Influenza infection Primary care

Chukwuma Iwundu, Clare MacRae, Eleftheria Vasileiou

PH806 / 2230 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
    Read codes v2SNOMED CT codesCTV3 codes
    Collections
    BREATHEPhenotype Library
    Tags
    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 % (487.0, (july 2001 2004)influenza-specific 2006to 3 487.1, 487.8), <21 a actual admission age al, all and assigned at be children's code codes cohort conducted consecutive determine diagnosis diagnostic discharge during et following for had hospital hospitalizations.< hospitalized however, icd-9 in influenza influenza-related influenza-specific influenza.keren june laboratory-confirmed li may number of or patients philadelphia positive predictive rapid retrospective routine seasons sensitivity setting study substantially testing the these through trends. underestimate useful value we will with without years>
    • 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

    • Clinical Code List

    • Publication

      • 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. PH806 / 2230 - Influenza infection Primary care. Phenotype Library [Online]. 04 August 2022. Available from: http://phenotypes.healthdatagateway.org/phenotypes/PH806/version/2230/detail/. [Accessed 25 June 2024]

    • API

      To Export Phenotype Details:

      FormatAPI
      JSON site_root/api/v1/phenotypes/PH806/version/2230/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(
       'PH806',
       version_id=2230
      )

      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(
       'PH806',
       version_id=2230
      )

      To Export Phenotype Code List:

      FormatAPI
      JSON site_root/api/v1/phenotypes/PH806/version/2230/export/codes/?format=json
      CSV site_root/phenotypes/PH806/version/2230/export/codes/
      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(
       'PH806',
       version_id=2230
      )

      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(
       'PH806',
       version_id=2230
      )

    • Version History

      Version IDNameOwnerPublish date
      2230 Influenza infection Primary care zinnurar2022-08-08currently shown
      1691 Influenza infection Primary care zinnurar2022-01-17