Cases

Click on the menu item Cases in the blue ribbon to access the list of cases.

Open

Case Directory

In the case directory, the cases entered in SORMAS are listed in table form and can be opened by clicking on the blue case ID in the first column (A). The case ID is assigned automatically by SORMAS.

The case directory shows "active cases" by default. After 90 days, cases are automatically closed in SORMAS unless your office has configured a different number of days using the AUTOMATIC_Archiving function. When cases are automatically closed, any associated contacts, samples, tasks and event participants are also closed. Until version 1.71, the closing function was referred to as "archiving". The function ensures that cases, contacts or events that are no longer relevant are hidden in the directories and can be found via the status of the respective entity under "closed". Write protection is generally applied to completed entries via the EDIT_ARCHIVED_ENTITIES function configuration - if this is not desired, this feature can be deactivated on an office-specific basis (see the Delete chapter). This applies to all entities (cases, contacts, events, event participations and entries). The selection window on the right above the table (B) can be used to select between active (default) and closed cases as well as all cases (active + closed cases). You can only see closed cases if you have the corresponding role authorization; they are no longer available on the user interface for other users.

Further filter options are located directly above the tabular directory (C) and are explained in more detail in chapter 2.1.1. Please note that the visibility and editing options of cases depend on your user role and the limited responsibilities assigned to it (example: a monitoring manager with the area of responsibility Baden-Württemberg does NOT see the case created by another user in the case directory and NOT in the list of persons if this case has a different responsibility, such as Bavaria). Detailed information on user:internal rights can be found in the document User:internal roles at www.sormas-oegd.de and in the admin manual.

The case directory data can be exported in various levels of detail as a csv file (D).

Cases can be entered using the New case or Line listing (E) fields.

The case directory can be displayed as a standard view, detailed view or in the tracking overview (F).

• The default view is the preselected view when calling up the case directory and contains a tabular overview of selected information, such as: Case definition category, course of the disease, vaccination status, examination status, if in use: symptom diary status (registered, not registered) and surname/first name.

• In the detailed view, in addition to the columns known from the standard view, further personal information on the respective case, such as: Gender, age, home address or telephone number.

The tracking view lists the tracking entries made for the respective cases. These can be created in two ways: Calls or Visitsare documented in the "Follow-up" tab in the corresponding case file. The time period can be selected on the right above the tabular tracking view (B). A legend of the call histories to be seen in the directory can be found below the directory (C).

Open

Filter functions

The case directory offers the option of filtering the displayed data according to various criteria. For this purpose, a series of selection fields can be found above the tabular display, which can be used, for example, to restrict the displayed cases exclusively to those whose investigation is still pending (A).

Further filter options can be found directly under the heading Case directory. Here, for example, only cases in a specific case definition category can be displayed or only cases that are currently being tracked (via the "Tracking status" filter). It is also possible to search specifically for the name (B), the case ID, the EPID number or an institution (C). Click on "Show more filters" to open further filter options, which can be activated by clicking on the "Apply filter" button or deactivated by clicking on the "Reset filter" button (D). There are also options to filter according to the type of isolation (status: Domestic, Institutional, None, Unknown or Other). Furthermore, the guarantee of care can also be selected as a checkbox for filter options. It is also possible to filter according to the type of responsibility of cases (selection options 'Area of responsibility', 'Location' or 'All'). The extended filter options can then be collapsed again via "Show fewer filters" (not shown in the illustration).

New Case

A new case can be created from the standard or detailed view of the case directory using the "New case" button.

Click on "New case" to open a separate input window in which you first enter person-specific information. Mandatory fields are marked with a red asterisk; these must be completed in order to save the case.

Attention! The "Case origin" field (A) is always left at the default setting "In country". The "Case origin" field is NOT intended for specifying trips (this is done in the Epidemiological data tab). The "Place of entry" setting exists for recording cases at e.g. airports.

The notification date (B) describes when the notification was received.

In addition to the field "Disease" for example (Covid-19), a mutation variant or the status of a corresponding detection (D) can be entered if evidence is available.

