Search

Simple Summary: Porcine reproductive and respiratory syndrome virus (PRRSV) can be controlled with vaccines and biosecurity measures. Uncovering local strain diversity is expected to help better understand the disease epidemiology and viral evolutionary dynamics, which will contribute to more effective disease control and prevention. In Hungary, although sporadic virus genetic information has been available since the 1990s, a more systematic data collection was initiated only in the mid-2000s and was maximized after the eradication program started in the mid-2010s. In this study, we report on the origin and spread of co-circulating genetic lineages and clades of PRRSV in Hungary till 2020. This longitudinal molecular epidemiological survey was an important element of the national disease eradication program to achieve PRRS-free status in our country. Porcine reproductive and respiratory syndrome (PRRS) is the cause of the most severe economic losses in the pig industry worldwide. PRRSV is extremely diverse in Europe, which poses a significant challenge to disease control within a country or any region. With the combination of phylogenetic reconstruction and network analysis, we aimed to uncover the major routes of the dispersal of PRRSV clades within Hungary. In brief, by analyzing >2600 ORF5 sequences, we identified at least 12 clades (including 6 clades within lineage 1 and 3 clades within lineage 3) common in parts of Western Europe (including Denmark, Germany and the Netherlands) and identified 2 novel clades (designated X1 and X2). Of interest, some genetic clades unique to other central European countries, such as the Czech Republic and Poland, were not identified. The pattern of PRRSV clade distribution is consistent with the route of the pig trade among countries, showing that most of the identified clades were introduced from Western Europe when fatteners were transported to Hungary. As a result of rigorous implementation of the national eradication program, the swine population was declared officially free from PRRSV. This map of viral diversity and clade distribution will serve as valuable baseline information for the maintenance of PRRSV-free status in the post-eradication era. [ABSTRACT FROM AUTHOR]

Simple Summary: Porcine reproductive and respiratory syndrome is a viral disease that causes significant economic losses in many countries worldwide. In this study, we employed a fast, inexpensive, target-specific next-generation sequencing method that can be used for both laboratory diagnosis and epidemiologic monitoring of the disease. We found the protocol to be highly sensitive and potentially effective on clinical serum samples. The method is suitable for the detection of mixed infections and provides a preliminary insight into the microevolution of the causative virus in affected swine herds. Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019–2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease. [ABSTRACT FROM AUTHOR]

Simple Summary: Two recent transmission chains of PRRSV-2-associated cases were documented in this study using field epidemiological and molecular genetic tools. The investigation highlighted the risks associated with the free movement of livestock in the European Union. To minimize this risk of re-infection of PRRS-free herds with PRRSV through animal imports, it is recommended that pigs are transported directly from the exporting holdings without the involvement of transit stations. Alternatively, the transit stations could be converted so that pigs in transit avoid contact with each other, thus preventing exposure to PRRSV infection. This study reports on the molecular epidemiology of Ingelvac-PRRS-MLV-associated cases in Hungary for the period 2020–2021. Field epidemiology investigations led the experts to conclude that imported pigs, which were shipped through transit stations in Denmark, introduced the vaccine virus. The movement of fatteners and the neglect of disease control measures contributed to the spread of the virus to PRRS-free pig holdings in the vicinity. Deep sequencing was performed to genetically characterize the genes coding for the virion antigens (i.e., ORF2 through ORF7). The study isolates exhibited a range of 0.1 to 1.8% nucleotide sequence divergence from the Ingelvac PRRS MLV and identified numerous polymorphic sites (up to 57 sites) along the amplified 3.2 kilo base pair genomic region. Our findings confirm that some PRRSV-2 vaccine strains can accumulate very high number of point mutations within a short period in immunologically naive pig herds. [ABSTRACT FROM AUTHOR]

