Public Health Division

Test Menu Details

SARS-CoV-2 Next Generation Sequencing (NGS)
Updated	2/19/2025
Search Terms	SARS-CoV-2 Sequencing; 2019 nCoV; COVID-19
How to Order	This assay is performed for public health SARS-CoV-2 surveillance projects and as a reflex test in the COVID-19 and Influenza Testing Algorithm (pdf).
Availability	This assay is performed for public health SARS-CoV-2 surveillance projects as a reflex test in the COVID-19 and Influenza Testing Algorithm (pdf).
Performed	As needed based on testing demand
Time to Reporting	Specimens are reflexed to this test if there is sufficient quality SARS-CoV-2 nucleic acid in the sample. Individual specimen testing priority will be determined by epidemiological significance and as capacity allows.
Data Sharing	Data from SARS-CoV-2 sequencing are submitted to national repository banks, GISAID or NCBI, as part of genomic surveillance and epidemiological data sharing. Additional details can be found in the COVID-19 Sequencing Educational Resources (pdf).
CPT Code

Specimen Collection Details
Collection	Acceptable specimen sources include: Nasopharyngeal swabs (preferred), nasal swabs, throat swabs, combination swabs (2 swabs from accepted specimen sources in one vial), nasal aspirates, nasal washes, bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates. Swabs must be submitted in appropriate media. Do not submit dry swabs for testing. Acceptable specimen transport media types include: VTM is preferred; UTM and sterile saline are accepted. DO NOT SUBMIT Molecular Transport Media (MTM) for this test. Media containing guanidine thiocyanate or similar chemicals are not acceptable for testing. This media inactivates the virus and cannot be used for all public health surveillance.
Optimal Volume	Primary specimen (preferred): 3.0 mL
Minimum Volume	Primary specimen (preferred): 1.0 mL
Handling	Store specimens at refrigerated temperatures (2-8°C) pending transport. Specimens that will not be tested within 72 hours of collection should be frozen at -70°C or lower pending transport. Specimens may also be stored at -20°C for up to 3 days. Minimize the potential for multiple freeze/thaw cycles during handling, storage, and testing to prevent viral degradation.
Transport	Package specimens with fully frozen ice packs to maintain refrigerated temperatures during transport. Transport for receipt at the OSPHL within 3 days of specimen collection. If specimen is frozen, package specimens with dry ice to maintain frozen temperatures during transport.
Rejection Criteria	Specimens are subject to the requirements of the OSPHL Specimen Submission Policy (pdf).
Comments	All specimens will be co-tested for COVID-19 (SARS-CoV-2) and influenza. Qualifying specimens may be sequenced for SARS-CoV-2. Sequencing priority will be determined by epidemiological significance and as capacity allows. For additional details about OSPHL's testing process, please review the COVID-19 and Influenza Testing Algorithm (pdf). Original material submitted for testing is retained for 7-10 calendar days after receipt at the laboratory.

Method Details
Methodology	ThermoFisher Ion Ampliseq SARS-CoV-2 Insight Research Assay ClearLabs Clear Dx Surveillance
Performance Specifications	The performance characteristics of this test were evaluated by the OSPHL following the requirements for clinical laboratory testing established by the Clinical Laboratory Improvement Amendments (CLIA). This test is intended for public health surveillance and infection control purposes. It should not be regarded as investigational or for research. For more information about the performance characteristics, please contact the OSPHL.

Change Log
2/19/2025	Updated How to Order; Availability; Performed; Public Health Data; Handling
10/19/2023	Updated Collection, Optimal Volume, Minimum Volume, Handling, and Comments sections
5/23/2023	Clarified Time to Reporting