Revision Log:
12/20/2022: Added the actual pdf document, since the HHS guidance link is broken
9/9/2022: Updated the OTC reporting guidance document so that the "Performing Organization Address (OBX-24)" does NOT use any state (OBX-24.4) or zip code (OBX-24-5)
3/8/2022: Updated with link to reporting guidance changes on CDC webpage effective 4/4/2022: https://www.cdc.gov/coronavirus/2019-ncov/lab/data-and-reporting.html and added a link to FAQs around OTC reporting
3/3/2022: Updated At Home test document and reference to SARS-CoV-2 variant spreadsheet.
4/13/2021: Updated the word document in the section on reporting variants of concern to fix some errors in the example messages - track changes on (and please accept my apologies for missing those!)
3/29/2021: Added a section on reporting variants of concern - CDC will publish this guidance soon (section: Reporting variants of concern) - it was published 4/10/2021 here: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/reporting-sequencing-guidance.html
11/3/2020: Updated the SCT code description for fever from 426000000^Fever over 104F^SCT to 426000000^Fever greater than 100.4 Fahrenheit^SCT to match HHS implementation guidance.6000000 | Fever greater than 100.4 Fahrenheit (finding) |
9/21/2020: Added note to NOT send Symptom Onset Date AOE, when unknown (as that creates a change in datatype).
9/14/2020: Updated syntax for the Device Identifier, when using the UDI definition (numeric values accessible via the FDA GUUID database)(section Device Identification).
The purpose of this page is to capture the goals and requirements to enhance ELR reporting in the context of the COVID pandemic, in light of HHS guidance, and in that context provide clear guidance to all parties in the communication flow to enhance their contributions to enhance the ELR transaction to a Public Health Authority.
| Name | Organization | Name | Organization | ||
|---|---|---|---|---|---|
| Rita Altamore | Department of Health Washington State | Janet Hamilton | CSTE | ||
| Ketty Andreasen | Epic | Ed Heierman | Abbott | ||
| Nancy Barrett | CT DPH | Christi Hildebrandt | GDIT | ||
| Brooke Beaulieu | CSTE | Jennifer Johnson | GDIT | ||
| Amy Bittrich | DHS Wisconsin | Riki Merrick | APHL, HL7 Orders & Observations Co-Chair, IHE Pathology and Laboratory Medicine Co-Chair | ||
| Laura Bleiel | Epic | Craig Newman | Altarum, HL7 Public Health Co-Chair | ||
| Hans Buitendijk | Cerner, HL7 Orders & Observations Co-Chair, EHRA Standards & Interoperability Chair | Tom Oswell | Sunquest Information Systems | ||
| David Burgess | LabCorp, HL7 Orders & Observations Co-Chair | Andrea Pitkus, PhD, MLS(ASCP)CM | Laboratory LOINC Committee Member, previously of Laboratory Interoperability Cooperative (LIC) focused on ELR | ||
| Coutney Fitzgerald | Cerner Public Health Surveillance | Dan Rutz | Epic | ||
| Freida Hall | Quest Diagnostics | Kathy Walsh | LabCorp | ||
| Jason Hall | CDC | Michael Waters | FDA | ||
| Mary Wedig | SLH Wisconsin | ||||
When ELRs are sent to PHA at times, they may not contain sufficient demographic, and other data as required by public health by law. This guidance aims to facilitate collection and transmission of these vital data at order entry, for transmission to the performing laboratory and on to the respective PHA. While some of the data may be part of a provider eCR report to public health, eCR is out of scope for this discussion, but ELR data would need to be aligned with eCR reporting. These data often available at order entry, and their transmission to the performing laboratory and in that lab's ELR report, may be the first notice to PHA and accelerate PHA processes.
Currently, the following are the data flows that would be impacted:
As certification to HL7 ELR R1 IG is not required for EHRs, nor LISs, and adoption of certified ELR capabilities is voluntary under CMS' Meaningful Use/Promoting Interoperability program for providers, while not addressed in other programs for Laboratory (e.g., CLIA), while states introduce further variations, and lab order transaction formats are not addressed anywhere, implementations across all data flows vary widely and production use of HL7 EHR R1 IG is limited. Additionally, the ELR reporting enhancements could almost all be addressed with the latest HL7 LRI R1 STU R3 IG, but that has not been adopted by anybody, since it was not included in MU regulation.
Additionally, as the PHA onboards the lab, they may accept a variety of fields, formats as long as they are receiving key information. Also it's unclear if point of care testing locations like pharmacies, drive up/drive through testing sites or state national guard collection sites for COVID-19 are 1) reporting ELR at all, 2) providing all required information and 3) those reporting on paper requisitions will not be providing LOINC or SNOMED CT codes and are often lacking demographics, specimen source and other required PHA elements.
