Objective of the Website

To publicly and transparently provide epidemiologic monitoring of the COVID-19 pandemic by monitoring the key indicators defined in the plan for the control of transmission of COVID-19 in Catalonia.

Justification of Key Concepts

Following is an explanation of 4 concepts that we use in all indicators and a justification for why we use them.

We use COVID-19 cases confirmed by means of PCR/RAT for epidemiologic monitoring.

First, the COVID-19 cases confirmed for epidemiologic monitoring are only those confirmed by PCR/RAT, as a positive PCR/RAT tells us that it is an active case and the date on which the case starts is important for epidemiologic monitoring.

We do not use COVID-19 cases confirmed by means of rapid serology tests or by ELISA.

Second, and as a result of the first point, we will not use the serology tests or ELISA tests that have been carried out for seroprevalence studies because the information they provide us is the immune status of the person, but the date when the case was active is not known. The date on which these tests were performed cannot be used, as this would give us a false sensation of an increase in cases when the opposite is the case; these are people who have achieved immunity and who were cases in the past.

We must differentiate monitoring of the general population and the care-home population.

Third, it is important to differentiate between two populations, the general population and the care-home population, as their epidemiologic behavior is completely different, as was seen in the first wave. The general population lives in the community and interacts and moves in a certain way, whereas people who live in geriatric care homes live in highly closed communities in very closed places and their mobility is considerably reduced. Given these characteristics, epidemiologic monitoring of these two populations together is not possible and this is why the website shows separate data.

Where do we attribute the case date?

Unlike other sources and for epidemiologic reasons, we attribute the start of the case based on the oldest date available to us, whether it sis the diagnosis of COVID-19 in primary care (if applicable) or the performance of a positive PCR/RAT test, as these two dates indicate the start of the case. See definition of case confirmed by PCR/RAT for more details.

 

Characteristics of the Website

The sources of the data on epidemiologic monitoring of COVID-19 in Catalonia are  varied and changing, making this a complex system to systematize and interpret. This document aims both to describe the data sources and to explain and help to interpret the data and their idiosyncrasies.

Data Sources

We will specify the data sources for all the data and indicators that you will find on the website. Here is a list of all the sources for the data being used.

SourceDescriptionData provided

ECAP (Primary Care Clinical Station)

This is the platform for primary care clinical records in Catalonia. It uses diagnoses coded using CIM10-MC and its own variables.

Acute respiratory diseases

Care home census

Hospital census register

Admissions to hospitals in Catalonia, only available since 29/04/2020

Admitted patients

Numeric declaration

Numeric declaration of UCI covid19 beds  Patients admitted to the ICU

Aggregated Health Care Register (RSA)

Centralized PCR/RAT register of the public health care system.

PCR

Deaths

Orfeu

Program for registering PCR/RAT tests, which was initially used to request and record the PCR/RAT tests carried out by health care professionals and from screening in care homes.

PCR

Central register of CatSalut insurees

Register of assignation of persons to their primary-care teams

Town

Age

Gender

Territory

Care-home census pilot app

Application containing the updated census of residents in geriatric care homes, currently in the pilot phase and only in some care homes.

Care home town


All data have gone through a process of anonymization and to avoid risks of re-identification some data have been generalized (age groups) or eliminated (deaths have been eliminated in territories where confidentiality of sensitive data cannot be that guaranteed) with technical applications of anonymization.

Start date

Data collection began on 01/03/2020.

Data update

The data are published every day at around 10am, but must take into account the following:

  • Only the data from up to 3 days previously are shown. The reason for this is given in the next section.
  • Although the post is at 10am, the data is updated at 8pm the day before.

The Data Are Dynamic

Given the uniqueness of the situation, the data may vary from day to day. That is, if we look at the data today, we see X, but if we look 24 hours later, we may see X+3. The reason for the variation differs depending on the datum.

Here is a list, but we will explain it in detain in the glossary for each concept.

Parameter

Reason

PCR

When a health care professional requests a PCR, this takes a length of time that may vary from hours to days. The website includes the PCR tests as the results are received and this is attributed to the day the test was carried out. For this reason, the number of PCR may increase retrospectively.

