Introduction
Methods
Study design
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Investigate frequency, severity and distinct phenotypes of COVID-19 and Post-COVID-19 Syndrome (PCS) in the German population and identify long-term clinical trajectories of PCS. POP
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Identify genomic, epigenomic, transcriptomic, proteomic, and metabolomic signatures predicting course and outcome of acute and post-acute COVID-19.
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Decipher further central pathophysiologic mechanisms of specific COVID-19 related pathologies in order to inform development of therapies.
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Establish commonalities and differences between COVID-19 and other forms of respiratory tract infections, pneumonia and acute respiratory distress syndrome (ARDS) in detail.
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Understand reasons for development of acute or post-acute COVID-19 in SARS-CoV- 2 vaccinated patients.
Each of the three cohort platforms focuses on one or multiple of the above scientific areas of interest. The following paragraphs will introduce the three cohort platforms and supporting infrastructure elements. Cross-sectoral platform
Category | Features | Collected in | ||
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SUEP | HAP | POP | ||
Socio-demographic data | Age, sex, residence, marital status | x | x | x |
Educational level and employment status (e.g. general education degree, vocational degree) | x | x | x | |
Clinical data: pre-infection anamnestic data | Pre-infection lifestyle (e.g. sports activity, dietary pattern) | x | x | |
Pre-infection smoking and alcohol consumption | x | x | x | |
Pre-infection health status and functionality (e.g. Barthel Index, care level, Clinical Frailty Scale) | x | x | x | |
Pre-infection medication | x | x | ||
Vaccination status | x | x | x | |
Comorbidities | x | x | x | |
Directives for medical decisions (e.g. power of attorney, patient decree) | x | x | ||
Clinical data: parameters in the observational period | Infrastructural treatment context (e.g. health care facility, involved disciplines) | x | x | x |
Smoking and alcohol consumption | x | x | ||
Health status and functionality (e.g. Barthel index, care level, Clinical Frailty Scale) | x | x | x | |
Symptoms, events | x | x | x | |
Clinically indicated diagnostics (vital signs, pulmonary diagnostics, laboratory parameters, microbiology & virology, radiological findings, functional diagnostics) | x | x | x | |
Intensive care scores (e. g. SOFA, SAPS) | x | x | ||
Therapeutic measures (medication, interventions, surgery, complementary medicine) | x | x | x | |
Pediatric-specific variable extensions (e.g. perinatal medical history, congenital defects, effects on development) | x | |||
Imaging data | Clinically indicated diagnostic imaging
data | x | x | |
Study-related MRI scans | x | x | ||
Study related CT-Thorax scans | x | |||
Study-related echocardiographies | x | x | x | |
Patient-reported outcome measures (PROM) | Cognitive function (e.g. PROMIS Kognition) | x | x | x |
Dypsnea (e.g. Modified Medical Research Council Dyspnea Scale, PROMIS Dyspnoe) | x | x | x | |
Fatigue (e.g. Chalder Fatigue Scale, FACIT-F) | x | x | x | |
Functional physical status (e.g. Activities of Daily Living) | x | x | x | |
Mental health (e.g. GAD-7, Brief Resilience Scale) | x | x | x | |
Pain (e.g. DN2, HIT-6) | x | x | x | |
Quality of life (e.g. EQ-5D-5L) | x | x | x | |
Metadata | Study-related metadata (e.g. data quality assessment, protocol deviation) | x | x | x |
Digital Imaging and Communications in Medicine (DICOM) header information | x | x | x | |
Biosample accompanying metadata (e.g. regarding transport, processing and storage) | x | x | x |
Study assessmenta | SUEP | HAP | POP |
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Abdominal ultrasonography | x | ||
Additional medical history and recording by study physician | x | x | x |
Basic endocrinological diagnostics | x | x | |
Computer tomography chest | x | ||
Electrocardiography | x | x | x |
Electroencephalography | x | ||
Fraction Exspiratory Nitric Oxide | x | ||
Fundus examination | x | ||
Home visit | x | ||
Impulse oscillometry | x | ||
Long-term ECG | x | ||
Long-term glucose measurement | x | ||
Long-term RR | x | ||
Magnetic resonance imaging brain | x | x | |
Magnetic resonance imaging heart | x | ||
Microbiome sampling | x | x | x |
Myocarditis panel | x | x | |
Basic neurological examination | x | x | |
6-Min walking test | x | ||
Smell test | x | x | |
Spiroergometry | x | ||
Standard laboratory outpatients | x | ||
Standardized spirometry with bodyplethysmography and diffusion capacity | x | x | x |
Taste test | x | x | |
Transthoracic echocardiography | x | x | x |
Vital sign monitoring | x | x | x |
High-resolution platform
Population-based platform
Infrastructure elements of the NAPKON
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The Interaction Core Unit (ICU) coordinates overall governance, support of the use & access processes, development of datasets, engagement of the scientific community via working parties and a scientific council, age-specific consideration of study aspects via a dedicated Pediatric Core Unit, convening of the general assembly, and other tasks related to internal project management or communication.