Throughout the data collections and flows there are numerous challenges in terms of data not being able to be collected (even if it could be available), not being documented, not using standard vocabulary, not including it in the order, not forwarding certain data, dropping standard vocabulary, not retaining data, not communicating data available to the PHA.
Currently the specific challenges in that area are:
As indicated before, there are many other challenges to ensure that data is fully, accurately, and consistently documented and communicated, including use of encoded standard vocabulary (at least along with any local coding that remains relevant), but that is not addressed here. Our goal is to provide guidance on how to address the above challenges in the necessary implementation guides that can be deployed as quickly as possible and as consistent as possible across ALL jurisdictions.
In short, the challenges this guidance is looking at is ensuring that the relevant data can be communicated from ordering provider through a potential intermediary lab to the performing lab and on to PHA as an ELR in a complete, standard, consistent format and with vocabulary, with the least amount of effort to meet the deadlines.
Considering the existing implementation guides and updates to them in flight, upgrading to the latest versions would support most of the requirements and address the challenges outlined above, but still would require various updates to address all requirements. The following updates need to be made in the base implementation guides for a next version to include the short-term Implementation Guidance provided in the next section.
We suggest that HHS works with the key stakeholders and HL7 to pursue these updates as quickly as possible to enable adoption. In the meantime, the following section outlines the specific short-term guidance to make substantive progress that also prepares the industry for future adoption of the guides referenced above.
As adoption of the latest guides is not an option short term, we recommend to adopt the following specific guidance to enable communication of the data in the HHS guidance.
This guidance is based on the technique of pre-adopting the relevant capabilities from more current HL7 v2 versions in context of the latest applicable implementation guides referenced in the prior section, which is an acceptable approach that is reflected in many HL7 implementation guides already. Thus this can be added to any existing HL7 v2.x based ELR specification, recognizing that certain software and integration engines may not recognize and therefore fail "mixed" content without further work.
The following identifies for each of the data elements called out by the HHS guidance where in a v2 message it should be communicated.
The embedded spreadsheet includes tabs for each of the tables below as an alternative format.
Optionality Legend: O-Optional, R-Required (cannot be blank), RE-Required but can be empty if not available, ND-Not Desired by HHS, NF-Not Forwarded to HHS, C-Conditional
| Seq | Name | Optionality | Definition | HL7 Mapping | Implementation guidance | Comments / Open questions |
|---|---|---|---|---|---|---|
| 1 | Patient date of birth | RE-PHA, O-HHS | This is the preferred field to populate. | PID-7 | ||
| 2 | Patient race | RE-PHA, RE-HHS | Used for socio-demographic analytics, and as permitted by jurisdiction. This may be different than the race used for clinical interpretation (e.g., reference range). If a race is needed for clinical interpretation as well, that must be communicated with an AOE in addition to this field. | PID-10 | Code using the expanded value set of HL70005 with these additonal values: UNK^Inknown^NULLFL We can use this existing value set in use in case notification UPDATED: instead of using PHC1175 will support ASKU^Asked but unknown^NULLFL, so need a different value set | We will need to define this value set for the LAB_PH_HHS_ELR_Guidance_Component; listing the new values as permitted . |
| 3 | Patient ethnicity | RE-PHA, RE-HHS | Used for socio-demographic analytics, and as permitted by jurisdiction. | PID-22 | If there is a desire to include refused to answer we will have to expand the traditional ELR R1 value set of HL70189 (PHVS_EthnicGroup_HL7_2x) to include: PHC1175^Refused to answer^CDCPHINVS UPDATED: instead of using PHC1175 will support ASKU^Asked but unknown^NULLFL, so need a different value set | We will need to define this value set for the LAB_PH_HHS_ELR_Guidance_Component; liting the additional value as permitted. |
| 4 | Patient sex | RE-PHA, RE-HHS | Used for socio-demographic analytics, and as permitted by jurisdiction. This may be different than the sex used for clinical interpretation (e.g., reference range). If a sex is needed for clinical interpretation as well, that must be communicated with an AOE in addition to this field. | PID-8 | Send only the codes from HL70001 table | |
| 5 | Patient residence zip code | RE-PHA, RE-HHS | PID-11.5 | Some jurisdictions consider a combination of age, sex and zipcode PII, because of the population densitiy - need to accommodate that by allowing creation of regions (and that may be better done in the county field) | ||
