lms african swine fever virus (asf) and classical swine

LMS African Swine Fever Virus (ASF) and Classical Swine Fever Virus (CSF) Data

Submission Program Guide

LMS ASF/CSF Messaging Guide V3 of 16

Contents Introduction .................................................................................................................................................. 3

Initial Vetting Process for Messaging ........................................................................................................ 3

Acknowledgment Message for Successful LMS Acceptance ................................................................ 5

Acknowledgment Message for Unsuccessful LMS Acceptance ............................................................ 5

Submission/Accession Assumptions ..................................................................................................... 6

ASF/CSF Messaging Specific Requirements by Sample Stream .................................................................... 7 Submission and Result Fields to be Included in Messages ....................................................................... 7

ASF/CSF Message Components .................................................................................................................... 9 Premises Information (PROL) .................................................................................................................... 9

Operation/Facility Site Type (ROL), HL7 User Defined Table 0305 Codes ................................................ 9

Animal Identifier (PID.3) ........................................................................................................................... 9

Date of Death (PID.29) .............................................................................................................................. 9

Animal Taxonomy/Species (PID.35) .......................................................................................................... 9

Production Class (PID.38), HL7 User Defined Table 0429 Codes .............................................................. 9

Clinical Sign(s) (PATIENT_OBSERVATION.OBX.3) .................................................................................... 10

Age Class (PATIENT_OBSERVATION/OBX.5/CWE.2) and Date of Birth (PID.7) ....................................... 10

Owner information (NK1) ....................................................................................................................... 12

Unique Specimen Identifiers (SPM.2) ..................................................................................................... 12

Samples being submitted to NVSL .......................................................................................................... 12

Specimen Type (SPM.4): SNOMED Codes .............................................................................................. 12

Referral Numbers (ORC.4/EI.1) ............................................................................................................... 13

APHIS Program OID (ORC.4/EI.3) ............................................................................................................ 13

Reason for Submission (OBR.31): Locally Defined Codes ....................................................................... 13

ASF and CSF Tests (RESULT.OBX.3): LOINC Codes .................................................................................. 14

Result Type (RESULT.OBX.2) ................................................................................................................... 14

Test Interpretation (RESULT.OBX.8) HL7 User Defined Table 0078 Codes ............................................. 14

Observation Instance Identifier (RESULT.OBX.21) .................................................................................. 15

Additional Guidance for Special Cases ........................................................................................................ 15 Reporting updated lab testing supporting information .......................................................................... 15

Reporting repeated testing results on the same specimen .................................................................... 15

LMS African Swine Fever Virus (ASF) and Classical Swine Fever Virus (CSF) Data

Submission Program Guide


Reporting an Internal Control Failure Scenario ...................................................................................... 15

Reporting “No Result Available” ............................................................................................................. 15

Contact Information .................................................................................................................................... 15 Document control ....................................................................................................................................... 16


Introduction This document is a reference guide intended to provide the summary information specific for messaging results to the Laboratory Messaging Services (LMS) for African Swine Fever (ASF) and Classical Swine Fever virus (CSF) as part of the combined ASF and CSF slaughter and diagnostic sick pig surveillance or as a Foreign Animal Disease (FAD) Investigation in which screening testing occurs in the NAHLN lab. This guide is intended to be used with the suite of reference material for NAHLN HL7 messaging that is available on the VTSL NAHLN Terminology Services web site at http://vtsl.vetmed.vt.edu/nahln/main.cfm.

NAHLN Foreign Animal Disease Investigation (FADI) test results are considered presumptive until NVSL’s confirmatory testing is complete. FADI presumptive results, including negative results, should not be messaged into LMS until results have been confirmed by NVSL, unless otherwise directed by the NAHLN program office.

Initial Vetting Process for Messaging The following list outlines the approval process for messaging to the production system. Labs are strongly encouraged to do schema validation on the message prior to sending a test message to expedite the process. Rhapsody or a number of programming editors and other free tools (such and Notepad ++, VHIS Validator and XML Tools) are available that provide this feature. Please see the ‘Hitchhikers Guide to NAHLN Messaging’ for more details.

Please note that there are two separate validation procedures during this review process. The first validation procedure is automatically performed when the message is submitted to the system. This validation procedure checks to see if the message is compliant with the HL7 standard with reference to the current LMS XML schema. The lab will receive system generated feedback from this process immediately after the message is sent. The second validation procedure is performed to make sure the data needed for analysis and reporting are available and valid. A member of the NAHLN IT team will review the message and give feedback to the lab via email.

