….and other standards
What are we capturing?
Morbidity
Surveillance
Virologic
Health Departments
Surveillance
•U.S. WHO Collaborating
Laboratories
•National Respiratory and Enteric
Virus System (NREVSS)
•Novel influenza A reporting
Mortality
Surveillance
CDC
State-level data to state surveillance
coordinators
Current Laboratory Reporting Methods*
NYC
District of
Columbia
DoD
SLO
Co.
Houston
Web
*As of 4/24/2014
PHLIS2
PHLIP

Influenza virologic surveillance data analyzed weekly for Flu
View:
◦ http://www.cdc.gov/flu/weekly/
◦ http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html




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
Orig Sub #1
LIMS
Orig Sub
#2 LIMS
PHL A
LIMS
ETOR
HL7
ELSM
PHL B
LIMS
ETOR
CDC Epi or Lab
JSK: 8-4-2010
Slide Courtesy of Joan
Knapp, CDC
Knapp: 7-26-2010



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:
Influenza Test Encoding Guideline : Test Overview
Display Name
502195|39528-5 HAdV DNA XXX Ql PCR
502195|34487-9 FluAV RNA XXX Ql PCR
502195|40982-1 FLUBV RNA XXX Ql PCR
502195|29908-1 HPIV1 RNA XXX Ql PCR
Usage of the Test Concept
To order and report at least the
individual targets listed here,
other respiratory virus targets
may be added - does not require
Flu A subtyping!
To order and report at least the
individual targets listed here,
other respiratory virus targets
may be added - does not require
Flu A subtyping!
To order and report at least the
individual targets listed here,
other respiratory virus targets
may be added - does not require
Flu A subtyping!
To order and report at least the
individual targets listed here,
other respiratory virus targets
may be added - does not require
Flu A subtyping!
PHLIP Test
ID or LOINC
Code
39528-5
34487-9
40982-1
29908-1
LOINC Short Name or PHLIP Name
HAdV DNA XXX Ql PCR
FluAV RNA XXX Ql PCR
FLUBV RNA XXX Ql PCR
HPIV1 RNA XXX Ql PCR
OBR-4.1
OBR-4.2
OBR-4.3
OBR-15.1
50219-5
Respiratory virus
DNA + RNA panel LN
Specimen
Value Set for
the Flu
Testing
50219-5
Respiratory virus
DNA + RNA panel LN
Specimen
Value Set for
the Flu
Testing
50219-5
Respiratory virus
DNA + RNA panel LN
Specimen
Value Set for
the Flu
Testing
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
OBR 4
48509-4
OBX 3 (LOINC)
FLUAV + FLUBV RNA
XXX PCR
40982-1
FLUBV RNA XXX Ql PCR
34487-9
FLUAV RNA XXX QI PCR
49521-8
FLUAV HA H1 RNA XXX Ql PCR
49524-2
FLUAV HA H3 RNA XXX Ql PCR
FLUAV swine origin RNA XXX Ql
PCR
FLUAV H1 2009 pandemic RNA
XXX Ql PCR
55464-2
55465-9
OBX 5 (SNOMED)
26041500
Not
0
Detected
26037300
Detected
1
26041500
Not
0
Detected
26037300
Detected
1
26037300
Detected
1
26041500
Not
0
Detected
VS.
OBR 4
48509-4
FLUAV + FLUBV RNA XXX PCR
OBX 3 (LOINC)
48509-4
FLUAV + FLUBV RNA XXX PCR
OBX 5 (SNOMED)
446645007
Influenza A virus subtype H3
LOINC only represents generic methods (and other stuff
that Riki detailed) – NOT the specific kit used.
OBR 4

Luminex:“To order and report the
individual targets used in the LUMINEX
Respiratory Multiplex test - must report
ALL targets” ---------------

OBX 3 (LOINC)
Other RVP codes have had the
more generic order code
OBR 4
502195
OBX 3 (LOINC)
Respiratory virus
DNA + RNA pane
Variable Targets/Tests
605667
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
Novel Influenza A H1N1
Swine Influenza Virus
Influenza A H1N1 swine-like
Novel Influenza A H1N1 swine-like
Influenza A H1, porcine
swine-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

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

Will discuss further in a few minutes.
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.
• Standardization
• Promote understanding of
codes
• Reinforce existing
vocabulary
• http://www.cdc.gov/flu/profess
ionals/diagnosis/rtpcr-testkits.htm
• -------------------------
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


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.
In 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




LRN – LIMSi project
VPD Reference Labs – second PHLIP project
NREVSS – data sharing project
Many others (ex. cancer registry)

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

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)
Thanks for your time!