| 6 | Patient residence county | RE-PHA, RE-HHS | PID-11.9 | ELR R1 requires use of numeric FIPS 6-4 codes (PHVS_County_FIPS_6-4) | Some jurisdictions consider a combination of age, sex and county PII, because of the population density - need to accommodate that by allowing creation of regions | |
| 7 | Patient name (Last name, First name, Middle Initial) | R-PHA, NF-HHS | PID-5 | |||
| 8 | Patient street address | RE-PHA, NF-HHS | PID-11.1 | |||
| 9 | Patient phone number with area code | RE PHA, NF HHS | PID-13 | This assumes it is the patient's home phone |
| Seq | Name | Optionality | Definition | HL7 Mapping | Implementation guidance | Comments |
|---|---|---|---|---|---|---|
| 1 | Ordering provider address | RE-PHA, NF-HHS | ORC-24.1 | The street information is not forwarded and sometimes the city (based on PHA request); state is forwarded (and zip is its own elemetn further down) | ||
| 2 | Ordering provider phone number | RE-PHA, NF-HHS | ORC-14/OBR-17 | |||
| 3 | Ordering provider name and NPI (as applicable) | RE-PHA, RE-HHS | If the ordering provider is not known, then the ordering facility should be included. | ORC-12 / OBR-16 | Ordering Provider Name is in ORC-12.2 / OBR-16.2 and ORC12.3 / OBR-16.3; NPI would be ORC-12.1 / OBR-16.1; when populating ORC-12.1 / OBR-16.1 also populate ORC-12.9/OBR-16.9 as: "NPI&2.16.840.1.113883.4.6&ISO" | For some testing there may not be a specific ordering provider (e.g. employment related testing, mass screening) - it is a CLIA requirement so need to ensure that this is provided. What about ordering provider for home test (is covered through doctor office or on-line doctor who ordered). For drive-thru it is possibly the Surgeon General or appropriate Medical officer |
| 4 | Ordering provider zip | RE-PHA, C-HHS | The zip code of the location where the ordering provider is located at the time of ordering. Condition: If patient is in a low density area this should not be forwarded to HHS. | ORC-24.5 | ||
| 5 | Date test ordered (date format) | RE-PHA, RE-HHS | ORC-15 | For the PH_HHS_ELR_Guidance_component this element will be RE | ||
| 6 | Test ordered – use harmonized LOINC codes provided by CDC | R-PHA, R-HHS | The test currently being reported to PHA as the test ordered | OBR-4 | LOINC is strongly recommended in ELR R1 Use the code from column "LOINC Order Code" and optionally description from colum "LOINC Order Code Long Name" in the CDC LIVD mapping file |
|
Valueset for Y/N/U - Use PHINVADS valueset (Y/N from HL70136 and UNK from V3 Nullflavor) that is used for Case notifications: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.888. U is replaced with UNK below, except as noted in the implementation guidance.
Note that the following OBX fields are not usually expected for AOEs:
Note that various AOEs do not have published LOINC codes yet. These have been created in the 2.69 pre-release and are marked with "2.69-pre". Once published they should be communicated with the published release number, likely "2.69".
Note that HHS and CDC are working on finalizing wording of the AOEs and associated LOINC coding. That may result in a different LOINC code and/or a change in questions. We will update this section as soon as HHS and CDC finalize the wording and associated LOINC coding.
NOTE: July 28th Updates are captured in red font below
| Seq | Name | Optionality | Definition | Allowable Answers | Implementation Guidance | Comments |
|---|---|---|---|---|---|---|
| 1 | First test Suggest to HHS to change to: Whether this is the patient's first test for the condition of interest | RE-HHS - changed to optional | Patient's first test for the condition of interest that is being ordered. | Y/N/UNK | OBX-2 = CWE OBX-3 = 95417-2^First test for condition of interest^LN OBX-5 OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 95417-2^Whether this is the patient's first test for the condition of interest^LN^^^^2.69-pre Questions for HHS:
|
| 1a | Type of most recent test | Optional | Condition: If First Test is N | Molecular Antigen Antibody Unknown | Questions to resolve: How is this expected to be reported? How are patients going to know what type of test was performed? How are providers going to know if the test results are not in their system? Depending on how this will be reported, how is this result going to be differentiated from the current result, so it is not counted again? Hasn't this result already been reported? Why do labs have to report this, when this is clinical data? | |
| 1b | Result of most recent test | Optional | Detected Not detected Unknown | |||
| 1c | Test performed date | Optional | YYYY[MM][DD]] | |||
| 2 | Employed in healthcare? Suggest to HHS to change to: Whether patient is employed in a healthcare setting | RE- HHS | The main focus is on patients who work in a high-risk setting with patients who could be a super spreader. (first responders, front line clinicians, environmental staff, therapists, in direct contact with patients or in their location). | Y/N/UNK | OBX-2 = CWE OBX-3 = 95418-0^Employed in a healthcare setting^LN OBX-5 OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 95418-0^Whether patient is employed in a healthcare setting^LN^^^^2.69-pre |