In the area of responsibility (E), the federal state, district/city and municipality of the responsible office that processes and reports the case are entered.

If the case has a location that differs from the area of responsibility (F), the corresponding documentation can be expanded by ticking the box below (G). For example, cases that are currently in a clinic can be better mapped if the location is decoupled from the area of responsibility. This means that if the clinic is located in a different district to the original location, this can be documented and has no negative impact on access rights. Observe the office's internal procedural instructions on how to proceed in the event of unclear responsibilities/different places of residence.

Under the selection "Whereabouts" (F), you specify whether the person is accommodated in a facility during the isolation or spends it at home/privately. An institution can be described in more detail using the additional fields that appear after selection

The date of birth (I) should definitely be entered for further identification, but it is not a mandatory field so that the case can be recorded even if the data is not yet complete. If applicable and available, a primary telephone number (other telephone numbers can be entered elsewhere), a primary e-mail address and the date of the onset of symptoms should also be noted (J). Using the magnifying glass symbol (K), you can search whether the person you are currently creating is already stored in the system. This function is supplementary to the duplicate detection in SORMAS and is another way of recognizing persons who may already exist in the system and not creating them twice.

When creating a case, you can enter details of the home address (L), if known. This is available at the end of the case creation window via the query "Enter the case person's home address now". Activating this checkbox opens a drop-down menu in which you can enter the home address. Saving takes you to the newly created case file (see Chapter 2.2). The address can then be found again in the case file under the Person case tab.

Mechanism for recognizing duplicates

This chapter explains the detection of potentially duplicate persons, cases, contacts and events in SORMAS - how the process works in general and which variables are taken into account:

General information

Duplicate detection is always based on the responsibility of the user who creates or imports persons, cases, contacts or event participants into the system. Data to which the user does not have access is not taken into account, meaning that it is theoretically possible for duplicates to be created even if every user makes consistent use of duplicate detection. To remedy this, users with the appropriate rights have access to the special "Merge duplicates" view (for cases and contacts), which is accessible via the respective directories. The system can be cleaned up here by merging duplicate data.

Please note that there is currently no duplicate detection when data is transferred to SORMAS via the ReST interface!

People

Whenever a user attempts to create data relating to persons - cases, contacts or event participants - the system is checked for similar persons before a subsequent duplicate detection of the actual case, contact or event participant is carried out. A person is recognized as a potential duplicate if it fulfills the following requirements. Any variable that is not specified for the person created is ignored in this calculation.

⮚ The person must have a similar name.

To recognize similar names, the pg_trgm module of PostgreSQL is used, which uses trigrams to calculate the similarity between two strings, in this case the names of two people. The default threshold for similarity is 0.65. This threshold can be adjusted by changing the value of the server property namesimilaritythreshold .The higher the value, the more similar the names must be for them to be recognized. A swap of first and last names is recognized; UE/Ü is recognized for first and last names (e.g. Müller and Mueller); separators are recognized for first and last names.

⮚ Both persons must have the same gender or no gender (if specified for the person created).

⮚ The gender "Unknown" matches any other gender, so that the system recognizes a person with the gender "Unknown" as a potential duplicate of a person with the gender "Unknown".

gender "Male", "Female" or "Other" as long as all other requirements are met.

⮚ Both persons must not have a different year, month or day of birth (the date of birth must be identical).

⮚ Persons are also recognized as potential duplicates if their year, month or day of birth is blank. They are only excluded if there is an actually different

value.

⮚ Both persons must not have a different national health identifier (not relevant for German systems).

health insurance number, this field is used for duplicate detection. Since version 1.68, the passport number and health insurance number fields are no longer available, so they can only be used to compare duplicates in previous cases if both cases have the fields titled. Otherwise, the fields are not taken into account in a comparison. If you have used this field for other purposes, this is a source of error in the duplicate detection; duplicates are then not recognized as these fields must match.

⮚ If available, both persons are stored with the same reinfection date.

A configuration option allows the following setting, which is deactivated by default, to be activated: The person must be linked to at least one case, contact or event participant. If the server property duplicatechecks.excludepersonsonlylinkedtoarchivedentries is activated, the associated case or contact or the event to which the event participant belongs must also be active, i.e. not deleted and not completed.

