., algorithm only without human-in-the-loop performance) was done:
- Yes, a standalone performance study was done. The entire clinical performance evaluation section (Section 7) describes the performance of the "cobas SARS-CoV-2 test" (the device/algorithm) against a composite comparator method (ground truth) without human intervention in the result interpretation of the device. The device itself is an automated RT-PCR test.
-
The type of ground truth used:
- The ground truth used was a composite comparator method based on the results from "three highly sensitive FDA-EUA-authorized laboratory-based RT-PCR assays." This is a form of laboratory reference standard.
-
The sample size for the training set:
- The document describes a clinical performance evaluation (test set) and analytical studies. It does not provide information about the sample size of a specific "training set" for the device, as it is a molecular diagnostic test rather than a machine learning algorithm that typically undergoes explicit training on large datasets in the way an AI image analysis product would. The development (implied "training" in a broader sense for assay optimization) would have used various samples, but these are not explicitly detailed as a distinct training set in the provided text.
-
How the ground truth for the training set was established:
- As no explicit "training set" with established ground truth is described in the context of typical AI/ML development, this question cannot be answered from the provided text. The assay development would involve extensive analytical validation using characterized viral samples and clinical specimens validated by reference methods, which broadly contribute to optimizing the assay's performance.
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December 4, 2023
Roche Molecular Systems, Inc. Alicja Stradomska Regulatory Affairs Specialist 4300 Hacienda Drive Pleasanton, California 94588-2722
Re: K223783
Trade/Device Name: cobas SARS-CoV-2 Nucleic acid test for use on the cobas Liat System Regulation Number: 21 CFR 866.3982 Regulation Name: Simple Point-Of-Care Device To Detect Sar-Cov-2 Nucleic Acid Targets From Clinical Specimens In Near-Patient Settings Regulatory Class: Class II Product Code: QWR Dated: September 1, 2023 Received: September 1, 2023
Dear Alicja Stradomska:
We have reviewed your section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food, Drug, and Cosmetic Act (the Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. Although this letter refers to your product as a device, please be aware that some cleared products may instead be combination products. The 510(k) Premarket Notification Database available at https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm identifies combination product submissions. The general controls provisions of the Act include requirements for annual registration. listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21, Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
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Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Part 801 and Part 809); medical device reporting of medical device-related adverse events) (21 CFR Part 803) for devices or postmarketing safety reporting (21 CFR Part 4, Subpart B) for combination products (see https://www.fda.gov/combination-products/guidance-regulatory-information/postmarketing-safetyreporting-combination-products); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820) for devices or current good manufacturing practices (21 CFR Part 4, Subpart A) for combination products; and, if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR Parts 1000-1050.
Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to https://www.fda.gov/medical-device-safety/medical-device-reportingmdr-how-report-medical-device-problems.
For comprehensive regulatory information about mediation-emitting products, including information about labeling regulations, please see Device Advice (https://www.fda.gov/medicaldevices/device-advice-comprehensive-regulatory-assistance) and CDRH Learn (https://www.fda.gov/training-and-continuing-education/cdrh-learn). Additionally, you may contact the Division of Industry and Consumer Education (DICE) to ask a question about a specific regulatory topic. See the DICE website (https://www.fda.gov/medical-device-advice-comprehensive-regulatoryassistance/contact-us-division-industry-and-consumer-education-dice) for more information or contact DICE by email (DICE(@fda.hhs.gov) or phone (1-800-638-2041 or 301-796-7100).
Sincerely. Himani Bisht -S
Himani Bisht, Ph.D. Assistant Director Viral Respiratory and HPV Branch Division of Microbiology Devices OHT7: Office of In Vitro Diagnostics Office of Product Evaluation and Quality Center for Devices and Radiological Health
Enclosure
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Indications for Use
510(k) Number (if known) K223783
Device Name
cobas SARS-CoV-2 Nucleic acid test for use on the cobas Liat System
Indications for Use (Describe)
The cobas SARS-CoV-2 Nucleic acid test for use on the cobas SARS-CoV-2) is an automated, realtime reverse transcriptase polymerase chain reaction (RT-PCR) test intended for the rapid in vitro qualitative detection of nucleic acid from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in anterior nasal (nasal) and nasopharyngeal swab specimens collected from individuals with signs and symptoms of respiratory tract infection (i.e., symptomatic). Additionally, this test is intended to be used with nasal and necimens collected from individuals without signs and symptoms suspected of COVID-19 (i.e., asymptomatic).
The cobas SARS-CoV-2 performed on the cobas Liat System is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiologic, and laboratory findings. SARS-CoV-2 RNA is generally detectable in nasal and nasopharyngeal swab specimens during the acute phase of infection.
Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out co-infection with other microorganisms.
