Samples

Selecting the Samples menu item in the blue ribbon takes you to the sample directory. There are overview has two possible views: Human (A) and Environment (B). You can switch between the two views by clicking on the respective button at the top right. The active view is highlighted in dark blue.

Here you will find for the selected view a list of all samples documented in SORMAS, regardless of whether they were recorded under cases, contacts or event participants (in the view ‘human’) as well as all documented environment-related samples for the ‘environment’ view. However, samples that belong to archived entities can no longer be edited (provided no other active entity is linked). Here you can get an overview of all available samples, filter, sort and export the overview according to certain criteria and edit existing samples, for example to add new test results.

Sample directory for the “human” view

In the upper area you will find the available filter options for the sample directory (A). You can combine the filters as required, for example to determine all positive samples from a specific laboratory. All selected filters must be activated using the "Apply filters" button or ENTER; the set filters are discarded using the "Reset filters" button.

You can use the predefined filters "Shipped", "Not shipped", "Received" and "Referred to other lab" with a light blue background to filter the list according to the status of the sample (B). You also have the option of filtering the list according to active or archived samples or according to their context (Case samples / Contact samples / Event participant samples) (C).

To edit an existing sample, click on the sample ID in the first column of the table (D). Editing an existing sample is not only possible via the sample directory, but also via opening a person (click on the pencil symbol in the sample which is displayed in the ‘Samples’ box on the right side of the window).

Opening and editing the sample information

To edit an existing sample, click on the sample ID in the sample directory or on the pencil icon of a sample that is displayed in the "Samples" box on the first page of a case, contact or event participant. All the information available for this sample is then displayed.

In the upper area (A) you will find the ID assigned by the system for this sample, the date on which the sample was taken and the ID of the associated case/contact/event participant.

The most important information and mandatory details for a sample are:

Purpose of the sample is usually "External lab testing " and preset accordingly
Date sample was collected is the date on which the sample was taken, whereby the time can also be specified
Type of sample, e.g. throat swab or nasopharyngeal swab
Laboratory is the name of the laboratory to which the sample is/was sent
Date sample was sent and date sample received at lab: if any of the fields "Sent/dispatched" or "Received" is checked, the respective date must be specified
Final laboratory result: test result still pending or positive/negative

Using the tabs (B), you can either go back to the sample directory or directly open the case, contact or event participant associated with the sample. The following options are offered in three boxes on the right-hand side of the screen:

In addition to the ID, the top box (C) contains the most important information on the case, contact or event participant to which the sample belongs.
The Pathogen tests box (D) shows the results of the pathogen tests already performed. You can use the "New test result" button to enter new test results, e.g. a new Covid-19 pathogen test.
In the "Additional tests" box (E), the results of other, non-COVID-19 related tests - if available - are displayed. The "New test result" button allows you to record such additional tests and their results, such as hemoglobin value in urine.

Visualization of samples in the sample and pathogen test area: The laboratory messages are displayed in the Messages menu item as follows: The menu item Messages is displayed as follows: An eye symbol is displayed for sample and pathogen test listings if a laboratory message is pending. Clicking on this symbol opens the corresponding laboratory message if it was previously processed in SORMAS. The arrows (bottom/center) can be used to switch between the stored laboratory messages.

Create new test results manually

To enter a new test result manually, either select the "New test result" in the "Pathogen tests" box on the sample page in the Samples menu or directly in the corresponding (already created) case using "New sample" (in the Samples box on the right-hand side). A new window will open in both situations.

If you create a new sample, the following information must be entered before entering the data for a new test result:

A Purpose of the sample: “external lab testing” or “internal/in-house testing” have to be selected. In case of “external lab testing” the field laboratory has to be specified, and the boxes ‘Request pathogen tests to be performed?’, ‘Sent/dispatched’, ‘Received’ ticked according to the actions taken.

B Date of sample was collected: the date has to be specified, the specification of the time is optional.

C Type of sample has to be chosen from the drop-down menu.

D Laboratory appears if the purpose of the sample is “external lab testing” and must be specified.

E Final laboratory result, with one of the following values: “Indeterminate”, “Pending”, “Negative”, or “Positive”.

Via the Add pathogen test button in the Create new sample window, a new pathogen test can be entered.
When adding a new test result via the Samples menu and the Pathogen tests box, a window opens with the same information to be specified.

The information to be entered for a new pathogen test result is the following:

A Type of test: The type of test used to examine the sample must be specified here, e.g. antigen detection test (rapid test, PCR test, etc.): Antigen detection test (rapid test), PCR test, etc. If “PCR/RT-PCR" is selected, the corresponding test specifications can be entered directly.

B Tested disease: must be selected from the diseases stored in the database.

C Test result: Result of the test, with one of the following values: “Indeterminate”, “Pending”, “Negative”, or “Positive”.

D Result verified by lab supervisor: Indication of whether a verification has taken place.

E Documentation of preliminary pathogen test results: Preliminary test results, e.g. in the form of antigen tests, which are later supplemented by final PCR test results, can be documented using the "preliminary" checkbox when creating new pathogen test results. After entering the final PCR test results, this checkbox can be deactivated again.

If the test result entered is “Positive”, a window opens and a new case for the selected disease can be created.

If you have created the sample in the Case ribbon directly within the case, it will be displayed inthesamples box on the right-hand side. You can use the pencil icon to edit further information about thissample afterwards.

If you have clicked on the pencil icon, you will automatically be directed to the sample itself within the Sample ribbon. You will then see the corresponding case on the left-hand side.

Positive test results for contact persons

If you change a contact's pending test result to "positive", a prompt to automatically convert the person into a case is displayed. Confirm with "Yes" to convert the contact into a case.

Sample directory for the environment view

Work in progress

Export sample directory

Export sample directory for the ‘human’ view

The data in the sample directory for the view ‘human’ can be exported. To do this, there is an "Export" button in the top right-hand corner of the overview, which can be used to start a basic or detailed export.

In both cases, a CSV file is downloaded. The basic export contains all columns that are displayed in the standard view of the sample directory. The detailed export includes all information that can be recorded for a sample. As this export takes a little longer, users are notified of this with a notification window.

Export sample directory for the ‘environment' view

The data in the sample directory for the view ‘environment’ can be exported. To do this, there is an "Export" button in the top right-hand corner of the overview, which can be used to start the export.

A CSV file is downloaded. The export contains all columns of the sample directory.

Delete test results (only for administrators)

The administrator user role has the authorization to delete test results in SORMAS. To do this, open the test result and select the red "Delete" button in the window.

Deletion of samples in mass editing mode is also possible. The mass editing mode can be selected in the sample directory. (Further information on the mass editing mode can be found in the admin manual).