Form 0920-20OS CSV Format Guide

COVID-19 Pandemic Response, Laboratory Data Reporting

3. CSV Format Guide.xlsx

CDC-provided CSV file or HL7 messages

OMB: 0920-1299

Document [xlsx]
Download: xlsx | pdf

Overview

CSV file input_COVID19
csv_headers
ExampleData_csv_format
CDC Guidance Elements


Sheet 1: CSV file input_COVID19

OMB Approved. 0920-XXXX
Exp. Date XX/XX/2020






























































































































































Public reporting burden of this collection of information is estimated to average 60 minutes per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. An agency may not conduct or sponsor, and a person is not required to respond to a collection of information unless it displays a currently valid OMB Control Number. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to CDC/ATSDR Reports Clearance Officer, 1600 Clifton Road NE, MS D-74, Atlanta, Georgia 30333; ATTN: PRA 0920-XXXX





















































































































































Legend


Abbreviations




































































field must be filled out







LN LOINC SCT SNOMED CT




































































either one of the highlighted fields must be filled out







PLT Public Health Lab Test PLR Public Health Lab Results




































































either one of the highlighted fields must be filled out







L Local HL70070 Specimen type table from V2.3.1




































































either one of the highlighted fields must be filled out









HL70487 Specimen type table from V2.5.1




































































either one of the highlighted fields must be filled out
















































































either one of the highlighted fields must be filled out
















































































either one of the highlighted fields must be filled out



































































































































































section separators














































































YYYYMMDD[HHMMSS]
Date format where the first 4 (Y) are the year, the next 2 (M) the month, then next 2 (D) the day - to use for reporting dates; [] indicates optionality - so in this case the time is optional: the next 2 (H) the hour, the next 2 (M) the minutes, the next 2 (S) the seconds














































































































































































































































Row "Use of csv file": Indicates if use is for CDC = CDC and PHA_ELR















































































Row "Mapping to HL7": Provides the mapping to the HL7 element, where it can be found based on V2.5.1 - mapping to other HL7 versions will be added at a later point in time















































































Row "Sections": Identifies the sections















































































Row "Instructions": Provides some instructions / allowed formats or values















































































Row "CSV Column name": CSV column headers and the only thing that will be in the upload file - see tab "csvFileHeadersOnly_CDC_COVID19" for CDC specific file

































































































































































Epi Questions For each disease there will be a list of required / desired EPI questions that are of interest - the appropriate list should be provided accordingly - a few generic questions would be Patient_age_at_specimen_collection, or Illness_onset_date or pregnancy_status





































































































































































































































































































































Use of csv file CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC
CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC CDC
CDC CDC CDC
Mapping to HL7 OBR-3 SPM-2.2.1 (v2.5.1) SPM-2.1.1 (v2.5.1) SPM-2.1.2 (v2.5.1) OBX-23.1 (v2.5.1) OBX-23.10 (v2.5.1) OBX-23.7 (v2.5.1) OBX-24.1 (v2.5.1) OBX-24.3 (v2.5.1) OBX-24.4 (v2.5.1) OBX-24.5 (v2.5.1) PID-3.1 PID-3.4 PID-3.5
PID-7 PID-8 PID-10.2 PID-11.3 PID-11.4 PID-11.5 PID-11.9 PID-22.2
OBX-5.1 if NM or OBX-5.2, if SN, where OBX-3.1 = 21612-7, 29553-5, 35659-2, 30525-0
OBX-6 should be years (not sure how to handle this given the bad HL7 I have seen, ideally we could use OBX-6.2, so maybe we need to add age unit for the HL7?!
OBX-5, where OBX-3.1 = 11368-8
OBX-2 = DT
OBX-2 = CE or CWE
OBX-5.2, where OBX-3.1 = 82810-3, 11449-6
expected answers would be Yes: Y^Yes^HL70136 or 77386006^Patient currently pregnant^SCT or 102874004^Possible pregnancy^SCT
No = N^No^HL70136 or 60001007^Not pregnant^SCT
UNK^Unknown^NULLFL
not sure what else - just take what we get
OBX-2 = CE or CWE
OBX-5.2, where OBX-3.1 = 75325-1, INV576(PHINQUESTION)
expected answers:
Y^Yes^HL70136
N^no^HL70136
UNK^Unknown^NULLFL
not sure what else - just take what we get
OBX-2 = CE or CWE
OBX-5.2, , where OBX-3.1 = 56816-2, LAB330 (PHINQUESTION)
expected answers:
I^Inpatient^HL70004 or 44065400^Inpatient environment^SCT
O^Outpatient^HL70004
309904001^Intensive Care Unit^SCT
282E00000X^Long Term Care Hospital^HCPT or 42665001^Nursing home^SCT
not sure what else - just take what we get
OR
PV1-2 coded with I = Inpatient
E = Emergency
O = Outpatient
NK1-11 may provide the job class code (NK1-5 = SEF for self, to give us information about the patient)

