Influenza infection Secondary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

PH807 / 2231 Clinical-Coded Phenotype

  1. Overview

    Phenotype Type
    Disease or syndrome
    Sex
    Both
    Valid Event Date Range
    01/01/2001 to 31/01/2021
    Coding System
    ICD10 codesICD9 codesICD11 codes
    Data Sources
    Hospital Episode Statistics Admitted Patient Care
    Civil Registration - Deaths
    Annual District Death Extract
    Patient Episode Dataset for Wales
    Collections
    BREATHEPhenotype Library
    Tags
    No data
    Ontology
    No data

  2. Definition

    • Not found code search
    • Wabe et al, 2021The aim of the study was to evaluate the accuracy of assigned International Classification of Diseases version 10-Australian Modification (ICD-10-AM) codes for influenza by comparing with patients’ results of their polymerase chain reaction (PCR)-based laboratory tests.Although ICD-10-AM coding for influenza demonstrated high accuracy when laboratory results were received before discharge, its sensitivity was substantially lower for patients whose test results were not available at discharge. The timely availability of laboratory test results during the episode of care could contribute to improved coding accuracy.The timely availability of laboratory test results during the episode of care could contribute to improved coding accuracy.Feemster et al, 2012We used Pediatric Health Information System data and laboratory records from 3 children's hospitals to determine whether administrative data accurately identify children with laboratory-confirmed influenza.The objective of this multicenter study was to validate influenza-specific ICD-9 codes for the identification of influenza cases among hospitalized childrenAmong 23 282 inpatients, diagnosis codes for influenza detected 73% of laboratory-confirmed influenza cases, whereas <1% of patients without a diagnosis code had laboratory-confirmed influenza.Keren et al, 2006To determine the sensitivity and positive predictive value of influenza-specific ICD-9 admission or discharge codes (487.0, 487.1, and 487.8), we conducted a retrospective cohort study of all patients <21 years of age hospitalized at the Children's Hospital of Philadelphia with laboratory-confirmed influenza during 3 consecutive influenza seasons (July 2001 through June 2004)Influenza-specific ICD-9 codes assigned in a setting of routine rapid diagnostic testing may be useful for following trends. However, these codes will substantially underestimate the actual number of influenza-related hospitalizations.

  3. Implementation

    Implementation

    These codes are not intended to be mandatory, but are to be used as a starting point for the identification of influenza infection in routine Electronic Health Record (EHR). Each study may differ in the sensitivity and specificity of the coding required.

    According to the National Health Service (NHS), Influenza is a common infectious viral illness spread by coughs and sneezes. Some of the main symptoms of influenza include: high temperature (fever) of 38C or above, tiredness and weakness, headache, general aches and pains and dry or chesty cough. Cold-like symptoms, such as a blocked or runny nose, sneezing, and a sore throat, can also be caused by influenza, but they tend to be less severe than the other symptoms.

    https://www.nhsinform.scot/illnesses-and-conditions/infections-and-poisoning/flu

    According to the National Institute for Health and Care Excellence (NICE) guidelines, Influenza is an acute respiratory illness caused by RNA viruses f the family Orthomyxoviridae (influenza viruses). There are three types of influenza virus: Influenza A occurs more frequently and is more virulent. It is responsible for local outbreaks, larger epidemics and pandemics. Influenza B often co-circulates with influenza A during the yearly outbreaks. Generally, influenza B causes less severe clinical illness, although it can still be responsible for outbreaks. Influenza C usually causes a mild or asymptomatic infection similar to the common cold.

    Influenza presents with symptoms appearing around 2 days after exposure. Uncomplicated influenza signs and symptoms include: coryza, nasal discharge, cough, fever, gastrointestinal symptoms, headache, malaise, myalgia, arthralgia, ocular symptoms, and sore throat. Complicated influenza is defined by signs and symptoms that: require hospital admission, involve the lower respiratory tract, central nervous system, or cause significant exacerbation of an underlying medical condition.

    https://cks.nice.org.uk/topics/influenza-seasonal/

    Not found code search

  4. Clinical Code List

  5. Publication

    Related publications

    • Publications in 2020-2021 identified in PubMed

    • Moss JWE, Davidson C, Mattock R, Gibbons I, Mealing S, Carroll S. Quantifying the direct secondary health care cost of seasonal influenza in England. BMC Public Health. 2020 Sep 29;20(1):1464. doi: 10.1186/s12889-020-09553-0. PMID: 32993588; PMCID: PMC7526100.

      (DOI: 10.1186/s12889-020-09553-0)

    • Ramsay J, Minton J, Fischbacher C, Fenton L, Kaye-Bardgett M, Wyper GMA, Richardson E, McCartney G. How have changes in death by cause and age group contributed to the recent stalling of life expectancy gains in Scotland? Comparative decomposition analysis of mortality data, 2000-2002 to 2015-2017. BMJ Open. 2020 Oct 7;10(10):e036529. doi: 10.1136/bmjopen-2019-036529. PMID: 33033012; PMCID: PMC7542937.

