Public Health Division

Test Menu Details

SARS-CoV-2 Next Generation Sequencing (NGS)
Updated	10/29/2026
Search Terms	SARS-CoV-2 Sequencing; 2019 nCoV; COVID-19; surveillance; whole genome sequencing; WGS
How to Order	This assay is not available for direct ordering. SARS-CoV-2 sequencing is performed for public health surveillance purposes as a reflex test according to the Respiratory Virus Testing Algorithm (pdf).
Availability	Testing is limited to specimens selected for public health SARS-CoV-2 surveillance based on epidemiological significance and laboratory capacity. Refer to the Respiratory Virus Testing Algorithm (pdf).
Performed	As needed based on testing demand
Time to Reporting	Turnaround time varies depending on specimen quality, testing demand, and sequencing capacity. Sequencing results are reported after initial SARS-CoV-2 results have been released.
Data Sharing	De-identified data from SARS-CoV-2 sequencing are submitted to national and international repositories, GISAID or NCBI, to support genomic surveillance and epidemiological investigations data sharing. Additional details can be found in the COVID-19 Sequencing Educational Resources (pdf).
CPT Code

Specimen Collection Details
Specimen Details	All specimens will be co-tested for SARS-CoV-2 and influenza. Please refer to the Influenza SARS-CoV-2 Multiplex Real-Time RT-PCR Test Menu. Qualifying SARS-CoV-2 positive specimens may undergo reflex sequencing if sufficient quality and quantity of viral nucleic acid are available. Specimen selection and testing priority are determined by epidemiological significance and laboratory capacity.

Method Details
Methodology	Ion Torrent Ampliseq™ SARS-CoV-2 Insight Research Assay Clear Labs Clear lx™ WGS SARS-CoV-2 v3.0 Assay
Performance Specifications	The performance characteristics of this assay were evaluated by the OSPHL following the requirements for clinical laboratory testing established by the Clinical Laboratory Improvement Amendments (CLIA). This assay is intended for public health surveillance and infection control purposes. It should not be regarded as investigational or for research.. Ion Torrent AmpliseqSARS-CoV-2 Insight Research Assay: Accuracy 89.47% Reproducibility 100.00% Sensitivity 89.47% Specificity 100.00% Clear lx™ WGS SARS-CoV-2: Accuracy 96.97% Reproducibility 100.00% Sensitivity 96.20% Specificity 100.00%

Change Log
10/29/2026	Changes made throughout; review as new
2/19/2025	Updated How to Order; Availability; Performed; Public Health Data; Handling