OBX-2 = CE or CWE
OBX-5.2, , but NOT SURE about the code they will use, if anyone even has this
expected answers:
Y^Yes^HL70136
N^no^HL70136
UNK^Unknown^NULLFL
not sure what else - just take what we get
OBX-2 = CX
OBX-5.1 &OBX-5.4, where OBX-3.1 = 94659-0, or PLT248 AND OBX-5.5. = "PHC"
- need to keep the assigning authority, if sent as well (just use the ^)

SPM-4.1 (v2.5.1)
OBR-15.1.1 (V2.3.1)
SPM-4.2 (v2.5.1)
OBR-15.1.2 (V2.3.1)
SPM-4.3 (v2.5.1)
OBR-15.1.3 (V2.3.1)
SPM-4.9 (v2.5.1)
OBR-15.3 (V2.3.1)
OBR-7
SPM-17.1 (v2.5.1 only)
OBR-14
SPM-18.1 (V2.5.1 only)

ORC-12 / OBR-16
or
ORC-21.1
ORC-12.2 / OBR-16.2 ORC-12.3 / OBR-16.3 ORC-24.1 ORC-24.3 ORC-24.4 ORC-24.5 ORC-21.1 ORC-22.1 ORC-22.3 ORC-22.4 ORC-22.5 ORC-23
OBR-25 OBR-22 OBR-4.1 OBR-4.2 OBR-4.3
OBX-3.1 OBX-3.2 OBX-3.3 OBX-5.1 CE or CWE OBX-5.2 CE or CWE OBX-5.3 CE or CWE OBX-5.1 ST or TX or OBX-5.9 CWE (2.5.1)
OBX-5.2 (2.3.1)
OBX-5.1 SN OBX-5.2 SN or OBX-5.1 NM OBX-5.3 SN OBX-5.4 SN OBX-6 OBX-7 OBX-8 OBX-17.5 or OBX-17.9 OBX-11 OBX-19.1
MSH-4.1 MSH-4.2 MSH-3
Sections Identifiers (will repeat across rows for each specimen / accession)
Patient Information (will repeat across rows for each patient, can span more than one specimen)
EPI Questions - pre-defined (will repeat across rows for each patient or specimen)
Specimen Information (will repeat across rows for each specimen)
Ordering Provider information (will repeat across rows for each order) Ordering Facility Information (will repeat across rows for each specimen)
Order Information (will repeat across rows for each specimen)
Lab Test Information - 1 row per test - either it or the Epi information section will be populated
Meta-Data: (values will repeat across rows for all rows in this file)
Instructions Must have either this or Testing_lab_specimen_ID valued
order number assigned by the testing lab
Must have either this or Testing_lab_accession_number valued (can have both)

If not available: Use another unique laboratory ID from your system if available. If not, it is suggested to: Create unique ID by concatenating
- Date/time initially entered (to millisecond)
- Specimen collection date (if present)
- SNOMED-CT of specimen type (if present)
- Name of laboratory (if present)

Name of the organization that created the specimen ID Must have either this or Testing_lab_ID valued (can have both)

