BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment

Descriptive analyses

Periods

Different time periods are specified for the analysis:

  • The data extraction period: Data extraction is foreseen from the first date of a documented SARS-CoV-2 infection in the population until the most recent date at which data is available at the time of analysis. All individuals vaccinated with at least one dose of the SARS-CoV-2 vaccine (any of the available brands) and all individuals eligible to be vaccinated with a documented positive diagnosis (irrespective of the type of test) for SARS-CoV-2 infection during the data extraction period are included in the study population.
  • The enrollment period: A sequence of nested (daily) trials are emulated with increasing time (t1, t2, …, tn), iterating over the days in the enrollment period. At each eligible time during the enrollment period, the vaccination status of eligible individuals is assessed and every individual who has completed a primary vaccination schedule at that time (treated/exposed) is matched to an individual who has not (yet) completed the primary vaccination schedule (control).
  • The study period: The study period is considered from the start of the enrollment period until one year after the end of the enrollment period, to allow a minimal possible follow-up period of one year.
Period Time range
Data extraction period 2020-03-05 - 2022-05-20
Enrollment period 2021-01-01 - 2021-08-31
Study period 2021-01-01 - 2022-08-31

Study population and enrollment

A flow diagram displaying the process of obtaining a matched study population considered for survival analysis.

Description of the study population: table 1

Table 1
Intervention group (Completed a primary vaccination schedule)
(N=8378)
Control group (Not completed a primary vaccination schedule)
(N=949)
P-value

ᵃ5-year age groups

sex_cd
Mean (SD) 1.47 (0.537) 1.48 (0.541) 0.356
Median [Min, Max] 1.00 [0, 2.00] 2.00 [0, 2.00]
age_cdᵃ
Mean (SD) 11.6 (2.96) 11.6 (3.00) 0.914
Median [Min, Max] 12.0 [2.00, 18.0] 12.0 [2.00, 18.0]
residence_area_cd
731 1170 (14.0%) 139 (14.6%) 0.574
732 1182 (14.1%) 123 (13.0%)
733 6026 (71.9%) 687 (72.4%)
institutionalized_bl
Yes 233 (2.8%) 28 (3.0%) 0.845
No 8145 (97.2%) 921 (97.0%)
foreign_bl
Yes 1271 (15.2%) 123 (13.0%) 0.0782
No 7107 (84.8%) 826 (87.0%)
pregnancy_bl
Yes 99 (1.2%) 20 (2.1%) 0.0241
No 8279 (98.8%) 929 (97.9%)
essential_worker_bl
Yes 231 (2.8%) 27 (2.8%) 0.959
No 8147 (97.2%) 922 (97.2%)
comorbidities_bl
Yes 3852 (46.0%) 451 (47.5%) 0.384
No 4526 (54.0%) 498 (52.5%)
immunestatus_bl
Yes 2349 (28.0%) 250 (26.3%) 0.287
No 6029 (72.0%) 699 (73.7%)
Table 1
Intervention group (Completed a primary vaccination schedule)
(N=8126)
Control group (Not completed a primary vaccination schedule)
(N=8126)
P-value

ᵃ5-year age groups

sex_cd
Mean (SD) 1.46 (0.537) 1.45 (0.549) 0.179
Median [Min, Max] 1.00 [0, 2.00] 1.00 [0, 2.00]
age_cdᵃ
Mean (SD) 11.6 (2.96) 11.6 (2.99) 0.607
Median [Min, Max] 12.0 [2.00, 18.0] 12.0 [2.00, 18.0]
residence_area_cd
731 1133 (13.9%) 1170 (14.4%) 0.00891
732 1144 (14.1%) 1012 (12.5%)
733 5849 (72.0%) 5944 (73.1%)
institutionalized_bl
Yes 225 (2.8%) 217 (2.7%) 0.736
No 7901 (97.2%) 7909 (97.3%)
foreign_bl
Yes 1234 (15.2%) 1232 (15.2%) 0.983
No 6892 (84.8%) 6894 (84.8%)
pregnancy_bl
Yes 97 (1.2%) 83 (1.0%) 0.33
No 8029 (98.8%) 8043 (99.0%)
essential_worker_bl
Yes 226 (2.8%) 224 (2.8%) 0.962
No 7900 (97.2%) 7902 (97.2%)
comorbidities_bl
Yes 3736 (46.0%) 3721 (45.8%) 0.826
No 4390 (54.0%) 4405 (54.2%)
immunestatus_bl
Yes 2280 (28.1%) 2287 (28.1%) 0.917
No 5846 (71.9%) 5839 (71.9%)

Two-by-two tables

The individuals in the imported dataset are counted by ‘fully_vaccinated_bl’ and ‘confirmed_case_bl’.