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The Biosample Core Unit (BCU) selects suitable biosamples together with clinical experts, defines standards of procedure for sampling, processing, storage, quality assurance, as well as regular auditing of biobanks.
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The Epidemiology Core Unit (ECU) is responsible for methodological consultation of the project and third parties applying for data/biosamples. It performs an external quality assurance and reporting of collected project data.
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The Integration Core Unit (IGCU) designs and manages the integration of external and existing cohort data into the NAPKON.
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Clinical data management electronic case report form (eCRF) for documentation of all clinical data, including additional tests performed as part of the study.
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Imaging data management central storage for clinical routine images and additional images collected by study protocol.
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Biosample management central laboratory information and management system (cLIMS).
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Ethics coordination coordination of ethical aspects regarding data-infrastructure and governance and professional communication with ethics committees and institutional review boards.
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Trusted third party centralized quality assurance and management of (electronic) informed consents, including supporting the invitation of patients to follow-up studies.
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Data transfer office provision of datasets and identification of the respective biosamples based on applications approved by the Use & Access committee.
Study population and recruitment
Case definition for SARS-CoV-2 infection (= inclusion criteria) | Control definition |
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Either: Positive polymerase chain reaction (PCR) for SARS-CoV-2 in either Oro/nasopharyngeal swab, BAL, sputum, tracheal secretions, stool, or blooda Or (all of the following): Negative polymerase chain reaction (PCR) for SARS-CoV-2 of a swab or body fluid Definitive infection of the respiratory system Characteristic radiographic imagery A negative test for influenza Exclusion of other potential causes (like chronic diseases of the respiratory system) | Case definition for SARS-CoV-2 case not applicable Applicable control inclusion criteria for one of the three control strata (pool) Outpatient (e.g., respiratory viral infection) Inpatient (e.g., community-acquired pneumonia) Intensive care unit (e.g., acute respiratory distress syndrome) Capacity for control recruitment with sufficient positive cases in the respective pool over the past eight weeks |
Visit schedules and follow-up
Clinical assessment
Biosample collection
Data collection
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Automatic predefined plausibility and completeness checks in the eCRFs
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Local (Review A) and central (Review B) quality assessment
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Random source data verification of 10%-20% of the cases.