The following steps are necessary to complete the approval process for messaging ASF and CSF results into the production system.

1. Use the following information for your lab’s initial FADI message for vetting:

HL7 Segment Description Comments

PV1.19/CX.1 Lab assigned accession number/case number

Use your lab’s accession number

PROL.13/PL.10/EI.1 Premises identification number 0034P2K PROL.11/XAD.4 Premises state CO nk.1/nk.12/xpn.1/fn.1 Owner last name Fakedude nk.1/nk.12/xpn.2 owner first name Joe srol.4/xcn.2/fn.1 submitter name I. R. Messaging, VMO srol.11/xad.1/sad.1 submitter address 1920 Dayton Ave. srol.11/xad.3 submitter city Ames srol.11/xad.4 submitter state IA srol.11/xad.5 submitter zip 50010 PID.3/CX.1 Animal ID 840 000 000 000 000

PID.35/CWE.1 & 2 Animal Taxonomy/Species SNOMED

78678003

http://vtsl.vetmed.vt.edu/nahln/main.cfm


HL7 Segment Description Comments PID.35/CWE.2 Animal Taxonomy/Species label Sus scrofa SPM.2/EIP.1/EI.1 Specimen ID assigned by the

submitter (Placer) A02176230 (tonsil) A02176231 (spleen)

SPM.2/EIP.2/EI.1 Specimen ID assigned by the lab (Filler)

Use your lab’s assigned specimen ID number

SPM.4/CWE.1 & 2 Specimen type SNOMED code & label 811000009103 Tonsil 551000009102 Spleen

SPM.17/DR.1 Specimen collection date Enter simulated date SPM.18 Date specimen received Enter simulated date ORC.4/EI.1 FAD/RCN number 00ST0000 ORC.4/EI.3 APHIS Program OID ASF = 2.16.840.1.113883.3.5.8.9.1

CSF = 2.16.840.1.113883.3.5.8.3.1 OBR.4/CWE.1 & 2 Test Ordered LOINC code & label LOINCs

73693-4 ASF PCR 44273-1 CSF PCR

OBR.31/CWE.1 & 2 Reason for submission code & label F - FAD Diagnostics

OBX.2 Results Type Code NM OBX.3/CWE.1 & 2 Test performed LOINC code & label LOINCs

73693-4 ASF PCR 44273-1 CSF PCR

OBX.5 Test result 0 OBX.8 Test interpretation NDET OBX.11 Test Result Status F OBX.19 Test date Enter simulated date OBX.21 Observation Instance ID Your lab’s LIMS system ID for the

instance of the result 2. The lab will message an example of ASF and CSF test results into the test system at:

https://vsapps.aphis.usda.gov/HL7ResultTest. The system will validate the message to determine if it is HL7 compliant and will immediately provide feedback to the lab via the Acknowledgement message response. The lab should contact the NAHLN IT messaging support team at [email protected] for assistance if a message cannot be successfully sent. Examples of Acknowledgement responses are described below.

If the lab has switched to messaging to EMS. MSH.11 must be set to “T” when sending a message intended for LMS Test. MSH.11 is used to direct the message into either LMS Test or LMS Production. The lab will message an example of ASF and CSF results to: https://mrpvsmsg.aphis.usda.gov/PublisherService/PublisherServiceApi/api/publish/LMS

3. Once a successful message is sent (i.e. Acknowledgement message of AA), the lab will send a notification email to [email protected] stating that a message has been sent successfully. That email will include the MSH.10, disease tested for, purpose of message (slaughter, diagnostic sick pig, or FAD investigation) and accession number used in the message. A member of the NAHLN IT messaging support team will review the message content and feedback will be provided to the lab via email. The lab is expected to make any corrections described in the feedback and send updated messages as needed.

https://vsapps.aphis.usda.gov/HL7ResultTest

mailto:[email protected]

https://mrpvsmsg.aphis.usda.gov/PublisherService/PublisherServiceApi/api/publish/LMS




4. The NAHLN Program Office (NPO) will approve the lab to begin messaging into production after the test message is successfully validated in both review procedures.

5. NPO will notify the lab that messaging into production has been approved. 6. The lab will email [email protected] informing them of the date messaging into production

will begin. The lab will message ASF and CSF test results into the production system at: https://vsapps.aphis.usda.gov/HL7Result MSH.11 must be set to “P” when messaging to LMS Production.