If BOTH Testing_lab_ID and Testing_lab_name are unavailable, populate with the literal value 'NULL'
Must have either this or Testing_lab_name valued (can have both)

This can be CLIA, NPI or OID
Expected values:
CLIA
NPI
OID



5 or 9 digits Must have this valued
This should uniquely identify the patient over time.
Preferred IDs are from the submitter or the PHA, to allow linking with case data.
Do NOT send SSI or Medical Record Number

If not available: Use PH-Case ID or internal surveillance ID, or specimen ID/accession number.
Name of the organization that created the patient ID Expected values:
PI = Patient Internal ID

Format YYYYMMDD[HHMMSS]
If this cannot be provided, please provide Patient age in EPI section
Expected Values:
(M) Male
(F) Female
(O) Other
(U) Unknown
(A) Ambiguous
Expected Values:
(1002-5) American Indian or Alaska Native
(2028-9) Asian
(2054-5) Black or African American
(2076-8) Native Hawaiian or Other Pacific Islander
(2106-3) White
(U) Unknown

Multiple race values are allowed and should be delimited using ";".

Must have either this or Ordering_facility_state or Ordering_provider_state valued

If not available: populate with the literal value 'NULL'
5 or 9 digits
Expected values:
(H) Hispanic
(N) Not-Hispanic
(U) Unknown

Report in years
Expected answers:
Yes
No
N/A
Fever, cough, shortness of breath, fatigue

Expected answers:
Yes
No
Expected answers:
(I) Hospitalized
ICU
Long term care
(O) Outpatient
(E) Emergency
These are healthcare workers, first responders, essential serivces worker

Expected answers:
Yes
No
The case ID assigned by the PHA - ideally this woud be the NCOV-ID in the following format: ZZNNNNNN, where ZZ is the 2 letter state abbreviation and N is a numeric (e.g. : AR000001)
Must have either this or specimen_type_description or specimen_type_free_text valued (can have all three)

If not available: populate with the literal value '119324002' (Specimen_type_code_system: SCT)
Must have either this or specimen_type_code or specimen_type_free_text valued (can have all three)

If not available: populate with the literal value 'Specimen of unknown material'
Allowed values:
HL70070
HL70487
SCT
PLR
L
Must have either this or specimen_type_code or or specimen_type_description valued (can have all three)

If not available: populate with the literal value 'Specimen of unknown material'
Format YYYYMMDD[HHMMSS]
If unknown populate with the literal value '0000'
Format YYYYMMDDHHMM[SS]
Must have this or Ordering_facility_name or Ordering_provider_name valued

If you capture only 1 instance of ordering provider information - regardless if person or facility - use this field

If Ordering_facility_name, Ordering_entity_name, and Ordering_provider_name are ALL unavailable, populate with the literal value 'NULL'
Must have this or Ordering_facility_name or Ordering_entity_name valued


Must have either this or Patient_state or Ordering_facility_state valued

If not available: populate with the literal value 'NULL'
5 or 9 digits Must have either this or Ordering_provider_name or Ordering_entity_name valued

Must have either this or Patient_state or Ordering_provider_state valued

If not available: populate with the literal value 'NULL'
5 or 9 digits Use format NNN-NNN-NNNN
Summary of all results under this order (this will only be different from Test_result_status for panels)
For CDC allowed values:
Final
Corrected
For PHA_ELR additionally allowed:
Partial
Preliminary
Must have either this or Test_Date valued
Expected Format YYYYMMDDHHMM[SS]
code should be from LOINC
Expected values:
LN = LOINC
PLT = Public Health Lab Test
L = Local

Must have either this or Test_performed_description valued

code should be from LOINC
Must have either this or Test_performed_code valued Expected values:
LN = LOINC
PLT = Public Health Lab Test
L = Local
Must have either this or Test_result_description or Test_result_free_text (can have all three) or Test_result_number valued Must have either this or Test_result_coded or Test_result_free_text (can have all three) or Test_result_number valued Expected Values:
SCT = SNOMED CT
PLR = Public Health Lab Results
L = Local
Must have either this or Test_result_description or Test_result_coded (can have all three) or Test_result_number valued

