SARS-CoV-2 Whole Genome Sequencing Assay

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 206-685-6656 Virology Laboratory, Ste 320 1616 Eastlake Ave E. Seattle, WA 98102

Frequency

Available STAT?

Billing & Coding