A negative result from an asymptomatic individual is presumptive. Additionally, a negative result obtained with a nasal swab collected from an asymptomatic patient should be followed up by testing at least twice over three days with at least 48 hours between tests.
Negative results do not preclude SARS-CoV-2 infection.
The results of this test should not be used as the sole basis for diagnosis, treatment management decisions.
This test is intended for prescription use only and can be used in Point-of-Care settings.
| Type of Use (Select one or both, as applicable) |
|---|
| ------------------------------------------------- |
| ☑ Prescription Use (Part 21 CFR 801 Subpart D) | □ Over-The-Counter Use (21 CFR 801 Subpart C) |
|---|---|
| ------------------------------------------------------------------------------------ | ----------------------------------------------- |
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cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System 510(k) Summary
This summary of 510(k) safety and effectiveness information is being submitted in accordance with the requirements of 21 CFR 807.92.
| Submitter Name | Roche Molecular Systems, Inc. |
|---|---|
| Address | 4300 Hacienda DrivePleasanton, CA 94588, USA |
| Contact | Dr. Alicja StradomskaPhone: (+41) 795-177-052Email: alicja.stradomska@roche.com |
| Date Prepared | December 1, 2023 |
| Proprietary Name | cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System |
| Common Name | cobas® SARS-CoV-2 |
| Classification Name | Simple Point-of-Care Device to Detect SARS-CoV-2 Nucleic Acid Targets fromClinical Specimens in Near-Patient Settings |
| Regulation Number | 21 CFR 866.3982 |
| Predicate Devices | ID NOW COVID-19 2.0 (K221925) |
| Establishment Registration | Roche Molecular Systems, Inc. (2243471) |
DEVICE DESCRIPTION 1.
The cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System (cobas® SARS-CoV-2) uses real-time reverse transcriptase polymerase chain reaction (RT-PCR) technology to rapidly (approximately 20 minutes) detect SARS-CoV-2 virus from nasopharyngeal and nasal swabs. The automation, small footprint, and easy-to-use interface of the cobas® Liat® System enable performance of this test to occur at the POC or in a clinical laboratory setting.
1.1. Principles of the procedure
The cobas® SARS-CoV-2 assay is performed on the cobas® Liat® Analyzer which automates and integrates sample purification, nucleic acid amplification, and detection of the target sequence in biological samples using real-time RT-PCR assays. The assay targets both the ORF1 a/b nonstructural region and nucleocapsid protein gene that are unique to SARS-CoV-2. An Internal Process
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Control (IPC) is also included. The IPC is present to control for adequate processing of the target virus through steps of sample purification, nucleic acid amplification, and to monitor the presence of inhibitors in the RT-PCR processes.
INDICATIONS FOR USE 2.
The cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System (cobas® SARS-CoV-2) is an automated, real-time reverse transcriptase polymerase chain reaction (RT-PCR) test intended for the rapid in vitro qualitative detection of nucleic acid from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in anterior nasal (nasal) and nasopharyngeal swab specimens collected from individuals with signs and symptoms of respiratory tract infection (i.e., symptomatic). Additionally, this test is intended to be used with nasal and nasopharyngeal swab specimens collected from individuals without signs and symptoms suspected of COVID-19 (i.e., asymptomatic).
The cobas® SARS-CoV-2 performed on the cobas® Liat® System is intended for use as an aid in the diagnosis of COVID-19 if used in conjunction with other clinical, epidemiologic, and laboratory findings. SARS-CoV-2 RNA is generally detectable in nasal and nasopharyngeal swab specimens during the acute phase of infection.
Positive results are indicative of the presence of SARS-CoV-2 RNA. Positive results do not rule out co-infection with other microorganisms.
A negative result from an asymptomatic individual is presumptive. Additionally, a negative result obtained with a nasal swab collected from an asymptomatic patient should be followed up by testing at least twice over three days with at least 48 hours between tests. Negative results do not preclude SARS-CoV-2 infection.
The results of this test should not be used as the sole basis for diagnosis, treatment, or other patient management decisions.
This test is intended for prescription use only and can be used in Point-of-Care settings.
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TECHNOLOGICAL CHARACTERISTICS 3.
