HIPS Helmholtz Institut für Pharmazeutische Forschung Saarland

Covid-Pool

 
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Database software for screening projects using a sample-pooling workflow

Covid-pool picture Extensive testing for SARS-CoV-2 is key to mitigating the current pandemic caused by the novel coronavirus. Capacity for testing is nowadays a precious asset and a crucial factor for success of any containment strategy. Thus, additional lab resources are currently being established worldwide. These activities come with a number of challenges: besides technical equipment, chemical supply and appropriate diagnostic protocols, considerable efforts have to be mastered concerning sample-taking, logistics and for data management. Sample-pooling is a method to efficiently utilize available testing capacity and has recently been shown to enable screening of populations with suspected low Covid-19 prevalence at good sensitivity, while consuming only a reduced number of valuable test kits.

► Literature: Lohse et al. (2020), Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. The Lancet Infectious Diseases

What can it do?

Covid-Pool is a software tool to manage a SARS-CoV-2 screening study based on sample pooling, starting with sample barcode generation, tracking of the pooling process in the lab and finally assigning test results to pools and samples. It has been developed to enable efficient collaboration across multiple sites. Due to its simple and intuitive design - focused on the essential functions to support the lab workflow - it has a very fast learning curve.

✉ Contact us if you are interested in using this tool.

How to get started

Covid-Pool is a free open-source software that runs on a standard webserver and requires no client-side installation. Users simply open the Covid-Pool startpage in their web browser. All data is stored in a MySQL database on the server. The application is not resource-hungry and only fairly basic IT skills are required for installation.

► Download - all components in one .zip file

► Software repository - sourcecode on GitHub


Questions & answers

What is the underlying study design?
The Covid-Pool software can be used with simple pooling designs where a number of samples are combined within one pool (typically comprising 20 to 30 samples) which is then tested, and with cascaded pooling setups where a set of smaller pools (typically containing 5 samples each) are combined into one larger pool for first-round testing. See for example these papers where the issue of sensitivity in sample pooling is addressed: Schmidt et al. 2020, Lohse et al. 2020

Has this tool been used in the field already?
The Covid-Pool system has been used during a field study run in southwestern Germany, where over 20,000 persons working or living in homes for the elderly have been screened for SARS-CoV-2 infection. Labs from several institutions as well as a mobile lab truck were involved in that study named "SaarCoScreen". Newspaper article (DE), Press release (EN), Mobile lab (EN)

Which languages does the software support?
Inside the Covid-Pool software the currently available languages are English and German.

How about extended data analysis/reporting?
Covid-Pool offers basic statistical overview functions for the sample pooling process and it can also create report sheets showing the results for pools and samples from any tested source. Moreover, the underlying MySQL database design is simple and makes development of custom data analysis queries easy.

Can the sofware be adapted to my specific requirements?
The Covid-Pool application is built on standard web technologies such as PHP using a MySQL database and is provided as open-source software. This makes it easy to extend or modify the system by any software engineer having the appropriate skills. You may also contact us with your ideas about additional functions.

Can my screening project be hosted remotely on this server?
Our primary aim is to supply Covid-Pool as a free open-source software that can be run by anyone on their own webserver, demanding only basic IT skills for installation and operating on inexpensive hardware. Please note that we are not a compute center/data-services provider. However, if you experience that your facility can absolutely not offer the necessary infrastructure please do contact us.


Installation instructions

Technical prerequisites
The Covid-Pool software runs on a standard webserver and requires no client-side installation. Users simply open the Covid-Pool link in their web browser. All data is stored in a MySQL database on the server. The server needs to operate a web service (usually Apache), PHP and the MySQL system, commonly referred to as a "WAMP" (Windows) or "LAMP" (Linux) configuration. Depending on the usage scenario it may run only on the intranet or also exposed to the internet.

Installing the web-application
When it has been verified that the web server is basically running, the PHP application files are simply copied to the /covid-pool folder inside the web documents directory. Prior to the first test, permissions should be checked and the connection information for the database needs to be entered. See also the detailled installation instructions that come with the software package.

Preparing the database
A database scheme including a small number of test datasets is delivered together with the software download. The setup.sql file needs to be imported into an empty database named 'corona' in order to initialize the MySQL database tables. In addition, a database user with SELECT, INSERT, UPDATE, DELETE permissions must be created and the account information entered into a connection file in the /covid-pool directory. This is also explained in the detailled installation instructions.

Adjust basic project settings
Several settings such as the project name, size of sample pools and constraints for input fields can be configured in a central settings file. Several other options are available through the web interface (some are only for use by the administrator).

User management
The Covid-Pool application comes with a pre-configured administrator account (and the password for this one should be changed upon first login). Additional user accounts can be easily created inside the web interface and the corresponding passwords set. No specialized database knowledge is required for these steps.

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