Merge pull request #63 from opensafely/Add_long_covid

Add long covid

.gitignore

@@ -9,3 +9,10 @@ venv/
 .DS_Store
 .Rproj.user
 .Rhistory
+reports/variation/*
+reports/coverage/table_prop_eligible_clinc_demo.csv
+reports/coverage/mabs_and_antivirals_coverage_report.html
+reports/coverage/figures/*
+reports/coverage/tables/*
+released_outputs/reports_wip/coverage/*
+reports/coverage_wip/*

analysis/codelists.py

@@ -414,3 +414,28 @@
   first_dose_declined, second_dose_declined
 )
 
+## Long COVID (used from openprompt vaccine work https://github.com/opensafely/openprompt-vaccine-long-covid/blob/main/analysis/codelists.py)
+long_covid_nice_dx = codelist_from_csv(
+    "codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv",
+    system = "snomed",
+    column="code",
+)
+long_covid_referral_codes = codelist_from_csv(
+    "codelists/opensafely-referral-and-signposting-for-long-covid.csv",
+    system = "snomed",
+    column="code",
+)
+long_covid_assessment_codes = codelist_from_csv(
+    "codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv",
+    system = "snomed",
+    column="code",
+)
+long_covid_combine = combine_codelists(
+    long_covid_nice_dx, long_covid_referral_codes, long_covid_assessment_codes
+)
+
+long_covid_hosp = codelist_from_csv(
+    "codelists/user-hendersonad-hes-long-covid.csv",
+    system = "icd10",
+    column="code"
+)

analysis/descriptive/coverage_report_data.R

@@ -430,7 +430,7 @@ write_csv(table_elig_treat_redacted2, fs::path(output_dir, "table_elig_treat_red
 ## Clinical and demographics table
 variables <- c("ageband", "sex", "ethnicity", "imd", "rural_urban", "region_nhs", "autism_nhsd", "care_home_primis",
                "dementia_nhsd", "learning_disability_primis", "serious_mental_illness_nhsd", 
-               "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd", "vaccination_status")
+               "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd", "long_covid", "vaccination_status")
 
 table_demo_clinc_breakdown_base <- data_processed_clean %>%
   select(all_of(variables)) %>%

analysis/process/process_data.R

@@ -120,7 +120,8 @@ data_extract0 <- read_csv(
     serious_mental_illness_nhsd = col_logical(),
     sickle_cell_disease_nhsd = col_date(format = "%Y-%m-%d"),
     vaccination_status = col_character(),
-
+    first_lc_code_date = col_date(format = "%Y-%m-%d"),
+
     # COVID VARIENT
     sgtf = col_character(),
     sgtf_first = col_character(),
@@ -209,6 +210,9 @@ data_processed <- data_extract %>%
 
     ## Convert sickle cell disease from date
     sickle_cell_disease_nhsd = ifelse(!is.na(sickle_cell_disease_nhsd), 1, 0),
+
+    ## Long COVID
+    long_covid = ifelse(!is.na(first_lc_code_date), 1, 0),
 
     # Combine subgoups of rare neurological conditions cohort
     rare_neurological_conditions_nhsd =  pmin(multiple_sclerosis_nhsd, motor_neurone_disease_nhsd, myasthenia_gravis_nhsd,
@@ -568,7 +572,7 @@ data_processed_clean <- data_processed_combined %>%
 
     # Clinical groups
     autism_nhsd, care_home_primis, dementia_nhsd, housebound_opensafely, learning_disability_primis, shielded_primis, 
-    serious_mental_illness_nhsd, sickle_cell_disease_nhsd, vaccination_status,
+    serious_mental_illness_nhsd, sickle_cell_disease_nhsd, long_covid, vaccination_status,
 
     # COVID variant
     sgtf, sgtf_first, variant,

analysis/study_definition.py

@@ -1391,6 +1391,34 @@
   ),
 
 
+
+  # # Long COVID
+
+  first_lc_dx_flag = patients.with_these_clinical_events(
+      long_covid_nice_dx,
+      on_or_before = "date_treated",
+      returning = "code",
+      include_date_of_match = True,
+      return_first_date_in_period = True,
+      date_format = "YYYY-MM-DD",
+      return_expectations = {"incidence": 0.1},
+      ),
+
+  first_lc_dxrx_flag = patients.with_these_clinical_events(
+      long_covid_combine,
+      on_or_before = "date_treated",
+      returning = "binary _flag",
+      include_date_of_match = True,
+      return_first_date_in_period = True,
+      date_format = "YYYY-MM-DD",
+      return_expectations = {"incidence": 0.1},
+      ),  
+
+  first_lc_code_date = patients.minimum_of(
+    "first_lc_dx_flag_date","first_lc_dxrx_flag_date"
+    ),
+
+
 