The cobas® SARS CoV-2 Nucleic acid test for use on the cobas® Liat® System is substantially equivalent to another legally marketed POC test intended for the qualitative detection of SARS-CoV-2 (K221925) as indicated in Table 1.
| Submitted Device:cobas® SARS-CoV-2 Nucleic acid test for use on thecobas® Liat® System | Predicate Device:ID NOW COVID-19 2.0(K221925) | |
|---|---|---|
| Regulation Name | 21 CFR 866.3982 | 21 CFR 866.3982 |
| Product Code | QWR | Same |
| Intended Use | The cobas® SARS-CoV-2 Nucleic acid test for use on thecobas® Liat® System (cobas® SARS-CoV-2) is an automated,real-time reverse transcriptase polymerase chain reaction (RT-PCR) test intended for the rapid in vitro qualitative detection ofnucleic acid from severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) in anterior nasal (nasal) andnasopharyngeal swab specimens collected from individualswith signs and symptoms of respiratory tract infection (i.e.,symptomatic). Additionally, this test is intended to be used withnasal and nasopharyngeal swab specimens collected fromindividuals without signs and symptoms suspected of COVID-19 (i.e., asymptomatic).The cobas® SARS-CoV-2 performed on the cobas® Liat®System is intended for use as an aid in the diagnosis ofCOVID-19 if used in conjunction with other clinical,epidemiologic, and laboratory findings. SARS-CoV-2 RNA isgenerally detectable in nasal and nasopharyngeal swabspecimens during the acute phase of infection.Positive results are indicative of the presence of SARS-CoV-2RNA. Positive results do not rule out co-infection with othermicroorganisms.A negative result from an asymptomatic individual ispresumptive. Additionally, a negative result obtained with anasal swab collected from an asymptomatic patient should befollowed up by testing at least twice over three days with atleast 48 hours between tests.Negative results do not preclude SARS-CoV-2 infection.The results of this test should not be used as the sole basis fordiagnosis, treatment, or other patient management decisions.This test is intended for prescription use only and can be usedin Point-of-Care settings. | ID NOW COVID-19 2.0 performed on the IDNOW Instrument is a rapid molecular in vitrodiagnostic test utilizing an isothermal nucleicacid amplification technology (NAAT)intended for the qualitative detection ofnucleic acid from SARS-CoV-2 in directanterior nasal (nasal) or nasopharyngealswabs from individuals with signs andsymptoms of respiratory tract infection. IDNOW COVID-19 2.0 performed on the IDNOW Instrument is intended for use as an aidin the diagnosis of COVID-19 if used inconjunction with other clinical, epidemiologic,and laboratory findings. SARS-CoV-2 RNA isgenerally detectable in nasal andnasopharyngeal swab specimens during theacute phase of infection.Positive results are indicative of the presenceof SARS-CoV-2 RNA. Positive results do notpreclude co-infection with bacteria or otherviruses and should not be used as the solebasis for diagnosis, treatment, or otherpatient management decisions.A negative test result is presumptive, and it isrecommended these results be confirmed byanother molecular SARS-CoV-2 assay.Negative results do not preclude SARS-CoV-2 infection and should not be used as thesole basis for diagnosis, treatment, or otherpatient management decisions. This test isintended for prescription use only and can beused in Point-of-Care settings. |
| Submitted Device:cobas® SARS-CoV-2 Nucleic acid test for use on thecobas® Liat® System | Predicate Device:ID NOW COVID-19 2.0(K221925) | |
| Sample Types | Healthcare provider-collected nasopharyngeal and nasalswabs, and self-collected nasal swabs | Nasal or nasopharyngeal swab |
| Analyte Targets | • SARS-CoV-2 ORF1 a/b non-structural region• SARS-CoV-2 nucleocapsid protein gene | RdRp gene of SARS-CoV-2 RNA |
| AncillaryCollection Kits | • Copan FLOQSwabs™ with UTM™, UVT and other swabswith other viral transport media (VTM) e.g., M4RT, M4, M5and M6• 0.9% and 0.85% Saline | UTM |
| SamplePreparation | Automated | Same |
| AmplificationTechnology | Real-time PCR for detecting the presence/absence of viralRNA in clinical specimens | Isothermal nucleic acid amplification fordetecting the presence/absence ofviral RNA in clinical specimens |
| DetectionChemistry | Assay using different reporter dyes for target and InternalControl | Fluorescently labeled molecular beaconprobes |
| Controls Used | • Internal Control (a process control for sample purification,nucleic acid amplification, and monitoring presence ofinhibitors)• External Positive and Negative Controls | • Internal Control (verifying assay reagents)• External Positive and Negative Controls |
| ResultInterpretation | Automated | Same |
Table 1: Comparison of the cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System and the predicate device
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4. SPECIAL CONTROLS/STANDARDS/GUIDANCE REFERENCED
Class II Special Controls as per 21 CFR 866.3982.
NON-CLINICAL PERFORMANCE EVALUATION 5.
Analytical sensitivity (Limit of detection) 5.1.1.
Limit of detection (LoD) studies determine the lowest detectable concentration of SARS-CoV-2 at which greater or equal to 95% of all (true positive) replicates test positive.
SARS-CoV-2 viral culture 5.1.1.1. -
To determine the LoD for SARS-CoV-2, a heat inactivated virus of an isolate from a US patient (USA-WA1/2020, lot number 324047, ZeptoMetrix, NY, USA) was serially diluted in pooled negative nasopharyngeal swab matrix. Five concentration levels were tested with 20 replicates
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except for the highest concentration level, which was tested with 10 replicates. Three lots of assay tubes (approximately equal numbers of replicates per lot) and two independent dilution series (equal numbers of replicates per dilution series) were used in the study.
