Sequencing Pathogens

I am getting more and more questions about sequencing of pathogen genomes. Most of existing LOINC content in this area is for identification of pathogens using molecular tools like PCR. But, especially in influenza, we are seeing more and more sophisticated analysis of the pathogens’ sequences analogous to what is included in the tests under the “Molecular genetics” method.

Two specific examples that I’ll describe in general terms:

I’m submitting a viral transport medium with influenza virus. Please use the viral genetic sequence to return a report on the specific taxonomy of this isolate.

I’m submitting a viral transport medium with influenza virus. Please sequence the M segment, put the sequence in GenBank and return its accession number as the “result” of this test.

I keep getting pointed to various LOINC codes that sound like these but have at least one part that isn’t right.

Can anyone point me in the right direction?

It is possible that LOINC does not have existing codes for the examples you provided. Without additional testing information, it is difficult to give more direction. We welcome submissions for new term requests (see With the submission, feel free to propose what you think should be included in the six parts (Component, Property, Timing, System, Scale and Method) of the LOINC term. Package insert (test kit information), test descriptions/significance of testing, and example results/reports are often necessary for the creation of a term.