Cases

If a user attempts to create a case and a potentially duplicate person has been identified and selected, the system is also checked for similar cases of the selected person. A case is classified as a potential duplicate if it meets the following requirements. Any variable that is not specified for the case created is ignored in this calculation. Only cases that have not been marked as deleted are considered, including closed cases.

⮚ Both cases must have the same disease.

⮚ Both cases must have the same region of residence or (if the region of residence is empty) the same responsible region.

⮚ The reporting dates for both cases must be within 30 days of each other.

Line listing

With this variant of case entry, outbreaks can be efficiently created in facilities where people live or are accommodated for a certain period of time (e.g. nursing homes, hospitals, etc.). To do this, the mandatory fields in the top line are first filled in before

"Registration date", "Municipality responsible" and the "Facility" in the second line.

The administrator stores the facilities relevant to the region so that they can be selected via the drop-down menu. By clicking on "Add line", the line with this information is listed again below. In this way, a different infected person can be created as a case for the same facility per line.

Case file

Once you have successfully entered and saved a new case, you will be taken to the case data. Like a file, this is divided into several pages running to the right, which are referred to as tabs (A). On the far left, marked with an arrow, you can return to the case directory if you want to leave the file (B).

In the top right-hand section of the page you will find linking options; here you can create or link tasks (C), samples (D),events (E) and immunizations (F) for the case.

Your office may have opted to activate automatic task creation. If this is the case, a task is automatically assigned to a user after creation. When a new case is created, the "Case investigation" task is then created automatically. This is assigned to the responsible monitoring officer in the area of responsibility (for more information, see chapter 4 Tasks).

Under Samples (D), you can directly insert a sample for the associated case (further information in chapter 7 Samples).

In the Events box, it is possible to note participation in an event (for more information, see chapter 5 Events).

Vaccinations (F) can be stored directly with the case in SORMAS and are then person-dependent, i.e. if further entities (e.g. contact situation or event participation) are created for this person, the vaccination for the corresponding disease is also displayed there. To create a vaccination for a case, click on the "New vaccination" button. The creation window opens to create a new vaccination. See chapter Vaccination status and entering vaccinations.

If the case has been reported by means of laboratory evidence, this is recorded via an entry under Samples (D); if the report originates from other sources such as a hospital report/medical diagnosis, this must be recorded under Reports (H).

It is also possible to create notifications in mass processing mode (for more information on mass processing mode, please refer to the Admin Manual). The files generated under the document template can also be uploaded directly to the respective entity (see illustration). A document repository (I) is available for this purpose, which enables documents to be uploaded and attached.

The following file formats can be uploaded: jpg, png, doc, docx, pdf, xls, xlsx, dot, dotx with a maximum size of 20MB per document. These attachments will not be displayed if a user without the corresponding rights has access. A reporting user always has full access, even if the case does not fall within their own area of responsibility.

Case

The first tab of a case file, "Case", shows you detailed information about the individual case and its classification. All the information that was entered on the input screen when the case was created has already been transferred here. Other details, such as the case definition category or the investigation status, still need to be entered here and will be explained in the following chapters.

Investigation status

The investigation status can be defined under the reference definition field. In the original logic of this field, an examination is considered "completed" if the case has been confirmed by a test result or a medical diagnosis. If the status is set to "performed", a field for entering the date of the examination appears next to it.

The investigation status is automatically linked to the task type "Case investigation" in the program: If a task of the type "Case investigation" has been created under the task function and this task is then set to completed after the investigation has been completed (task status

"completed") You can then see the completed task highlighted in grey in the box on the right. Conversely, this is also automatic: if the task "Case investigation" exists (task status open) and the investigation status is set to "Completed", this automatically results in the task

"Case investigation" is set to "Completed". Read more information on this in the chapter on automatisms.

File Number/Token

You can use the internal/external file token field to enter your own file number or similar. This is used exclusively for internal documentation in the public health department and has no effect on sending to the reporting software or similar. This field is intended to improve the mapping of work processes.