As shown in Table 2, the lowest concentration level with observed hit rates greater than or equal to 95% was 0.012 TCID50/mL (12 copies/mL) for SARS-CoV-2.
Table 2 LoD determination using USA-WA1/2020 strain
Strain - USA-WA1/2020 (stock concentration 3.16E+06 TCID50/mL) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Co atratic ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Total valid ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| Concentration [TCID50/mL] | Concentration[copies/mL]* | Total validresults | Hit rate [%] | Mean Ct** |
|---|---|---|---|---|
| 0.048 | 49 | 10 | 100 | 33.0 |
| 0.024 | 24 | 20 | 100 | 33.6 |
| 0.012 | 12 | 20 | 95 | 34.7 |
| 0.006 | 6 | 20 | 90 | 35.4 |
| 0.003 | 3 | 20 | 55 | 35.5 |
*Concentration of each viral stock in copies/mL was quantified using Reverse transcriptase digital PCR with target specific PCR primers and probe sets designed to amplify SARS-CoV-2.
**Calculations only include positive results.
WHO International Standard 5.1.1.2.
The LoD using WHO International Standard for SARS-CoV-2 RNA (NIBSC code: 20/146) was determined by reconstituting the WHO Standard to 0.5 mL according to the WHO NIBSC code: 20/146 Instructions for use (Version 1.0, Dated 14/12/2020). Following reconstitution, the WHO Standard was diluted to an intermediate stock (IS) concentration in UTM.
WHO Standard IS was serially diluted in pooled negative clinical nasopharyngeal swabs matrix. Six concentration levels were tested with 24 replicates at each level across three lots of assay tubes (8 replicates per lot). Three independent dilution series were used in the study with approximately equal numbers of replicates per dilution series. The LoD was determined to be 30 IU/mL.
The results of the LoD study are shown in Table 3 below.
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Table 3 Hit rate and mean Ct results of SARS-CoV-2 LoD determination
| Concentration [IU/mL] | Valid Positive Results | Total Valid Results | Hit Rate [%] | Mean Ct* |
|---|---|---|---|---|
| 120 | 24 | 24 | 100 | 32.74 |
| 60 | 24 | 24 | 100 | 33.81 |
| 30 | 24 | 24 | 100 | 34.28 |
| 20 | 21 | 24 | 88 | 34.97 |
| 15 | 19 | 24 | 79 | 35.48 |
| 7.5 | 9 | 24 | 38 | 36.05 |
Strain - WHO International Standard for SARS-CoV-2 RNA (NIBSC code: 20/146)
*Calculations only include positive results
5.1.2. Reactivity/inclusivity
The inclusivity study evaluates the assay ability to detect SARS-CoV-2 isolates/variants. In this study, sixteen (16) SARS-CoV-2 isolates/variants were tested. The isolates/variants were tested as inactivated viruses diluted into pooled clinical negative nasopharyngeal swab matrices. The isolates/variants tested in the study and the concentrations that they can be detected at 100%, i.e., in 3 out of 3 replicates are listed in Table 4. In silico analysis of the oligo sets for SARS-CoV-2 (taxonomy ID 2697049) have been continuously performed since the onset of the pandemic and cobas®SARS-CoV-2 test will detect all analyzed SARS-CoV-2 sequences in the GISAID (>14 M) database (as of 15th November, 2023).
Summary of SARS-CoV-2 inclusivity testing Table 4
| Isolate/Variant | Pango Lineage | WHO Label | Lowest ConcentrationDetected (cp/mL) |
|---|---|---|---|
| Italy-INMI1 | not listed | N/A | 5.0E+00 |
| Hong Kong/VM20001061/2020 | A | N/A | 2.0E+01 |
| UK variant | B.1.1.7 | Alpha | 5.0E+00 |
| South Africa Variant | B.1.351 | Beta | 2.0E+01 |
| USA/COR-22-063113/2022 | BA5.5 | Omicron | 6.0E+00 |
| USA/GA-EHC-2811C/2021 | BA.1 | Omicron | 1.5E+00 |
| hCoV-19/USA/MD-HP40900/2022 | B.1.1.529, XBB.1.5 | Omicron | 6.0E+00 |
| hCoV-19/USA/MD-HP38861/2022 | B.1.1.529, BQ.1.1 | Omicron | 1.2E+01 |
| hCoV-19/USA/MD-HP38288/2022 | B.1.1.529, BF.7 | Omicron | 1.2E+01 |
| hCoV-19/USA/MD-HP30386/2022 | B.1.1.529, BA.4 | Omicron | 6.0E+00 |
| USA/MD-HP24556/2022 | BA.2.3 | Omicron | 1.2E+01 |
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| Isolate/Variant | Pango Lineage | WHO Label | Lowest ConcentrationDetected (cp/mL) |
|---|---|---|---|
| USA/MD-HP20874/2021 | B.1.1.529 | Omicron | 6.0E+00 |
| USA/CA-Stanford-15_S02/2021 | B.1.617.1 | Kappa | 1.2E+01 |
| USA/NY-Wadsworth-21025952/2021 | B.1.526 | lota | 1.2E+01 |
| USA/PHC658/2021 | B.1.617.2 | Delta | 3.6E+01 |
| Japan/TY7-503/2021 (Brazil P.1) | P.1 | Gamma | 3.6E+01 |
Cross- reactivity and microbial interference 5.1.3.
