KAMC_COVID-19

We retrospectively collected data of admitted confirmed COVID-19 patients (positive RT-PCR test) to King Abdulaziz Medical City in Riyadh. Starting from the first case, which was on April 2, 2020, till June 18, 2020. We retrieved 5,739 patients records from the EHR system. However, 1513 COVID-19 patients passed the criteria set to be included for mortality endpoint, and 1508 patients passed the inclusion criteria for the ventilatory support requirement endpoint. For ventilatory support requirement, any patient that is lacking one of the following are excluded: 1) confirmed RT-PCR for COVID-19, 2) age >18, 3) CXR, 4) CBC test results, 5) availability of medical history, and 6) Full code status at the time of COVID-19 diagnosis. For mortality inclusion criteria is same as ventilatory support endpoint except that COVID-19 patients who are assigned no-code before the SARS-CoV-2 test are also included. The data include the 36 variables and we below describe how it is obtained and:
1) Gender
2) Age at diagnosis
3) Ventilation support status
4) Vital status
5) Haematocrit
6) Hemoglobin
7) MCHC
8) MCH
9) MCV
10) MPV
11) RBC
12) Platelet_count
13) RDW
14) WBC:
15) CXR zone 1
16) CXR zone 2
17) CXR zone 3
18) CXR zone 4
19) CXR zone 5
20) CXR zone 6
21) CXR zone 7
22) CXR zone 8
23) CXR zone 9
24) CXR zone 10
25) CXR zone 11
26) CXR zone 12
27) cancer_ICD-10_C00-C97
28) chronic_ischaemic_heart_disease_coronary_artery_disease_ICD-10_I25_I250-I259
29) hypertension_ICD-10_I10
30) asthma_ICD-10_J45_J450-J459
31) chronic_obstructive_pulmonary_disease_ICD-10_J44_J440-J449
32) type_2_diabetes_mellitus_ICD-10_E11
33) liver_cirrhosis_ICD-10_K74_K740-K746
34) chronic_viral_hepatitis_B_ICD-10_B181
35) chronic_viral_hepatitis_C_ICD-10_B182
36) chronic_kidney_disease_all_stages_ICD-10N18_N181-N189

Variable 1 is obtained from EHR. Variable 2 obtained from the EHR system as date of birth and converted to age using Covid-19 test date. Variable 3 is filled manually by a physician from the Infectious Disease Department at KAMC, the value MV assigned for mechanical ventilation, NIV for noninvasive ventilation. MV label is assigned if the patient received MV within 30 days of diagnosis. Variable 4: Filled manually by looking at EHR system discharge charts. If the patient is not discharge after 30 days of follow-up and the patient is still alive. The vital status is then reported as Alive. Variables 5-14 are obtained from CBC test results (within 3 days of DX). Variables 15-26, are annotated for CXR severity by four radiologists at KAMC. The images are baseline (within 3 days of DX). The radiologist are blinded to the outcome (mortality, or ventilator support requirement). A value of 0 is assigned for no presence of ground glass opacity (GGO) , a value of 1 for moderate GGO, and a value of 2 for severe manifestation of GGO (see included CXR figure for CXR zones). Variables 27-36 are obtained from the EHR system a value of 0 for disease absence and 1 for disease presence.