If the lab has switched to messaging to EMS, MSH.11 must be set to “P” when sending a message intended for LMS Production. The lab will message results into the production system to: https://mrpvsmsg.aphis.usda.gov/PublisherService/PublisherServiceApi/api/publish/LMS .

Acknowledgment Message for Successful LMS Acceptance An Acknowledgement (ACK) message is returned to the lab to indicate successful or unsuccessful receipt of the message by LMS. If receipt was successful, the ACK message will include an Acknowledgment Code which indicates success (MSA.1 = AA). The ACK report also includes the Message Control ID (MSH.10 value), the lab’s accession number (pv1.19/cx.1 value) and the Processing ID (MSH.11 value) received in the lab’s message. This information may be used by the lab’s staff or the message sending system to match the acknowledgement message to the original message sent. An abbreviated successful ACK message example is provided below. In the example the Message Control ID is shown in MSA.2 as 1.197568928512.2123, the accession number in ERR.7 shown as 046399-18 and the Processing mode also in ERR.7 is shown as “T”.

Acknowledgment Message for Unsuccessful LMS Acceptance If receipt was unsuccessful, the ACK message will include one of two Acknowledgment Codes to indicate either that there was an error in the message structure or content (MSA.1 = AE) or rejection (MSA.1 = AR). Messages may be rejected either because of a problem with the message type, structure, or

<?xml version='1.0' encoding='UTF-8'?> <ACK_R25 xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns:hl7='urn:hl7-org:v2xml' xsi:noNamespaceSchemaLocation='ackMessage.xsd'> <MSH> . . . </MSH> <MSA> <MSA.1>AA</MSA.1> <MSA.2>1.197568928512.2123</MSA.2> MSH.10 value from lab’s message </MSA> <ERR> <ERR.3>0</ERR.3> <ERR.4>I</ERR.4> <ERR.7>Accession:046399-18 Processing Mode:T</ERR.7> </ERR> </ACK_R25>


https://vsapps.aphis.usda.gov/HL7Result




processing ID or because of an LMS issue such as database failure. An abbreviated unsuccessful ACK message example is provided below. Also included in the example is a cryptic, yet sometimes useful description of the problem with the message structure or content. The description in the example below indicates that the required lab specimen ID (SPM.3) and specimen type (SPM.4) are missing (“Invalid content was found starting with element 'SPM.11'. One of '{SPM.3, SPM.4}' is expected.”).

Submission/Accession Assumptions For ASF and CSF Slaughter Surveillance testing only: Only labs that are participating in and have task orders in place for slaughter surveillance will need to have a message vetted for this sample stream. The collector or submitter will create a submission in CLSM-ASF and assign a referral number and specimen IDs. The referral number and specimen IDs will be included on the submission form and must be included in the message. The general format for submitter created referral numbers is [2 letter (Collection) state][2-3 letter initials][date of collection using 2 digit month, 2 digit day, 4 digit year (i.e. MMDDYYYY)] Diagnostic lab sick pig surveillance testing: Only labs that are participating in and have task orders in place for diagnostic sick pig surveillance will need to have a message vetted for this sample stream. Additional submission information is required when messaging results for diagnostic laboratory sick pig surveillance submissions. ASF and CSF testing must be done in conjunction with each other.

<?xml version='1.0' encoding='UTF-8'?> <ACK_R25 xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns:hl7='urn:hl7-org:v2xml' xsi:noNamespaceSchemaLocation='ackMessage.xsd'> <MSH> . . . </MSH> <MSA> <MSA.1>AE</MSA.1> <MSA.2>2420962</MSA.2> </MSA> <ERR> <ERR.3> <ERR.3.1>0</ERR.3.1> <ERR.3.2 /> <ERR.3.3>NAHLN</ERR.3.3> </ERR.3> <ERR.4 /> <ERR.7><![CDATA[Error occurred processing message on filter 'NAHLN LMS Base Schema': XML Message validation fails.,Nested exception was 'com.orchestral.rhapsody.module.api_2_0.module.filter.FilterProcessingException': XML Message validation fails.,Nested exception was 'org.xml.sax.SAXParseException': cvc-complex-type.2.4.a: Invalid content was found starting with element 'SPM.11'. One of '{SPM.3, SPM.4}' is expected.]]></ERR.7> </ERR> </ACK_R25>


ASF/CSF Messaging Specific Requirements by Sample Stream

Submission and Result Fields to be Included in Messages The following chart lists which fields in the message are:

• R = Required. Fields must have valid values in the message. • O = Optional. If your lab receives and captures this information, it must be sent in the message. • NA = not applicable

Additional details for some of these fields are found in the ASF/CSF Message Components section.