Cross-reactivity and microbial interference of cobas® SARS-CoV-2 were evaluated by testing a panel of multiple unique sub-species of microorganisms. High titer stocks of the potentially crossreacting microorganisms were spiked into pooled negative nasopharyngeal swab clinical matrix and tested for cross-reactivity with cobas® SARS-CoV-2, and into pooled negative nasopharyngeal swab clinical matrix spiked with 3x LoD concentrations of SARS-CoV-2 and tested for microbial interference. The testing concentrations for potentially interfering microorganisms are ≥1.0E+05 units/mL for viruses and ≥1.0E+06 units/mL for other microorganisms unless otherwise noted (Table 5).
None of the organisms tested interfered with cobas® SARS-CoV-2 performance.
Results show that the presence of the microorganisms at the concentrations tested did not interfere with the detection of SARS-CoV-2 by generating false negative results. Note that in presence of SARS-coronavirus (SARS-CoV-1) at 1e5 pfu/mL, 3x LoD concentrations of SARS-CoV-2 was not detected, when SARS-CoV-1 was at 1e4 pfu/mL, 3x LoD of SARS-CoV-2 can be detected indicating SARS CoV-1 at 1e5 pfu/mL or higher may interfere with SARS-CoV-2 detection. However, the likelihood of a co-infection with SARS CoV-1 is remote as the last confirmed case of SARS-CoV-1 was reported in 2004.
Cross-reactivity/Microbial interference: list of organisms tested Table 5
| Description | ConcentrationTested* | Description | ConcentrationTested* |
|---|---|---|---|
| Human coronavirus 229E | 2.80E+05 | Aspergillus Flavus var. flavus | 1.00E+06 |
| Human Coronavirus HKU1 | 1.38E+07 | Bordetella parapertussis | 1.00E+06 |
| Human coronavirus OC43 | 3.16E+05 | Bordetella pertussis | 1.74E+06 |
| Human Coronavirus, NL63 | 1.38E+06 | Candida albicans | 1.58E+07 |
| SARS Coronavirus** | 1.00E+05 | Chlamydia pneumoniae | 6.88E+06 |
| SARS Coronavirus** | 1.00E+04 | Corynebacterium flavescens | 1.00E+06 |
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| Description | ConcentrationTested* | Description | ConcentrationTested* |
|---|---|---|---|
| MERS Coronavirus | 1.50E+07 | Escherichia coli | 1.00E+06 |
| Adenovirus | 2.88E+05 | Fusobacterium necrophorum subsp.necrophorum | 1.00E+06 |
| Cytomegalovirus | 1.00E+05 | Haemophilus influenzae | 2.00E+06 |
| Enterovirus Type 71 | 1.05E+05 | Lactobacillus crispatus | 1.00E+06 |
| Epstein-Barr virus | 1.00E+05 | Legionella pneumophila | 1.38E+08 |
| Human Metapneumovirus (hMPV) | 1.60E+05 | Moraxella catarrhalis | 1.00E+06 |
| Influenza A (Brisbane 59/07) H1N1 | 1.00E+05 | Mycobacterium tuberculosis | 5.75E+06 |
| Influenza A (Kansas-14/2017) | 1.99E+07 | Mycoplasma genitalium | 1.00E+06 |
| Influenza B (Colorado-06/2017) | 6.10E+08 | Mycoplasma pneumoniae | 3.45E+06 |
| Influenza B (Florida/04/06) | 1.00E+05 | Nasal Wash | 1:10 |
| Measles | 1.00E+05 | Neisseria flava | 1.00E+06 |
| Mumps | 1.00E+05 | Neisseria meningitidis | 1.00E+06 |
| Parainfluenza Virus (hPIV) | 1.60E+05 | Pneumocystis jirovecii | 1.59E+07 |
| Parainfluenza Virus Type 1 | 1.26E+05 | Pneumocystis jirovecii (Clinical sample) | 1:10 |
| Parainfluenza Virus Type 3 | 3.45E+05 | Pseudomonas aeruginosa | 2.03E+07 |
| Parainfluenza Virus Type 4A | 2.88E+05 | Staphylococcus aureus | 1.00E+06 |
| Respiratory Syncytial Virus Type A | 1.26E+05 | Staphylococcus epidermis | 1.20E+07 |
| Rhinovirus | 5.50E+05 | Streptococcus pneumoniae | 1.22E+06 |
| Streptococcus pyogenes | 6.25E+06 | ||
| Streptococcus salivarius | 6.63E+06 |
- TCID50/mL, EID50/mL, cp/mL PFU/mL, genome equiv/mL for viruses; CFU/mL, IFU/mL for bacteria and fungi.
