PHLIP usage of LOINC….and other standards

Background on Flu SurveillanceWhat are we capturing?

U.S. Influenza Surveillance

CDC

Health Departments

VirologicSurveillance

MortalitySurveillance

Morbidity Surveillance

State-level data to state surveillance coordinators

•U.S. WHO Collaborating Laboratories•National Respiratory and Enteric Virus System (NREVSS)•Novel influenza A reporting

WHO U.S. Collaborating Laboratories

Current Laboratory Reporting Methods*

District of Columbia

PHLIP PHLIS2Web

*As of 4/24/2014

NYC

DoD

Houston

SLO Co.

Routine Products Influenza virologic surveillance data analyzed weekly for Flu

View:◦ http://www.cdc.gov/flu/weekly/◦ http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html

Overview of PHLIP Partnership between Association of Public

Health Labs, CDC, state and local health labs, standards organizations

Started in 2005 Influenza and salmonella were chosen as test

cases Aimed to facilitate surveillance, detection and

response Reduce manual workload/increase efficiency Improve data quality Continuity of Operations/surge capacity

Knapp: 7-26-2010

Slide Courtesy of Joan Knapp, CDC

PHL A LIMS

Orig Sub #2 LIMS

PHL B LIMS

Orig Sub #1 LIMS

JSK:

8-4

-201

0

CDC -Epi or Lab

ETOR

ETOR ELSM

HL7 HL7

HL7

More on PHLIP

PHLIP Standards Standardized message format (ORU^R01 HL7

2.3.1) Standardized transport (PHINMS/RnR hubs) Standardized vocabulary/harmonized vocabulary

Standard demographic information LOINC SNOMED PHLIP codes

Change Requests

Encoding Guide:

Encoding Guidelines/CCB

Influenza Test Encoding Guideline : Test Overview

Display Name Usage of the Test Concept

PHLIP Test ID or LOINC Code LOINC Short Name or PHLIP Name OBR-4.1 OBR-4.2 OBR-4.3 OBR-15.1

50219-5|39528-5 HAdV DNA XXX Ql PCR

To order and report at least the individual targets listed here, other respiratory virus targets may be added - does not require Flu A subtyping! 39528-5 HAdV DNA XXX Ql PCR 50219-5

Respiratory virus DNA + RNA panel LN

Specimen Value Set for the Flu Testing

50219-5|34487-9 FluAV RNA XXX Ql PCR

To order and report at least the individual targets listed here, other respiratory virus targets may be added - does not require Flu A subtyping! 34487-9 FluAV RNA XXX Ql PCR 50219-5

Respiratory virus DNA + RNA panel LN

Specimen Value Set for the Flu Testing

50219-5|40982-1 FLUBV RNA XXX Ql PCR

To order and report at least the individual targets listed here, other respiratory virus targets may be added - does not require Flu A subtyping! 40982-1 FLUBV RNA XXX Ql PCR 50219-5

Respiratory virus DNA + RNA panel LN

Specimen Value Set for the Flu Testing

50219-5|29908-1 HPIV1 RNA XXX Ql PCR

To order and report at least the individual targets listed here, other respiratory virus targets may be added - does not require Flu A subtyping! 29908-1 HPIV1 RNA XXX Ql PCR 50219-5

Respiratory virus DNA + RNA panel LN

Specimen Value Set for the Flu Testing

LIMS affects a sites ability to adhere to standards

RVP/other panels Virus naming Pyrosequencing Rapidity of obtaining LOINC and SNOMED

codes Aligning with other standards and

messaging projects

Challenges for PHLIP Flu standards

“LIMS affects a sites ability to adhere to standards”

OBR 4 OBX 3 (LOINC) OBX 5 (SNOMED)

48509-4 FLUAV + FLUBV RNA XXX PCR 48509-4 FLUAV + FLUBV RNA XXX PCR 446645007 Influenza A virus subtype H3

