When a new pathogen arises at the horizon that is contagious and harbours a real risk to generate a pandemic, it is of utmost importance to develop tools based on the genetic content of the pathogen to rapidly detect this emerging infectious agent. In STAMINA, we therefore focused on technologies developed by BioCoS and IPT that can do this quickly and accurately. When an existing pathogen re-emerges, it is easier to respond, because more genetic information of such a pathogen is available or rapid diagnostic tests might already exist that can be re-applied to track and trace the spread of the pathogen in the hope that infected people and their close contacts can be isolated.
For a new pathogen, this is more complex. When there is an outbreak, first responders will try to obtain genetic information from a potential causative agent from infected persons, wastewater or food sources. This will result in new genetic information that is collected at the start of a pandemic of the pathogen obtained from maybe 10 to a few hundred infected people. This genetic information obtained from the causative agent can then be used for the development of a rapid detection method.
One of the first goals in the STAMINA project was to answer the question on how we can use the genetic information of new and emerging pathogens to train the software tools of BioCoS and IPT to then accurately identify genetic regions that are specific for the pathogen that has been identified during the start of a pandemic. In this process, we focused on five pathogens – SARS-CoV-2, Influenza A, Measles, West-Nile Virus and an antibiotic resistant Escherichia coli – and thereby taking into account the area from the human body that is the most optimal region to perform the rapid diagnostic test or the liquid biopsy. For example, for SARS-CoV-2 this is the nasopharynx. In all of these samples, specific bugs can be present that can interfere with the detection process because there is overlap with the genetic information between the newly identified pathogen and the host and between the pathogen and commensal bacteria or other pathogens that can enter the host at the same site where the collection of the genetic material occurs. The work done by our team (in particular by the partners BioCoS and IPT) led to the identification of genetic targets that are specific for SARS-CoV-2, Influenza A, Measles, West-Nile virus and the antibiotic resistant Escherichia coli.
In the next phase, the targets will be analysed with different rapid detection tools to confirm they are specific for a certain pathogen. Also, the sensitivity is determined to get an idea of what the detection limits are of the rapid detection tools, i.e., can we detect, one, ten, a hundred a or thousand pathogenic particles in a one-millilitre urine or blood sample. At the moment, this work in STAMINA project is particularly fascinating, as the team can follow in real-time the things that are going well in the pandemic response and the things that aren’t, which includes the development and usage of a newly developed rapid detection tool.