** SARS CoV-1 at 1e5 pfu/mL or higher may interfere with SARS-CoV-2 detection. It did not interfere with the SARS-CoV-2 detection at 1e4 pfu/mL.
Endogenous and exogenous interference 5.1.4.
Potentially interfering substances that may be commonly encountered in respiratory specimens were evaluated. Medically and/or physiologically relevant concentrations of potential interferents were tested with cobas® SARS-CoV-2. Each substance was tested, by introducing potential interferents into pooled negative nasopharyngeal swab specimens (NNPS) in UTM and tested with and without 3x LOD of SARS-CoV-2 target. As shown in Table 6 substances at the concentrations tested did not interfere in the detection of SARS-CoV-2.
Table 6 Endogenous and exogenous interference
| Potential Interferent | Active Ingredient | Concentration Tolerated |
|---|---|---|
| ----------------------- | ------------------- | ------------------------- |
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| Potential Interferent | Active Ingredient | Concentration Tolerated |
|---|---|---|
| Mucin | Purified mucin protein | 5 mg/mL |
| Human Whole Blood | - | 5% (v/v) |
| Peripheral blood mononuclear cell (PBMC) | - | 1.0E+06 cells/mL |
| Nasal spray - Afrin / Anefrin | Oxymetazoline | 5% (v/v) |
| Nasal corticosteroids - Flonase | Fluticasone | 5% (v/v) |
| Nasal gel - Zicam | Galphimia glauca, Histaminum hydrochloricum,Luffa operculata, Sulphur | 5% (v/v) |
| Throat lozenges, oral anesthetic and analgesic -Cepacol | Benzocaine, Menthol | 5 mg/mL |
| Antibiotic, nasal ointment - Bactroban | Mupirocin | 5 mg/mL |
| Antiviral drug - Relenza | Zanamivir | 5 mg/mL |
| Antiviral drug - Tamiflu | Oseltamivir | 7.5 mg/mL |
| Antimicrobial, systemic | Tobramycin | 4 µg/mL |
| Influenza vaccine - FluMist | Live Quadrivalent 2022-2023A/Victoria/1/2020 (H1N1) (anA/Victoria/2570/2019 (H1N1) pdm09 - like virus),A/Norway/16606/2021 (H3N2) (anA/Darwin/9/2021 (H3N2) - like virus),B/Phuket/3073/2013 (B/Yamagata lineage), andB/Austria/1359417/2021 (B/Victoria lineage)lineage) | 5.93E+06 FFU/mL |
REPRODUCIBILITY 6.
Reproducibility study assesses the total variability of the assay in detecting SARS-CoV-2 across operators, study sites, testing days, Analyzers, and assay tube lots. The reproducibility was evaluated at 3 study sites representative of CLIA-waived intended use settings. Two operators at each of the 3 sites tested a 3-member reproducibility panel in triplicate on 5 different days, for a total of ~270 runs (3 panel members x 3 replicates x 2 operators x 5 days x 3 sites). Nine Analyzers and 3 assay tube lots were used. The reproducibility panel comprises a low positive and a moderate positive for SARS-CoV-2, in addition to a negative sample. The expected result for the true negative panel member is "Not Detected," while the expected result for the low positive and moderate positive panel member is "Detected." Percent agreement with expected result, mean Ct, Ct SD, and Ct %CV are shown in Table 7.
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| PanelMember | Total numberof valid testruns | Site 1 | Site 2 | Site 3 | All sites | All sites |
|---|---|---|---|---|---|---|
| Agreementwith ExpectedResults | Agreementwith ExpectedResults | Agreementwith ExpectedResults | Avg. Ct ± SD(%CV) | Agreement (n/N)and (95% CI) | ||
| Negative | 268 | 100.0% (90/90) | 100.0% (88/88) | 98.9% (89/90) | 99.6% (267/268)(97.9%-99.9%) | |
| SARS-CoV-2Low Positive | 266 | 100.0% (89/89) | 100.0% (90/90) | 97.7% (85/87) | 33.4±0.96(2.9%) | 99.2% (264/266)(97.3%-99.8%) |
| SARS-CoV-2ModeratePositive | 268 | 100.0% (88/88) | 100.0% (90/90) | 100.0% (90/90) | 32.5±0.54(1.7%) | 100.0% (268/268)(98.6%-100.0%) |
Table 7 SARS-CoV-2 reproducibility
CLINICAL PERFORMANCE EVALUATION 7.