OBR 4 OBX 3 (LOINC) OBX 5 (SNOMED)

48509-4 FLUAV + FLUBV RNA XXX PCR

40982-1 FLUBV RNA XXX Ql PCR 260415000

Not Detected

34487-9 FLUAV RNA XXX QI PCR 260373001 Detected

49521-8 FLUAV HA H1 RNA XXX Ql PCR 260415000

Not Detected

49524-2 FLUAV HA H3 RNA XXX Ql PCR 260373001

Detected

55464-2 FLUAV swine origin RNA XXX Ql PCR

260373001

Detected

55465-9FLUAV H1 2009 pandemic RNA

XXX Ql PCR26041500

0Not

Detected

VS.

LOINC only represents generic methods (and other stuff that Riki detailed) – NOT the specific kit used.

Luminex:“To order and report the individual targets used in the LUMINEX Respiratory Multiplex test - must report ALL targets” ---------------

Other RVP codes have had the more generic order code

“RVP/other panels”

OBR 4 OBX 3 (LOINC)

60566-7

Resp virus 12 Pnl XXX PCR^LN

29908-1 HPIV1 RNA XXX Ql PCR

29909-9 HPIV2 RNA XXX Ql PCR

29910-7 HPIV3 RNA XXX Ql PCR

38917-1 hMPV RNA XXX Ql PCR

39528-5 HAdV DNA XXX Ql PCR

7993-9 Rhinovirus RNA XXX Ql PCR

30075-6 RSV A RNA XXX Ql PCR

30076-4 RSV B RNA XXX Ql PCR

40982-1 FLUBV RNA XXX Ql PCR

34487-9 FluAV RNA XXX Ql PCR

49521-8 FLUAV H1 RNA XXX Ql PCR

49524-2 FLUAV H3 RNA XXX Ql PCR

OBR 4 OBX 3 (LOINC)

50219-5

Respiratory virus DNA + RNA pane

Variable Targets/Tests

“Virus naming”

Novel Influenza A H1N1Swine Influenza Virus

Influenza A H1N1 swine-likeNovel Influenza A H1N1 swine-like

Influenza A H1, porcineswine-origin influenza virus

Swine-origin Influenza A (H1N1)SOIV

Flu A/SW H1

Used to detect mutations in flu associated with antiviral resistance

Added to PHLIP reporting in 2012-13 season Only have two sites currently sending this to

production Difficult to code – use temporary codes right

now

“Pyrosequencing”

Have had three recent “opportunities” to test emergency response: ◦ Pandemic – we were still new – bumpy ride◦ H3N2v – we did this fairly easily (no LOINC, only

SNOMED, which we cannot get – results are presumptive)

◦ H7 – still getting codes – not as urgent right now b/c not in the US

Also recently added new PCR to test for flu B lineage, which will be discuss in detail later

“Rapidity of obtaining LOINC and SNOMED codes”

Will discuss further in a few minutes.

“Aligning with other standards and messaging projects”

Adding Reporting Codes to Package Insert

Adding Reporting Codes to Package Insert

Prior to Adding Standard Info

What was added?