Confirmed case Not confirmed case Total
Completed a primary vaccination schedule 2990 6010 9000
Not completed a primary vaccination schedule 361 639 1000
Total 3351 6649 10000

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 0.9202832

The individuals eligible for analysis are counted by ‘fully_vaccinated_bl’ and ‘confirmed_case_bl’.

Confirmed case Not confirmed case Total
Completed a primary vaccination schedule 2639 5739 8378
Not completed a primary vaccination schedule 329 620 949
Total 2968 6359 9327

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 0.9085929

The matched individuals are counted by ‘fully_vaccinated_bl’ and ‘confirmed_case_bl’.

Confirmed case Not confirmed case Total
Completed a primary vaccination schedule 2617 5715 8332
Not completed a primary vaccination schedule 242 560 802
Total 2859 6275 9134

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 1.0409107

Survival in un-matched population

Variable Beta (SE) HR (95% CI) P
fully_vaccinated_blTRUE -0.02 (0.07) 0.98 (0.86, 1.11) 0.71

Strata Time Number at risk Cumulative sum of number of events Cumulative sum of number censored Survival Std. error Cumulative hazard Std. error cumulative hazard
Not fully vaccinated 0 902 1 0 0.9988914 0.0011080327 0.0011086475 0.0011086475
Not fully vaccinated 1 901 2 0 0.9977827 0.0015661251 0.0022185254 0.0015687346
Not fully vaccinated 100 887 15 0 0.9833703 0.0042579213 0.0167601671 0.0043275070
Not fully vaccinated 200 881 21 0 0.9767184 0.0050209720 0.0235436859 0.0051377719
Not fully vaccinated 300 869 33 0 0.9634146 0.0062511087 0.0372477521 0.0064843714
Not fully vaccinated 400 693 212 0 0.7649667 0.0141183086 0.2674750096 0.0184246060
Not fully vaccinated 500 621 281 0 0.6884701 0.0154201697 0.3726241520 0.0223575550
Not fully vaccinated 600 620 282 0 0.6873614 0.0154351407 0.3742344580 0.0224154712
Fully vaccinated 0 8378 1 0 0.9998806 0.0001193531 0.0001193602 0.0001193602
Fully vaccinated 1 8377 2 0 0.9997613 0.0001687807 0.0002387347 0.0001688109
Fully vaccinated 100 8253 126 0 0.9849606 0.0013297021 0.0151514274 0.0013498093
Fully vaccinated 200 3885 594 3997 0.9149921 0.0034433135 0.0887960657 0.0037611165
Fully vaccinated 300 2645 1072 4665 0.7759389 0.0065510625 0.2534754869 0.0084351389
Fully vaccinated 400 2307 1195 4885 0.7394797 0.0070201758 0.3015773379 0.0094855960
Fully vaccinated 500 786 1200 6446 0.7378440 0.0070426699 0.3037910797 0.0095371385
Fully vaccinated 600 7 1200 7171 0.7378440 0.0070426699 0.3037910797 0.0095371385
Variable Beta (SE) HR (95% CI) P
fully_vaccinated_blTRUE -0.02 (0.07) 0.98 (0.86, 1.11) 0.73
age_cd 0.00 (0.01) 1.00 (0.99, 1.02) 0.64
sex_cd -0.05 (0.05) 0.95 (0.86, 1.04) 0.26
residence_area_cd
     731 (ref)
     732 0.04 (0.10) 1.04 (0.85, 1.28) 0.67
     733 0.14 (0.08) 1.15 (0.99, 1.34) 0.07
essential_worker_blTRUE 0.03 (0.15) 1.03 (0.76, 1.39) 0.84
institutionalized_blTRUE 0.20 (0.14) 1.22 (0.92, 1.61) 0.17
foreign_blTRUE -0.04 (0.07) 0.96 (0.83, 1.11) 0.60
comorbidities_blTRUE 0.02 (0.05) 1.02 (0.92, 1.13) 0.75
immunestatus_blTRUE 0.01 (0.06) 1.01 (0.90, 1.13) 0.93