| 2a | If Yes - What is your occupation? | Optional for Aug 1, 2020 | Condition: If Employed in Healthcare is Y | OBX-2 = CWE OBX-3 = 85658-3^Occupation [Type]^LN OBX-5 = SNOMED CT codes from this list: 223366009 Healthcare Professional More Detailed Healthcare Professional List OBX-11 = F | Suggested LOINC: 85658-3^Occupation [Type]^LN^^^^2.68 Comments/Questions: Has NIOSH weighed in on the use of SNOMED CT codes? APHL suggests to allow use of OTH^Other^NULLFL, so that other settings can be reported in OBX-5.9 This is really not lab related data and should be available in the case report / case notification. | |
| 3 | Symptomatic as defined by CDC? Suggest to HHS to change to: Whether patient has symptoms related to condition of interest | RE-PHA, RE-HHS | Symptomatic per current CDC guidance at time of order for the reportable condition/illness | Y/N/UNK | OBX-2 = CWE OBX-3 = 95419-8^Has symptoms related to condition of interest^LN OBX-5 OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 95419-8^Whether patient has symptoms related to condition of interest^LN^^^^2.69-pre (Note that no LOINC is currently listed on the CDC FAQ page but it is expected to be corrected soon) |
| 3a | Date of Symptom Onset
| C-PHA, C-HHS | Condition: If Symptomatic is Y. | mm/dd/yy | OBX-2 = DT
NOTE: Do NOT send Symptom Onset Date AOE, when unknown (as that creates a change in datatype) | UPDATED LOINC 65222-2^Date and time of symptom onset^LN^^^^2.68
|
| 3b | If Yes - What were the symptoms experienced? | Optional for Aug 1, 2020 | Condition: If Symptomatic is Y. | OBX-2 = CWE OBX-4 = if needed for more than one symptom (suggest to number sequentially starting with "1" for each occurrence) OBX-5 can be one of: 49727002^Cough^SCT OBX-11 = F When more than one symptom apply send each as a separate OBX segments using OBX-4 to differentiate individual answers - in the future it is anticipated that the LAB_PH_HHS_ELR_Guidance_Component will also support multiple repeats of OBX-5 when OBX-29 is valued 'QST' | Suggested LOINC: 75325-1^Symptom^LN^^^^2.68 Comments: APHL suggests to allow use of OTH^Other^NULLFL, so that other settings can be reported in OBX-5.9 This is really not lab related data and should be available in the case report / case notification. | |
| 5 | Hospitalized? Suggest to HHS to change to: Whether patient was hospitalized because of this condition | RE-PHA, RE-HHS | Patient has been hospitalized for the reportable illness/condition that this order has been placed for (suspected or diagnosed) When ordered during ER duration, the answer would be N. | OBX-2 = CWE OBX-3 = 77974-4^Patient was hospitalized because of this condition^LN OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 77974-4^Whether patient was hospitalized because of this condition^LN^^^^2.68 When interested in whether hospitalized at time of order, use PV1-2 (Patient Class). Comment: The CDC web page lists a follow up question here with these expected answers: 840544004^Suspected disease caused by 2019 novel coronavirus (situation) This seems to indicate the case status, which is something that is determined during case investigation, not at time of test order expect this to be removed | |
| 6 | ICU? Suggest to HHS to change to: Whether patient was admitted to intensive care unit for condition of interest | RE-PHA, RE-HHS | Patient has been admitted/transferred to the ICU at any time during the encounter for the reportable illness/condition that the order has been placed for (suspected or diagnosed). | Y/N/UNK | OBX-2 = CWE OBX-3 = 95420-6^Admitted to intensive care unit for condition of interest^LN OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 95420-6^Whether patient was admitted to intensive care unit for condition of interest^LN^^^^2.69-pre When interested in whether in ICU at time of order, use PV1 location/organization providing care. Comment: On the CDC page a single SNOMED CT code is listed If ICU is Yes, which is ICU - expect this to be removed, as it does not provide further information. |
| 7 | Resident in a congregate care setting (including nursing homes, residential care Suggest to HHS to change to: Whether patient resides in a congregate care setting | RE-PHA, RE-HHS | This is at time of exposure where they normally live. | Y/N/UNK | OBX-2 = CWE OBX-3 = 95421-4^Resides in a congregate care setting^LN OBX-5 can be one of: Y^Yes^HL70136 N^No^HL70136 UNK^Unknown^NULLFL OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 95421-4^Whether patient resides in a congregate care setting^LN^^^^2.69-pre |
| 7a | If YES, what type of residence is the congregate care setting? | Optional for August 1, 2020 | Condition: If Congregate Care setting is Yes | OBX-2 = CWE OBX-3 = 75617-1^Residence type^LN OBX-5 can be one of: 22232009^Hospital^SCT 2081004^Hospital ship^SCT 32074000^Long term care hospital^SCT 224929004^Secure hospital^SCT 42665001^Nursing home^SCT 30629002^Retirement home^SCT 74056004^Orphanage^SCT 722173008^Prison-based care site^SCT 20078004^Substance abuse treatment center^SCT 257573002^Boarding house^SCT 224683003^Military accommodation^SCT 284546000^Hospice^SCT 257628001^Hostel^SCT 310207003^Sheltered housing^SCT 257656006^Penal institution^SCT 285113009^Religious institutional residence^SCT OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | Suggested LOINC: 75617-1^Residence type^LN^^^^2.68 Comments: APHL suggests to allow use of OTH^Other^NULLFL, so that other settings can be reported in OBX-5.9 This is really not lab related data and should be available in the case report / case notification. | |