For this reason, the website only shows data for up to 3 days previously, which is when most PCR results are published, although a variable number may be published on subsequent days.

Acute respiratory infections

When entering the diagnosis into the clinical records, it is possible to specify the date of onset of the disease, and this may be earlier than the day the patient was seen. For this reason, there may be increases in the number of diagnosed cases after the date.

 

It may also be the case that, after receiving the results of a test, the diagnosis of acute respiratory infection may be changed to something else. In this case, the number of acute respiratory infections on the website will drop.

Deaths

Deaths may experience some delay in notification. On the website, deaths are attributed to the day of death and not the day of notification. For this reason, the number of deaths may increase retrospectively.

Levels of Territorial Aggregation

The website can be browsed by territorial level and we have included 2 complementary levels of aggregation:

  1. Region and Care Management Areas (CMA): division by CatSalut health care regions
  2. Counties: provinces, counties, municipalities of >20,000 inhabitants and those that are subject to active monitoring.

Downloads

There are daily and weekly data by CMA or by county. They include age and gender. The data are also available at -3 days. 

Glossary

Following is a definition of the different concepts used to calculate the indicators constructed to carry out the epidemiologic monitoring of COVID-19.

Concepts 

Concept

Definition

Source

Town

All people resident in Catalonia.

RCA

Care home census

Patients living in a geriatric care home. They come from 2 different sources:

  • ECAP care-home census and RSA
  • The new pilot app where the census of residents is centralized

ECAP, RSA, care-home census app (pilot)

Acute respiratory infection (ARI)

Each of the episodes of acute respiratory disease diagnosed in ECAP is taken into account.

 

The diagnostic codes taken into consideration are all those associated with COVID-19 (not contacts) and the diagnostic codes for ARIs (see dditional data).

ECAP

PCR/RAT (Rapid Antigenic Test)

The PCR/RAT test to detect SARS-CoV-2 can be performed at different levels: in primary care, in hospitals, in the workplace, at the public-health level, etc. The vast majority are registered in the RSA. The results of the PCR/RAT performed in the private sector on patients visiting primary care are retrieved from ECAP.

 

PCR/RAT tests are generally used to confirm a suspected case of COVID-19 or to screen the contacts of a confirmed case and to follow up the case. The result of the test may take from a few hours to a few days to arrive, depending on where it is performed. On the website, the PCR/RAT result is attributed to the date on which the test was performed, and the number may increase retrospectively as the results are received from the laboratories, as we have already mentioned.

 

The PCR/RAT results are attributed to the territory where the patient is assigned to the RCA.

RSA, Orfeu, ECAP

Case confirmed by PCR/RAT

Patient with a positive PCR/RAT result. The date to which the case is attributed is the start date for the case and is the oldest of these two dates:

  • The date on which the COVID-19 health problem is diagnosed in primary care, provided that the diagnosis is made 14 days before the PCR/RAT test
  • The date on which the positive result of the PCR/RAT test arrives

If a patient has more than one diagnosis of COVID-19, the first diagnosis in the past 14 days is taken.

If a patient has more than one positive PCR/RAT test performed, the first one is taken, as that is the one that confirms the case.

The serology tests used for the population-immunity study, which began on 29/06/2020 (variable depending on the territory), are not taken into account for the epidemiologic evolution of the pandemic.

See PCR/RAT

ECAP for diagnoses of COVID-19

Confirmed cases

A case can be confirmed by PCR/RAT, but also by other methods that are not taken into account for the epidemiologic monitoring, but which are shown in the daily situation of the total population (start), in the Accumulated confirmed cases box.

As well as PCR/RAT, cases can be confirmed by:

  • Epidemiology: this is where an epidemiologist has confirmed the case.
  • Probable case, as they have a high probability of being confirmed.
  • Serology: ELISA and rapid tests that tell us the patient’s immunity. We do not use them for epidemiologic monitoring because it is not possible to determine the start date of the case.
 

Admitted patients

Patients admitted due to COVID-19 the last day of the period shown.

These are attributed to the territory where the patient is assigned to the RCA.

Hospital census register

Patients admitted to ICU

Patients in the ICU due to COVID-19  the last day of the period shown.

These patients are included in admitted patients, to be admitted to the ICU they must first have been admitted to hospital.

