SARS-CoV-2 Next Generation Sequencing (NGS)
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| Updated | 10/19/2023
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| Search Terms | SARS-CoV-2 Sequencing; 2019 nCoV; COVID-19
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| 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.
If the specimen is associated with an identified outbreak, include the outbreak number in the Outbreak Number box on the test request form. |
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| Availability |
With state Acute and Communicable Disease Prevention Program (ACDP) approval only. Please review the Criteria for Requesting COVID-19 Sequencing at OSPHL (pdf).
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| Performed | Once per week or more, depending on demand |
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| 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.
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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).
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| CPT Code |
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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.
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| Optimal Volume | Primary specimen (preferred): 3.0 mL
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| Minimum Volume | Primary specimen (preferred): 1.0 mL
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| 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. Minimize the potential for multiple freeze/thaw cycles during handling, storage, and testing to prevent viral degradation.
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| 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. |
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| Rejection Criteria | Specimens are subject to the requirements of the OSPHL Specimen Submission Policy (pdf). |
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| 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.
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Method Details |
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Methodology | ThermoFisher Ion Ampliseq SARS-CoV-2 Insight Research Assay
ClearLabs Clear Dx Surveillance
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| 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.
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