opensafely / disparities-comparison

Repository for OpenSAFELY project comparing disparities between RSV, Influenza and COVID-19
MIT License
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Outcome Phenotypes #1

Open emprestige opened 2 months ago

emprestige commented 2 months ago

Maximally Specific

Mild RSV

Severe RSV

At least one ICD-10 diagnosis code for RSV or bronchiolitis in the first or second position in the HES APC (codelist)

Maximally Sensitive

Mild RSV

Inclusion Criteria

Exclusion Criteria

Diagnosis code in SNOMED CT for influenza, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, bronchitis, sinusitis, tonsillitis, laryngitis, pertussis, or coronavirus, including COVID-19, within the one-month period (±) of respiratory symptoms or receipt of a relevant prescription as noted in the inclusion criteria above (codelist)

Severe RSV

Inclusion Criteria

Exclusion Criteria

ICD-10 diagnosis code in any position in HES APC for influenza, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, bronchitis, sinusitis, tonsillitis, laryngitis, pertussis, or coronavirus, including COVID-19, within the one-month period (±) of respiratory symptoms (codelist)

Maximally Specific

Mild Influenza

At least one SNOMED CT code for influenza (codelist)

Severe Influenza

At least one ICD-10 diagnosis code for influenza in the first or second position in the HES APC (codelist)

Maximally Sensitive

Mild Influenza

Inclusion Criteria

Exclusion Criteria

Diagnosis code in SNOMED CT for RSV, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, tonsillitis, pertussis, or coronavirus, including COVID-19, within the one-month period (±) of respiratory symptoms or receipt of a relevant prescription as noted in the inclusion criteria above (codelist)

Severe Influenza

Inclusion Criteria

Exclusion Criteria

ICD-10 diagnosis code in any position in HES APC for RSV, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, tonsillitis, pertussis, or coronavirus, including COVID-19, within the one-month period (±) of respiratory symptoms (codelist)

Maximally Specific

Mild COVID-19

At least one SNOMED CT code for COVID-19 (codelist)

Severe COVID-19

At least one ICD-10 diagnosis code for COVID-19 in the first or second position in the HES APC (codelist)

Maximally Sensitive

Mild COVID-19

Inclusion Criteria

Exclusion Criteria

Diagnosis code in SNOMED CT for RSV, influenza, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, bronchitis, sinusitis, tonsillitis, pertussis, laryngitis, or specific coronavirus strains which are not COVID-19 within the one-month period (±) of respiratory symptoms or receipt of a relevant prescription as noted in the inclusion criteria above (codelist)

Severe COVID-19

Inclusion Criteria

Exclusion Criteria

ICD-10 diagnosis code in any position in HES APC for RSV, influenza, pneumonia, human metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia, bronchitis, sinusitis, tonsillitis, pertussis, laryngitis, or specific coronavirus strains which are not COVID-19 within the one-month period (±) of respiratory symptoms (codelist)

Maximally Sensitive

Mild Overall Respiratory Virus

Inclusion Criteria

Exclusion Criteria

Diagnosis code in SNOMED CT for metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia or pertussis within the one-month period (±) of respiratory symptoms (codelist)

Severe Overall Respiratory Virus

Inclusion Criteria

Exclusion Criteria

ICD-10 diagnosis code in any position in HES APC for metapneumovirus, rhinovirus, adenovirus, parainfluenza, enterovirus, mycoplasma pneumonia or pertussis within the one-month period (±) of respiratory symptoms (codelist)

emprestige commented 2 months ago

edited to add clarity of diagnosis positions for emergency admissions and exclusion criteria

emprestige commented 2 months ago

edited to change definition of influenza-like-illness for Maximally Sensitive Mild Influenza definition - presence of code from cough codelist no longer required

emprestige commented 1 month ago

edited to add detail to maximally sensitive phenotypes for RSV, flu, and COVID-19