The clinical performance of the cobas® SARS-CoV-2 test was evaluated using prospectively collected fresh paired clinical nasopharyngeal swab (NPS) and nasal swab (NS) specimens and unpaired frozen specimens collected from either symptomatic individuals suspected of respiratory viral infection consistent with COVID-19 or asymptomatic individuals. Testing of clinical samples was performed with the cobas® SARS-CoV-2 test at 10 point-of-care healthcare facilities (e.g., emergency rooms, outpatient clinics, and physician offices). Results from clinical specimens tested with cobas® SARS-CoV-2 were compared to results from three highly sensitive FDA-EUAauthorized laboratory-based RT-PCR assays (composite comparator method).
Prospective clinical specimens were tested February-June 2022. In total, 1874 evaluable NPS samples and 1872 evaluable NS samples were included in the analysis for the performance evaluation of the cobas® SARS-CoV-2 assay. Of these, 673 NPS specimens were collected from individuals with signs and symptoms of respiratory tract infection and 1201 were from asymptomatic individuals (413 suspected of SARS-CoV-2 infection due to recent exposure or other reasons and 788 from individuals without symptoms or other reasons to suspect COVID-19). Among the NS specimens tested in the study, 674 were collected from individuals with signs and symptoms of respiratory tract infection and 1198 were from asymptomatic individuals (411 suspected of SARS-CoV-2 infection due to recent exposure or other reasons and 787 from individuals without symptoms or other reasons to suspect COVID-19).
For each specimen type (NPS and NS), 23 each frozen SARS-CoV-2-positive and -negative specimens from 92 symptomatic individuals earlier during the COVID-19 pandemic (March—June
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- were distributed to 3 of the 10 sites and worked into the daily workflow of sites for testing.
Clinical performance evaluation using nasopharynqeal swab specimens 7.1.
The clinical performance of the cobas® SARS-CoV-2 test for the detection of SARS-CoV-2 from healthcare-provider collected NPS specimens collected in UTM/UVT was evaluated based on test results from a total of 1876 individual fresh and frozen (23 prospective frozen SARS-CoV-2-positive NPS specimens were tested at sites; one frozen negative specimen was included for each frozen positive specimen) NPS specimens. Of these, 2 NPS specimens were non-evaluable due to invalid/failed tests. The remaining 1874 NPS specimens were evaluable and included in the clinical performance evaluation of cobas® SARS-CoV-2.
As shown in Table 8 for symptomatic individuals, 125 NPS specimens tested positive for SARS-CoV-2 with both the cobas® SARS-CoV-2 test on cobas® Liat® System and the composite comparator; six SARS-CoV-2-positive specimens tested negative for SARS-CoV-2 with the cobas® SARS-CoV-2 test. A total of 539 NPS specimens tested negative for SARS-CoV-2 with both the cobas® SARS-CoV-2 test and the composite comparator; three SARS-CoV-2-negative specimens tested positive for SARS-CoV-2 with the cobas® SARS-CoV-2 test.
For NPS specimens prospectively collected from symptomatic individuals, cobas® SARS-CoV-2 demonstrated 95.4% PPA (125/131; 95% score CI: 90.4%-97.9%) and 99.5% NPA (539/542; 95% score CI: 98.4%-99.8%).
Clinical performance comparison with the composite comparator method - NPS Table 8 specimens from symptomatic individuals
| Composite Comparator MethodSARS-CoV-2 Result | |||
|---|---|---|---|
| Positive | Negative | ||
| cobas® SARS-CoV-2 on cobas® Liat® SystemNasopharyngeal Swab | Positive | 125 | 3 |
| Negative | 6 | 539 |
PPA 95.4% (95% CI: 90.4% - 97.9%) NPA 99.5% (95% CI: 98.4% - 99.8%)
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As shown in Table 9 for asymptomatic individuals, 52 NPS specimens tested positive for SARS-CoV-2 with both the cobas® SARS-CoV-2 test on cobas® Liat® System and the composite comparator; two SARS-CoV-2-positive specimens tested negative for SARS-CoV-2 with the cobas® SARS-CoV-2 test. A total of 1142 NPS specimens tested negative for SARS-CoV-2 with both the cobas® SARS-CoV-2 test and the composite comparator; five SARS-CoV-2-negative specimens tested positive for SARS-CoV-2 with the cobas® SARS-CoV-2 test. For NPS specimens prospectively collected from asymptomatic individuals, cobas® SARS-CoV-2 demonstrated 96.3% PPA (52/54; 95% score CI: 87.5%-99.0%) and 99.6% NPA (1142/1147; 95% score CI: 99.0%-99.8%).