Study organization
Governance and use and access
Project management infrastructure
Study budget
Results
Governance and use and access
Cohorts and study population
Variable | N1 | Statistic | HAP, N = 544 | POP, N = 2346 | SÜP, N = 1837 |
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Age (numeric) | 4727 | Median (IQR) | 57 (47, 65) | 46 (31, 57) | 56 (42, 68) |
Age (categorical) | 4727 | ||||
< 18 | n (%) | 0 (0%) | 0 (0%) | 50 (2.7%) | |
18–29 | n (%) | 33 (6.1%) | 501 (21%) | 138 (7.5%) | |
30–39 | n (%) | 51 (9.4%) | 446 (19%) | 205 (11%) | |
40–49 | n (%) | 83 (15%) | 360 (15%) | 280 (15%) | |
50–59 | n (%) | 156 (29%) | 608 (26%) | 368 (20%) | |
60–69 | n (%) | 128 (24%) | 260 (11%) | 379 (21%) | |
70–79 | n (%) | 69 (13%) | 140 (6.0%) | 255 (14%) | |
80+ | n (%) | 24 (4.4%) | 31 (1.3%) | 162 (8.8%) | |
Gender | 4726 | ||||
Female | n (%) | 174 (32%) | 1305 (56%) | 723 (39%) | |
Male | n (%) | 370 (68%) | 1040 (44%) | 1114 (61%) | |
Non-binary | n (%) | 0 (0%) | 0 (0%) | 0 (0%) | |
Missing or review A pending | n | 0 | 1 | 0 | |
Smoking (past or current smoker) | 3867 | ||||
Yes | n (%) | 28 (6.8%) | 1068 (49%) | 128 (9.9%) | |
No | n (%) | 381 (93%) | 1100 (51%) | 1162 (90%) | |
Missing or review A pending | n | 135 | 178 | 547 | |
Alcohol | 2433 | ||||
Never | n (%) | 0 (NA%) | 183 (13%) | 516 (50%) | |
Up to 4 times monthly | n (%) | 0 (NA%) | 676 (48%) | 377 (36%) | |
Multiple times weekly | n (%) | 0 (NA%) | 536 (38%) | 145 (14%) | |
Missing or review A pending | n | 544 | 951 | 799 | |
Obesity at inclusion (BMI ≥ 30 kg/m2) | 4169 | ||||
No | n (%) | 311 (65%) | 1758 (76%) | 900 (66%) | |
Yes | n (%) | 167 (35%) | 566 (24%) | 467 (34%) | |
Missing or review A pending | n | 66 | 22 | 470 | |
SARS-CoV-2 vaccined | 3581 | ||||
Yes | n (%) | 93 (19%) | 1189 (55%) | 459 (49%) | |
No | n (%) | 393 (81%) | 965 (45%) | 482 (51%) | |
Missing or review A pending | n | 58 | 192 | 896 | |
In-patient ever | 4161 | ||||
Yes | n (%) | 544 (100%) | 170 (7.3%) | 1120 (88%) | |
No | n (%) | 0 (0%) | 2172 (93%) | 155 (12%) | |
Missing or review A pending | n | 0 | 4 | 562 | |
Intensive stay ever | 3997 | ||||
Yes | n (%) | 208 (38%) | 36 (1.5%) | 367 (33%) | |
No | n (%) | 336 (62%) | 2301 (98%) | 749 (67%) | |
Missing or review A pending | n | 0 | 9 | 721 | |
Covid-associated oxygenation | 4619 | ||||
Invasive/non-invasive ventilation | n (%) | 141 (26%) | 17 (0.7%) | 299 (17%) | |
O2-therapy only | n (%) | 260 (48%) | 93 (4.0%) | 746 (43%) | |
No assistance | n (%) | 142 (26%) | 2222 (95%) | 699 (40%) | |
Missing or review A pending | n | 1 | 14 | 93 | |
Extracorporeal membrane oxygenation (ECMO) | 4047 | ||||
Yes | n (%) | 60 (13%) | 1 (<0.1%) | 47 (3.8%) | |
No | n (%) | 417 (87%) | 2334 (100%) | 1188 (96%) | |
Missing or review A pending | n | 67 | 11 | 602 | |