Under the disease variant, you can record the mutation variant of the virus or the status of a corresponding detection if required.

Responsible Jurisdiction

Under Area of responsibility, you will find the responsible region, district or city and community entered when the case was created. However, if the case is located at a location other than the area of responsibility (e.g. in a clinic in a neighbouring district), this can be marked by ticking the box below, whereupon further fields for localizing the location will appear.

Pre-existing conditions

Previous illnesses can be entered in the Case tab below the isolation of a case person.

Enter vaccination status and vaccinations via vaccination module

Under the subheading Additional medical information on the page, you will see the Immunization status (A) field.

This is automatically filled by the program if one or more vaccinations have been entered in the link options (shown as boxes) on the right under Vaccinations (B). Although it is possible to open the drop-down menu of the Vaccination status field and manually select a value such as Vaccinated, this will not generate an entry in the Vaccinations box. Enter vaccinations directly in the box on the right-hand side (B) so that the information is automatically complete in both places. Attention - if a vaccination is entered and the vaccination status is then set to "Vaccinated", but this vaccination is subsequently deleted again, the vaccination status does NOT jump back to "Unvaccinated"!

The relevance of a vaccination for the corresponding entity (case, contact, event participation) is compared in the following hierarchy based on the vaccination date:

• at symptom start > reporting date for case situations of this immunized person

• on the date of the last contact > reporting date for contact situations of this immunized person

• on the start or end date of the event > reporting date for event participation of this immunized person

A vaccination entry that is made in a record is automatically displayed in all existing records for this person (case, contact situation, event participation, as the vaccination module is linked to the person entity (dependent on the person entity). Vaccinations without dates are not used to calculate the vaccination status and are greyed out as irrelevant. The visual representation of relevance is intended to highlight vaccinations that took place before the relevant dates. The display of relevance has no influence on the possibility of editing vaccinations.

The vaccine manufacturer is filled in automatically after selecting the vaccine name. Each vaccination entry is stored as a single line.

The date on which the vaccination was carried out may differ. In field B, the reporting user is listed in a vaccination. A selection of common vaccine names is provided in the Vaccine name (D) field. The appropriate vaccine manufacturer is automatically added by the system after the vaccine name has been entered. The F field is a free text field for documenting the vaccine type - here you can manually enter, for example: Vector-based or mRNA vaccine can be entered here manually. The vaccination information source (G) also contains a selection (vaccination certificate, oral communication, no proof, unknown). The vaccine dose can be entered in the free text field H. Codes can be entered in fields I, J, K and L to verify the vaccine batch. The INN stands for International nonproprietary name. This name is for the BioNTech Covid-19 vaccine e.g: "tozinameram". As soon as a vaccination has been created, the vaccination status is automatically adjusted to "Vaccinated". However, if this vaccination is deleted again, the vaccination status is NOT reset to "Unvaccinated" or "Unknown".

The documentation of a vaccination for contacts or event participants is carried out exactly as shown above in the case.

Enter vaccinations via import

Vaccination data can also be imported via the case directory using the "Import" button. It is important to note that the vaccine names in the csv files can be arbitrarily assigned to the manufacturers. There is no validation during import. This only exists for manual entry directly in the system.

Export of vaccination data for cases, contacts and event participants

There are different ways to export vaccinations in SORMAS. The user-defined export for cases and contacts can be used for this purpose, for example. To create a custom case export, you can select the cases to be exported in mass processing mode or go directly to the "Export" button and select "User-defined case export" (for more information on mass processing mode, see the Admin Manual).

You can then use the "New export setting" button in the window that opens to create a new export with the selection shown in the following illustration. This data is created in the standard csv format.

With the help of the detailed case export, all vaccination data available for selection in the "user-defined export" can be exported in full. To create a detailed case export, you can select the cases to be exported in mass processing mode or go directly to the "Export" button and select "Detailed export". This data is also made available in the standard csv format.

Vaccination data can also be exported from SORMAS using a database export. To do this, go to the "Statistics" section (with the Administrator user role) and click on the "Database export" tab. After selecting "Immunizations and vaccinations" plus other required fields, please click on "Export".