   # CLINICAL CO-MORBIDITIES TBC ----
 

codelists/codelists.json

@@ -129,7 +129,7 @@
     "nhsd-immunosuppresant-drugs-pra-dmd.csv": {
       "id": "nhsd/immunosuppresant-drugs-pra-dmd/526d9f5f",
       "url": "https://www.opencodelists.org/codelist/nhsd/immunosuppresant-drugs-pra-dmd/526d9f5f/",
-      "downloaded_at": "2024-02-14 13:10:23.166362Z",
+      "downloaded_at": "2024-03-05 16:43:26.365935Z",
       "sha": "b86c1ff06c9208851b40b668fc846e25ccabcbb1"
     },
     "nhsd-immunosuppresant-drugs-pra-snomed.csv": {
@@ -141,7 +141,7 @@
     "nhsd-oral-steroid-drugs-pra-dmd.csv": {
       "id": "nhsd/oral-steroid-drugs-pra-dmd/44292c02",
       "url": "https://www.opencodelists.org/codelist/nhsd/oral-steroid-drugs-pra-dmd/44292c02/",
-      "downloaded_at": "2024-02-14 13:10:23.423657Z",
+      "downloaded_at": "2024-03-05 16:43:26.614328Z",
       "sha": "c0008e3734ad82744e3643d4a0f692d76a70085f"
     },
     "nhsd-oral-steroid-drugs-snomed.csv": {
@@ -285,7 +285,7 @@
     "primis-covid19-vacc-uptake-eth2001.csv": {
       "id": "primis-covid19-vacc-uptake/eth2001/v1",
       "url": "https://www.opencodelists.org/codelist/primis-covid19-vacc-uptake/eth2001/v1/",
-      "downloaded_at": "2024-02-14 13:10:26.407595Z",
+      "downloaded_at": "2024-03-05 16:43:29.656369Z",
       "sha": "2ff9aea91a05f41fe911a885eee50d2494247d58"
     },
     "nhsd-primary-care-domain-refsets-autism_cod.csv": {
@@ -353,6 +353,30 @@
       "url": "https://www.opencodelists.org/codelist/opensafely/covid-19-vaccination-second-dose-declined/27d8bb36/",
       "downloaded_at": "2022-02-16 16:33:44.441520Z",
       "sha": "5f79648b7682f0fc85eb0c47c1da6dc180c5a89d"
+    },
+    "opensafely-nice-managing-the-long-term-effects-of-covid-19.csv": {
+      "id": "opensafely/nice-managing-the-long-term-effects-of-covid-19/64f1ae69",
+      "url": "https://www.opencodelists.org/codelist/opensafely/nice-managing-the-long-term-effects-of-covid-19/64f1ae69/",
+      "downloaded_at": "2024-03-05 16:43:31.119028Z",
+      "sha": "8ba3006b5e3d054bbc6ed1861d08fdc682a52a31"
+    },
+    "opensafely-referral-and-signposting-for-long-covid.csv": {
+      "id": "opensafely/referral-and-signposting-for-long-covid/12d06dc0",
+      "url": "https://www.opencodelists.org/codelist/opensafely/referral-and-signposting-for-long-covid/12d06dc0/",
+      "downloaded_at": "2024-03-05 16:43:31.254016Z",
+      "sha": "4574b35cc14eee04bd149d0226f1dae0dfadcb3e"
+    },
+    "opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv": {
+      "id": "opensafely/assessment-instruments-and-outcome-measures-for-long-covid/79c0fa8a",
+      "url": "https://www.opencodelists.org/codelist/opensafely/assessment-instruments-and-outcome-measures-for-long-covid/79c0fa8a/",
+      "downloaded_at": "2024-03-05 16:43:31.367401Z",
+      "sha": "f09228d28e9a43ea823b4570e7d82ff3714a0010"
+    },
+    "user-hendersonad-hes-long-covid.csv": {
+      "id": "user/hendersonad/hes-long-covid/7565af4d",
+      "url": "https://www.opencodelists.org/codelist/user/hendersonad/hes-long-covid/7565af4d/",
+      "downloaded_at": "2024-03-05 16:43:31.490204Z",
+      "sha": "49812e5b946cd87c1a84a293e11a2f01a4d7a233"
     }
   }
 }

codelists/codelists.txt

@@ -57,4 +57,8 @@ primis-covid19-vacc-uptake/nonshield/v1
 nhsd-primary-care-domain-refsets/mh_cod/20210127
 opensafely/covid-19-vaccination-first-dose-declined/0c16880b
 opensafely/covid-19-vaccination-second-dose-declined/27d8bb36
+opensafely/nice-managing-the-long-term-effects-of-covid-19/64f1ae69
+opensafely/referral-and-signposting-for-long-covid/12d06dc0
+opensafely/assessment-instruments-and-outcome-measures-for-long-covid/79c0fa8a
+user/hendersonad/hes-long-covid/7565af4d
 

codelists/opensafely-assessment-instruments-and-outcome-measures-for-long-covid.csv