Standards-Based Electronic Laboratory Reporting for Influenza Background This section contains the recommendations for uniform coding and vocabulary for CDC Human Influenza Virus Real-time RT-PCR Diagnostic Panel. The following information is provided to assist the performing laboratory in complying with new federal guidelines for the meaningful use of electronic health information systems. The implementation of adopted standards should be harmonized across all performing laboratories to ensure semantic interoperability to better support electronic data exchange. The CDC developer of this assay through collaboration has established Standard English terminology for the test name and test results with the testing community and expert knowledge of the processes involved. It is recognized that this terminology will differ in countries outside the United States. However, through the use of national and international agreements, it is possible to establish a universal set of codes and terms to accurately characterize laboratory observations. Recommendations in this package insert apply to the reporting of results of this assay only within the United States. Process for achieving uniformity in laboratory test results The laboratory performing the influenza assay may utilize a Laboratory Information Management Systems (LIMS) with connections to a hospital or medical system Electronic Health Record (EHR). The coding systems include LOINC - Logical Observation Identifiers Names and Codes (LOINC® -- http://www.loinc.org) and SNOMED CT – Systematic Nomenclature of Medicine--Clinical Terms (http://www.ihtsdo.org/). These coding systems have specific capabilities that are essential for achieving uniformity. The test request and results are to be incorporated into a standard Health Level 7 (HL7) electronic format for laboratory test messaging. More information about HL7 can be found at http://www.hl7.org. LOINC provides for a common understanding of the medical procedure or process related to the specific assay, in this case the process of detecting the presence of influenza virus and the potential sub-typing of the detected influenza virus. The LOINC codes specified here describe the important information about the methodology employed by the assay; recovery and amplification of one or more RNA targets. Multiple LOINC codes are utilized to convey that the assay is composed of multiple components, i.e. it is a panel or a battery of subtests. In the case of the CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel, the LOINC also provides for conveying that an interpretive test summary is appropriate. SNOMED CT codes provide for unambiguous representation of the test results and allow the application of specific concepts such as “detected” or “positive” or the identification of detected organism names. Though not further defined in this document, SNOMED CT can also be used to provide for description of the type and source/ location of the specimen being tested or for conveying information about failures of the test procedure or the lack of adequate specimen. Specific Recommendations for Standards-Based Electronic Data Exchange for Influenza Laboratories can find more information regarding implementation of HL7 messaging for CDC FLU rRT-PCR Dx Panel, including applicable LOINC test codes and SNOMED result codes at http://www.cdc.gov/flu/professionals/diagnosis/rtpcr-test-kits.htm

• http://www.cdc.gov/flu/professionals/diagnosis/rtpcr-test-kits.htm

• -------------------------

Goals:• Standardization• Promote understanding of

codes• Reinforce existing

vocabulary

Unique opportunity to test the codes on the insert PCR for B lineage typing is a brand new test

◦ No coding existed for it◦ Wanted to have coding ready when test was released

LOINC code requests had started requiring an FDA approved insert before issuing new LOINC

Manufacture and distribution occurs rapidly after FDA approval Need codes earlier in the process (Clem agreed)

Followed the usual CCB process for adding these codes.

First added a “PHLIP” code temporarily. Waited for the FDA approval, then applied for the LOINC. This process needed to be simultaneous so that our reporting

standards and the coding on the insert could be in sync.

B lineage typing

ETOR for CDC Flu LabIn progress…

In developmental stages Main “orders” currently received:

◦ Surveillance◦ Diagnostic◦ Antiviral Resistance Surveillance◦ Antiviral Resistance Diagnostic◦ Undetermined/Unknown

Lab requires flexibility with these – does not consistently run same tests for each

CDC Flu ETOR

Other Programs

LRN – LIMSi project VPD Reference Labs – second PHLIP project NREVSS – data sharing project Many others (ex. cancer registry)

Other programs using LOINC

Aligning with NREVSS◦ Collaborating on PHLIP vocabulary◦ Any changes can affect them

Aligning with LRN and VPD when necessary◦ Potential crossover with flu on any respiratory

viruses (Ex. MERS)◦ VPD and Flu share models and infrastructure as

well Our programs can impede each other if we

do not coordinate

“Aligning with other standards and messaging projects”

More collaboration◦ Cross-center◦ Cross discipline◦ Cross agencies

Need to make coding information accessible◦ “Physically” accessible◦ Reduce jargon – or teach it gradually

Create standard procedure for coordinating application for codes (in conjunction with APHL and other partner agencies)

Future for Coding at CDC

Thanks for your time!

For more information please contact :

Desiree Mustaquim dwc6@cdc.gov404-639-2578