HL7 Segment Description Comments Slaughter Sick Pig FAD

MSH.11 Processing ID T=test, P=production, D=debugging R R R PV1.19/CX.1 Lab assigned accession

number/case number Specimen and animal identifiers: It must be possible to differentiate individual animals. An accession number assigned by the lab (Filler) is required

R R R

PROL.13/PL.6 Operation/Facility site type

Location of animal at time of sample collection. O O O

PROL.13/PL.10/EI.1 Premises identification number

PROL = ROL segment with ‘PREM’ in the ROL.3 role field. Prem State is required. PremID is required when provided.

R O R

PROL.11/XAD.4 Premises state R R R SROL.4 Submitter name

Information for individual who submitted sample to the lab

O O O SROL.11 Submitter premises site

address SROL.12 Submitter phone

number PID.3/CX.1 Animal ID Even though the Animal ID is optional, if

it is known it is required to be sent. O O O

PID.7 Date of birth See the component section below for disease-specific information. O O O

PID.29 Date of Death

PID.35/CWE.1 Animal taxonomy SNOMED code

An indicator of a disease-appropriate species is required.

R R R

PID.35/CWE.2 Animal taxonomy label PID.38/CWE.1 Production class code

See the component section below for disease-specific information.

O O O PID.38/CWE.2 Production class label POBX/OBX.3 & 5 Clinical Signs POBX/OBX.5/CWE.

Age class

NK1.4 Owner premises ID or address

Owner information O O O


HL7 Segment Description Comments Slaughter Sick Pig FAD SPM.2/EIP.1/EI.1 Specimen ID assigned

by the submitter (Placer)

This is the barcode or other specimen identifier from the submission form. Field is required for slaughter surveillance. For FADI and diag sick pig surveillance these fields are optional, but data must be sent if provided to lab.

R O O

SPM.2/EIP.2/EI.1 Specimen ID assigned by the lab (Filler)

Specimen and animal identifiers: It must be possible to differentiate individual animals.

R R R

SPM.4/CWE.1 Specimen type SNOMED code See the component section below for

disease-specific information. R R R SPM.4/CWE.2 Specimen type label SPM.17/DR.1 Specimen collection

date Date specimen was collected. Even though this is optional, if it is known it is required to be sent.

R O O

SPM.18 Date specimen received

Date specimen received at the lab. R R R

ORC.4/EI.1 FAD or referral number R NA R ORC.4/EI.3 APHIS Program OID See the component section below for

disease-specific information. R R R ORC.5 Order Status OBR.4/CWE.1 Test Ordered LOINC

See the component section below for disease-specific information. R R R OBR.4/CWE.2 Test Ordered label

OBR.31/CWE.1 Reason for submission code Submission reason will be F or N. See

the component section below for sample stream specific information.

R R R OBR.31/CWE.2 Reason for submission

label OBX.2 Results Type Code Examples are SN, NM, ST, CWE. See the

component section below for result specific information.

R R R

OBX.3/CWE.1 Test performed LOINC code

Test performed or planned to be performed if a test result could not be obtained (result status = X)

R R R OBX.3/CWE.2 Test performed label OBX.5 Test result Test result if a test result could be

obtained (result status = F) R R R

OBX.8 Test interpretation Examples are DET, NDET, and IND. See the component section below for disease-specific information.

R R R

OBX.11 Test Result Status Examples are F or X. The list of options is on the VTSL site. R R R

OBX.19 Test date Date test is completed. R R R OBX.21 Observation Instance

ID Unique result identifier *required with implementation of schema 2.1* R R R


ASF/CSF Message Components

Premises Information (PROL) Location of animal at the time the specimen was taken. PROL is the ROL segment with ‘PREM’ in the ROL.3 role field. NEW: The premises state (PROL.11/XAD.4) is required in the message. If the premises ID (PROL.13/PL.10/EI.1) is available, it is also required to be sent in the message. (A premises ID might be required for payment.) If a premises does not have a PIN, the full address including the state may be included (PROL.11/XAD.1, XAD.3-5). When labs switch to messaging to EMS both premises ID and state should be included in the message if provided. If the state is not present and an invalid premises ID is sent, the message will not go through to LMS.

