Guidance for Reporting SARS-CoV-2 Sequencing Results

Summary of Recent Changes

Key Points

• 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.

Regulatory Position on Reporting Sequencing Results to Public Health Departments

The Centers for Medicare and Medicaid Services (CMS) published information that allows both non 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 the methods used to perform the sequencing have met CLIA requirements for establishing performance specifications and have received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA). If the SARS-CoV-2 genetic sequencing result is reported to the ordering provider, reported to the patient, or appears in the patient record — 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 and FDA regulations.

In a November 15, 2021 update to the Policy for Coronavirus Disease-2019 Tests During the Public Health Emergency (Revised), FDA now requires COVID-19 diagnostic test developers to submit an EUA request for review and authorization prior to offering a test for diagnostic use or reporting test results to a healthcare provider, patient, or medical record. If a test was in use prior to November 15, 2021, and an EUA request was submitted to FDA within 60 days of the date of this policy update, FDA does not intend to object to the continued offering of a COVID-19 diagnostic test without EUA while FDA reviews the EUA request.

In both scenarios, CDC strongly recommends and requests that laboratories send sequencing results to state, local, tribal, or territorial public health departments.

How to Report SARS-CoV-2 Sequencing Results to 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 SARS-CoV-2 lineages, including variants, should upload sequence data to a public database (e.g., GISAID, NCBI Gene Bank)

Technical Guidance for Reporting Sequencing Results to Public Health Departments

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.

*Note: Follow all applicable CLIA and FDA regulations when reporting sequencing results to an ordering provider.

Reporting Scenarios

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 Confluence.

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)

Previous Updates