BackgroundThe occurrence of the novel porcine circovirus type 3 (PCV3) was reported from the Americas, Asia and Europe. Although this virus was detected in association with various clinical syndromes in pigs, its role as possible swine pathogen remains unclear. PCV3 was detected with high prevalence in Polish farms, but to date no genome sequences were available from European PCV3 strains.MethodsWe collected 1060 serum samples from piglets at the age of 20–24 weeks from 53 farms distributed all over Germany. PCV3 DNA was detected using a real-time PCR and subsequently complete PCV3 genome sequences were obtained after multiply primed rolling circle amplification and sequencing of overlapping PCR products. Phylogenetic analysis was performed by neighbor-joining method and maximum likelihood method.ResultsWe obtained 15 complete PCV3 genome sequences as well as nine partial sequences including the putative ORFs 1, 2 and 3 from PCV3 viremic animals in German pig farms. Phylogenetic analysis of these German as well as 30 full genome sequences received from GenBank divided the PCV3 strains into two main groups and several subclusters. Furthermore, we were able to define group specific amino acid patterns in open reading frame 1 and 2.ConclusionPCV3 is distributed with high prevalence in German pig industry. Phylogenetic analysis revealed two clearly separated groups of PCV3 strains, which might be considered as PCV3 genotypes. Specific nucleotide and amino acid marker positions may serve for easy and fast intraspecies classification and genotyping of PCV3 strains. No correlation between PCV3 variants with their geographical origin was evident. We found the same diversity of PCV3 strains in Germany as in other countries. We hypothesize that PCV3 is not a newly emerging virus in the German pig population. Future studies will have to show, if PCV3 genotype specific biological properties are evident.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-0929-3) contains supplementary material, which is available to authorized users.

Background Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) continues to be a major economic issue for the swine industry worldwide, not only due to acute outbreaks but also endemic infections. PRRS disease severity and consequently financial losses can vary greatly between endemically infected farms and estimation of damage is challenging. This study aimed to assess the economic effect of PRRS in a systematic way at individual farm-level for endemically infected herds, using a PRRS cost simulation tool. In total 21 German sow herds with endemic PRRSV infection were investigated. Data on health and production performance, farm management and environment to be fed into the calculator was collected on each farm, and blood samples taken to confirm the PRRSV status. Results All study farms experienced a significant loss attributable to PRRS. The median farm budget across all farms was − 31 € per sow and year, compared to a median simulated farm budget of 248 € if these farms had been PRRSV negative. The median total loss attributable to PRRS was 74,181 € per farm per year, corresponding to a median total loss per sow and year of 255 €. The impact of PRRS on farm profits was − 19.1% on average and − 41% in the worst case. Conclusions The calculated losses give a good hint of the economic damage due to PRRS for the pig industry. Even in endemically infected farms, farmers face a non-negligible damage and profit from a concerted PRRS control. The calculator has proven itself in the field to render a valid estimation of losses due to PRRS in endemically infected farms.