Operation/Facility Site Type (ROL), HL7 User Defined Table 0305 Codes The type of facility where the animal was located at the time of sample collection. This field is optional and would be sent in a ROL segment as ROL.13/PL.6 with Role Code = PREM.

Local Code Text label Use for Messaging Results for: M Market/Collection Point FAD E Exhibition FAD N Non-producer participants FAD, Diagnostic Sick Pig P Production Unit FAD, Slaughter, Diagnostic Sick Pig S Slaughter Plant FAD, Slaughter

Animal Identifier (PID.3) If available, this is often either the animal identification (tag/number) or the animal group/lot identifier. If not available, this can be the subject identifier as recorded in the LIMS (sent with the laboratory facility OID as the identifier assigning authority in PID.3.4). Otherwise, this can be empty.

Date of Death (PID.29) If available, provide the date of death for animals that are submitted dead. The date of death does not apply to those animals sacrificed or euthanized for necropsy.

Animal Taxonomy/Species (PID.35) An indicator that a pig was tested is required. The level of taxonomy (e.g. species, breed) reported will be determined by the level of detail available in the LIMS. By default, the species Sus scrofa (SNOMED code 78678003) may be used. Additional child SNOMED codes are available on the VTSL site.

Production Class (PID.38), HL7 User Defined Table 0429 Codes This field is optional. The production class codes are as follows:

Local Code

Text label Description

BR Breeding/genetic stock Animal intended for reproductive purposes to produce offspring. C Companion Animal intended for personal pleasure, recreation or hobby use. MT Meat Animal intended to be slaughtered for human consumption. MP Multipurpose Animal used for multiple purposes. U Unknown Purpose of the animal is unknown.


Clinical Sign(s) (PATIENT_OBSERVATION.OBX.3) Serving as the context for what was observed by a caretaker (e.g. abortion, CNS signs, septicemia) or what was reported to the caretaker (e.g. clinical history), the LOINC listed below should be used in OBX.3.

LOINC Code LOINC Short name (Text label)

Description

10187-3 Review of Systems a relevant collection of signs and functions systematically gathered by an animal health caretaker

The narrative text for the clinical signs should be reported in OBX.5. The following list contains the clinical signs that may be present for an animal to be tested for ASF and CSF:

Example:

Age Class (PATIENT_OBSERVATION/OBX.5/CWE.2) and Date of Birth (PID.7) These fields are optional. If the lab’s LIMS can capture age class, use the following codes and send it as a patient observation (OBX). The LOINC listed below should be used in OBX.3 and one the following codes should be sent as patient observation in OBX.5. Do not convert age class to date of birth (DOB).

LOINC Code LOINC Short name (Text label)

46251-5 Age Group

Antemortem Observations Postmortem Observations Increased mortality rate Lymph nodes, lungs, kidneys, spleen, myocardium,

etc Fever, lethargy, anorexia, depression, abortion Splenomegaly Lameness, recumbency, paddling Erosions, hemorrhage, necrosis, proliferation Eythema, petechiae, hematoma, subcutaneous hemorrhage, epistaxis

Acute or chronic ulcers, button ulcers

<OPU_R25.PATIENT_OBSERVATION> <OBX> <OBX.2>ST</OBX.2> <OBX.3> <CWE.1>10187-3</CWE.1> <CWE.2>Review of Systems</CWE.2> <CWE.3>LN</CWE.3> </OBX.3> <OBX.5>fever, skin hemorrhage, and diarrhea</OBX.5> <OBX.11>F</OBX.11> </OBX> </OPU_R25.PATIENT_OBSERVATION>


Age Classifications for Swine

Description SNOMED Code Text label Sow/Boar 28811000009104 Adult pig for meat production (organism)

Grower/Finisher 356661000009103 Grower/finisher pig for meat production (organism)

Nursery 28901000009106 Starting pig for meat production (organism)

Suckling 28911000009108 Suckling pig for meat production (organism)

If the lab’s LIMS captures DOB, please send the raw date and do not convert it to age class. The DOB may need to be approximated.

If both age class and DOB are available, please send both.

