COVID-19 Test Overview

The Color COVID-19 testing platform supports testing at multiple laboratories. The laboratory where testing is completed is listed in the methodology and limitation section on each individual report. Test details for each laboratory are described below:

 

 

 

Color SARS-CoV-2 RT-LAMP Diagnostic Assay

Assay Overview

The Color SARS-CoV-2 RT-LAMP Diagnostic Assay is a real time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay intended for the qualitative detection of nucleic acid from the SARS-CoV-2 virus collected in respiratory swabs. Testing is performed at the Color laboratory which is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests.

 

Results are intended for the detection of SARS-CoV-2 RNA. The SARS-CoV-2 RNA is generally detectable in the upper respiratory system during the acute phase of infection. Positive results are indicative of active infection with SARS-CoV-2 but do not rule out bacterial infection or co-infection with other viruses. The agent detected may not be the definite cause of illness. In addition, nucleic acid detection can persist following clearance of active viral replication. Laboratories within the United States and its territories are required to report all positive results to the appropriate public health authorities, and in some jurisdictions (including where Color is located), all results (positive, negative, and indeterminate) will be reported to local public health authorities.

 

Negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient treatment or other patient management decisions. Negative results must be combined with clinical observations, patient history, and epidemiological information.

Testing with the Color SARS-CoV-2 RT-LAMP Diagnostic Assay is intended for use by trained and competency-certified clinical laboratory personnel, specifically instructed and trained in the techniques and in vitro diagnostic procedures. The Color SARS-CoV-2 RT-LAMP Diagnostic Assay has been validated in accordance with the FDA’s Guidance Document (Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency Immediately in Effect Guidance for Clinical Laboratories, Commercial Manufacturers, and Food and Drug Administration Staff Document) issued on March 16, 2020 (the “FDA Guidance of March 16, 2020”). This Test has been authorized by FDA under an Emergency Use Authorization (EUA) for use by the Color lab, but is not FDA cleared or approved. This test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens. This test is only authorized for the duration of time the declaration that circumstances exist justifying the authorization of the emergency use of in vitro diagnostic tests for detection of SARS-CoV-2 virus and/or diagnosis of COVID-19 infection under section 564(b)(1) of the Act, 21 U.S.C. 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.

Expected Turnaround Time

24-72 hours. Turnaround time is the usual number of hours from the time a specimen is accessioned at the laboratory to when the result is released to the ordering provider. Test results are most typically reported electronically, which generally allows for faster delivery. Schedules may vary.

Specimen Requirements
  • Specimen
    • This test has currently been validated for use with AN, NP, and OP swabs.
  • Media
    • Acceptable transport media include: DNA/RNA shield, VTM or UTM, 1ml minimum.
    • Samples can also be sent “dry” (a swab with no media, in a sterile tube), using a Color-provided collection kit. 
  • Storage and Transport Instructions
    • Ship all samples as Category B (UN3373 – Biological Substances) material.
    • Specimens collected without media (dry swabs) or swabs collected in DNA/RNA shield may be handled and shipped at room temperature
    • VTM and UTM should be refrigerated at 2-8℃ prior to and during transport within 24 hrs. If the specimen is to be submitted greater than 24 hrs post collection, freeze the specimens at -20℃ or below and then ship on dry ice.
    • Sample may be rejected or significantly delayed if they arrive with:
      • Insufficient, incompatible or congealed media in specimens collected in transport media
      • Dry swabs that arrive more than 56 hours after sample collection
      • Improperly capped or labeled tubes
      • Swabs inverted in collection tubes (i.e. swab bud facing up)
      • Missing physician order
      • Incomplete or missing patient information
      • Not in compliance with Color’s Terms of Service
Test Details
  • Use: 
    • Detection of SARS-CoV-2 to assist in the diagnosis of COVID-2019 infections
  • Result types: 
    • Positive for SARS-CoV-2. Positive indicates that SARS-CoV-2 (the virus that causes COVID-19) was detected in the patient’s sample. False positives are possible.
    • Negative for SARS-CoV-2. Negative indicates that SARS-CoV-2 (the virus that causes COVID-19) was not detected in the patient’s sample. False negatives are possible.
    • Inconclusive result for SARS-CoV-2. Inconclusive indicates that the test results were internally inconsistent and cannot be classified as either positive or negative.
    • Unsatisfactory sample. Test could not be completed.
  • Test method for Color SARS-CoV-2 Amplification Assay
      • This test was developed and its performance characteristics determined by Color Genomics, Inc. (“Color”), a clinical laboratory accredited by the College of American Pathologists (CAP) and certified under the Clinical Laboratory Improvement Amendments (CLIA) to perform high-complexity testing (CAP #8975161 – CLIA #05D2081492).
      • RNA is extracted from the primary sample and analyzed using a colorimetric loop-mediated isothermal amplification (LAMP) based assay. The presence of SARS-CoV-2 is assessed by analyzing two viral targets (N & E genes, or Orf1A & S genes). The human RNAseP gene is analyzed as an extraction control. 
      • Test Limitations include:
        • This assay has a >99% accuracy with a limit of detection of 0.75 copies/uL for samples processed up to 72 hours from collection time.
        • Positive results are indicative of an active infection with SARS-CoV-2 but do not rule out bacterial infections or co-infection with other viruses. Negative results do not eliminate the possibility of a SARS-CoV-2 infection. 
        • The sample collection technique can meaningfully impact test sensitivity. False positives and false negatives are possible. False negatives can occur for several reasons including (but not limited to) reduced sensitivity due to a viral load below the limit of detection of this assay, or mutations in the targeted viral sequence, or the presence of amplification inhibitors.