If you are not differentiating between qualitative and quantitative results use this field
Expected values:
>
<
=
<=
>=
Must have this or either Test_result_coded, Test_result_description or Test_result_free_text (can have all three) valued

If you are not breaking out quantitative results into structured numerics (like less than / titers) and numbers, use this field for ANY quantitative result
Expected values:
- (use for ranges)
: (use for titers)




Include the kit name, if available MUST have this valued

For CDC expected Values:
Final
Corrected

If not available: Populate with the literal value 'NULL'
Must have either this or Results_Released_Date valued (can have both)
Expected Format YYYYMMDD[HHMMSS]

If BOTH Test_date and Date_result_released are unavailable AND specimen_collection_date_time is populated with a real date, not the literal value '0000' use the literal value '0000'

Must have either this or Reporting_facility_ID valued

If not available: Map to Testing_lab_name. Alternatively, can be populated with your own info in Reporting_facility_name as long as Testing_lab_name is populated.
Must have either this or Reporting_facility_name valued

If not available: Map to Testing_lab_ID

This is a static entry - for this version populate with the literal value 'V2020-04-18'
CSV Column name Testing_lab_accession_number Testing_lab_specimen_ID Submitter_unique_sample_ID Submitter_sample_ID_assigner Testing_lab_name Testing_lab_ID Testing_lab_ID_type Testing_lab_street_address Testing_lab_city Testing_lab_state Testing_lab_zip_code Patient_ID Patient_ID_assigner Patient_ID_type
Patient_DOB Patient_gender Patient_race
Patient_city Patient_state
Patient_zip_code Patient_county
Patient_ethnicity

Patient_Age Illness_Onset_Date Pregnant Symptomatic_for_disease Patient_location Employed_in_high_risk_setting Public_Health_Case_ID
Specimen_type_code Specimen_type_description Specimen_type_code_system Specimen_type_free_text Specimen_collection_date_time Specimen_received_date_time
Ordering_entity_name Ordering_provider_last_name Ordering_provider_first_name Ordering_provider_street Ordering_provider_city Ordering_provider_state Ordering_provider_zip_code Ordering_facility_name Ordering_facility_street Ordering_facility_city Ordering_facility_state Ordering_facility_zip_code Ordering_facility_phone_number
Order_result_status Date_result_released Ordered_test_code Ordered_test_description Ordered_test_code_system
Test_performed_code Test_performed_description Test_performed_code_system Test_result_coded Test_result_description Test_result_code_system Test_Result_free_text Test_result_comparator Test_result_number Test_result_number_separator Test_result_number2 Test_result_units Reference_range Abnormal_flag Test_method_description
Test_result_status Test_date
Reporting_facility_name Reporting_facility_ID Report_facil_data_source_app csv_file_version_no

Sheet 2: csv_headers

Testing_lab_accession_number Testing_lab_specimen_ID Submitter_unique_sample_ID Submitter_sample_ID_assigner Testing_lab_name Testing_lab_ID Testing_lab_ID_type Testing_lab_street_address Testing_lab_city Testing_lab_state Testing_lab_zip_code Patient_ID Patient_ID_assigner Patient_ID_type Patient_DOB Patient_gender Patient_race Patient_city Patient_state Patient_zip_code Patient_county Patient_ethnicity Patient_Age Illness_Onset_Date Pregnant Symptomatic_for_disease Patient_location Employed_in_high_risk_setting Public_Health_Case_ID Specimen_type_code Specimen_type_description Specimen_type_code_system Specimen_type_free_text Specimen_collection_date_time Specimen_received_date_time Ordering_entity_name Ordering_provider_last_name Ordering_provider_first_name Ordering_provider_street Ordering_provider_city Ordering_provider_state Ordering_provider_zip_code Ordering_facility_name Ordering_facility_street Ordering_facility_city Ordering_facility_state Ordering_facility_zip_code Ordering_facility_phone_number Order_result_status Date_result_released Ordered_test_code Ordered_test_description Ordered_test_code_system Test_performed_code Test_performed_description Test_performed_code_system Test_result_coded Test_result_description Test_result_code_system Test_Result_free_text Test_result_comparator Test_result_number Test_result_number_separator Test_result_number2 Test_result_units Reference_range Abnormal_flag Test_method_description Test_result_status Test_date Reporting_facility_name Reporting_facility_ID Report_facil_data_source_app csv_file_version_no