Example age class segment:

Example DOB segment:

<OPU_R25.PATIENT> ... <OPU_R25.PATIENT_OBSERVATION> <OBX> <OBX.2>CWE</OBX.2> <OBX.3> <CWE.1>46251-5</CWE.1> <CWE.2>Age Group</CWE.2> <CWE.3>LN</CWE.3> </OBX.3> <OBX.5> <CWE.1>28911000009108</CWE.1> <CWE.2>Suckling pig for meat production (organism)</CWE.2> <CWE.3>SCT</CWE.3> </OBX.5> <OBX.11>F</OBX.11> </OBX>

</OPU_R25.PATIENT_OBSERVATION>

<OPU_R25.PATIENT> <PID> <PID.3><CX.1>PIGID</CX.1><CX.4 /></PID.3> <PID.5><XPN.1><FN.1>NOT PROVIDED</FN.1></XPN.1></PID.5> <PID.7>20200215</PID.7> <PID.8>F</PID.8> <PID.30>N</PID.30> . . . </PID> </OPU_R25.PATIENT>


Owner information (NK1) Animal’s owner name and location information for location where the animal normally resides.

Unique Specimen Identifiers (SPM.2) If a submitter assigned specimen (Placer) ID is provided this should be sent in SPM.2/EIP.1/EI.1. A barcode is required for reimbursement, otherwise a non-unique submitter ID is acceptable. If the lab assigns the barcode to the specimen that number should be sent in this field. Note: For a matrix positive sample, the barcode ties together the matrix and all subsequent testing.

All samples must be submitted with a UNIQUE laboratory assigned specimen (Filler) ID in SPM.2/EIP.2/EI.1.

For more information, see the current version of ‘Hitchhikers Guide to NAHLN Messaging’ or the “NAHLN/LMS HL7 Implementation Guide for Laboratory Results Messaging".

Example SPM.2 segment:

Samples being submitted to NVSL All 10-4s must include the BARCODE in Sample ID field on the form. The A0 barcodes can be obtained from NAHLN by emailing [email protected] .

Specimen Type (SPM.4): SNOMED Codes

The specimen types that are currently approved for the NAHLN ASF/CSF testing protocols are included in the following table. If the codes do not represent the specimens that are to be messaged, please contact NPO for guidance. Note: Specific sample testing must follow guidelines provided in the ASF-CSF Surveillance NAHLN Laboratory Manual and WI-NAHLN-0038, NAHLN Test Reference Chart.

Text label SNOMED Code ASF CSF Comments Whole blood sample (specimen) 258580003 ✓ ✓ FADI only Tissue specimen from spleen 551000009102 ✓ ✓ Tissue specimen from Tonsil 811000009103 ✓ ✓ Lymph node tissue sample 309078004 ✓ ✓ Tonsil Scraping 4241000009102 ✓ FADI only Blood swab 362231000009100 ✓ FADI only Swab of spleen 362221000009102 ✓ FADI only Dried blood spot specimen* 440500007 ✓ FADI only;

*Common name is nucleic acid blood card or FTA card

<SPM.2> <EIP.1> <EI.1>1</EI.1> </EIP.1> <EIP.2> <EI.1>A97E7EA2-B410-470A-82B9-39D6752AF2DB</EI.1> <EI.3>2.16.840.1.113883.3.5.1.9.10</EI.3> <EI.4>ISO</EI.4> </EIP.2> </SPM.2>



Referral Numbers (ORC.4/EI.1) • For ASF and CSF slaughter surveillance testing only, use the referral number that is provided on

the CLSM or MiCoForm submission paperwork. The standard convention is: [2 letter state code][submitters initials][date using format mmddyyyy] followed by a,b,c if more than one submission was created on the same day by the same submitter. Do NOT generate this number if not provided, contact the submitter for this number.

• All samples that are tested for ASF and CSF in the NAHLN laboratory that are part of or initiate a Foreign Animal Disease (FAD) investigation MUST have an FAD number/ RCN number in ORC.4/EI.1 in order to be reimbursed for the test. The FAD number format is generally [2-digit year][2-letter state][4-digit number]

APHIS Program OID (ORC.4/EI.3) The Program OID will be very important for routing messages internally to the VS data systems. This must be included in the ORC.4 segment. If one or more samples tested for multiple diseases are to be submitted in the same message, each set of disease specific test results must be included under a unique ORDER group with the applicable program OIDs in each ORC segment.

