Guidance for Reporting SARS-CoV-2 Sequencing Results
- CDC requests laboratories that are sequencing SARS-CoV-2 positive specimens to report those data to state, local, tribal, or territorial public health departments.
- The technical guidance provides detailed instructions and examples for how to report SARS-CoV-2 sequencing results to state, local, tribal, or territorial public health departments.
It is critically important for the nation’s COVID-19 pandemic response to understand the genetic diversity, spread, and evolution of SARS-CoV-2, including variant viruses.
The Centers for Medicare and Medicaid Servicespdf iconexternal icon (CMS) published information that allows both non-CLIA Clinical Laboratory Improvement Amendments (CLIA) and CLIA-certified facilities that perform SARS-CoV-2 genetic sequencing on identified specimens to report patient-specific results to state, local, tribal, or territorial public health departments. Any sequencing data can be reported to public health.
Laboratories should only report results to patients or providers when sequencing is done under a CLIA certification. If the SARS-CoV-2 genetic sequencing result is reported to the ordering provider or patient and is intended to be used for the purposes of a person’s diagnosis, prevention, treatment, or health assessment, then the test must be performed in a CLIA-certified laboratory or facility and must comply with all applicable CLIA regulations.
In both scenarios, CDC strongly recommends and requests that labs send sequencing results to state, local, tribal, or territorial public health departments.
This guidance outlines the process for adding a SARS-CoV-2 genetic sequencing result to an existing electronic laboratory report to provide that information to the state, local, tribal, or territorial health departments. SARS-CoV-2 sequencing results should be reported as a follow-up to the original positive viral test result and reported to the same public health department. The electronic reporting of the sequencing data should include all the original patient demographic data, along with both the viral test report content and the second ordered test with viral genetic lineage identified. Laboratories and facilities that have SARS-CoV-2 positive specimens and intend to report -CoV-2 lineages, including variants, should upload sequence data to a public database (National Center for Biotechnology Information [NCBI] , Global Initiative on Sharing Avian Influenza Data [GISAID]).
The table below provides detailed guidance on reporting SARS-CoV-2 sequencing results to state, local, tribal, or territorial public health departments and includes examples for packaging data elements. This technical guidance is subject to change as new information becomes available about the impact of SARS-CoV-2 evolution on public health. For simplicity, only the fields needing more guidance in the additional observations for the variant lineage and the ID for the sequence sample are highlighted here. Other data elements normally part of each Observation/Result Segment (OBX), such as the result date, still need to be packaged as well.
|Data Element||Reporting Requirement||Technical Specifications||Notes||Example||HL7 Field|
|Federal / CDC / HHS||State / Local / Tribal / Territorial PHD||Ordering Provider / EHR*|
|Test result (performed and values)
|Yes||Yes||Requested||Must use harmonized LOINC codes, when available
|SARS-CoV-2 pango lineage identified through sequencing from the original specimen
|LOINC: 96741-4external icon:
SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing
OBX-2 = ST
Example answers so far:
SARS-CoV-2 – B.1.1.7 lineage
SARS-CoV-2 – B.1.351 lineage
SARS-CoV-2 – P.1 lineage
SARS-CoV-2 variant CA-B.1.429 lineage
SARS-CoV-2 variant NCY B.1.526 lineage
SARS-CoV-2 variant CA-B.1.427 lineage
SARS-CoV-2 variant P.2 lineage
|Test result date||Yes||Yes||Requested||YYYY[MM[DD]]||Date the test result was obtained||Example: 20200716||OBX-19.1external icon|
|Device Identifier||Yes||Yes||Requested||Must use harmonized Device Identifiers, when available. The DI is contained within the UDI, created by manufacturer||Manufacturer requests UDI issuanceexternal icon, then provides DI, or pull from GUDID databaseexternal icon
If DIs unavailable: Use the Unique Trade Name (controlled under 21 CFR 209.10(b)(1)external icon)
|Example DI: 01234567891011
Example Trade Name:
|Sequence ID||Yes||Yes||N/A||Lab assigned Sequence ID
|Add as an additional observation to the original report||PLT2397^Filler Lab Assigned Genetic Sequence Identifier^PLT
OBX-2 = ST
<WHATEVER FORMAT THE LAB USES>
|Performing facility name; CLIA #||Yes; if known||Yes; if known||N/A||Alpha; ##D#######||CLIA Laboratory Search||Example: 21D1234567||OBX-23.10external icon|
CDC: Centers for Disease Control and Prevention
CFR: Code of Federal Regulations
CLIA: Clinical Laboratory Improvement Amendments
CX: Extended Composite ID
DI: Device Identifier
EHR: Electronic Health Record
GISAID: Global Influenza Surveillance AID
GUDID: Global Unique Device Identification Database
HHS: Department of Health and Human Services
HL7: Health-Level Seven
LOINC: Logical Observations Identifiers Names and Codes
NAAT: Nucleic Acid Amplification Test
NCBI: National Center for Biotechnology Information
OBX: Observation/Result Segment
PHD: Public Health Department
RT-PCR: Reverse Transcription Polymerase Chain Reaction
ST: Structured Text
UDI: Universal Device Identification
*Note: Follow CLIA regulations when reporting sequencing results to an ordering provider.
Below are scenarios that provide examples of how to report SARS-CoV-2 sequencing results to public health departments. The first two examples are the preferred methods, and the third is an alternative method. Specific details for each example can be found on Confluenceexternal icon.
Preferred scenario (1): Send the sequencing results/SARS-CoV-2 lineage with the original (RT-PCR) or NAAT result that led to the decision to perform sequencing, if performed at the same laboratory or facility (parent-child test result linkage, if possible)
Preferred scenario (2): Send the sequencing results/SARS-CoV-2 lineage with the original RT-PCR or NAAT result that resulted in the decision to perform sequencing, if performed at the same laboratory or facility (no parent-child test result linkage)
Alternative scenario: Send only the sequencing results/SARS-CoV-2 Lineage as a new report with reference to the laboratory generated sequence ID (sent as a ST datatype, if CX (HL-7 datatype) is not possible)