Sphaerospora molnari Lom, Dyková, Pavlásková and Grupcheva, 1983 often causes severe infections in the gills and skin of common carp fingerlings Cyprinus carpio carpio in Central Europe. Although most Sphaerospora spp. are coelozoic and affect the excretory system of fish, S. molnari develops mature spores in the epithelia of gill filaments, making it a rare representative of histozoic freshwater species within the genus. On the basis of a partial 18S rDNA sequence assigned as belonging to S. molnari, previous phylogenetic studies located the species within the Myxobolus clade. In the present study, S. molnari isolates from Hungary and the Czech Republic were characterized based on morphology, DNA sequence analysis and phylogenetic comparison. The obtained 3714 bp final consensus 18S rDNA sequence of the parasite showed several, sometimes extremely long inserts in the variable regions of the gene and differed considerably from the one published in GenBank in 2002. In situ hybridization confirmed the validity of the obtained DNA sequence and detected pre-sporogonic blood stages in the interstitium and blood vessels of the kidney. Phylogenetic analysis showed that S. molnari clusters within the Sphaerospora sensu stricto clade with a high support, revealing it as the first known histozoic member of the Sphaerospora subclade comprising parasites of freshwater fish.

Myxobolus pseudodispar Gorbunova, 1936 (Myxozoa) is capable of infecting and developing mature myxospores in several cyprinid species. However, M. pseudodispar isolates from different fish show up to 5% differences in the SSU rDNA sequences. This is an unusually large intraspecific difference for myxozoans and only some of the muscle-dwelling myxozoan species possess such a high genetic variability. We intended to study the correlation between the host specificity and the phylogenetic relationship of the parasite isolates, and to find experimental proof for the putatively wide host range of M. pseudodispar with cross-infection experiments and phylogenetic analyses based on SSU rDNA. The experimental findings distinguished 'primary' and less-susceptible 'secondary' hosts. With some exceptions, M. pseudodispar isolates showed a tendency to cluster according to the fish host on the phylogenetic tree. Experimental and phylogenetic findings suggest the cryptic nature of the species. It is likely that host-shift occurred for M. pseudodispar and the parasite speciation in progress might explain the high genetic diversity among isolates which are morphologically indistinguishable.

The genome sequence of a novel avian cyclovirus is described in this study. The genome size and orientation of predicted genes was similar to those described in other vertebrate and insect origin cycloviruses. The greatest genome sequence identity was shared with a dragonfly cyclovirus (nt, 60.6%). Phylogenetic analysis showed marginal relatedness with another avian cyclovirus, the chicken associated cyclovirus 1. In contrast, along a short fragment of the replication-associated protein coding gene (rep) (spanning nt 1240-1710) the duck origin cyclovirus was very similar to human origin and honey bee origin rep sequences (human - TN4, 98%; honey bee - hb10, 100%). Related cyclovirus strains existing amongst various animal species living in diverse ecosystems and separated by large geographic distances show the need for additional studies to better understand the ecology and epidemiology of cycloviruses.

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Circular replication associated protein (Rep)-encoding ssDNA (CRESS DNA) viruses have diverse genomic architecture and are widely distributed in different ecosystems. In this study we characterized the complete genomic sequence of a novel circovirus-like virus, Garrulus glandarius associated circular virus-1 (GgaCV-1). The genome size (1971 nt) and other features (the nonanucleotide, rolling circle replication motif and SF3 helicase motif) are also reminiscent of circoviruses. Similar genomes with uni-directionally localized and overlapping rep and cap genes are typical of type V CRESS DNA viruses that were identified in invertebrates and environmental samples of aquatic ecosystems. GgaCV-1 showed the highest aa identity with partial rep sequences detected in bat feces (77%) and with the rep (54%) and cap (42%) of Lake Sarah-associated circular virus-23 of New Zealand freshwater mussel origin. A dietary origin for GgaCV-1 could not be excluded as the virus was detected in the cloacal swab specimen of an Eurasian jay. Further studies may help to reveal the linkage among variable organisms regarding virus transmission.

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Porcine reproductive and respiratory syndrome virus 1 is a major cause of swine morbidity and mortality in various parts of the world, including Hungary. A national elimination programme to reduce the associated economic burden was initiated in Hungary in 2012. Using extensive laboratory surveillance, we identified and isolated an unusual PRRSV strain. The complete coding sequence of this isolate was determined and analyzed. The genome of this Hungarian PRRSV1 strain, HUN60077/16, is 15,081 nucleotides in length. Phylogenetic and recombination analysis showed a mosaic structure of the genome where a large fragment of ORF1b and the genomic region coding for ORF3 to ORF7 showed a very close genetic relationship to the vaccine virus Unistrain, while the ORF1a region, the 3’ end of ORF1b, and the whole ORF2 were only distantly related to this or any other PRRSV1 strain whose genome sequence is available in the GenBank database. Genomic characterization of PRRSV strains is crucial when possible vaccine-associated cases are identified. This approach not only helps to identify genetic interactions between vaccine and wild-type PRRSV1 strains but may also be needed to prevent trust in commercial vaccines from being undermined.

To analyze the methylation status of wild-type adeno-associated virus type 2 (AAV2), bisulfite PCR sequencing (BPS) of the packaged viral genome and its integrated form was performed and 262 of the total 266 CG dinucleotides (CpG) were mapped. In virion-packaged DNA, the ratio of the methylated cytosines ranged between 0–1.7%. In contrast, the chromosomally integrated AAV2 genome was hypermethylated with an average of 76% methylation per CpG site. The methylation level showed local minimums around the four known AAV2 promoters. To study the effect of methylation on viral rescue and replication, the replication initiation capability of CpG methylated and non-CpG methylated AAV DNA was compared. The in vitro hypermethylation of the viral genome does not inhibit its rescue and replication from a plasmid transfected into cells. This insensitivity of the viral replicative machinery to methylation may permit the rescue of the integrated heavily methylated AAV genome from the host’s chromosomes.