Sheet 3: ExampleData_csv_format

Testing_lab_accession_number Testing_lab_specimen_ID Submitter_unique_sample_ID Submitter_sample_ID_assigner Testing_lab_name Testing_lab_ID Testing_lab_ID_type Testing_lab_street_address Testing_lab_city Testing_lab_state Testing_lab_zip_code Patient_ID Patient_ID_assigner Patient_ID_type Patient_DOB Patient_gender Patient_race Patient_city Patient_state Patient_zip_code Patient_county Patient_ethnicity Patient_Age Illness_Onset_Date Pregnant Symptomatic_for_disease Patient_location Employed_in_high_risk_setting Public_Health_Case_ID Specimen_type_code Specimen_type_description Specimen_type_code_system Specimen_type_free_text Specimen_collection_date_time Specimen_received_date_time Ordering_entity_name Ordering_provider_last_name Ordering_provider_first_name Ordering_provider_street Ordering_provider_city Ordering_provider_state Ordering_provider_zip_code Ordering_facility_name Ordering_facility_street Ordering_facility_city Ordering_facility_state Ordering_facility_zip_code Ordering_facility_phone_number Order_result_status Date_result_released Ordered_test_code Ordered_test_description Ordered_test_code_system Test_performed_code Test_performed_description Test_performed_code_system Test_result_coded Test_result_description Test_result_code_system Test_Result_free_text Test_result_comparator Test_result_number Test_result_number_separator Test_result_number2 Test_result_units Reference_range Abnormal_flag Test_method_description Test_result_status Test_date Reporting_facility_name Reporting_facility_ID Report_facil_data_source_app csv_file_version_no
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94307-6 Probe.amp.tar.primer-probe set N1 LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0604 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94308-4 2019 Novel Coronavirus N gene LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0605 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 68993-5 Human RNase P RNA LN 260373001 Detected SCT Detected




detected N CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0606 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94309-2 2019 Novel Coronavirus RNA LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94307-6 Probe.amp.tar.primer-probe set N1 LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0604 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94308-4 2019 Novel Coronavirus N gene LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0605 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 68993-5 Human RNase P RNA LN 260373001 Detected SCT Detected




detected N CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595 100031 Arkansas Heart Hospital Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No Yes ICU No AR000002 430238007 Specimen from nasal sinus (specimen) SCT nasal swab 202002051800-0600 202002060707-0600
Everman Anna 1701 S. Shackleford Suite 203 Little Rock AR 72205 Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0606 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94309-2 2019 Novel Coronavirus RNA LN 260373001 Detected SCT Detected




not detected A CDC 2019-nCoV RT-PCR F 202002060715-0600 Public Health Laboratory, AR 04D1044169 STARLIMS.AR.STAG V2020-04-18
M00000594-999 M00000999

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No



430238007 Specimen from nasal sinus (specimen) SCT
202002051800-0600 202002060707-0600
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94307-6 Probe.amp.tar.primer-probe set N1 LN 260373001 Detected SCT Detected






PCR F 202002060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-999 M00000999

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No



430238007 Specimen from nasal sinus (specimen) SCT
202002051800-0600 202002060707-0600
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0604 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94308-4 2019 Novel Coronavirus N gene LN 260373001 Detected SCT Detected






PCR F 202002060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-999 M00000999

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No



430238007 Specimen from nasal sinus (specimen) SCT
202002051800-0600 202002060707-0600
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0605 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 68993-5 Human RNase P RNA LN 260373001 Detected SCT Detected






