Monkeypox Testing LOINC-SNOMED codes

Hi all,
I have been working with CDC on the LOINC/SNOMED CTs for the PCR based test - here they all are:
Initial Test:

41853-3^Orthopoxvirus DNA [Presence] in Specimen by NAA with probe detection^LN

 

260415000^Not Detected^SCT

260373001^Detected^SCT

419984006^Inconclusive^SCT

373121007^Test not performed^SCT

 

100370-6^Orthopoxvirus DNA [Identifier] in Specimen by NAA with probe detection^LN

 

59201000284109^Presumptive positive for variola virus^SCT

59211000284106^Presumptive positive for varicella virus^SCT

59221000284102^Presumptive positive for non-variola virus^SCT

59231000284100^Presumptive positive for orthopoxvirus^SCT

59241000284107^Unable to rule out variola virus^SCT

419984006^Inconclusive^SCT

260415000^Not detected^SCT

373121007^Test not done^SCT

 

100434-0^Orthopoxvirus.non-variola DNA [Presence] in Specimen by NAA with probe detection^LN

 

260415000^Not Detected^SCT

260373001^Detected^SCT

419984006^Inconclusive^SCT

373121007^Test not performed^SCT

 

100383-9^Monkeypox virus DNA [Presence] in Specimen by NAA with probe detection^LN

 

260415000^Not Detected^SCT

260373001^Detected^SCT

419984006^Inconclusive^SCT

373121007^Test not performed^SCT

Can you share the SOPs or package inserts for the other targeted test, so I can finish putting together a guidance document with all the monkeypox related codes?
Riki

OK - so I got ahead of myself - CDC is working on an official guidance document for the PCR testing, so please for now use only these and wait for official guidance document from CDC specifically:

100434-0            Orthopoxvirus.non-variola DNA [Presence] in Specimen by NAA with probe detection      

260373001         Detected

419984006         Inconclusive

280414007         Equivocal result 

260415000         Not detected                                                                              

373121007         Test not done                                                                                                                                    

And then to cover the MPX  that was published https://www.cdc.gov/poxvirus/monkeypox/lab-personnel/index.html)

 

100383-9            Monkeypox virus DNA [Presence] in Specimen by NAA with probe detection

260373001         Detected                                                                                                    419984006         Inconclusive       

280414007         Equivocal result 

260415000         Not detected      

373121007         Test not done    

I am still looking for the SOPs for the other test types you are mentioning :)

Riki

Hi Riki!
Let us know when these codes based on the guidance are Ready!
Nancy

Will do.
Do you have any SOPs for the other test types?

Robb, there is lab guidance being created but not final yet for reporting from labs. The question of reporting lab results to CDC has been raised. Guidance not cleared yet so further info not ready to be shared.

Thanks! I thought of that after as well.

The offical CDC guidance has been posted here:
https://www.cdc.gov/poxvirus/monkeypox/lab-personnel/report-results.html?ACSTrackingID=USCDC_2146-DM85261&ACSTrackingLabel=Lab%20Advisory%3A%20CDC%20Publishes%20New%20Online%20Guidance%20on%20Orthopoxvirus%2C%20Non-Variola%20Orthopoxvirus%2C%20and%20Monkeypox%20Virus%20Test%20Result%20Rep&deliveryName=USCDC_2146-DM85261#how 
There was some discussion on the Open ELR call about not including positive / negative in the value set (as that is what is used in the package insert - however detected not detected is the preferred terminology for PCR resulting and in the SARS-CoV-2 LIVD file all positive is mapped to detected and negative is mapped to not detected) - they may update / add some guidance around that.
I will be submitting 10 PLT codes for tests performed at the CDC which are more specific target PCRs as well as Elisa for Orthopox IgG and IgM next week, hopefully in time for the next release in July.

HI Robb,
I am no longer working on LRN vocab, but I checked and the LRN messaging guide will be updated today to include the published LOINC code.  If you want to update your LRN message to use the published LOINC code, LRN will be able to support its use. 
If you are worried about the LOINC being a pre-release code - LOINC release shoudl be coming out officially in the next 2 weeks I think, if that affects your timing.

Hi - our State Lab is not going to process these under BT to expand the number of staff who can run the tests (if under BT need to have a background check), so the results would not be included in the LRN. Have we heard anything about reporting to CDC except for their RedCap? What has PHLIP said?

Note: I am opposed to adding these to CELR, but adding to GenV2 is feasible. 

Thanks!

Nancy  we are talking with CDC about that - hang tight...