DOI: 10.5061/dryad.ksn02v78v
title: Monocentric retrospective cohort of 30,423 COVID-19 patients

description: Population and design: Monocentric cohort comparing COVID-19 patients
 exposed or not exposed to the treatment hydroxychloroquine
 (HCQ)+azithromycin (AZ) used as a standard of care in our center (Institut
 Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France).
 The inclusion period was from 2 March 2020 to 31 December 2021, with a
 follow-up period of 6 weeks. Inclusion and exclusion criteria: Data
 included were those of patients ≥ 18 years of age with PCR-proven COVID-19
 disease regardless of symptoms (asymptomatic or symptomatic) and treated
 in our centre, i.e. having had a medical examination by one of the doctors
 in our centre (Institut Hospitalo-Universitaire (IHU) Méditerranée
 Infection, Marseille, France) either as outpatients or as inpatients, i.e.
 hospitalized on the day of the visit in our outpatient unit following
 evaluation or directly transferred from another medical ward except
 intensive care unit. The reasons for exclusion were an erroneous patient
 identification (identity surveillance and duplicates), lack of available
 medical data, lack of COVID-19 after checking the medical record
 (including patients without COVID-19 consulting for a post-COVID-19
 syndrome), expression of opposition to the use of their medical data for
 research purposes (in accordance with European General Data Protection
 Regulation), and data from patients hospitalized in our center after
 intensive care. Data from COVID-19 outpatients left without medical advice
 were excluded.
description: Data
 source For inpatients: Between 03.03.20 and
 12.03.2021, i.e. the first year of the epidemic, data were collected using
 the Electronic Patient Record. The DPI ‘”Dossier Patient Informatisé”)
 centralized all the medical information of a patient concerning his stays
 at the Assistance Publique - Hôpitaux de Marseille. During this input, a
 large amount of medical data concerning the treatment was collected (2799
 patients). Between 13.03.21 and 31.12.2021, the data were extracted from
 the APHM administrative database (PASTEL). PASTEL does not contain medical
 data but only the following information: IPP (“Identifiant Permanent du
 Patient”) which is a unique identifier for each patient, age, sex, date of
 entry, the different services in which the patient may have been
 hospitalised and the date of discharge (1791
 patients). For the outpatients, the medical cards
 of the patients who came to the outpatient unit filled in by the medical
 staff (11,725 patients). The content of these medical forms evolved during
 the epidemic, particularly with regard to the collection of patients'
 vaccination status and risk factors. At the outset, they contained
 information on prescribed treatments (29752
 patients). The fusion of these databases was
 carried out via the IPP, and made it possible to obtain the total
 population of patients treated at the IHU with the following information:
 IPP, age, sex, outpatient care (Y/N), inpatient care (Y/N), date of entry
 and date of exit. If a patient had more than one episode of SARS-CoV-2
 treated at the IHU, only the first stay was taken into account. If a
 patient was treated as an outpatient and then hospitalized, both pieces of
 information were kept. In the end, we obtain a database of 30,669
 patients To this merged database were added
 only for the hospitalized patients the data concerning the treatment from
 the PHARMA database which is the pharmaceutical prescription file.
 Similarly, for each patient, the Sars-Cov2 variant was merged with the
 biology database (NEXLAB Medical Software) which lists all the samples and
 their associated genotype via an extraction. Finally, the information on
 death from all causes was obtained via an extraction from the Medical
 Information Department (DIM). Indeed, if the patient died during his
 inpatient care, the information system retrieves this information in the
 discharge mode. For patients discharged alive from the APHM stay, we
 queried the French National Death Registry (29) to find out whether they
 died within 42 days of their IHU treatment. All the data were quality
 controlled, looking for duplicates and aberrant
 data. Finally, the construction of the
 database and the quality controls carried out were verified by a
 bailiff.