Copy of Hemagglutination Inhibition Assay - updates from Influenza-TAUG

For SDTMIG 3.4, and using the IS domain, detailed taxonomic names can be mapped to the OI domain, thusly liberating the ISBDAGNT variable from having to house and control sub-strain level taxonomic information.

The OI example below shows how to represent two strains of Influenza virus, Influenza B virus (B/Acre/117700/2012) and Influenza A/Michigan/45/2015, at various taxonomic and non-taxonomic levels.

The IS example below shows how to represent data collected from running the Hemagglutination Inhibition Assay on Influenza A and B viruses. NHOIDs generated from the OI domain above are used in the IS dataset below to show that the following tests are performed against the two specific flu A and B strains. We are assessing whether or not the antibody would prevent influenza-driven Hemagglutination process. Note the OI dataset and NHOID are used to describe and identify fully the taxonomic classification and information about the two flu strains - so such details do not have to appear elsewhere in the IS dataset.

Questions and Concerns:

The use-case describes a seasonal influenza vaccine study conducted in healthy subjects, this means none of the subjects is presumably naturally infected by the influenza viral strains of interest in the study.

1. OI domain definition indicates that OI should be used for a bug that's been identified in a study/assay or be a known reference strain. In our use-case the influenza vaccine is a prophylactic vaccination in healthy subjects. Are the Influenza strains tested for vaccine in healthy subjects considered as "known reference strains"?
   1. Jon N: Yes, this is the correct use-case for OI and the Flu strains used in seasonal vaccines are known reference strains against which you test for vaccine immunogenicity and protective effects/strength. In this case to represent complicated taxonomic information of the strains OI dataset is recommended. NHOID is a test qualifier, it is not meant to represent a result, hence NHOID should not be created as the result of an identification test. In most studies you first identify an microorganism in an infected individual first (MB) and then create a OI dataset and NHOID for the said microorganism for subsequent testing (PF, IS, MS). Similarly for prophylactic vaccine studies you would run immunodeficiency tests against a known reference strain of bug.
2. Ine's comments: If OI doesn't work, and we don't want to control sub-strain level taxonomic INFO, can we use NSPCES from PGx and add it to the IS domain? (Note that this approach will also entail deprecation of the –NSTRN variable. –NSPCES will still be available to allow for findings based on organisms where the species name alone is sufficient, or for sorting records based on species in a co-infection study.) Variables for Identifying Pathogens
   1. Jon N: the PGx IG is being updated; both –NSTRN and –NSPCES will be deprecated in the new version of the PGx IG. They will no longer be in use for SDTM, they are still allowed in SEND. Moving forward, tests that further characterize and assess an "identified" microorganism in PF, IS MS or non-MB findings domains should use NHOID to represent the identified bug.