The CRSP SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic 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.
The test was validated on 103 positive and 50 negative specimens representing nasopharyngeal (NP) and oropharyngeal (OP) swabs and found to have 100% accuracy with a lower limit of detection of 0.20 copies/µl.
Results are presumptive for the detection and identification of SARS-CoV-2 RNA. The SARS-CoV-2 RNA is generally detectable in the nasopharynx and oropharynx 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 disease. 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.
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 CRSP SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Assay is intended for use by trained and competency-certified clinical laboratory personnel, specifically instructed and trained in the techniques of real-time PCR and in vitro diagnostic procedures. The CRSP SARS-CoV-2 Real-time Reverse Transcriptase (RT)-PCR Diagnostic Assay is only for use under the Food and Drug Administration’s Emergency Use Authorization.
We support 2 options for sending samples for testing to Broad. Please note that choice of tube submission may impact turnaround times and testing capacity. We are happy to discuss these options with you in more detail to figure out the most effective, safe way to transfer.
|Option 1 - Matrix tubes||Option 2 - Swab VTM tubes|
For larger, automation savvy labs that have the ability to print scannable barcode labels to affix to the tube.
Tubes provided by CRSP: ThermoFisher catalog #3732
For smaller labs with lower test volume. If needed, we can provide scannable barcode labels.
We do NOT supply swabs or collection tubes.
Requires a matrix tube labeled with:
Requires a swab collected in a VTM tube labeled with:
A manifest file is required for all options. Please include both:
The file should be named as follows: SITENAME_ManifestNumber_Date.csv, e.g. st.elsewhere_Manifest203_3.25.20.csv
Regardless of option chosen above, samples may be rejected or significantly delayed if they arrive with any of the following nonconformances:
Although we do not expect this to happen any time soon, in the event that we become capacity constrained, we will follow the CDC and Massachusetts Department of Public Health guidelines for prioritization of testing. Tier A includes Categories 1-3 from the CDC and 1-6 from the MA DPH. Click on the links in the table below to obtain details from each source.
Please add a Tier level in your manifest for each sample according to the following criteria:
|Tier A||CDC Priorities 1-3 or MA DPH Categories 1-6|
|Tier B||All other symptomatic|
|Tier C||All other non-symptomatic|
We have deployed multiple options for transfer of manifest files. Please choose the version that best fits with your lab workflow.
Send us your .csv manifest file in one of the following ways:
CRSP will provide a results file with the following format:
If PDF reports were required by the facility, you will receive PDFs that look similar to this:
Individuals designated to receive test results will be provided with one of the following options to access results:
The test result code (column I of the report) may be any of the following:
|Result||Description ("reason" or column J in the results file)|
|NEG||2019-novel Coronavirus (2019-nCoV) not detected by the qRT-PCR assay. Consider testing for other respiratory viruses or re-collecting for 2019-nCoV testing. Note: Optimum timing for peak viral levels during infections caused by 2019-nCoV have not been determined. Collection of multiple specimens from the same patient may be necessary to detect the virus.|
|INCONCLUSIVE||Inconclusive for 2019-novel Coronavirus (2019-nCoV) by qRT-PCR with one of the two viral probes (either N1 or N2) being positive while the other is not detected after two attempts on this specimen. Consider re-collection of specimen. Note: Optimum timing for peak viral levels during infections caused by 2019-nCoV have not been determined. Collection of multiple specimens from the same patient may be necessary to detect the virus.|
|POS||Positive for detection of 2019-novel Coronavirus (2019-nCoV) by qRT-PCR.|
|INVALID||This specimen failed to produce a valid result after two attempts. An invalid result means no nucleic acids (viral or human) were detected by qRT-PCR. Consider re-collection of specimen.|
|UNSATISFACTORY_1||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: improper specimen transport medium.|
|UNSATISFACTORY_2||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: inappropriate timing of collection relative to specimen receipt. Specimens must be received within 72 hrs of collection unless frozen.|
|UNSATISFACTORY_3||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: sample tube unlabeled.|
|UNSATISFACTORY_4||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: insufficient volume.|
|UNSATISFACTORY_5||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: tube sample data does not match the submission form.|
|UNSATISFACTORY_6||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: laboratory accident.|
|UNSATISFACTORY_7||Unsatisfactory for 2019-novel Coronavirus (2019-nCoV) testing by PCR: leaking/broken tube.|
|CANCELED||Testing canceled per submitter.|
This RT-PCR test, a high throughput version of the CDC 2019-nCoV Realtime RT-PCR test, was performed by the Clinical Research Sequencing Platform at the Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, CLIA #22D2055652. This test is not FDA-cleared but its performance characteristics were established by a CLIA-certified high-complexity laboratory in accordance with CLIA regulations. The test was validated on 103 positive and 50 negative specimens representing nasophryngeal (NP) and oropharyngeal (OP) swabs and found to have 100% accuracy with a lower limit of detection of 0.2 copies/µl. Subsequently, we validated oropharyngeal swabs (OP) which also showed 100% concordance with a second lab’s results. Further, we have validated the use of Saline as an alternate media (to VTM) for collection and transport of swabs.
Medical Director: Heidi Rehm Ph.D., FACMG
Project Manager: Maegan Harden, Ph.D. (617-714-7569)
Clinical Research Sequencing Platform, LLC
Broad Institute of MIT and Harvard
320 Charles St. Cambridge, MA 02141
CLIA ID: 22D2055652
CAP # 8707596