| 8 | Pregnant? | C-PHA, C-HHS | Condition: If patient is female Current pregancy status of the patient | Pregnant, Not pregnant, Unknown | OBX-2 = CWE OBX-3 = 82810-3^Pregnancy status^LN OBX-5 can be one of: 77386006^Patient currently pregnant^SCT 60001007^Not pregnant^SCT UNK^Unknown^NULLFL (Note: Expect to have 261665006^Unknown^SCT on the CDC page be updated to UNK^Unknown^NULLFL) OBX-11 = F OBX-14 = Date question was answered OBX-29 = QST | LOINC: 82810-3^Pregnancy status^LN^^^^2.68 LOINC from https://loinc.org/sars-cov-2-and-covid-19/ |
| 9 | Patient age | C-PHA, RE-HHS | For reporting from PHA to HHS (CDC), when DOB may not be included or in ELR, when DOB is not available. Condition for PHA: If Patient Date of Birth is not available or cannot be calculated correctly to reflect the age at time of order, then include the age at time of specimen collection using the methodless LOINC (30525-0^Age^LN). | Send as AOE OBX: OBX-2 = NM (can be SN) | Questions for HHS: Can HHS accept DoB and figure out the age so we don't need to calculate? |
| Seq | Name | Optionality | Definition | HL7 Mapping | Implementation guidance | Comments |
|---|---|---|---|---|---|---|
| 1 | Date specimen collected (date format) | R-PHA, R-HHS | OBR-7 also in SPM-17 (2.5 and up) | OBR-7 is required; | ELR allows use of 0000, when date is unknown | |
| 2 | Specimen Source - use appropriate LOINC, SNOMED-CT, or SPM4 codes, or equivalently detailed alternative codes | R-PHA, R-HHS | SPM-4 (after 2.5) OBR-15.1 SPM-8 (after 2.5) OBR-15.4 | Code to SNOMED CT codes for SPM-4 as provided in the "Vendor Specimen Description" column of the "LOINC Mapping" tab in the CDC LIVD mapping file; ELR also allows use of both SNOMED CT codes from the speicmen hierarchy (PHVS_Specimen_CDC) and HL70487 codes (PHVS_SpecimenType_HL7_2x) Some labs may support the sending of source site information; ELR R1 uses SNOMED CT codes compiled in the HITSP body site value set (PHVS_BodySite_HITSP) | ||
| 3 | Accession #/Specimen ID | R-PHA, R-HHS | ORC-3/OBR-3 SPM-2 (V2.5 and up) | This is the testing lab's specimen ID or accession number - may also send the submitters specimen ID / accession number In older versions of HL7 only ORC-3/OBR-3 can be used; for the submitter's accession number use ORC-2/OBR-2. |
| Seq | Name | Optionality | Definition | HL7 Mapping | Implementation guidance | Comments |
|---|---|---|---|---|---|---|
| 1 | Performing facility name and/or CLIA number, if known | R-PHA, R-HHS | OBX-23 (V2.5.1 and up) ORC-15 | In older versions of HL7 OBX-15 (Producer's ID can be used for the Performing Lab ID) or it can be conveyed in the NTE following the result OBX, ensuring it is included on the report. | ||
| 2 | Performing facility zip code | R-PHA, R-HHS | OBX-24 (V2.5.1 and up) | In older versions of HL7 this information can be conveyed in the NTE following the result OBX, ensuring it is included on the report. | ||
| 3 | Device Identifier | RE-PHA, RE-HHS | The test kit/reagent(s) used to perform the test, and as necessary the instrument platform(s) when used off-label. The EUA may be used when used as authorized. | OBX-17 OBX-18 (v2.4 and up) | Use OBX-17 when describing the manufacturer and model of either test kit (reagent) or instrument used; or when referencing the EUA (see more detailed guidance below). Use OBX-18 when passing the serial number or UDI of the test kit (reagent) or instrument | The model is acceptable. It is allowed to use the Device Identifier (as defined per FDA's UDI definition) or the UDI Carrier (the full human readable form of the barcode) instead or as well if that can be obtained. For the PH_HHS_ELR_Guidance_component OBX-18 will be RE |
| 4 | Test result | R-PHA, R-HHS | This is the code of the test being resulted. | OBX-3 | LOINC Is required in LRI and ELR R1, when an appropriate LOINC exists - since this points to LIVD, as long as LOINC is listed there for the manufactueer test kit, MUST use. | Include the fully structured test code, name, and code system of the applicable LOINC code in accordance with the CDC guidance for the reportable illness/condition |
| 5 | Test result value | R-PHA, R-HHS | The result value. | OBX-5 | For coded results use the appropriate SNOMED CT code for qualitative result values in accordance with the CDC guidance for the reportable illness/condition. For numeric results include units in OBX-6 when appropriate (code units in UCUM) | Suggest to HHS to clarify, that not all results are coded. |
| 6 | Test Result date | RE-PHA, R-HHS | The date the test result was obtained and approved for release | OBX-19 (V2.4 and later) OBR-22 (as proxy in V2.3.1 and earlier) | Must be sent for each result - may not be populated for AOE OBX segments | Note: For v2.3.1 and earlier, OBR-22 should reflect the date/time when OBR-25 was set to F. Generally, for an OBR including multiple OBX segments it would be equal to or later than the most recently finalized OBX, but without OBX-19 available OBR-22 is the closest one can get. |
There are four components that are potentially of interest for which to include an "identifier":
There is no need to include identification information for calibrators, controls, or collection devices.