      (DOI: 10.1136/bmjopen-2019-036529)

    • Wabe N, Li L, Lindeman R, Post JJ, Dahm MR, Li J, Westbrook JI, Georgiou A. Evaluation of the accuracy of diagnostic coding for influenza compared to laboratory results: the availability of test results before hospital discharge facilitates improved coding accuracy. BMC Med Inform Decis Mak. 2021 May 22;21(1):168. doi: 10.1186/s12911-021-01531-9. PMID: 34022851; PMCID: PMC8141245.

      (DOI: 10.1186/s12911-021-01531-9)

    • Fitzpatrick T, Malcolm W, McMenamin J, Reynolds A, Guttmann A, Hardelid P. Community-Based Antibiotic Prescribing Attributable to Respiratory Syncytial Virus and Other Common Respiratory Viruses in Young Children: A Population-Based Time-series Study of Scottish Children. Clin Infect Dis. 2021 Jun 15;72(12):2144-2153. doi: 10.1093/cid/ciaa403. PMID: 32270199.

      (DOI: 10.1093/cid/ciaa403)

    • Code repositories

    • ID- 1 - Repository- Manchester Clinical Codes - Description- Trends in antibiotic prescribing in primary care for clinical syndromes subject to national recommendations to reduce antibiotic resistance, UK 1995-2011: analysis of a large database of primary care consultations - Conditions- URTI - Publication- https://doi.org/10.1093/jac/dku291 - Clinical codes- Read Version 2

      (DOI: 10.1093/jac/dku291)

    • ID- 2 - Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Infections of other or unspecified organs - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI: 10.1016/S2589-7500(19)30012-3)

    • ID- 3 - Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Lower respiratory tract infections - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI: 10.1016/S2589-7500(19)30012-3)

    • ID- 4 - Repository- HDR UK National Phenomics Resource Project - Description- A chronological map of 308 physical and mental health conditions from 4 million individuals in the English National Health Service - Conditions- Viral diseases (excl chronic hepatitis/HIV) - Publication- https://doi.org/10.1016/S2589-7500(19)30012-3 - Clinical codes- ICD-10

      (DOI: 10.1016/S2589-7500(19)30012-3)

    • ID- 5 - Repository- HDR UK National Phenomics Resource Project - Description- Incidence of Community-Acquired Lower Respiratory Tract Infections and Pneumonia among Older Adults in the United Kingdom: A Population-Based Study - Conditions- Pneumonia - Publication- https://doi.org/10.1371/journal.pone.0075131 - Clinical codes- ICD-10

      (DOI: 10.1371/journal.pone.0075131)

    • ID- 6 - Repository- OpenSAFELY - Description- Codes indicating a diagnosis of influenza or influenza-like illness - Conditions- Documented influenza illness - Publication- - Clinical codes- CTV3 (Read V3) with TPP extensions

    • ID- 7 - Repository- OpenSAFELY - Description- Codes indicating a diagnosis of a lower respiratory tract infection excluding pneumonia - Conditions- Lower respiratory tract infection - Publication- - Clinical codes- CTV3 (Read V3) with TPP extensions

    • ID- 8 - Repository- OpenSAFELY - Description- Pneumonia ICD-10 codes - Conditions- Pneumonia secondary care - Publication- - Clinical codes- ICD-10

    • ID- 9 - Repository- LSHTM Data Compass - Description- Code list: ICD-10 codes for pneumonia - Conditions- Pneumonia - Publication- https://doi.org/10.17037/DATA.00000847 - Clinical codes- ICD-10

      (DOI: 10.17037/DATA.00000847)

    • ID- 10 - Repository- LSHTM Data Compass - Description- Clinical codelist: Read codes and terms used for pneumonia (CPRD) - Conditions- Pneumonia - Publication- https://doi.org/10.17037/DATA.00001654 - Clinical codes- Medcodes

      (DOI: 10.17037/DATA.00001654)

    Citation Example

    Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou. PH807 / 2231 - Influenza infection Secondary care. Phenotype Library [Online]. 04 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH807/version/2231/detail/. [Accessed 15 February 2025]

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH807/version/2231/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH807',
     version_id=2231
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_detail(
     'PH807',
     version_id=2231
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH807/version/2231/export/codes/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH807',
     version_id=2231
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH807',
     version_id=2231
    )

  7. Version History

    Version IDNameOwnerPublish date
    Influenza infection Secondary care zinnurar2022-08-08 14:14
    1693 Influenza infection Secondary care zinnurar2022-01-17 14:47