@@ -0,0 +1,11 @@
+code,term
+1325051000000101,Newcastle post-COVID syndrome Follow-up Screening Questionnaire
+1325061000000103,Assessment using Newcastle post-COVID syndrome Follow-up Screening Questionnaire
+1325071000000105,COVID-19 Yorkshire Rehabilitation Screening tool
+1325081000000107,Assessment using COVID-19 Yorkshire Rehabilitation Screening tool
+1325091000000109,Post-COVID-19 Functional Status Scale patient self-report
+1325101000000101,Assessment using Post-COVID-19 Functional Status Scale patient self-report
+1325121000000105,Post-COVID-19 Functional Status Scale patient self-report final scale grade
+1325131000000107,Post-COVID-19 Functional Status Scale structured interview final scale grade
+1325141000000103,Assessment using Post-COVID-19 Functional Status Scale structured interview
+1325151000000100,Post-COVID-19 Functional Status Scale structured interview

codelists/opensafely-nice-managing-the-long-term-effects-of-covid-19.csv

@@ -0,0 +1,3 @@
+code,term
+1325161000000102,Post-COVID-19 syndrome
+1325181000000106,Ongoing symptomatic disease caused by severe acute respiratory syndrome coronavirus 2

codelists/opensafely-referral-and-signposting-for-long-covid.csv

@@ -0,0 +1,4 @@
+code,term
+1325021000000106,Signposting to Your COVID Recovery
+1325031000000108,Referral to post-COVID assessment clinic
+1325041000000104,Referral to Your COVID Recovery rehabilitation platform

codelists/user-hendersonad-hes-long-covid.csv

@@ -0,0 +1,4 @@
+code,term
+B948,Sequelae of other specified infectious and parasitic diseases
+U09,Post COVID-19 condition
+U099,"Post COVID-19 condition, unspecified"

reports/coverage/mabs_and_antivirals_coverage_report.Rmd

@@ -50,13 +50,15 @@ library(magick)
 source(here("analysis", "lib", "custom_functions.R"))
 
 # Input directory ----
+
 input_dir_os <- here("released_outputs", "reports", "coverage")
 #input_dir_os <- here("output", "coverage")
 
 # Output directory ----
 output_dir_rmd <- here("reports", "coverage")
 fs::dir_create(output_dir_rmd)
 
+
 # Import data ----
 report_stats <- read_csv(fs::path(input_dir_os, "table_report_stats_redacted.csv"))
 flowchart_non_elig <- read_csv(fs::path(input_dir_os, "table_non_elig_flowchart_redacted.csv")) 
@@ -524,9 +526,9 @@ table_demo_clinc_breakdown_redacted <-
   mutate(Group = factor(Group, 
                         levels = c("All", "ageband", "sex", "ethnicity", "imd", "rural_urban", "region_nhs", "autism_nhsd", "care_home_primis",
                                    "dementia_nhsd", "learning_disability_primis", "serious_mental_illness_nhsd", 
-                                   "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd", "vaccination_status"),
+                                   "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd", "long_covid", "vaccination_status"),
                         labels = c("All", "Age band", "Sex", "Ethnicity", "IMD", "Rurality", "Region", "Autism", "Care home", "Dementia",
-                                   "Learning disability ", "Serious mental illness", "Housebound", "CEV", "Sickle cell disease",
+                                   "Learning disability ", "Serious mental illness", "Housebound", "CEV", "Sickle cell disease", "Long COVID",
                                    "Vaccination status")),
          Variable = factor(Variable, 
                            levels = c("-", "12-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80+", 
@@ -539,7 +541,7 @@ table_demo_clinc_breakdown_redacted <-
                                       "South West", "West Midlands", "Yorkshire and the Humber",
                                       "autism_nhsd", "care_home_primis",
                                       "dementia_nhsd", "learning_disability_primis", "serious_mental_illness_nhsd", 
-                                      "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd",
+                                      "housebound_opensafely", "shielded_primis", "sickle_cell_disease_nhsd", "long_covid",
                                       "Un-vaccinated (declined)", "Un-vaccinated" , "One vaccination", "Two vaccinations", 
                                       "Three or more vaccinations", "Unknown"),
                            labels = c("-", "12-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80+", 
@@ -551,7 +553,7 @@ table_demo_clinc_breakdown_redacted <-
                                       "East Midlands", "East of England", "London", "North East", "North West", "South East",
                                       "South West", "West Midlands", "Yorkshire and the Humber",
                                       "Autism", "Care home", "Dementia", "Learning disability ", "Serious mental illness",
-                                      "Housebound", "CEV", "Sickle cell disease",
+                                      "Housebound", "CEV", "Sickle cell disease", "Long COVID", 
                                       "Un-vaccinated (declined)", "Un-vaccinated" , "One vaccination", "Two vaccinations", 
                                       "Three or more vaccinations", "Unknown")))  %>%
   arrange(Group, Variable) %>%