These devices can be identified as a kind of using three different approaches:
The device identification information will be captured in either OBX-17 when describing the kind and OBX-18 when describing an instance.
In order to differentiate which of the devices is being described we propose a list of abbreviations to represent each kind (for use in OBX-17)
| Element | Type of identifier | Abbreviation for the type |
|---|---|---|
| Emergency Use Authorization | EUA | EUA |
| Testkit/reagent | Model | MNT |
| Testkit/reagent | Device ID | DIT |
| Instrument Platform | Model | MNI |
| Instrument Platform | Device ID | DII |
| Manual kit | Model | MNM |
| Manual kit | Device ID | DIM |
Sept 14, 2020 update:
In OBX-17 use OBX-17.1 for the device identification information using the format <Model name or Diagnostic (Letter of Authorization)>_<Manufacturer name>_<Abbreviation for the type> and in OBX-17.3 "99ELR". For Device ID omit "_<Manufacturer name>" resulting in <Device ID>_<Abbreviation for the type> in OBX-17.1.
Best place to obtain these values is the CDC LIVD file (https://www.cdc.gov/csels/dls/sars-cov-2-livd-codes.html):
<Model name or Diagnostic (Letter of Authorization)>_<Manufacturer name> is provided in the in Testkit Name ID (column M); the <Abbreviation for the type> in Testkit Name ID Type (column N) and concatenate: <Testkit Name ID>_<Testkit Name ID Type>.
<Device ID> in Equipment UID (column O); the <Abbreviation for the type> is in Equipment UID Type (column P)
Using Abbotts ID Now as example:
Using the EUA ID = ID NOW COVID-19_Abbott Diagnostics Scarborough, Inc. EUA
Using the Device ID = 10811877011269_DII^^99ELR
Where OBX-17.1 length limits interfere with the full identification use the following approach:
OBX-17: ID NOW COVID-19_Abb#^^99ELR
Full ID for the NTE: ID NOW COVID-19_Abbott Diagnostics Scarborough, Inc._EUA
Alternatively these devices can be identified as the specific instance used in testing by their UDI as defined by FDA (for use in OBX-18).
Since the OBX-17 and OBX-18 fields can repeat, multiple values can be communicated. While the newer PRT segment can improve on this somewhat, it still would require a new field to maintain these relationships. Shifting to FHIR where this already can be addressed is not realistic in the timelines needed and given most LIS/LIMS currently lack FHIR functionality. However, given the likely configurations being used, we do not believe we need to address that yet while data curation in the analtyics phase can address this challenge.