Vaccinations are listed in SORMAS as a means of immunization. Other means of immunization can be e.g: Recovery, or Vaccination & Recovery. The management of immunizations is possible in principle with the IMMUNIZATION_MANAGEMENT feature, but currently remains inactive in Germany due to the higher administrative effort for immunizations. Immunizations are superordinate to vaccinations and are referenced by them in the database. Immunizations, in turn, are linked to the person in the database. This means that immunizations can now be displayed in all entities attached to a person.

Tracking Period

The follow-up period is normally set at 10 days from the onset of symptoms. If a case is asymptomatic, the sample collection date is used, but only if a positive pathogen test result is stored here. The notification date is only used if the date of the first sample is after the notification date.

The hierarchy of the calculation is therefore as follows:

⮚     Symptom onset > Date of first sample taken > Notification date.

Thanks to the server configuration activated by default for overriding any tracking duration, the end of tracking can be switched off and on or overwritten as required (e.g. for free tests). If your office decides against this option, it can be deactivated.. Please discuss this option with a SORMAS administrator in your office. However, an extension is possible at any time. A comment must be entered if the process is aborted. If the tracking status is canceled before the actual/expected end, the date of the interruption and the processing user will be documented. In addition, the scheduled/expected end of tracking is displayed next to the actual tracking date.

If the office works with the role distribution of the monitoring officers, this can be selected below. The user roles are set up by your administrator.

At the end of the Case tab, you can see the "Deletion date". This shows when the case will be deleted from your SORMAS instance. Samples, documents, follow-up calls and tasks associated with the case are also deleted. Deleting or closing cases, contacts and events is only possible with the administrator user role. Further information can be found in the deletion chapter or in the admin manual.

Case Person

All personal information can be documented or viewed in the Person case tab. This includes, for example, title, first and last name, gender, date of birth and contact addresses. If a date of birth has been saved, the person's current age is automatically calculated and also displayed. Under Current status of the person, you can specify whether the person is alive or deceased.

The external Token (external ID) is related to the national health ID and internal number can be used for a specific numeration within your organization,

Important!

The External ID on this Case Person page is not identical to the External ID on the "Case" page, as the latter is the External ID of the case situation and the External ID here on the case person by the external ID that is assigned to the natural person. As it is possible for the same person to be listed several times as a "case" in the case of reinfection, a distinction must be made between the "case" situation and the "natural person". The internal file number field is available for an office-specific file number (not shown in the figure).

In addition, information on employment (e.g. "working in the healthcare sector") and place of residence can be entered.

If the home address is a facility such as a retirement home or hospital, this should have been entered by the administrator in the drop-down menu in your SORMAS instance. In order for the facilities to be selected, it is important to select the federal state and the municipality beforehand.

The address of the facility is filled in automatically if the administrator has entered it. If the administrator has not yet entered the facility they are looking for, the facility can be entered manually by selecting "Other facility".

If an exact address is available, it can be linked to GPS coordinates to enable it to be displayed on the overview map in the dashboard (see section 1.1.5). To do this, click on the geo button after entering the address. The GPS coordinates are then automatically transferred to the two fields provided for latitude and longitude and linked to the dashboard. Clicking on the eye symbol displays a small overview map with the calculated position. Information on contact persons (first and last name, telephone number, e-mail address) of facilities can also be stored.

Additional addresses, such as a second home or workplace, can be added using the "New entry" button above the "Addresses" table.

A window opens that corresponds to the input mask for the home address. Please note, however, that only the entry under "Home address" is listed in the case directory. You will find the entries under the other addresses, apart from the entry in the respective case file, in a database export in the Statistics section. There, in the "locations" table, you can search or sort according to the addresses themselves or the address type, for example.

Additional contact information such as telephone numbers or email addresses can be entered at the end of the Case Person tab. You can specify which details are the primary contact details. This selection is displayed in the case directory (detailed view) and is also used for making contact via the symptom diary - if this is used in the office. You can create multiple entries using "New entry".

Hospitalization

Further information on the case person's stay in a medical facility can be stored in the Hospitalization tab. If the location of the person has already been set accordingly when creating the case or in the Case tab, the information on the facility will already be available in the upper area, "Current hospital stay".

