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Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY

Description
Descriptive analysis of the use of long-COVID codes in English primary care.
Authors
Alex J Walker, Brian MacKenna, Peter Inglesby, Laurie Tomlinson, Christopher T Rentsch, Helen J Curtis, Caroline E Morton, Jessica Morley, Amir Mehrkar, Seb Bacon, George Hickman, Chris Bates, Richard Croker, David Evans, Tom Ward, Jonathan Cockburn, Simon Davy, Krishnan Bhaskaran, Anna Schultze, Elizabeth J Williamson, William J Hulme, Helen I McDonald, Rohini Mathur, Rosalind M Eggo, Kevin Wing, Angel YS Wong, Harriet Forbes, John Tazare, John Parry, Frank Hester, Sam Harper, Shaun O’Hanlon, Alex Eavis, Richard Jarvis, Dima Avramov, Paul Griffiths, Aaron Fowles, Nasreen Parkes, Ian J Douglas, Stephen JW Evans, Liam Smeeth, Ben Goldacre and (The OpenSAFELY Collaborative)
Contact
Get in touch and tell us how you use this report or new features you'd like to see: [email protected]
First published
03 Aug 2021
Last released
17 Mar 2022
DOI
http://doi.org/10.53764/rpt.3917ab5ac5
Links

Long COVID coding in primary care.

This OpenSAFELY report is a routine update of our peer-review paper published in the British Journal of General Practice on the Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY.

It is a routine update of the analysis described in the paper. The data requires careful interpretation and there are a number of caveats. Please read the full detail about our methods and discussionis and the full analytical methods on this routine report are available on GitHub.

OpenSAFELY is a new secure analytics platform for electronic patient records built on behalf of NHS England to deliver urgent academic and operational research during the pandemic. You can read more about OpenSAFELY on our website.

Results

Counts and rates of long COVID coding stratified by demographic variable

This is equivalent to Table 2 from the paper

There were 162,881 people who have been given a diagnostic code for long COVID to date. Counts for each software system are:

TPP       40,096.0
EMIS     122,785.0
Totals   162,881.0
dtype: float64

The overall rate of long COVID coding in the population was 287.6 per 100,000 people. Rates for each software system are:

TPP      164.9
EMIS     379.9
Totals   287.6
dtype: float64
TPP EMIS Totals
Long COVID Rate per 100,000 % Long COVID Rate per 100,000 % Long COVID % Rate per 100,000
age_group 0-17 3185 65.3 7.9 11136 169.4 9.1 14321 8.8 125.1
18-24 2546 132.6 6.3 8463 321.8 6.9 11009 6.8 242.0
25-34 5747 170.5 14.3 19448 423.1 15.8 25195 15.5 316.2
35-44 8459 259.9 21.1 26725 591.5 21.8 35184 21.6 452.7
45-54 9489 290.0 23.7 27475 626.9 22.4 36964 22.7 482.9
55-69 8545 200.4 21.3 23613 429.0 19.2 32158 19.7 329.2
70-79 1627 77.0 4.1 4436 169.8 3.6 6063 3.7 128.3
80+ 498 40.4 1.2 1489 97.8 1.2 1987 1.2 72.1
sex F 25004 205.7 62.4 75759 469.9 61.7 100763 61.9 356.3
M 15092 124.2 37.6 47026 290.0 38.3 62118 38.1 219.0
region East of England 6848 120.3 17.1 6165 490.8 5.0 13013 8.0 187.3
East Midlands 5260 125.4 13.1 1809 246.1 1.5 7069 4.3 143.4
London 1616 95.5 4.0 22429 304.2 18.3 24045 14.8 265.3
North East 4103 354.3 10.2 4359 382.8 3.6 8462 5.2 368.5
North West 4504 214.0 11.2 35612 540.2 29.0 40116 24.6 461.3
South East 3594 221.4 9.0 17687 257.9 14.4 21281 13.1 250.9
South West 6003 180.6 15.0 15925 672.0 13.0 21928 13.5 385.2
West Midlands 1210 120.9 3.0 15866 326.3 12.9 17076 10.5 291.3
Yorkshire and The Humber 6951 198.1 17.3 2822 253.7 2.3 9773 6.0 211.5
imd Missing 897 151.4 2.2 310 322.2 0.3 1207 0.7 175.3
Most deprived 1 6900 141.9 17.2 26556 398.9 21.6 33456 20.5 290.4
2 7664 160.8 19.1 26134 381.6 21.3 33798 20.8 291.0
3 8288 165.1 20.7 24171 385.4 19.7 32459 19.9 287.4
4 8717 184.6 21.7 23028 377.9 18.8 31745 19.5 293.5
Least deprived 5 7630 175.6 19.0 22586 354.5 18.4 30216 18.6 282.0
ethnicity Missing 9575 143.2 23.9 34655 332.8 28.2 44230 27.2 258.7
White 26762 180.8 66.7 70019 409.8 57.0 96781 59.4 303.5
Mixed 447 139.2 1.1 2011 361.4 1.6 2458 1.5 280.1
South Asian 2290 152.5 5.7 10252 422.7 8.3 12542 7.7 319.4
Black 591 114.5 1.5 4198 370.9 3.4 4789 2.9 290.6
Other 431 90.4 1.1 1650 227.2 1.3 2081 1.3 173.0

Volume of code use in individual practices

Stratified by the electronic health record provider of the practice (TPP/SystmOne or EMIS).