The Broad Institute’s Clinical Research Sequencing Platform (CRSP)

Samples tested at the Broad Institute’s Clinical Research Sequencing Platform (CRSP) are processed using the CRSP SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Assay. The assay is a real-time RT-PCR test intended for the qualitative detection of nucleic acid from the SARS-CoV-2 in nasopharyngeal and oropharyngeal swabs collected from individuals who may have contracted the virus. Testing is limited to the Clinical Research Sequencing Platform at the Broad Institute which is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests. 

Further details about this assay can be found here

California Department of Public Health (CDPH) Branch Laboratory

Assay Overview

The SARS-CoV-2 RT-PCR test is a real-time polymerase chain reaction (RT-PCR) based diagnostic laboratory developed test (LDT) for the direct detection of SARS-CoV-2 virus RNA from patient samples. The test is indicated for use as an aid in diagnosis of SARS-CoV-2 infection in patients. This SARS-CoV-2 RT-PCR based test uses the chemagic™ 360 for the isolation of the viral nucleic acids followed by the RT-PCR assay on an Analytik Jena thermal cycler. The SARS-CoV-2 RT-PCR test detects N and ORF1ab sequences from the SARS-CoV-2 virus using sequence-specific primers and probes. An internal control is used to monitor the processes from nucleic acid extraction to fluorescence detection in clinical samples.

 

The SARS-CoV-2 RT-PCR test is not FDA cleared. The test has been validated and was submitted to FDA for emergency use authorization (EUA). FDA has been notified of the LDT (with modifications) and FDA has deemed that EUA is not necessary. The SARS-CoV-2 RT-PCR test is a RT-PCR based qualitative diagnostic test intended for the qualitative detection of nucleic acid from the SARS-CoV-2 in nasopharyngeal swabs, oropharyngeal swabs, and anterior nasal swabs from individuals suspected of SARS-CoV-2 infection. This test has been developed as a LDT. Additional sample types are accepted subject to a validation by the laboratory.

Disclaimer

This assay is intended for use by CLIA certified high-complexity laboratories with experience in developing molecular diagnostics and is only for use under the Food and Drug Administration’s Emergency Use Authorization. This SARS-CoV-2 RT-PCR Assay does not constitute a definitive report for all infected individuals and hence interpreted with caution. The detection of viral nucleic acids depends on proper sample collection, handling, transportation, storage, and preparation (including extraction). There are many possible sources of diagnostic errors that can result from trace contamination of polymerase chain reactions and from rare genetic variants that interfere with analysis. Failure to observe proper procedures in any one of these steps can lead to an incorrect result. False negative results may occur due to improperly collected, transported, or handled swab samples. False negative results may also occur due to the presence of sequence variants in the targets of the assay, procedural errors, and amplification inhibitors in samples or inadequate numbers of organisms for amplification. False positive results may occur due to potential cross-contamination by target organisms, their nucleic acid or amplified product, or from non-specific signals in the assay. This SARS-CoV-2 RT-PCR test does not detect or differentiate any other respiratory virus types. Results from this test should be interpreted in conjunction with other clinical and laboratory findings.

 

Pursuant to the requirements of CLIA ’88, this technical component and the professional component was performed by CDPH Branch Laboratory. This test was developed and its performance characteristics determined by the CDPH Branch Laboratory, Valencia, CA. It has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. This test is used for clinical purposes. PKIG is accredited by the College of American Pathologists and CLIA for high complexity clinical testing.