PCR F 202002060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-999 M00000999

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234567 STARLIMS.AR.Prod PI 19540622 Female White Indianapolis IN 46203 Marion County Hispanic or Latino 66 20200105 No



430238007 Specimen from nasal sinus (specimen) SCT
202002051800-0600 202002060707-0600
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0606 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94309-2 2019 Novel Coronavirus RNA LN 260415000 Not Detected SCT Not Detected






PCR F 202002060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234568 STARLIMS.AR.Prod PI 19640630 Male Asian Beech Grove IN 46203 Marion County Not Hispanic or Latino 56 20200331 No



258500001 Nasopharyngeal swab (specimen) SCT
20200402 20200404104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200406073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94311-8 SARS-CoV-2 N gene Ct XXX Qn NAA N1 LN




20

CrossingThreshold


F 202004060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234568 STARLIMS.AR.Prod PI 19640630 Male Asian Beech Grove IN 46203 Marion County Not Hispanic or Latino 56 20200331 No



258500001 Nasopharyngeal swab (specimen) SCT
20200402 20200404104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200318 94500-6 SARS-CoV-2 RNA Resp Ql NAA+probe LN 94500-6 SARS-CoV-2 RNA Resp Ql NAA+probe LN 419984006 Inconclusive SCT






A Cepheid Xpert Xpress SARS-CoV-2 F 20200318 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234568 STARLIMS.AR.Prod PI 19640630 Male Asian Beech Grove IN 46203 Marion County Not Hispanic or Latino 56 20200331 No



258500001 Nasopharyngeal swab (specimen) SCT
20200402 20200404104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0605 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 68993-5 Human RNase P RNA LN 260373001 Detected SCT Detected







F 202004060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-231 M00000595

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234568 STARLIMS.AR.Prod PI 19640630 Male Asian Beech Grove IN 46203 Marion County Not Hispanic or Latino 56 20200331 No



258500001 Nasopharyngeal swab (specimen) SCT
20200402 20200404104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0606 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94309-2 2019 Novel Coronavirus RNA LN 260415000 Not Detected SCT Not Detected





A Cepheid Xpert Xpress SARS-CoV-2 F 20200318 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-555 M00000795

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234569 STARLIMS.AR.Prod PI 19740630 Female Black Indianapolis IN 46203 Marion County Hispanic or Latino 46 20200315 No



430238007 Specimen from nasal sinus (specimen) SCT
20200320 20200331104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94307-6 Probe.amp.tar.primer-probe set N1 LN 260373001 Detected SCT Detected







F 202004060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-555 M00000795

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234569 STARLIMS.AR.Prod PI 19740630 Female Black Indianapolis IN 46203 Marion County Hispanic or Latino 46 20200315 No



430238007 Specimen from nasal sinus (specimen) SCT
20200320 20200331104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200206073248-0604 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94308-4 2019 Novel Coronavirus N gene LN 260373001 Detected SCT Detected





A Cepheid Xpert Xpress SARS-CoV-2 F 20200318 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-555 M00000795

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234569 STARLIMS.AR.Prod PI 19740630 Female Black Indianapolis IN 46203 Marion County Hispanic or Latino 46 20200315 No



430238007 Specimen from nasal sinus (specimen) SCT
20200320 20200331104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200406073248-0603 94306-8 2019-nCoV RNA Pnl XXX NAA+probe LN 94311-8 SARS-CoV-2 N gene Ct XXX Qn NAA N1 LN




20

CrossingThreshold


F 202004060715-0600 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18
M00000594-555 M00000795

Public Health Laboratory, AR 04D1044169 CLIA 202 South Monroe Little Rock AR 72205 234569 STARLIMS.AR.Prod PI 19740630 Female Black Indianapolis IN 46203 Marion County Hispanic or Latino 46 20200315 No