Use of long COVID codes over time

Stratified by the electronic health record provider of the practice (TPP/SystmOne or EMIS). Reporting lag may affect recent dates.

This is distinct from the above table in that it counts all coded events, including where patients have been coded more than once.

There were 278,245 long COVID codes used in total. Counts for each software system were:

TPP      60,005.0
EMIS    218,240.0
Total   278,245.0
dtype: float64
TPP EMIS Total
term Total records % Total records % Total records %
1325161000000102 Post-COVID-19 syndrome 8,941.0 14.9 117,489.0 53.8 126,430.0 45.4
1325181000000106 Ongoing symptomatic disease caused by severe acute respiratory syndrome coronavirus 2 8,205.0 13.7 27,777.0 12.7 35,982.0 12.9
1325021000000106 Signposting to Your COVID Recovery 16,727.0 27.9 44,654.0 20.5 61,381.0 22.1
1325031000000108 Referral to post-COVID assessment clinic 16,881.0 28.1 20,548.0 9.4 37,429.0 13.5
1325041000000104 Referral to Your COVID Recovery rehabilitation platform 7,272.0 12.1 3,046.0 1.4 10,318.0 3.7
1325051000000101 Newcastle post-COVID syndrome Follow-up Screening Questionnaire 144.0 0.2 2,100.0 1.0 2,244.0 0.8
1325061000000103 Assessment using Newcastle post-COVID syndrome Follow-up Screening Questionnaire 78.0 0.1 866.0 0.4 944.0 0.3
1325071000000105 COVID-19 Yorkshire Rehabilitation Screening tool 699.0 1.2 478.0 0.2 1,177.0 0.4
1325081000000107 Assessment using COVID-19 Yorkshire Rehabilitation Screening tool 1,016.0 1.7 271.0 0.1 1,287.0 0.5
1325091000000109 Post-COVID-19 Functional Status Scale patient self-report 9.0 0.0 [REDACTED] [REDACTED] 9.0 0.0
1325101000000101 Assessment using Post-COVID-19 Functional Status Scale patient self-report NaN NaN 202.0 0.1 202.0 0.1
1325121000000105 Post-COVID-19 Functional Status Scale patient self-report final scale grade NaN NaN [REDACTED] [REDACTED] [REDACTED] [REDACTED]
1325131000000107 Post-COVID-19 Functional Status Scale structured interview final scale grade 0.0 0.0 10.0 0.0 10.0 0.0
1325141000000103 Assessment using Post-COVID-19 Functional Status Scale structured interview 33.0 0.1 799.0 0.4 832.0 0.3
1325151000000100 Post-COVID-19 Functional Status Scale structured interview [REDACTED] [REDACTED] [REDACTED] [REDACTED] [REDACTED] [REDACTED]

Characteristics of the cohort

This is equivalent to Table 1 in the paper

There were 56,644,992 people in the cohort in total. In practices that use TPP software, there were 24,306,447, while in practices that use EMIS software, there were 32,338,545 people.

TPP EMIS Totals
Patient count % Patient count % Patient count %
age_group 0-17 4879370 20.1 6572407 20.3 11451777 20.2
18-24 1920315 7.9 2629710 8.1 4550025 8.0
25-34 3371356 13.9 4596788 14.2 7968144 14.1
35-44 3254684 13.4 4517972 14.0 7772656 13.7
45-54 3272485 13.5 4382355 13.6 7654840 13.5
55-69 4262947 17.5 5504815 17.0 9767762 17.2
70-79 2113544 8.7 2612137 8.1 4725681 8.3
80+ 1231746 5.1 1522361 4.7 2754107 4.9
sex F 12153953 50.0 16123631 49.9 28277584 49.9
M 12152494 50.0 16214914 50.1 28367408 50.1
region East of England 5691132 23.4 1256152 3.9 6947284 12.3
East Midlands 4195792 17.3 734975 2.3 4930767 8.7
London 1691631 7.0 7371970 22.8 9063601 16.0
North East 1157909 4.8 1138644 3.5 2296553 4.1
North West 2104354 8.7 6592085 20.4 8696439 15.4
South East 1623650 6.7 6858824 21.2 8482474 15.0
South West 3323532 13.7 2369813 7.3 5693345 10.1
West Midlands 1001027 4.1 4861837 15.0 5862864 10.4
Yorkshire and The Humber 3508237 14.4 1112223 3.4 4620460 8.2
imd Missing 592434 2.4 96224 0.3 688658 1.2
Most deprived 1 4862444 20.0 6656608 20.6 11519052 20.3
2 4764715 19.6 6848561 21.2 11613276 20.5
3 5020652 20.7 6272367 19.4 11293019 19.9
4 4722234 19.4 6094347 18.8 10816581 19.1
Least deprived 5 4343968 17.9 6370438 19.7 10714406 18.9
ethnicity Missing 6685995 27.5 10414061 32.2 17100056 30.2
White 14805442 60.9 17084649 52.8 31890091 56.3
Mixed 321021 1.3 556372 1.7 877393 1.5
South Asian 1501153 6.2 2425523 7.5 3926676 6.9
Black 516160 2.1 1131851 3.5 1648011 2.9
Other 476676 2.0 726089 2.2 1202765 2.1