Sample stream ASF CSF Slaughter surveillance 2.16.840.1.113883.3.5.8.9 2.16.840.1.113883.3.5.8.3 Diagnostic Sick pig surveillance or FAD investigation

2.16.840.1.113883.3.5.8.9.1 2.16.840.1.113883.3.5.8.3.1

Reason for Submission (OBR.31): Locally Defined Codes For messaging Slaughter or Diagnostic Sick Pig surveillance test results the National Surveillance (N) reason should be used. For messaging FAD investigation results the FAD Diagnostics (F) reason should be used.

Local Code

Text label Description

F FAD Diagnostics Samples that are submitted as part of the original FAD investigation or for testing directly associated with the outbreak and that meet the requirements for the State/Federal response

N Surveillance, National

Used for submission of specimens by a recognized national animal health surveillance program

T Traceback Epidemiologic traceback investigation


ASF and CSF Tests (RESULT.OBX.3): LOINC Codes The currently supported LOINC codes for ASF or CSF testing is in the following table.

LOINC Code LOINC short name (text label)

LOINC Long Name

73693-4 ASFV DNA Ct Tiss Qn NAA+probe

African swine fever virus DNA [Cycle Threshold #] in Tissue by NAA with probe detection

44273-1 CSFV RNA Spec NAA+probe-aCnc

Classical swine fever virus RNA [Units/volume] (viral load) in Specimen by NAA with probe detection

Result Type (RESULT.OBX.2) For PCR tests, the result type is a CT value. Obx.2 should be NM for numerical to denote the type of result that will be in obx.5. An example of the result segment using NM:

Test Interpretation (RESULT.OBX.8) HL7 User Defined Table 0078 Codes The current valid test interpretation code is:

Local Code Description NDET Not Detected DET Detected

In the case of a non-negative result, please contact (NPO) for instructions on how to submit the sample to NVSL and the result via messaging. FADI presumptive results, including negative results, should not be messaged into LMS until results have been confirmed by NVSL, unless otherwise directed by the NAHLN program office. Contact NPO for additional guidance. This does not apply to “quality control failure” nor “no result available” results (as outlined below) which can be messaged routinely.


Observation Instance Identifier (RESULT.OBX.21) With implementation of schema 2.1, obx.21 is a required field. This field is used to help identify duplicate results. Specifically, when the same result is sent more than once for the same accession, animal, specimen, and test performed. Its main function is to distinguish the case when the same observation is resent or corrected from that in which a new observation is made in the same order such as when a test is repeated due to some issue with testing discovered after recording the first observation. This can be anything that the sending system uses to distinguish unique results from the same result being sent again. This is usually a database key of some sort. If the system does not have a database key, several fields can be concatenated together to create an observation instance ID.

Additional Guidance for Special Cases

Reporting updated lab testing supporting information If updated or corrected supporting information needs to be reported (e.g. the collection site premises ID PIN; this does not include test result), contact the NPO for guidance.

Reporting repeated testing results on the same specimen If a specimen is tested more than once and then finalized, additional testing results should be maintained, with the new testing result uniquely identified using the Observation Instance Identifier (OBX.21). Refer to the ‘Hitchhiker’s Guide to NAHLN Messaging’ (Repeated Testing or Re-Sent Results) and the ‘NAHLN/LMS HL7 Implementation Guide For Laboratory Result Messaging’ for more details.

Reporting an Internal Control Failure Scenario If a result cannot be reported because of an internal control failure (e.g. it was not possible to run the test as needed to obtain a valid result) report this with an indicator that a result could not be obtained (OBX.11 = “X”) because of a ‘Quality Control Failure’ (OBX.8 = “QCF”)

Reporting “No Result Available” If a result cannot be reported for any reason other than Quality Control Failure, report this with an indicator that a result could not be obtained (OBX.11 = “X”) with an empty or excluded result interpretation (OBX.8 IS NULL or the OBX.8 tags not sent).

Contact Information To contact the NAHLN Program Office (NPO), please send an email to [email protected].

To contact the NAHLN IT team or the LMS support group, please send an email to [email protected].




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NAHLN Program Office – designee

4/11/2019 2.1 Updated guide for surveillance, added Program OIDs, required fields. Delineate messaging requirements for Slaughter and Diagnostic Sick Pig messaging for routing purposes.

NAHLN Program Office - designee

6/14/2021 3.0 Combined ASF/CSF guides together, reordered list of HL7 fields, included section on obx.21, added sample accession information for initial message, updated tables including new specimen types, updated information on CLSM and VSLS

Cindy Chard-Bergstrom, Beth Harris, Jennifer Rodriguez

lms african swine fever virus (asf) and classical swine

Documents