| Scenario | Location in message | Format to be used | Instructions | Where to find the information |
|---|---|---|---|---|
| Cepheid Xpert Xpress SARS-CoV-2 test used as described in EUA | OBX-17 | Xpert Xpress SARS-CoV-2 test_Cepheid _EUA | OBX-17.1 = <Diagnostic (Letter of Authorization)>_<Manufacturer name>_EUA OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Testkit Name ID" column, when identified as EUA in "Testkit Name ID Type" column |
| Abbott ID now as described in EUA | OBX-17 | ID NOW COVID-19_Abbott Diagnostics Scarborough, Inc. _EUA | OBX-17.1 = <Diagnostic (Letter of Authorization)>_<Manufacturer name>_EUA OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Testkit Name ID" column, when identified as EUA in "Testkit Name ID Type" column |
| LDT listed in Appendix A | OBX-17 | Cormeum SARS-CoV-2 Assay_Cormeum Laboratory Services_EUA | OBX-17.1 = <Letter Granting Inclusion under EUA>_<Laboratory>_EUA OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Testkit Name ID" column, when identified as EUA in "Testkit Name ID Type" column |
| CDC test run on Abbott m2000 using model names | OBX-17 for test kit | CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel_CDC_MNT | OBX-17.1 = <Test kit name>_<Manufacturer name>_MNT OBX-17.3 = "99ELR" | Name used in package insert (or "Testkit Name ID" column, when identified as MNT in "Testkit Name ID Type" column in the CDC LIVD mapping file) |
| CDC test run on Abbott m2000 using model names | OBX-17 for instrument | m2000 RealTime System_Abbott_MNI | OBX-17.1 = <Instrument name>_<Manufacturer name>_MNI OBX-17.3 = "99ELR" | Name used in package insert (or "Testkit Name ID" column, when identified as MNT in "Testkit Name ID Type" column in the CDC LIVD mapping file) |
| bioMérieux ARGENE SARS-COV-2 R-GENE test run on ABI 7500 Fast Dx Real-Time PCR Instrument using device ID | OBX-17 for test kit | 423735_bioMérieux_DIT | OBX-17.1 = <Device ID>_<Manufacturer name>_DIT OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Testkit Name ID", when identified as DIT in "Testkit Name ID Type" column |
| bioMérieux ARGENE SARS-COV-2 R-GENE test run on ABI 7500 Fast Dx Real-Time PCR Instrument using device ID | OBX-17 for instrument | 4351106_Applied Biosystems_DII | OBX-17.1 = <Device ID>_<Manufacturer name>_DII OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Product UID" column |
| Manual test kit for AB testing using model name | OBX-17 for manual test kit | SARS-CoV-2 IgM/IgG Antibody Test Kit_Biohit Healthcare_MNM | OBX-17.1 = <Manual kit name>_<Manufacturer name>_MNM OBX-17.3 = "99ELR" | CDC LIVD mapping file in the "Testkit Name ID" column, when identified as MNT in "Testkit Name ID Type" column |
| PH Lab developed test kit on Roche Cobas 6800 using model name for both | OBX-17 for test kit | SARS-COV-2 rt-PCR_SLOPHL_MNT | OBX-17.1 = <modelname = whatever the lab calls it>_<Labname = manufacturer name>_MNT OBX-17.3 = "99ELR" | PH lab documentation |
| PH Lab developed test kit on Roche Cobas 6800 using model name for both | OBX-17 for instrument | cobas® 6800/8800 Systems_Roche_MNI | OBX-17.1 = <IVD platform model name>_<Manufacturer name>_MNI OBX-17.3 = "99ELR" | LIVD file from Roche in the "Model" column |
| PH Lab developed test kit on Roche Cobas 6800 using model name for kit | OBX-17 for test kit | SARS-COV-2 rt-PCR_SLOPHL_MNT | OBX-17.1 = <modelname = whatever the lab calls it>_<Labname = manufacturer name>_MNT OBX-17.3 = "99ELR" | PH lab documentation |
| PH Lab developed test kit on Roche Cobas 6800 usingUDI for instrument | OBX-18 for instrument | [udi carrier]^2.16.840.1.113883.3.3719^ISO | OBX-18.1 = [udi carrier] OBX-18.3 = "2.16.840.1.113883.3.3719" OBX-18.4 = "ISO" | Device documentation (package insert/label) |
| Using Roche COBAS INTEGRA 400 plus using Device Identifier | OBX-17 | 4015630924592_Roche_DII | OBX-17.1 = <Device ID>_<Manufacturer name>_DII OBX-17.3 = "99ELR" | LIVD file from Roche "Product Reference UID" provides the identifier; "Product Reference UID Type" was listed as GITN, indicating it is a device ID |
| UDI carrier scanned on barcode using OID | OBX-18 | OBX-18.1 = [udi carrier] OBX-18.3 = "2.16.840.1.113883.3.3719" OBX-18.4 = "ISO" | Device documentation (package insert/label) on instrument, test kit (or box), or manual kit | |
| UDI carrier scanned on barcode using URI | OBX-18 | OBX-18.1 = [udi carrier] OBX-18.3 = "http://hl7.org/fhir/NamingSystem/fda-udi" OBX-18.4 = "URI" | Device documentation (package insert/label) on instrument, test kit (or box), or manual kit |
Added 3/29/2021
With the rise of more variants some variants require close tracking to ascertain if they have clinical implications (higher infection rates, or more severe illness). Which variants are of concern may vary over time and not all may remain of importance, while new ones may be detected in the future, so for now we opted to use ST datatype to report them. For the researchers and epidemiologists the sequence itself may be of importance as well, so we are including the ID assigned by the lab to the sequence (PLT2397^Filler Lab Assigned Genetic Sequence Identifier^PLT) - this is the one that is expected to be sent at minimum, and optionally a pointer to the sequence stored in the GISAID (96766-1^GISAID sequence accession number^LN) or Genbank database (87396-8^GenBank accession number^LN) or potentially also NCBI's Sequence Read Archive Number (SRA# = PLT2251^NCBI Sequence Read Archive Number [Identifier]^PLT ) or NCBI's Sample Accession Number (SAMN#) for the BioSample data repository (PLT2402^NCBI's BioSample data repository Accession Number (Identifier)^PLT). All of these identifiers ideally should be sent as CX, datatype, using 'ACSN' as the identifier type in CX.5, but may be sent as ST.