All (further) information on a current hospital stay is noted in the upper area, while previous hospital stays can be recorded by setting "Yes" in the lower area and making an entry in the following table field.

If you are now recording a current hospitalization for a case whose current location was previously set to "Home" or another facility, first select "Yes" for "Was the patient admitted to a hospital" at the top. The option to specify the exact hospital where the patient was admitted only appears after the first save in an input window that then appears. You can then enter the date of hospitalization and, if known, the date of discharge as well as the reason for the stay (reported illness, isolation, other reason or unknown).

You can also select the facility that your administrator has stored. Before or after this, fill in the remaining data for the current hospital stay. The details are automatically changed and added in the Case tab under Location (following figure).

The name of the selected facility now appears in the Hospitalization tab and further information on length of stay, inpatient treatment and discharge can be entered. If a case is transferred from one facility to another, selecting "Transfer case" in the "Infrastructure data has been changed" query will result in the previous facility automatically appearing as a table entry under "Previous hospital stays". This does not happen if "Edit data" is selected instead.

 If, on the other hand, you first change the location to a hospital via the Case tab, you must select the "Transfer case" button in the "Infrastructure data has been changed" query after saving the change.

Symptoms

In the Symptoms tab, existing and new signs of illness as well as the date of symptom onset can be entered. The information in this tab is also automatically supplemented by newly reported symptoms from the follow-up as soon as a new follow-up call is recorded (see also section 2.2.6). The entries are used for the automatic calculation of the case definition categories.

There are also three buttons that can speed up data entry:

• Delete all: Removes all entries from the list of symptoms (if a symptom start date was previously saved, this will be grayed out).

• Set blank to No: Sets all symptoms for which no entry has been made to "No".

• Set blank to Unknown: Sets all symptoms for which no entry has been made to "Unknown".

Epidemiological Data

All known information on the incidence of infection is summarized under the Epidemiological data tab. Detailed information, also with additional entry of the exposure localization, can be entered under "Exposure details known". Click on "Yes" to display a table. New entries are then added using the "New entry" button.

In the input window that opens, you can enter the details of the exposure, such as the start and end dates and a detailed description. The only mandatory information is the type of activity, such as work or returning from a trip.

In addition, information can be provided on the circumstances of the exposure (e.g.: "Were masks worn?", "Did the exposure take place indoors or outdoors?", "Was the distance less than 1.5m?", "Was the exposure longer than 15min?") and the location of the exposure can be entered. The entry of the location is based on the already known mask from the Person case tab.

It is also possible to enter information on the person's activity as a case that relates to care, accommodation or activities in facilities. For example, if the person continued to work as a caregiver AFTER their infection, click on

"Yes" under "Activity details known", a new entry can be generated using the table that appears.

After clicking on "New entry", a window opens to describe this activity as a case, which is similar to the input window for exposure.

Contacts

All contact persons linked to this case are listed in the Contacts tab. Clicking on the respective contact ID opens the respective contact file directly. New contacts can be created via the "New contact" button (a single contact) or via "Line listing" (several at the same time).

A form for entering the contact person opens (see section 3.2). Here, the current index case is

automatically linked directly to the contact. When creating a new contact with an associated case, a checkbox "Transfer address of case person" with an eye symbol appears under the "Relationship with case" field if the "Living in the same household" option is selected. This function automatically transfers the home address of the case for the contact if the case and contact live in the same household. When you click on the eye, a window appears with the address of the case. This option is also available when creating contacts via the line listing. After creating a new contact situation via "New contact", the respective contact file is opened directly or the contact directory is opened afterwards via "Line listing".

Duplicate detection / duplicate recognition when entering contact persons

If a person is entered whose name is similar to a person already stored in SORMAS, the duplicate detection window appears after saving (for the duplicate detection mechanism, see section 2.1.2.1). Here you can check whether it is the same person. If this is the case, select this person from the table and save. If this is not the case, check the "Create a new person" box at the bottom left. Duplicate detection searches the database for both active and completed persons.