Mapping of the Influenza-A Hemagglutinin Serotypes Evolution by the ISSCOR Method

Analyses and visualizations by the ISSCOR method of influenza virus hemagglutinin genes of different A-subtypes revealed some rather striking temporal relationships between groups of individual gene subsets. Based on these findings we consider application of the ISSCOR-PCA method for analyses of large sets of homologous genes to be a worthwhile addition to a toolbox of genomics - allowing for a rapid diagnostics of trends, and ultimately even aiding an early warning of newly emerging epidemiological threats.Comment: 26 pages with figures (Figs. 1-4 in the main text, and Figs. S1-S5 in supplementary materials

Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland

In this study we describe a simulation platform used to create a virtual society of Poland, with a particular emphasis on contact patterns arising from daily commuting to schools or workplaces. In order to reproduce the map of contacts, we are using a geo-referenced Agent Based Model. Within this framework, we propose a set of different stochastic algorithms, utilizing available aggregated census data. Based on this model system, we present selected statistical analysis, such as the accessibility of schools or the location of rescue service units. This platform will serve as a base for further large scale epidemiological and transportation simulation studies. However, the first approach to a simple, country-wide transportation model is also presented here. The application scope of the platform extends beyond the simulations of epidemic or transportation, and pertains to any situation where there are no easily available means, other than computer simulations, to conduct large scale investigations of complex population dynamics.Agent Based Model, Educational Availability, Daily Commuting, Social Network, Virtual Society Simulations

Characterization of mAb6-9-1 monoclonal antibody against hemagglutinin of avian influenza virus H5N1 and its engineered derivative, single-chain variable fragment antibody

Hemagglutinin (HA), as a major surface antigen of influenza virus, is widely used as a target for production of neutralizing antibodies. Monoclonal antibody, mAb6-9-1, directed against HA of highly pathogenic avian influenza virus A/swan/Poland/305-135V08/2006(H5N1) was purified from mouse hybridoma cells culture and characterized. The antigenic specificity of mAb6-9-1 was verified by testing its cross-reactivity with several variants of HA. The mimotopes recognized by mAb6-9-1 were selected from two types of phage display peptide libraries. The comparative structural model of the HA variant used for antibody generation was developed to further facilitate epitope mapping. Based on the sequences of the affinity- selected polypeptides and the structural model of HA the epitope was located to the region near the receptor binding site (RBS). Such localization of the epitope recognized by mAb6-9-1 is in concordance with its moderate hemagglutination inhibiting activity and its antigenic specificity. Additionally, total RNA isolated from the hybridoma cell line secreting mAb6-9-1 was used for obtaining two variants of cDNA encoding recombinant single-chain variable fragment (scFv) antibody. To ensure high production level and solubility in bacterial expression system, the scFv fragments were produced as chimeric proteins in fusion with thioredoxin or displayed on a phage surface after cloning into the phagemid vector. Specificity and affinity of the recombinant soluble and phage-bound scFv were assayed by suitable variants of ELISA test. The observed differences in specificity were discussed