NOTE: PLT2397 has been assigned a NEW LOINC = 98062-3^Sequencing study identifier^LN.
NOTE: The example messages in this document provide ORC segments with every OBR, but some PHAs may be able to handle ONLY the FIRST ORC segment.
Here is a list of PLR codes that represent the SARS-CoV-2 variants of interest / concern, in case you need some codes: https://confluence.hl7.org/download/attachments/4489770/SARS-CoV-2_PLR_VOC_VOI_r3.xlsx?api=v2 - UPDATED 7/22/2021 = this file is is not being updated on a regular basis, but APHL has a list of ALL PLR codes with a column indicating if VOC or VOI that can be accessed in row 24 of this page: https://app.smartsheet.com/b/publish?EQBCT=b585e5a5e0c2430398db60b0f0d5c72e - since Feb2022 APHL is publishing the SNOMED CT concept IDs in the APHL namespace extension (1000284) instead of the legacy PLR codes - still in the same place though - file is now called "SARS-CoV-2_APHLSCT_Codes.xlsx".
Note that PHINVADS has a valueset: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.3301 that contains 3 US extension SNOMED CT concepts, that have not officially been published. Due to the fluent nature of variants we do not plan on requesting more SNOMED CT concepts for the PLR codes and these code may not ever be published, so use with caution.
Example messages: - updated 6/16/2021 based on updated guidance:
OFFICAL CDC GUIDANCE PUBLISHED HERE: https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/reporting-sequencing-guidance.html
Added 4/30/2021:
Please follow this guidance document when reporting at home tests: - UPDATED WITH THIS document 3/3/2022 to support 4 different levels of OTC tests:
- here are the example HL7 messages, one for each level:
Added this link 3/8/2022: Over-The-Counter (OTC) Home Testing and CLIA Applicability Frequently Asked Questions - Updated March 4, 2022
Updated 9/9/2022: Update the "Performing Organization Address (OBX-24)" to NOT use any state (OBX-24.4) or zip code (OBX-24-5) - see updated guidance document:
ONLY if no HL7 v2.x support then use flat file to HL7 converter excel file - first box on this page: https://preparedness.cste.org/?page_id=136. But if you have a HL7 v2 feed continue to use and upgrade as quickly as possible.
If you do not have an HL7 v2 feed, work with your PHA to determine when you can put that in place.
Do we need multiple test kits? Ed will check if 1 or 2 UDIs
ROMA is a 2 step immunoassay. see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996955/
If only device identifier, OBX-18 can handle multiple
If UDI Carrier or UDI, multiple PRTs can handle that.
(a) The laboratory must have a written or electronic request for patient testing from an authorized person.
(b) The laboratory may accept oral requests for laboratory tests if it solicits a written or electronic authorization within 30 days of the oral request and maintains the authorization or documentation of its efforts to obtain the authorization.
(c) The laboratory must ensure the test requisition solicits the following information:
(1) The name and address or other suitable identifiers of the authorized person requesting the test and, if appropriate, the individual responsible for using the test results, or the name and address of the laboratory submitting the specimen, including, as applicable, a contact person to enable the reporting of imminently life threatening laboratory results or panic or alert values.
(2) The patient's name or unique patient identifier.
(3) The sex and age or date of birth of the patient.
(4) The test(s) to be performed.
(5) The source of the specimen, when appropriate.
(6) The date and, if appropriate, time of specimen collection.
(7) For Pap smears, the patient's last menstrual period, and indication of whether the patient had a previous abnormal report, treatment, or biopsy.
(8) Any additional information relevant and necessary for a specific test to ensure accurate and timely testing and reporting of results, including interpretation, if applicable.
(d) The patient's chart or medical record may be used as the test requisition or authorization but must be available to the laboratory at the time of testing and available to CMS or a CMS agent upon request.
(e) If the laboratory transcribes or enters test requisition or authorization information into a record system or a laboratory information system, the laboratory must ensure the information is transcribed or entered accurately.