These are attributed to the territory where the patient is assigned to the RCA.

Hospital census register

Deaths

Deaths have the following characteristics that affect the data we present:

  • Date of death: the date on which the patient dies.
  • Date of notification: the date on which the system is notified of the death.
  • Cause of death. 

In the case of the COVID website, deaths are attributed to the date of death but first appear on the day they are notified.

Only deaths linked to COVID-19 are taken into account: whn the cause of death on the death certificated specifies that the person has diad due to COVID-19 regardless of whether they have a positive PCR/RAT or not.

RSA

Descriptive Data

Description of the counts that appear on the website. 

Descriptive data

Description

Mean age

 

This is the mean age of the people who are confirmed COVID-19 cases for the period and territory selected.

% Women

Percentage of women of the cases of COVID-19 confirmed by PCR/RAT.

PCR/RAT performed

count

Total number of PCR/RAT performed during the period selected for the territory selected.

Cases confirmed by PCR/RAT

count

Number of cases of COVID-19 confirmed by PCR/RAT according to the period and territory selected.

Accumulated confirmed cases

count

Total number of patients with a positive diagnostic test for COVID-19 accumulated since 1 March 2020. They include the cases confirmed by rapid serologic tests and ELISA, probable PCR/RAT and epidemiologically confirmed.

Patients hospitalized

count

Number of COVID-19 patients hospitalized (prevalent) by territory.  

Patients in ICU

count

Number of COVID-19 patients hospitalized (prevalent) by territory.

Deaths

count

Number patients with COVID-19 who have died, by territory and period selected.

Indicators

We calculate the indicators based on the concepts defined in the previous section. Each indicator has its own formula and in the description, we explain its characteristics so that it can be interpreted correctly.

Indicator

Formula

Description

Acute respiratory infection rate

in graphic

(acute respiratory infection/population)×100,000

This is the earliest indicator, as it does not depend so directly on the PCR/RAT rate. It is directly linked to primary-care activity.

PCR/RAT rate

(number of PCR/RAT/population)×100,000

This serves to compare the number of PCR/RAT tests being performed in each territory.

It also depends on the rate of confirmed cases, as the more cases are confirmed, the more contacts and PCR/RAT tests carried out.

Rate of cases confirmed by PCR/RAT

(confirmed cases/pobulation)×100,000

This rate allows us to compare territories with each other.

It should be noted that this rate may be unstable for small territories. 

It is very closely related to the PCR/RAT rate, as the more PCR/RAT tests are carried out, the more cases are found.

It begins to be reliable 3 days after the PCR/RAT test has been performed (explained in the section “The Data Are Dynamic”).

AI14 (Acumulated Incidence)

(confirmed cases int he last 14 days/pobulation)×100,000

 

Case variation (%)

[(t(-1)-t)/t(-1)]×100

This is the relative variation in the rate of cases of COVID-19 confirmed by PCR/RAT in the last period with respect to the previous period.

It tells us whether the rate has increased (red) or decreased (green) with respect to the previous period.

% Positive PCR/RAT

 (total PCR+ or RAT+/total PCR+ or RAT+ performed)×100

 The proportion of all the PCR/RAT tests carried out that obtain a positive result. This indicator measures the intensity with which an active search for cases is being made by means of strategies to control outbreaks and trace contacts.

The more intensely cases are searched for among asymptomatic people, the lower the percentage of positive cases will be.
And conversely, if PCR/RAT tests are only performed on symptomatic cases, this percentage will be higher.

Risk of outbreak or EPG (effective growth potential) 

 It is made up of two elements:

  • The mean reproduction rate of the past 7  days  (ρ7), which allows us to evaluate the reproduction rate of the disease. This is  calculated as the mean of the cases confirmed#in the last 3 days divided by the confirmed cases from 5 days earlier, also as a mean of three days: ρt = (N(t) + N(t-1) + N(t-2))/(N(t-5)+ N(t-6) + N(t-7)). We then take the mean of the past 7 days.
  • The second component is the accumulated incidence of the past 14 days (IA14), which is calculated as the number of new cases from the current day plus the cases from the previous 13 days per 100,000 inhabitants. This incidence allows us to estimate how many people are able to contract the disease at a given moment (active cases).

