In a first phase of the project, the prevalence and importance of rotavirus infections on Flemish swine farms was investigated using extensive longitudinal field studies on 13 farms, an approach which was unique in the world. Rotavirus was endemically present on all Flemish farms. During the suckling period in the farrowing house, infections break-through in absence of good maternal (lactogenic) immunity or by the end of the farrowing stages when maternal antibodies become more diluted. Rotavirus A infections in the farrowing house were not always leading to clinical problems. The emergence of clinical signs is likely dependent on co-infections (enteric disease complex) and environmental factors (e.g. low environmental temperature). Nevertheless, a reduced growth was observed in presence of severe rotavirus C shedding. On all pig farms studied, several replication waves of different genotypes of rotavirus A and C infections break-through after weaning. Depending on the presence of co-infections (different viruses or bacteria), this situation was leading to diarrheic problems. When a high hygiene standard is pursued, e.g. in high health farms, a reduced rotavirus shedding in nursery pigs was observed. A first strategy to control rotavirus infections and enteric disease problems in general is the use of standardized hygiene protocols as a high health approach is not practically feasible on all farms. Therefore, the protocols developed by companies such as CID Lines, Agrologic, DGZ and Dialab are recommended for the swine industry. However, it is impossible to eliminate rotavirus completely, as the virus is very resistant in the environment. However, using hygiene procedures the infection pressure can be kept under control, leading to fewer replication break-throughs and improved gut health.

In this project, another aim was the refinement of diagnostic assays for rotaviruses. Since the start of the project, there was an enormous revolution ongoing in the diagnostics of infectious diseases using novel sequencing technologies. It was originally foreseen to develop genotype-specific real-time PCR assays to rapidly characterize strains. This would need specific primers for each genotype and is thus not efficient. Viral metagenomics was successfully implemented to enable rapid rotavirus strain characterization in a fast manner. This readout also immediately gives a full overview of all viruses that are part of the enteric disease complex. Using this information, the selection of vaccines and nutraceuticals will be facilitated in the long-term.

To control rotavirus infections, an attenuated rotavirus A vaccine candidate was developed in parallel to the present project. After several passages in cell cultures and upon peroral inoculation this strain was not able to replicate efficient in the gut of conventional neonatal piglets. As a consequence, the vaccine would not be useful to elicit a local and lactogenic immune response in nursery piglets or gilts/sows. This development path was abandoned. In parallel, a recombinant vaccine is now being developed to induce short term protection in the first week(s). The recombinant proteins will also be used for screening of nutraceuticals which can be added to the feed of young piglets around weaning and in order to postpone the moment of a virulent rotavirus infection as long as possible. This has led to a new project (Baekeland) following on the present trajectory.