General

EMPERIE started its activities in May 2009, at the start of the first influenza pandemic of the 21st century. A strong reminder of the rationale of EMPERIE, this new pandemic of the novel Influenza A/H1N1v prompted EMPERIE to postpone a significant share of its originally planned activities at the benefit of refocusing its first year efforts to influenza A/H1N1v. Several studies on the epidemiology, antigenic and genetic characteristics, replication-kinetics, reassortment potential, pathogenesis and transmission of this novel pandemic virus were conducted by partners in EMPERIE, providing valuable information for the development of risk assessment and containment strategies. In addition novel serological assays, pan-influenza and influenza A/H1N1v –specific real-time RT PCR methods and indexed (multiplex) 454 whole influenza genome sequencing methods were developed (for more information: see the section on Influenza A/H1N1 response).

Since year two, EMPERIE has shifted its main focus back to the originally planned deliverables. Since its start EMPERIE has collected and analysed a wide range of samples (blood, faecal, respiratory, CSF) covering different viruses (e.g., Influenzaviruses, WNV, Coronaviruses, Bluetongue virus, CCHFV) and different reservoir species (e.g., bats, pigs, arthropods and birds and from humans) from different regions in Europe, Asia and Africa. These samples are used for virus discovery and for the development and validation of EMPERIE’s technological platforms. SOPs for generic PCRs for Adeno-. Annello-, Asfar-, Astro-, Corona-, Flavi-, Herpes-, Orthomyxo-, Pappilloma-, Paramyxo-, Picorna-, Picornabirna-, Polyoma-, Pox-, Reo- and Rhabdoviruses are available as well as different cell cultures and SOPs for RNA purification for rapid prescreening, characterisation and identification of (novel) (sub)types of viruses as well as for next generation sequencing.

In the first three years of EMPERIE more than a dozen novel viruses, or known viruses identified in certain host species for the first time have been identified and characterised using the technologies established in EMPERIE. Examples include novel astroviruses and a novel orthobunya virus (Schmallenberg virus). For more information see the section on Viruses discovered.

Important steps were made in the field of Coronaviruses, with new findings on virus persistence and underlying mechanisms of host innate immunity, host tropism and virulence. In year 3 significant progress can also be reported in our modeling work. Models for modeling emerging or endemic vector-borne diseases, and analyses techniques for integrating multiple epidemiological data streams in pandemics and for inferring epidemic dynamics from sequence data were published and the work on optimizing syndromic surveillance for detecting case clusters is nearing completion.

Several papers on phylogenetic/antigenic methods for predicting pathogen emergence have been published that are foundational for the development of strategies to minimize antigenic evolution of an emerging pathogen—to be able to minimize antigenic evolution; one must (likely) first have to understand the potential variation.

Clinical microbiology training programmes have been conducted at various sites in Indonesia, Nepal and Ghana on GCP, QA/QC, safety, ethics, database entry and maintenance. Laboratories in Ha Noi Vietnam have been upgraded and staff has been trained in the molecular diagnostic procedures.