Sign in →

Test Code LAB8572 SARS Coronavirus 2 (COVID-19) by PCR

Additional Codes:

SARS-CoV-2-MP

Notes:

Impact of New SARS-CoV-2 Genetic Variants on Molecular Testing for COVID-19

Both the COVID-19 Genomics United Kingdom Consortium and the WHO have reported that mutations that have occurred in the Spike (S) gene, particularly the 69-70 deletion, is responsible for a “dropout” in the S gene target in certain molecular tests that target this gene.  Among the six different molecular tests deployed across MUSC Health only one test targets the S gene, the Thermo Fisher TaqPath test.   However, this test also amplifies two other gene targets, the ORF 1a and N genes, so the test itself is not compromised should this variant become common in the US.  Although we will remain vigilant for new variants that could potentially impact the performance of our molecular tests for COVID-19, the primer and probe sequences used in these tests are proprietary information, and consequently we are dependent on the manufacturers to alert us to any potential problems.  Now that we have the capacity to sequence for variants and we know the gene targets of the assays we have deployed we should be in a better position to identify any variants that might comprise diagnostics.  The South African and Brazilian variants should have no impact on the performance characteristics on molecular diagnostic tests we use. 

Collection:

Specimen: Nasopharyngeal (NP) swabs, oropharyngeal swabs, nasal aspirates, BAL

Saliva collection is limited to symptomatic patients at the fixed tent sites that have been evaluated by MUSC Health virtual urgent care only.


Container: Nasopharyngeal (NP) swabs in Universal Transport Media (MUSC Health Charleston Division inpatient units may call laboratory at 2-0707 to obtain) OR swab in 3mL sterile saline in sterile tube if UTM unavailable are preferred. E-swab collection kits are not preferred, but may be submitted if UTM and sterile saline are both unavailable. 

Nasal aspirates and BAL, submit in a sterile container.

Saliva, submit in an IsoHelix Collection tube.


Volume: 3 mL; Minimum 1 mL; Saliva requires 2 mL

Storage Instructions:

Send specimen to Lab immediately after collection. Refrigerate NP swabs, nasal aspirates, or BAL specimens at 2 – 8C or keep on wet ice if specimen cannot be sent immediately. Specimens are stable 72 hours refrigerated, and should be stored at -70C for storage beyond 72 hours. Saliva specimens collected in the IsoHelix collection devices should be stored and transported at room temperature. Do NOT store or transport refrigerated or on wet ice.

Turnaround Time (TAT):

Reported within 24-48 hours of receipt in laboratory

Methodology

The Abbott RealTime SARS-CoV-2 assay is real-time reverse transcription polymerase chain reaction (rRT-PCR) test on the Abbott m2000 System.

Request Form:

Routine Laboratory Request Form

Send To:

Central Processing – EH318 University Extension Hospital (former Children’s Hopsital)

Reference Interval:

Not Detected

Interpretive Data:

The oligonucleotide primers and probes for detection of SARS-CoV-2 were selected from regions of the virus nucleocapsid (N) and RNA dependent RNA polymerase (RdRp) genes.  RNA is isolated and purified from respiratory specimens and reverse transcribed to cDNA and subsequently amplified and detected by real-time PCR. Negative : A Negative result does not preclude SARS-CoV-2 infection and should not be used as the sole basis of patient management/treatment or public health decisions. A negative result should be combined with clinical observations, patient history, and epidemiological information.