Clinical performance comparison with the composite comparator method - NPS Table 9 specimens from asymptomatic individuals
| Composite Comparator MethodSARS-CoV-2 Result | |||
|---|---|---|---|
| Positive | Negative | ||
| cobas® SARS-CoV-2 on cobas® Liat® System | Positive | 52 | 5 |
| Nasopharyngeal Swab | Negative | 2 | 1142 |
PPA 96.3% (95% CI: 87.5% - 99.0%) NPA 99.6% (95% CI: 99.0% - 99.8%)
Clinical performance evaluation using nasal swab specimens 7.2.
The clinical performance of the cobas® SARS-CoV-2 test for the detection of SARS-CoV-2 from nasal (NS) specimens collected in UTM/UVT was evaluated from a total of 1950 individual fresh and frozen (twenty-three prospective frozen SARS-CoV-2-positive NS specimens were tested at sites; one frozen negative specimen was included for each frozen positive specimen) NS specimens; NS specimens were comprised of either healthcare provider-collected (49.6%) or self-collected swabs (50.4%). Overall, 77 NS specimens were non-evaluable due to not being tested, protocol deviation, or invalid/failed tests. The remaining 1873 NS specimens (including 1 indeterminate result) were evaluable and included in the clinical performance evaluation of cobas® SARS-CoV-2.
As shown in Table 10 for symptomatic individuals, 129 NS specimens tested positive for SARS-CoV-2 with both the cobas® SARS-CoV-2 test on cobas® Liat® System and the composite
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comparator; five SARS-CoV-2-positive specimens tested negative for SARS-CoV-2 with the cobas® SARS-CoV-2 test. A total of 539 NS specimens tested negative for SARS-CoV-2 with both the cobas® SARS-CoV-2 test and the composite comparator; one SARS-CoV-2-negative specimens tested positive for SARS-CoV-2 with the cobas® SARS-CoV-2 test.
Overall, for NS specimens prospectively collected from symptomatic individuals, cobas® SARS-CoV-2 demonstrated 96.3% PPA (129/134; 95% score CI: 91.6%-98.4%) and 99.8% NPA (539/540; 95% score CI: 99.0%-100.0%).
Clinical performance comparison with the composite comparator method - NS Table 10 specimens from symptomatic individuals
| Composite Comparator MethodSARS-CoV-2 Result | |||
|---|---|---|---|
| Positive | Negative | ||
| cobas® SARS-CoV-2 on cobas® Liat® SystemNasal Swab | Positive | 129 | 1 |
| Negative | 5 | 539 |
PPA 96.3% (95% CI: 91.6% - 98.4%) NPA 99.8% (95% CI: 99.0% - 100.0%)
Note: The nasal swabs were comprised of healthcare provider-collected nasal swab specimens self-collected on-site with healthcare provider instructions.
As shown in Table 11 for asymptomatic individuals, 45 NS specimens tested positive for SARS-CoV-2 with both the cobas® SARS-CoV-2 test on cobas® Liat® System and the composite comparator; five SARS-CoV-2-positive specimens tested negative for SARS-CoV-2 with the cobas® SARS-CoV-2 test. A total of 1147 NS specimens tested negative for SARS-CoV-2 with both the cobas® SARS-CoV-2 test and the composite comparator; one SARS-CoV-2-negative specimens tested positive for SARS-CoV-2 with the cobas® SARS-CoV-2 test.
Overall, for NS specimens prospectively collected from asymptomatic individuals, cobas® SARS-CoV-2 demonstrated 90.0% PPA (45/50; 95% score CI: 78.6%-95.7%) and 99.9% NPA (1147/1148; 95% score CI: 99.5%-100.0%).
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Table 11 Clinical performance comparison with the composite comparator method - NS specimens from asymptomatic individuals
| Composite Comparator MethodSARS-CoV-2 Result | |||
|---|---|---|---|
| Positive | Negative | ||
| cobas® SARS-CoV-2 on cobas® Liat® SystemNasal Swab | Positive | 45 | 1 |
| Negative | 5 | 1147 |
| PPA | 90.0% (95% CI: 78.6% - 95.7%) |
|---|---|
| ----- | ------------------------------- |
NPA 99.9% (95% CI: 99.5% - 100.0%)
Note: The nasal swabs were comprised of healthcare provider-collected nasal swab specimens self-collected on-site with healthcare provider instructions.
8. CONCLUSIONS
A comparison of the intended use, technological characteristics, and the results of non-clinical analytical and clinical performance studies demonstrate that cobas® SARS-CoV-2 Nucleic acid test for use on the cobas® Liat® System is substantially equivalent to the predicate device.
N/A