Important update: Healthcare facilities
CDC has updated select ways to operate healthcare systems effectively in response to COVID-19 vaccination. Learn more
To maximize protection from the Delta variant and prevent possibly spreading it to others, get vaccinated as soon as you can and wear a mask indoors in public if you are in an area of substantial or high transmission.
UPDATE
Given new evidence on the B.1.617.2 (Delta) variant, CDC has updated the guidance for fully vaccinated people. CDC recommends universal indoor masking for all teachers, staff, students, and visitors to K-12 schools, regardless of vaccination status. Children should return to full-time in-person learning in the fall with layered prevention strategies in place.
UPDATE
The White House announced that vaccines will be required for international travelers coming into the United States, with an effective date of November 8, 2021. For purposes of entry into the United States, vaccines accepted will include FDA approved or authorized and WHO Emergency Use Listing vaccines. More information is available here.
UPDATE
Travel requirements to enter the United States are changing, starting November 8, 2021. More information is available here.

Guidance for Reporting SARS-CoV-2 Sequencing Results

Guidance for Reporting SARS-CoV-2 Sequencing Results
Updated June 23, 2021

Summary of Recent Changes

  • Provides clarification on how laboratories may report sequencing results to patients and providers in compliance with CLIA
  • Addition of 96895-8 as the preferred LOINC code to report sequencing results by molecular genetic methods and 98062-3 as the preferred code to identify sequencing studies.

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.

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.

Regulatory Position on Reporting Sequencing Results to Public Health Departments

The Centers for Medicare and Medicaid Servicesexternal icon (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. 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 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 -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]).

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.

Test Result (Performed and Values)
Required Reporting
Federal / CDC / HHS
State / Local / Tribal / Territorial PHD
Requested Reporting
Ordering Provider / EHR*
Technical Specifications
Must use harmonized LOINC codes, when available
Notes
SARS-CoV-2 pango lineage identified through sequencing from the original specimen
Example
LOINC: Preferred = 96895-8:
SARS-CoV-2 (COVID-19) lineage [Identifier] in Specimen by Molecular genetics method
Allowable = 96741-4:
SARS-CoV-2 (COVID-19) variant [Type] in Specimen by Sequencing
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 B.1.429 lineage
SARS-CoV-2 variant B.1.526 lineage
SARS-CoV-2 variant B.1.427 lineage
SARS-CoV-2 variant P.2 lineage
Test Result Date
Required Reporting
Federal / CDC / HHS
State / Local / Tribal / Territorial PHD
Requested Reporting
Ordering Provider / EHR*
Technical Specifications
YYYY[MM[DD]]
Notes
Date the test result was obtained
Example
Example: 20200716
Device Identifier
Required Reporting
Federal / CDC / HHS
State / Local / Tribal / Territorial PHD
Requested Reporting
Ordering Provider / EHR*
Technical Specifications
Must use harmonized Device Identifiers, when available. The DI is contained within the UDI, created by manufacturer
Notes
Manufacturer requests UDI issuanceexternal icon, then provides DI, or pull from GUDID databaseexternal iconIf DIs unavailable: Use the Unique Trade Name (controlled under 21 CFR 209.10(b)(1)external icon)
Example
Example DI: 01234567891011

Example Trade Name:
SARS-CoV-2 Test_Company_MNT^^99ELR

HL7 Field
OBX-17external icon
OBX-18external icon

Sequence ID
Required Reporting
Federal / CDC / HHS
State / Local / Tribal / Territorial PHD
Requested Reporting
N/A
Technical Specifications
Lab assigned Sequence ID
Notes
Add as an additional observation to the original report
Example
LOINC: 98062-3 Sequencing study identifier

Allowable = PLT2397^Filler Lab Assigned Genetic Sequence Identifier^PLT

OBX-2 = ST

<WHATEVER FORMAT THE LAB USES>

HL7 Field
OBX-3external icon
OBX-2external icon
OBX-5external icon

Performing Facility Name: CLIA#
Reporting – If Known
Federal / CDC / HHS
State / Local / Tribal / Territorial PHD
Requested Reporting
N/A
Technical Specifications
Alpha; ##D#######
Example
Example: 21D1234567

*Note: Follow CLIA 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 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)