Chronic cardiovascular disease | 3842 | ||||
Yes | n (%) | 269 (50%) | 601 (29%) | 622 (50%) | |
No | n (%) | 265 (50%) | 1456 (71%) | 629 (50%) | |
Missing or review A pending | n | 10 | 289 | 586 | |
Chronic lung disease | 4013 | ||||
Yes | n (%) | 109 (21%) | 425 (19%) | 235 (19%) | |
No | n (%) | 417 (79%) | 1822 (81%) | 1005 (81%) | |
Missing or review A pending | n | 18 | 99 | 597 | |
Chronic kidney disease | 4088 | ||||
Yes | n (%) | 88 (17%) | 8 (0.3%) | 142 (12%) | |
No | n (%) | 436 (83%) | 2323 (100%) | 1091 (88%) | |
Missing or review A pending | n | 20 | 15 | 604 | |
Chronic liver disease | 3722 | ||||
Yes | n (%) | 44 (8.4%) | 181 (9.2%) | 84 (6.8%) | |
No | n (%) | 480 (92%) | 1788 (91%) | 1145 (93%) | |
Missing or Review A pending | n | 20 | 377 | 608 | |
Rheumatological/immunological disease | 4053 | ||||
Yes | n (%) | 32 (6.1%) | 219 (9.5%) | 60 (4.9%) | |
No | n (%) | 492 (94%) | 2075 (90%) | 1175 (95%) | |
Missing or review A pending | n | 20 | 52 | 602 | |
Diabetes mellitus | 4001 | ||||
Yes | n (%) | 110 (21%) | 101 (4.5%) | 266 (21%) | |
No | n (%) | 418 (79%) | 2129 (95%) | 977 (79%) | |
Missing or review A pending | n | 16 | 116 | 594 | |
Solid tumor disease | 4092 | ||||
Yes | n (%) | 57 (11%) | 39 (1.7%) | 150 (12%) | |
No | n (%) | 478 (89%) | 2294 (98%) | 1074 (88%) | |
Missing or review A pending | n | 9 | 13 | 613 | |
Haematological-oncological disease | 4074 | ||||
Yes | n (%) | 29 (5.5%) | 7 (0.3%) | 63 (5.2%) | |
No | n (%) | 498 (94%) | 2323 (100%) | 1154 (95%) | |
Missing or review A pending | n | 17 | 16 | 620 | |
HIV infection | 3948 | ||||
Yes | n (%) | 3 (0.6%) | 2 (<0.1%) | 17 (1.5%) | |
No | n (%) | 473 (99%) | 2336 (100%) | 1117 (99%) | |
Missing or review A pending | n | 68 | 8 | 703 | |
Chronic neurological or psychiatric disease | 3997 | ||||
Yes | n (%) | 81 (15%) | 570 (25%) | 159 (13%) | |
No | n (%) | 451 (85%) | 1690 (75%) | 1046 (87%) | |
Missing or review A pending | n | 12 | 86 | 632 | |
History of organ transplantation | 4106 | ||||
Yes | n (%) | 56 (10%) | 8 (0.3%) | 60 (4.9%) | |
No | n (%) | 479 (90%) | 2327 (100%) | 1176 (95%) | |
Missing or review A pending | n | 9 | 11 | 601 | |
General symptoms | 3711 | ||||
Yes | n (%) | 246 (59%) | 1964 (95%) | 979 (80%) | |
No | n (%) | 172 (41%) | 110 (5.3%) | 240 (20%) | |
Missing or Review A pending | n | 126 | 272 | 618 | |
Respiratory symptoms | 3726 | ||||
Yes | n (%) | 253 (61%) | 1974 (95%) | 979 (80%) | |
No | n (%) | 165 (39%) | 110 (5.3%) | 245 (20%) | |
Missing or review A pending | n | 126 | 262 | 613 | |
Gastrointestinal symptoms | 2626 | ||||
Yes | n (%) | 93 (22%) | 900 (89%) | 448 (37%) | |
No | n (%) | 325 (78%) | 110 (11%) | 750 (63%) | |
Missing or review A pending | n | 126 | 1336 | 639 | |
Neurological symptoms | 2829 | ||||
