SARS-CoV-2 Whole Genome Sequencing Assay – Epidemiology
General Information
- Lab Name
- SARS CoV 2 Epidemiology
- Lab Code
- SAREPI
- Epic Ordering
- SARS CoV 2 Epidemiology
- Description
This assay recovers the whole genome sequence of a series of SARS-CoV-2 specimens and reports the SARS-CoV-2 strain, including variants of concern, as well as specific coding mutations found in the SARS-CoV-2 spike protein relative to the Wuhan-Hu1 isolate SARS-CoV-2 reference sequence. It also reports the pairwise nucleotide distance between the batch of isolates submitted, which may be of use for epidemiological investigations into clusters. The limit of detection of the assay is Ct 33.
- Synonyms
- SARS-CoV-2 Epidemiology, SARS CoV 2 Resistance, SARS CoV 2 Spike Mutations, SARS CoV 2 Spike Mutations, SARS-CoV-2 Transmission, SARS CoV 2 Variant Sequencing
- Components
-
Code Name SARSMP SARS CoV 2 NGS Sample Type SARSTR SARS CoV 2 NGS Variant Analysis SARSPK SARS CoV 2 NGS Mutations in Spike SARWGS SARS CoV 2 NGS Pair Wise NT Distance SAEINT SARS CoV 2 Epidemiology Interpretation
Interpretation
- Reference Range
- See individual components
Ordering & Collection
- Specimen Type
- Swab
- Collection
-
Instructions for Nasopharyngeal Swab: Gently insert mini-tipped flocked nasopharyngeal swab (swab on flexible plastic shaft) through the nostril and into the nasopharynx, reaching the posterior nasopharynx. Leave swab in place for 2-3 seconds then rotate completely around for 10-15 seconds. Remove swab and repeat the same process in the other nostril with the same swab.
After the second swab is completed, immediately place into the sterile vial containing media (UTM is preferred). Make sure that the swab is fully immersed in media, and that the shaft is short enough to completely tighten the cap. Obtaining columnar epithelial cells will enhance reliability of viral detection. - Handling Instructions
Send to the laboratory as soon as possible. Sample may be stored at 2-8°C for up to 72 hours of collection. Ship immediately to lab at 2-8°C (ice pack). If collection to receipt in the lab will exceed 72 hours freeze at -10°C or colder and ship on dry ice. Do not freeze/thaw.
- Quantity
-
requested: 0.5mL
minimum: 0.5mL
Processing
- Processing
Sample must be positive for SARS-CoV-2 by PCR to proceed with testing. Transport and store tube at 2 to 25°C for up to 48 hours. Send to UW Virology Lab via courier.
Performance
- LIS Dept Code
- Virology, Eastlake (EVIR)
- Performing Location(s)
-
Other Virology, Eastlake
206-685-6656Virology Laboratory, Ste 320
1616 Eastlake Ave E.
Seattle, WA 98102 - Frequency
- Available STAT?
- No
Billing & Coding
- CPT codes
- LOINC
- 69581-7
- Interfaced Order Code
- UOW4178