‹ Home
Exported

CSTE National ELR Workgroup

Welcome to the CSTE National ELR Workgroup Basecamp! We hope you will utilize the space to share resources with colleagues, start discussion threads, and identify topics for the workgroup to tackle on future calls. All workgroup members will have the opportunity to join. Please note that you may edit your notification preferences to suit your needs (and your email inbox). If you are not already on the ELR distribution list and would like to receive call communications, please enroll using this subscription form (copy and paste in browser): https://app.smartsheet.com/b/form/5a91a4579952496682084796b82112e6
Becky Lampkins, Manager, Surveillance/Informatics Program at CSTEMegan Toe, CSTEScott Troppy, Surveillance Epidemiologist at MA DPHMeredith Lichtenstein, CSTEAmy Drake, NMJohn RobertsNancy Barrett, Epi 4/PH Informatics SpecialistErin Holt, TDHRita Altamore, EpidemiologistDavid DiCesareJason HallWalter Kemper, ELR Coordinator, NC DHHS Div of Public HealthJulie LuepkeCarmen Pugh, Labcorp Manager State Reporting at LabCorpTom Safranek +399 others
Posted by Keilina ·

MonkeyPox Sequencing Standard Codes?

Hello,

We have a submitter in LA County running MP Sequencing. Would any jurisdictions know if there are standard codes or preliminary standard codes floating around? The results may be in 3 parts. 

  1. Clade
  2. Linage
  3. GISAID

Thank you, 
Keilina

Comments & Events

Riki Merrick, Terminologist at APHL Riki Merrick, Terminologist at APHL
I am working on that LOINC submission for sequencing - if someone has a de-identified example report I can submit, I can finish that off next week (and request an emergency use label, so we can get it back faster).

LOINC for GISIAD: https://loinc.org/96766-1/

Riki
Notified 295 people
Hyung-Suk "Sue" Lee Hyung-Suk "Sue" Lee
Hi Riki,
Here is the example from LA County Public Health Lab on how they want to report Monkeypox Sequencing data so was inquiring the specific LOINC codes to be used. Would you be able to assist on this? Ashu from LAC PHL sent the reply email with the example to me and cc’d you as I sent your message from CSTE Basecamp to him earlier, but I’m also sending his message to you again.

Hi all,

Below is an example on how PHL would like to report the Monkeypox Whole Genome Sequencing. PHL needs the LOINC codes for the following ASAP to implement this test.


1) Clade

2) Linage

3) GISAID

[cid:image001.png@01D8D7CA.CD8AF030]

Thank you.

Ashutosh (Ashu) Ruparelia MT (ASCP), CLS
Principal Information System Analyst
Los Angeles Public Health Laboratory IT
CoPath (Anatomic Pathology) Consultant
Office: (562) 658-1349

Thank you in advance for your help!

Sue


Hyung-Suk "Sue" Lee, CLS, MT (ASCP)
ELR Project Manager
Acute Communicable Disease Control (ACDC) Program
Los Angeles County Department of Public Health
(213) 288-7206
hylee@ph.lacounty.gov<mailto:hylee@ph.lacounty.gov>
~WRD0000.jpg 823 Bytes • Download

image001.png 58.8 KB • Download
Notified 295 people
Riki Merrick, Terminologist at APHL Riki Merrick, Terminologist at APHL
I should be able to share the LOINCs for all of these tomorrow by EOD :)

Do you want / need codes for the Clades and lineages, or is free text good enough at the moment - the scale for these tests is nominal (based on the fact that there will alwyas be a limited set). If so, I will create them in the APHL SNOMED CT extension, as SNOMED is not eager to get those as submissions at the moment.
Notified 295 people
Hyung-Suk "Sue" Lee Hyung-Suk "Sue" Lee
Hi Riki,
Thank you so much for your prompt actions and updates! We are looking forward to getting the new LOINCs soon.

For your other questions on whether to use free text or SNOMED CT for Clades, Lineage, GISAID, I’ll need to check with Ashu at LAC PH Lab as I’m not exactly sure how they would be built in their lab system. I’ll get back to you on that later.

Thanks,
Sue


Hyung-Suk "Sue" Lee, CLS, MT (ASCP)
ELR Project Manager
Acute Communicable Disease Control (ACDC) Program
Los Angeles County Department of Public Health
(213) 288-7206
hylee@ph.lacounty.gov<mailto:hylee@ph.lacounty.gov>
~WRD0002.jpg 823 Bytes • Download
Notified 295 people
Riki Merrick, Terminologist at APHL Riki Merrick, Terminologist at APHL
Here is the LIVD file for this – I am not sure what to put for manufacturer and model, so I put LDT.
I listed the ABI 7500 Fast DX as the instrument (using its UDI), but if there are other instruments that can be used, we can add more rows.
The GISAID and the Genbank ID both don’t need to be included with the results, but one of them probably should. If there are other Sequence ID record locators that we should add, let me know.
 
The Publication tab has a link to the CDC webpage where the LIVD file for the FDA approved MPX tests will be hosted, but it is NOT yet up.
 
Notified 294 people
Hyung-Suk "Sue" Lee Hyung-Suk "Sue" Lee
Thanks so much Riki for sharing the LOINC codes for MPX Genome Sequencing tests with us! I’m relaying your message with LOINCs to the LAC PHL as well as CDPH ELR/MPX team for their information.

Best,
Sue
~WRD0000.jpg 823 Bytes • Download
Notified 294 people