Yes | n (%) | 94 (22%) | 1094 (91%) | 424 (35%) | |
No | n (%) | 324 (78%) | 110 (9.1%) | 783 (65%) | |
Missing or review A pending | n | 126 | 1142 | 630 | |
Other symptoms | 2750 | ||||
Yes | n (%) | 93 (22%) | 1019 (90%) | 387 (32%) | |
No | n (%) | 325 (78%) | 110 (9.7%) | 816 (68%) | |
Missing or review A pending | n | 126 | 1217 | 634 | |
Asymptomatic | 4012 | ||||
Yes | n (%) | 4 (0.8%) | 110 (4.9%) | 62 (5.0%) | |
No | n (%) | 520 (99%) | 2134 (95%) | 1182 (95%) | |
Missing or review A pending | n | 20 | 102 | 593 | |
Early outcome | 1800 | ||||
Discharged home/ambulatory care | n (%) | 413 (79%) | 0 (NA%) | 834 (65%) | |
Unknown or no change yet | n (%) | 0 (0%) | 0 (NA%) | 185 (14%) | |
Transferred to or from another facility | n (%) | 47 (9.0%) | 0 (NA%) | 107 (8.4%) | |
Deceased | n (%) | 62 (12%) | 0 (NA%) | 152 (12%) | |
Missing or review A pending | n | 22 | 2346 | 559 | |
3M follow-up conducted | 1258 | ||||
Yes | n (%) | 162 (69%) | 0 (NA%) | 534 (52%) | |
No | n (%) | 74 (31%) | 0 (NA%) | 488 (48%) | |
Missing or review A pending | n | 308 | 2346 | 815 | |
6M follow-up conducted | 182 | ||||
Yes | n (%) | 113 (62%) | 0 (NA%) | 0 (NA%) | |
No | n (%) | 69 (38%) | 0 (NA%) | 0 (NA%) | |
Missing or review A pending | n | 362 | 2346 | 1837 | |
12M follow-up conducted | 694 | ||||
Yes | n (%) | 37 (35%) | 0 (NA%) | 219 (37%) | |
No | n (%) | 68 (65%) | 0 (NA%) | 370 (63%) | |
Missing or review A pending | n | 439 | 2346 | 1248 |
Biosamples
Total | SUEP | HAP | POP | ||
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Patients with biosamples | 4349 | 1442 | 439 | 2469 | |
Visits with biosampling | 8845 | 3915 | 2445 | 2485 | |
Follow-up visits total | 2920 | 754 | 346 | 1822 | |
3 months | 740 | 583 | 155 | 2 | |
6 months | 1942 | 3 | 120 | 1819 | |
12 months | 209 | 166 | 43 | 0 | |
24 months | 29 | 0 | 28 | 1 | |
Average visit with biosampling per patient | 2 | 3 | 6 | 1 | |
Intended use | |||||
EDTA blood | Plasma: proteome, metabolome, biomarker analysis; DNA: genome, epigenome | 10,988 | 3974 | 2470 | 4544 |
Serum | Clinical and biomarker analysis | 8636 | 3760 | 2435 | 2443 |
Respiratory samplea | Determination of virus subtype, microbiome | 7077 | 3644 | 950 | 2483 |
Oro/nasopharyngeal swaba | 2916 | 2358 | 468 | 90 | |
Salivaa | 4091 | 1217 | 482 | 2392 | |
ENTAa,b | 65 | 64 | 0 | 1 | |
BALa,b | 5 | 5 | 0 | 0 | |
PAXgene RNA | Transcriptome | 8362 | 3627 | 2407 | 2328 |
Citrate blood | Analysis of coagulation factors, biomarkers | 10,727 | 4187 | 2470 | 4070 |
PBMC (all variants) | Analysis of cellular immune response | 11,484 | 4701 | 4361 | 2422 |
CPT | 5918 | 3337 | 936 | 1645 | |
EDTA | 1139 | 632 | 507 | 0 | |
Heparine | 4427 | 732 | 2918 | 777 | |
Urinea | Metabolome, kidney measures | 6358 | 3055 | 959 | 2344 |