Consider addition of pathogen type/strain/subtype

[sadiekelly]

ISARIC Core CRF captures serology or genomic results indicating the type of pathogen. For example Influenza A/H3N2, Dengue DENV1, Hepatitis type B. WHO T0 form indicates collection of pathogenic agent, strain and subtype as appropriate.
Would it be useful to add this, in addition to the more general pathogen_type variable, to indicate any serology results that are indicated in the source data?
Genomic clade is captured in a separate variable in the G.h schema.

[sadiekelly]

The existing variable 'pathogen' is a constant pre-filled value for the high level name of the pathogen of interest e.g. Hepatitis.
Additional variable(s) can be added to capture types as identified from testing e.g. Hepatitis type A | Hepatitis type B. To be determined for each pathogen type and a dictionary list created. New types may need to be captured as an 'other' free text field initially and coded post data collection.

[abhidg]

@sadiekelly taking a look at ICD-11 for this, https://icd.who.int, seems to have the use cases we are thinking of, including major variants of COVID-19, Influenza A subtypes and many other diseases. ICD is for diseases, so may need a subclass for pathogen only

[sadiekelly]

If strain is not known (or not provided in the source) but strain is indicated to be not the same as another known strain, is this important to capture in the linelist? Using this source for Aus H5N1 as an example; "Whilst the Victorian case is HPAI (H5N1), it is not the same as the strains that have caused these outbreaks in the United States of America".

https://www.health.vic.gov.au/health-advisories/human-case-of-avian-influenza-bird-flu-detected-in-returned-traveller-to-victoria

[sadiekelly]

Additionally is it important to capture record of mutations;

https://www.cdc.gov/flu/avianflu/spotlights/2023-2024/h5n1-technical-update-may-24-2024.html

[sadiekelly]

Recommendation: capture available pathogen type, strain, subtype as separate variables, that can be coded using ICD-11 codelists.