430238007 Specimen from nasal sinus (specimen) SCT
20200320 20200331104700
Everman Anna



Arkansas Heart Hospital 1701 S. Shackleford Little Rock AR 72205 501^2197386 M 20200318 94500-6 SARS-CoV-2 RNA Resp Ql NAA+probe LN 94500-6 SARS-CoV-2 RNA Resp Ql NAA+probe LN 419984006 Inconclusive SCT






A Cepheid Xpert Xpress SARS-CoV-2 F 20200318 Public Health Laboratory, AR AR.LittleRock.SPHL STARLIMS.AR.STAG V2020-04-18

Sheet 4: CDC Guidance Elements

Field Name HL7 Segment (if using HL7) Riki Notes
Sending application MSH-3 mapped to Reporting _facility_data_source_application
Sending Facility MSH-4 mapped to Reporting _facility_name and Reporting_facility_ID
Receiving Application MSH-5 no need to map for csv
Receiving Facility MSH-6 mapped to Program_or_pathogen
Date Time of Message MSH-7 mapped to Date_time_of_file_creation
Message Type MSH-9 no need to map for csv
Message Control ID MSH-10 no need to map for csv
Processing ID indicating these are production messages MSH-11 no need to map for csv
Version ID MSH-12 no need to map for csv
Patient Identifier PID 3 mapped to Patient_ID and Patient_ID_Assigner and Patient_ID_Type
Date Time of Birth PID-7 mapped to Patient_DOB
Administrative Sex PID-8 mapped to Patient_Sex
Zip Code PID-11.5 mapped to Patient_zip_code
Race PID-10 mapped to Patient_race
Ethnicity PID-22 mapped to Patient_ethnicity
County or parish PID-11.9 mapped to Patient_county
Ordering Facility Name ORC-21 mapped to Ordering_facility_name
Ordering Facility Address ORC-22 mapped to Ordering_facility_street and Ordering_facility_city and Ordering_facility_state and Ordering_facility_zipcode
Ordering Facility Phone Number ORC-23 mapped to Ordering_facility_phone_number
Ordering Provider OBR-16 mapped to Ordering_provider_last_name and Ordering_provider_first_name and Ordering_provider_ID and Ordering_provider_ID_Assigner
Ordering Provider Address ORC-24 mapped to Ordering_provider_street and Ordering_provider_city and Ordering_provider_state and Ordering_provider_zipcode
Filler Order Number / Accession number OBR-3 mapped to Testing_lab_accession_number
Ordered Test OBR-4 mapped to Ordered_test_code and Ordered_test_name and Ordered_test_code_system
Observation Date Time OBR 7 / 8 for 2.3.1
SPM 17 for ver 2.5.1
mapped to Specimen_collection_date
Specimen Type OBR-15 for ver 2.3.1 and mapped to Specimen_type_code and Specimen_type_description and Specimen_type_code_system and Specimen_type_free_text
SPM 4 for ver 2.5.1
Specimen Received date and time OBR 14 for ver 2.3.1 mapped to Specimen_received_date
SPM 18 for ver 2.5.1
Result Status indicating these are final results OBR-25 mapped to Order_result_status
Observation Result Segment Set ID OBX-1 no need to map for csv
Value Type OBX-2 no need to map for csv
Observation Identifier OBX-3 mapped to Test__performed_code and Test__performed_name and Test__performed_code_system
Observation Sub ID OBX-4 no need to map for csv???
Observation Value OBX-5 mapped to Test_Result_Coded and Test_Result_Description and Test_Result_code_system and Test_Result_Free_Text and Test_Result_Comparator and Test_Result_Number and Test_Result_Number_Separator and Test_Result_Number2
Units OBX-6 mapped to Test_units
Reference Range OBX-7 mapped to Reference_range
Abnormal flags OBX-8 mapped to Abnormal_flag
Observation Result Status OBX-11 mapped to Test_result_status
Date Time of the Observation OBX-14 - is actually OBX-19 mapped to Test_date
Performing organization name including the CLIA number OBX-23 mapped to Testing_lab_name and Testing_lab_ID and Testing_lab_ID_type
File Typeapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheet
File Modified0000-00-00
File Created0000-00-00

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