On-demand evaluation of future epidemiological scenarios caused by COVID-19, with UPV seal of approval
What would be the effect of a 50% reduction in contact between children and elderly people, with or without masks, what would happen if schools were reopened, and what about confinement in neighborhoods? These and many other scenarios can be simulated with LOIMOS, a new software tool in whose development researchers from the Polytechnic University of Valencia (UPV) are participating.
LOIMOS will make it possible to simulate and evaluate the effects of different epidemiological scenarios of COVID-19 and to predict the evolution of the pandemic in the face of future mutations of the virus in possible new waves of the disease.
The project is led by the Foundation for Biomedical Research of the Ramón y Cajal University Hospital (FIBio-HRC) and has the collaboration of the technology company Biotech Vana S.L. It is also one of the proposals selected from the call for research projects on SARS-COV-2 and COVID-19 promoted by the Ministry of Science and Innovation through the Carlos III Health Institute.
Evaluation of virus incidence in custom-designed scenarios
According to José Mª Sempere, from the Research Group on Automata, Formal Languages and their Applications (ALFA) belonging to the VRAIN-UPV Institute, LOIMOS will be developed under the paradigm of membrane computing, which makes it possible to design the behavior of the virus in different environments.
«The virtual design of the biological behavior of the virus and the actions of all the elements that surround it, such as infected, healthy and recovered people, decisions on isolation in public spaces (hospitals, schools, companies…), the hierarchization of territories in physical areas (neighborhoods, municipalities, provinces…), etc. will make it possible to evaluate the incidence of the virus under different situations designed a la carte and to observe its evolution in time projections,» explains Sempere.
In this way, the model will focus on an initial set of parameters and will make it possible to simulate changes in each of them and predict what the repercussions of these variations would be. «We can draw multiple scenarios, ask multiple questions, even varying different rates or actions, and with our model, predict their effects,» says Marcelino Campos, also a member of the ALFA-VRAIN group at the UPV.
Parámetros que incluye el modelo
Among the parameters to be included in LOIMOS are the basic population structure of the study area (children, young people, the elderly), the rate of individuals carrying COVID-19 in each group by age group, and the rate of contact by age group or daily contact times at less than two meters.
The model also allows working with variations in the viral propagule -minimum amount of virus to infect a healthy person-, the rate of viral transmission per minute to an uninfected person, as well as the rate as a function of time since infection and the level of virus survival on surfaces.
Other variables included are the rate of transmission reduction, the time to onset of antiviral immune response in children, young people, adults and the elderly, and even the rate of protection with an eventual antiviral vaccine as a proportion of vaccinated individuals.
«The essential advantage of the model,» says Sempere, «is that it is possible to assign values to each of these parameters according to the expected, desired, or effectively proven ranges, and to observe the effect they will have on the dynamic structure of the epidemic. But, above all, it gives the possibility of simultaneously modifying different values or study ranges, which makes it possible to make predictions of the effects that could result from carrying out certain interventions, thus aiding decision making.»
«The system is easily scalable,» he adds, «as it allows the introduction of new observations or knowledge, forming a true virtual test laboratory.»
Membrane computing
La computación con membranas en que se basa la herramienta LOIMOS es un paradigma de computación natural propuesto por el Gheorghe Paun en 1998. Su fundamento está inspirado en el comportamiento de la célula eucariota viva como procesador de información bioquímica de forma paralela, distribuida y no determinista, permitiendo una aproximación estocástica fundamental para el modelado de sistemas biológicos, tal y como el que se aplica en este proyecto.
La principal ventaja y novedad que incorpora la computación con membranas con respecto a otras herramientas epidemiológicas es la interacción multijerárquica y multinivel de los diversos actores de los escenarios de la pandemia. Estas interacciones se propagan a todos los niveles del sistema, lo que permite variar diversos elementos simultáneamente y conocer sus efectos en franjas temporales y, por tanto, ayudar a la toma de decisiones a nivel socio-sanitario.
ARES, a useful previous experience
In 2015, the team from the VRAIN Institute of the UPV, the Foundation for Biomedical Research of the Ramón y Cajal University Hospital, and Biotech Vana, developed the ARES (Antibiotic Resistance Evolution Simulator) platform, which has been internationally recognized for the study of the transmission dynamics of antibiotic resistance.
«Now,» concludes Campos, «we are taking advantage of our experience in the development of ARES for the design and implementation of LOIMOS, and it is expected that, in a short period of time, the first version of the tool will be ready to be validated and tested in various decision-making environments, mainly in hospitals and healthcare management».
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