Simple Summary: Gizzard erosion is an important pathology in chickens. Aviadenoviruses, in particular, fowl adenovirus 1, have been associated with the etiology of gizzard erosion. Clinical and pathology data from the field and from infection experiments suggested that both virulent and avirulent strains are circulating, although the genetic differences between these two FAdV-1 pathotypes have not been clarified. In this study, we analyzed a total of 40 FAdV-1 genomes, including 32 newly determined genome sequences, and demonstrated that a set of viral genes differ phylogenetically between the two pathotypes. These findings may help select suitable naturally attenuated FAdV-1 strains that can be used as an effective live vaccine acting directly on the mucosal surface of the gizzard. Fowl adenovirus 1 (FAdV-1) is the main cause of gizzard erosion in chickens. Whole genome sequencing and sequence analyses of 32 FAdV-1 strains from a global collection provided evidence that multiple recombination events have occurred along the entire genome. In gene-wise phylogenies, only the adenoviral pol gene formed a tree topology that corresponded to whole genome-based phylogeny. Virus genetic features that were clearly connected to gizzard erosion were not identified in our analyses. However, some genome variants tended to be more frequently identified from birds with gizzard erosion and strains isolated from healthy birds or birds with non-specific pathologies tended to form common clusters in multiple gene phylogenies. Our data show that the genetic diversity is greater, and the evolutionary mechanisms are more complex within FAdV-1 than previously thought. The implications of these findings for viral pathogenesis and epidemiology await further investigation. [ABSTRACT FROM AUTHOR]

We determined the genomic sequence of a Ukrainian strain of fowl adenovirus B (FAdV-B). The isolate (D2453/1) shared 97.2% to 98.4% nucleotide sequence identity with other viruses belonging to the species Fowl aviadenovirus B. Marked genetic divergence was seen in the hexon, fiber, and ORF19 genes, and phylogenetic analysis suggested that recombination events had occurred in these regions. Our analysis revealed mosaicism in the recombination patterns, a finding that has also been described in the genomes of strains of FAdV-D and FAdV-E. The shared recombination breakpoints, affecting the same genomic regions in viruses belonging to different species, suggest that similar selection mechanisms are acting on the key neutralization antigens and epitopes in viruses of different FAdV species. [ABSTRACT FROM AUTHOR]

Duck hepatitis A virus (DHAV), an avian picornavirus, causes high-mortality acute disease in ducklings. Among the three serotypes, DHAV-1 is globally distributed, whereas DHAV-2 and DHAV-3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV-1 strains using extant GenBank records and genomic sequences of 10 DHAV-1 strains originating from a large disease outbreak in 2004–2005, in Hungary. Recombination analysis revealed intragenotype recombination within DHAV-1 as well as intergenotype recombination events involving DHAV-1 and DHAV-3 strains. The intergenotype recombination occurred in the VP0 region. Diversifying selection seems to act at sites of certain genomic regions. Calculations estimated slightly lower rates of evolution of DHAV-1 (mean rates for individual protein coding regions, 5.6286 × 10−4 to 1.1147 × 10−3 substitutions per site per year) compared to other picornaviruses. The observed evolutionary mechanisms indicate that whole-genome-based analysis of DHAV strains is needed to better understand the emergence of novel strains and their geographical dispersal. [ABSTRACT FROM AUTHOR]

A novel gyrovirus was detected in an intestinal specimen of a common pheasant that died due to poult enteritis and mortality syndrome. The genome of the pheasant-associated gyrovirus (PAGyV) is 2353 nucleotides (nt) long and contains putative genes for the VP1, VP2, and VP3 proteins in an arrangement that is typical for gyroviruses. Gyrovirus-specific motifs were identified in both the coding region and the intergenic region of the PAGyV genome. The VP1 of PAGyV shares up to 67.6% pairwise nt sequence identity with reference sequences and forms a distinct branch in the phylogenetic tree. Thus, according to the recently described species demarcation criteria, PAGyV belongs to a novel species in the genus Gyrovirus, family Anelloviridae, for which we propose the name "Gyrovirus phaco 1". [ABSTRACT FROM AUTHOR]