The EPG is the product of the above two components:
EPG = ρ7*IA14

#In this case, to perform the calculations, patients in geriatric care homes are excluded because their epidemiologic behavior is different.

It allows us to evaluate the growth of an epidemic.


It measures the potential new cases diagnosable in the next 14 days and is linked to the probability of the appearance of new epidemic outbreaks.   

The methodology used is that provided by  Computational Biology and Complex Systems. BIOCOMSC 
 

Reproduction rate - Rt Rt = N(t) + N(t-1) + N(t-2) / N(t-5)+ N(t-6) + N(t-7) 

N is the number of cases confirmed by PCR/RAT. 
Where the mean of the past 7 days is calculated every day (t). 
Rt is an empirical measurement to evaluate the speed at which an epidemic propagates. It is a measure of the mean number of persons infected by an infectious person.  

Additional Information

COVID-19 Diagnostic Codes in ECAP (ICD-10-CM + Thesaurus)

ECAP uses the  ICD-10-CM codes, together with an internal coding system, the Thesaurus, which helps us to adapt the term search and coding to the specific needs of primary care. 

  • B97.29 OTHER CORONAVIRUS AS THE CAUSE OF DISEASES CLASSIFIED ELSEWHERE
  • B34.2 CORONAVIRUS INFECTION, UNSPECIFIED. This was the recommended code before 1 July 2020.
  • B97.21 SARS-ASSOCIATED CORONAVIRUS AS THE CAUSE OF DISEASES CLASSIFIED ELSEWHERE
  • J12.81 PNEUMONIA DUE TO SARS-ASSOCIATED CORONAVIRUS
  • J12.89 OTHER VIRAL PNEUMONIA. This code is not specific to COVID-19, but it has been used as such based on the  recommendations of CatSalut.
  • U07.1 COVID-19. This was the code  recommended by CatSalut  from 1 July 2020.
  • Z20.828 with the thesaurus of SUSPECTED COVID-19

Diagnostic codes considered to be ARI (ICD-10-CM)

We have selected the codes associated with the following SNOMED terms: Influenza, Adenoviral respiratory disease, Viral respiratory infection, Viral upper respiratory tract infection, Viral lower respiratory infection, Viral pleurisy, and Severe acute respiratory syndrome. And we have excluded the codes associated with influenza.

They include the diagnoses of  COVID-19 +

  • B25.0 CYTOMEGALOVIRAL PNEUMONITIS
  • B30.2 VIRAL PHARYNGOCONJUNCTIVITIS
  • B33.4 HANTAVIRUS (CARDIO)-PULMONARY SYNDROME
  • J00 ACUTE NASOPHARYNGITIS [COMMON COLD]
  • J12 VIRAL PNEUMONIA, NOT ELSEWHERE CLASSIFIED
  • J12.0 ADENOVIRAL PNEUMONIA
  • J12.1 RESPIRATORY SYNCYTIAL VIRUS PNEUMONIA
  • J12.2 PARAINFLUENZA VIRUS PNEUMONIA
  • J12.3 HUMAN METAPNEUMOVIRUS PNEUMONIA
  • J12.8 OTHER VIRAL PNEUMONIA
  • J12.9 VIRAL PNEUMONIA, UNSPECIFIED
  • J20.3 ACUTE BRONCHITIS DUE TO COXSACKIEVIRUS
  • J20.4 ACUTE BRONCHITIS DUE TO PARAINFLUENZA VIRUS
  • J20.5 ACUTE BRONCHITIS DUE TO RESPIRATORY SYNCYTIAL VIRUS
  • J20.6 ACUTE BRONCHITIS DUE TO RHINOVIRUS
  • J20.7 ACUTE BRONCHITIS DUE TO ECHOVIRUS
  • J21.0 ACUTE BRONCHIOLITIS DUE TO RESPIRATORY SYNCYTIAL VIRUS
  • J21.1 ACUTE BRONCHIOLITIS DUE TO HUMAN METAPNEUMOVIRUS
  • P23.0 CONGENITAL PNEUMONIA DUE TO VIRAL AGENT
 

Document last updated: 10/11/2020