Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe

Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or a small number of genotypes, yet the underlying factors driving invasions are poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated the North American chestnut, and a more recent outbreak threatens European chestnut stands. To unravel the chestnut blight invasion of southeastern Europe, we sequenced 230 genomes of predominantly European strains. Genotypes outside of the invasion zone showed high levels of diversity with evidence for frequent and ongoing recombination. The invasive lineage emerged from the highly diverse European genotype pool rather than a secondary introduction from Asia or North America. The expansion across southeastern Europe was mostly clonal and is dominated by a single mating type, suggesting a fitness advantage of asexual reproduction. Our findings show how an intermediary, highly diverse bridgehead population gave rise to an invasive, largely clonally expanding pathogen.

New circulation of genotype V of Crimean-Congo haemorrhagic fever virus in humans from Spain

Background Crimean-Congo haemorrhagic fever (CCHF) is a widespread tick-borne viral disease caused by the Crimean-Congo haemorrhagic fever virus (CCHFV). CCHFV has been implicated in severe viral haemorrhagic fever outbreaks. During the summer of 2016, the first two cases with genotype III (Africa 3) were reported in Spain. The first aim of our study was to determine the presence of CCHFV among patients with febrile illness during the spring and summer periods in 2017 and 2018. Finally, we perform a phylogenetic analysis to determine the genotype of the virus. Methodology We prospectively evaluated patients older than 18 years who came to the emergency unit at the University Salamanca Hospital (HUS) with fever. Specific IgM and IgG antibodies against CCHFV by ELISA and one immunofluorescence assay against two different proteins (nucleoprotein and glycoprotein C) was done. Moreover, molecular detection by Real Time PCR was performed in all collected samples. A phylogenetic analysis was carried out to genetically characterize CCHFV detected in this study. Principal findings A total of 133 patients were selected. The mean age was 67.63 years and 60.9% were male. One-third of the patients presented an acute undifferentiated febrile illness. Three patients had anti-CCHFV IgG antibodies, suggesting a previous infection. One patient was found confirmed anti-CCHFV IgM antibodies and positive RT-PCR was detected. Phylogenetic analysis indicated that the virus corresponds to the European genotype V. This patient came to the emergency unit at HUS in August 2018 presenting an acute febrile syndrome with thrombopenia and liver impairment. Conclusions We describe a new circulation of European genotype V CCHFV in Spain. Moreover, this study suggests that CCHFV is an identifiable cause of febrile illness of unknown origin in Spain. Thus, CCHF could be suspected in patients with fever, liver damage, and/or haemorrhagic disorders, particularly in people with risk activities who present in the spring or summer.

Commercial PRRS Modified-Live Virus Vaccines

Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) presents one of the challenging viral pathogens in the global pork industry. PRRS is characterized by two distinct clinical presentations; reproductive failure in breeding animals (gilts, sows, and boars), and respiratory disease in growing pigs. PRRSV is further divided into two species: PRRSV-1 (formerly known as the European genotype 1) and PRRSV-2 (formerly known as the North American genotype 2). A PRRSV-2 modified-live virus (MLV) vaccine was first introduced in North America in 1994, and, six years later, a PRRSV-1 MLV vaccine was also introduced in Europe. Since then, MLV vaccination is the principal strategy used to control PRRSV infection. Despite the fact that MLV vaccines have shown some efficacy, they were problematic as the efficacy of vaccine was often unpredictable and depended highly on the field virus. This paper focused on the efficacy of commercially available MLV vaccines at a global level based on respiratory disease in growing pigs, and maternal and paternal reproductive failure in breeding animals.

A Seasonal Study of Koi Herpesvirus and Koi Sleepy Disease Outbreaks in the United Kingdom in 2018 Using a Pond-Side Test

Fluorescence real-time LAMP assays were designed for the orf43 gene of CyHV-3 European genotype and the p4a gene of the CEV genogroup I. A third LAMP assay to detect the ef1a gene of the host common carp was designed as an internal control. The limit of detection was 102 and 103 viral copies under 25 min for CyHV-3 and CEV, respectively. The specificity of the CyHV-3 LAMP assay was 95.6% of 72 fish herpesviruses tested. Sixty-three non-lethal common carp mucus swabs were collected across 16 sites during disease investigations. DNA extractions were performed in under 10 min using the QuickExtract™ digestion buffer. The LAMP amplification of CyHV-3 DNA in mucus swabs from clinical cases was detected from 4 to 13 min in 13 sites, while a co-infection of CyHV-3 and CEV was confirmed by LAMP in a single site. The LAMP results agreed with the results of the reference laboratory. The common carp ef1a was amplified only in 61% of the mucus swabs collected, preventing its use as a robust internal control to distinguish false negatives from invalid tests. After further optimization, these tests could be implemented for border inspection posts surveillance and decentralizing testing during disease outbreaks.

