Moment approximation of infection dynamics in a population of moving hosts

Individual-Based Models for Public Health

Today, infectious diseases represent a threatening concern for human health. Understanding their transmission, and possibly forecasting the dynamics of these pathogens, represents both a scientific and sanitary emergency. To this goal, mathematical modeling has been a widely used tool. Nevertheless, they have important limitations to explicitly model the mechanisms involved in the infectious processes at the individual level. Thanks to the increase of computing capacity, computational models such as individual-based models (IBMs) are very relevant for understanding the complexity of mechanisms at the individual level that can be involved in disease outbreaks. Their computational formalism allows a large flexibility, while they rely on the same philosophy than current models in mathematical epidemiology that have proved their relevance. In this chapter, we review the main qualities of IBMs, what kind of new knowledge they can bring and they have already produced in epidemiological modeling. Then, we highlight their caveats and what could be developed during the future years to make IBMs a more reliable and useful approach.

SimFlu: a simulation tool for predicting the variation pattern of influenza A virus

Since the first pandemic outbreak of avian influenza A virus (H5N1 subtype) in 1997, the National Center for Biotechnology Information (NCBI) has provided a large number of influenza virus sequences with well-organized annotations. Using the time-series sequences of influenza A viruses, we developed a simulation tool for influenza virus, named SimFlu, to predict possible future variants of influenza viruses. SimFlu can create variants from a seed nucleotide sequence of influenza A virus using the codon variation parameters included in the SimFlu package. The SimFlu library provides pre-calculated codon variation parameters for the H1N1, H3N2, and H5N1 subtypes of influenza A virus isolated from 2000 to 2011, allowing the users to simulate their own nucleotide sequences by selecting their preferred parameter options. SimFlu supports three operating systems - Windows, Linux, and Mac OS X. SimFlu is publicly available at http://lcbb.snu.ac.kr/simflu.