Complete Chromosomal Sequences of Two Borrelia miyamotoi Samples Obtained from Ixodes ricinus Eggs in Czechia

Here, we present complete chromosome sequences of Borrelia miyamotoi samples CZ-F1E and CZ-F190E, which were obtained from Ixodes ricinus eggs from Czechia. The chromosome sequences, assembled from Illumina and Sanger sequencing data, had average coverage values of 647× and 3,216×, respectively. They belong to the European genotype, distinct from the Asian and American strains.

Complete Genome Sequence of an American Isolate of Pepino Mosaic Virus

Pepino mosaic virus (PepMV) is a widely distributed tomato virus. The complete genome sequence of the PepMV isolate US3 from infected tomato fruit was determined. The genome is 6,410 nucleotides long and has a poly(A) tail. US3 shares the highest similarity with strains belonging to the European genotype.

Diseases of different aetiologies in salmonids in Ukraine

The paper contains the results of the studies into the ichthyopathological situation of the invasion and infectious diseases of salmonids carried out by the Ichthyopathology Laboratory of the Institute of Fisheries of Ukraine from 2013 to 2016. The investigated salmonid species included: the rainbow trout Oncorhynchus mykiss, the brown trout Salmo trutta morpha fario, the brook trout Salvelinus fontinalis, and the European grayling Thymallus thymallus. The fish were sampled from aquatculture farms as well as natural water bodies and their diseases included invasive (parasitic) and infectious (viral and bacterial). The most frequently encountered invasions in the brown and brook trout were ciliates: Chilodonella pisci­cola and Apiosoma conicum, Trichodina (in particular T. truttae and T. nigra), Ichtyophthirius multifiliis; monogenea Gy­rodactylus birmani, and diplostoma Diplostomum spathaceum. Aeromonas and Flavobacterium bacteria were isolated from fry and young-of-the-year rainbow trout and brook trout. Y. ruckeri positive samples were isolated from the fish with the signs of yersiniosis. As for viral diseases, IPNV isolates (the first time in Ukraine) of the rainbow trout were first isolated in fish farms in the western regions of Ukraine. A phylogenetic analysis of these IPNV isolates was performed, which showed that they belonged to Sp strain and the European genotype.

Prevalence of UGT1A1 Genetic Variants in Argentinean Population, Potential Implications for Pharmacogenomic Testing

ABSTRACTThe four groups of uridine diphosphate glucuronosyltransferase (UGT) enzymes form a superfamily responsible for the glucuronidation of target substrates. These include hormones, flavonoids, environmental mutagens and pharmaceutical drugs. Thus, UGT enzymes are relevant for pharmacogenetic research.Most of the members of the UGT family are expressed in the liver, but are also present in intestinal, stomach or breast tissue.The incidences and types of polymorphisms for different enzymes vary with geographical regions and ethnic groups. This is the first study that examined the frequency of polymorphisms for UGT1 isozymes for a population of 100 healthy argentinians.The distribution of UGT1A1 in our population was: 70.5% (70.5) for the *1 allele, 21.5% for the *28 allele and 1% for the *36 allele. 48% (48) presented the *1/*1 genotype, while 43 % (43) had *1/*28, 2% (2) had *1/*36 and 7% (7) showed *28/*28. There was no preferential sex distribution.Since most Argentinians are of Caucasian descent, a European genotype frequency profile is to be expected. That is evident in the wild type prevalence in our population. However, the contribution of Native American ancestry to gene pool components may in part explain the higher prevalence of the *28 genotype in UGT1A1 *1 in our population, in comparison with European cohorts.

QTL mapping of a natural genetic polymorphism for long-term parasite persistence in Daphnia populations

SUMMARYKnowing the determinants of the geographic ranges of parasites is important for understanding their evolutionary ecology, epidemiology and their potential to expand their range. Here we explore the determinants of geographic range in the peculiar case of a parasite species – the microsporidian Hamiltosporidium tvaerminnensis – that has a limited geographic distribution in a wide-spread host – Daphnia magna. We conducted a quantitative trait loci (QTLs) analysis with monoclonal F2D. magna populations originating from a cross between a susceptible northern European genotype and a resistant central European genotype. Contrary to our expectations, long-term persistence turned out to be a quantitative trait across the F2 offspring. Evidence for two QTLs, one epistatic interaction and for further minor QTL was found. This finding contrasts markedly with the previously described bimodal pattern for long-term parasite persistence in natural host genotypes across Europe and leaves open the question of how a quantitative genetic trait could determine the disjunct geographic distribution of the parasite across Europe.