Search

After emerging in Wuhan, China, in December 2019, coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rapidly became a serious threat to human health worldwide (1-3). [...]

Astroviruses are an emerging hazard in hatchery management, and they are responsible for great economic losses in poultry farms worldwide. Chicken astrovirus (CAstV) and avian nephritis virus (ANV) are involved in decreased hatching rate, mainly due to embryo deaths, and pale and runted chicks too weak to hatch. Hatchery diseases occur through direct egg infection or vertical transmission. However, the specific role of astroviruses in these diseases is still largely unknown. To elucidate this a high-quality Piedmont hatchery (Italy) was selected based on farm clinical signs and the astrovirus serological positivity in the breeder farm. The viral dynamics were followed from the hatchery to the farm. The presence of both CAstV and ANV was monitored by evaluating the viral load in environmental and bird samples. Interestingly, both viruses were detected in chick yolk sacs at 18 days of incubation, and in the gut contents of 1-day chicks, whereas in the hatchery environmental samples, the eggs' external surfaces and the embryos' intestinal contents were negative. The CAstV copy number was higher in bird tissues from the hatchery, while a greater ANV load was detected in bird tissues from the farm. Moreover, our data suggest vertical transmission of both viruses. Frequent co-infection was also observed in samples from both the hatchery and the farm. Lastly, the first Italian full-length genome and molecular characterization of ANV was obtained. RESEARCH HIGHLIGHTS: Identified the role of the hatchery in astrovirus transmission. Sequenced the avian nephritis virus complete genome. Investigated tissue distribution of astrovirus from egg to chicks. Demonstrated co-infection of ANV/CAstV. [ABSTRACT FROM AUTHOR]

The presence of bocaparvoviruses (BoVs) and bufaviruses (BuVs) in the European hedgehog (Erinaceus europaeus) was investigated by screening duodenal and liver samples collected from 183 carcasses, delivered to wildlife rescue centers located in northwestern Italy. BoV DNA was detected in 15 animals (8.2%), with prevalences of 7.1% (13/183) and 2.7% (5/183) in intestine and liver samples, respectively. Upon the sequence analyses of the NS1 gene, two highly divergent BoVs (65.5–67.8% nt identities) were identified. Fourteen strains showed the highest identity (98.3–99.4% nt) to the hedgehog BoV strains recently detected in China in Amur hedgehogs (Erinaceus amurensis), whilst four strains were genetically related (98.9–99.4% nt identities) to the porcine BoVs identified in pigs and classified in the species Bocaparvovirus ungulate 4, which included related viruses also found in rats, minks, shrews, and mice. BuV DNA was detected in the duodenal samples of two hedgehogs, with a prevalence rate of 1.1%. The nearly full-length genome of two BuV strains, Hedgehog/331DU-2022/ITA and Hedgehog/1278DU/2019/ITA, was reconstructed. Upon phylogenetic analysis based on the NS and VP aa sequences, the Italian hedgehog BuVs tightly clustered with the BuVs recently identified in the Chinese Amur hedgehogs, within a potential novel candidate species of the genus Protoparvovirus. [ABSTRACT FROM AUTHOR]

Simple Summary: This preliminary study aimed to assess the presence of bacteria in pregnancy tissues belonging to healthy canine and feline feto-maternal units at term. Specifically, it included bitches and queens undergoing elective cesarean sections and their first extracted fetus. The placental side of the endometrium, amniotic fluid, and meconium were sampled as tissue representative of the intra-uterine environment during pregnancy. Sampling and laboratory protocols were elaborated to contrast the possibility for contamination and included strict selection criteria (only elective cesarean sections, no recent treatments with antimicrobials), sterility during sample collection, and sampling and laboratory controls. Samples were processed using both culture and molecular techniques (16S rRNA bacterial gene sequencing). When positive, culture revealed the presence of bacteria that are common contaminants and sequencing yielded a very low bacterial load. A difference was highlighted between canine and feline samples, suggesting a possible contamination from the skin of the dam, although the small sample size prevents any definitive conclusion. This study suggests that healthy canine and feline fetuses might develop in the presence of low amounts of bacterial components, although future research should include stricter protocols to check for contamination and provide information on bacterial viability. At present, there are no data on the presence of bacteria in healthy canine and feline pregnancies at term. Here, we investigated the uterine microbiome in bitches (n = 5) and queens (n = 3) undergoing elective cesarean section in two facilities. Samples included swabs from the endometrium, amniotic fluid, and meconium, and environmental swabs of the surgical tray as controls. Culture and 16S rRNA gene sequencing were used to investigate the presence of bacteria. Culture was positive for 34.3% of samples (uterus n = 3, amniotic fluid n = 2, meconium n = 4, controls n = 0), mostly with low growth of common contaminant bacteria. With sequencing techniques, the bacterial abundance was significantly lower than in environmental controls (p < 0.05). Sequencing results showed a species-specific pattern, and significant differences between canine and feline bacterial populations were found at order, family, and genus level. No differences were found in alpha and beta diversities between feto-maternal tissues and controls (p > 0.05). Dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria in different proportions based on tissue and species. Culture and sequencing results suggest that the bacterial biomass is very low in healthy canine and feline pregnancies at term, that bacteria likely originate from contamination from the dam's skin, and that the presence of viable bacteria could not be confirmed most of the time. [ABSTRACT FROM AUTHOR]

Simple Summary: The massive use, often without any real rationale, of antivirals such as Oseltamivir has as a side effect a significant increase in environmental pollution levels. The effect of the spread of these drugs, especially in aquatic basins, has manifested itself in changes in animal behavior with consequent implications for ecological and evolutionary balances. We focused on the effects that can be detected on avian influenza, which today represents one of the most important viral infectious diseases with possible dramatic pandemic repercussions. We evaluated the evolutionary rate of highly pathogenic H5N1 avian influenza strains and a potentially different evolutionary behavior of the H5N1 2.3 viral clade in the presence of environmental pollution by Oseltamivir. Antiviral (AV) drugs are the main line of defense against pandemic influenza. However, different administration policies are applied in countries with different stocks of AV drugs. These policies lead to different occurrences of drug metabolites in the aquatic environment, altering animal behavior with evolutionary consequences on viruses. The aim of this study was to investigate the potential impact of environmental pollution by human antivirals, such as oseltamivir carboxylate (OC), on the evolutionary rate of avian influenza. We used NA, HA, NP, and MP viral segments from two groups of neighboring countries sharing migratory routes of wild birds and characterized by different AV stockpiles. BEAST analyses were performed using the uncorrelated lognormal clock evolutionary model and the Bayesian skyline tree prior model. The ratios between the rate of evolution of the NA gene and the HA, NP, and MP segments were considered. The two groups of countries were compared by analyzing the differences in the ratio distributions. Our analyses highlighted a possible different behavior in the evolution of H5N1 2.3 clade viral strains when OC environmental pollution is present. In conclusion, the widespread consumption of antivirals and their presence in wastewater could influence the selective pressure on viruses. [ABSTRACT FROM AUTHOR]

Bubaline herpesvirus 1 (BuHV-1), Bovine herpesvirus 1 (BoHV-1) and Bovine herpesvirus 5 (BoHV-5) are classified in the genus Varicellovirus, subfamily Alphaherpesvirinae. BoHV-1 is the causative agent of infectious bovine rhinotracheitis, BoHV-5 induces moderate disease in adult cattle while BuHV-1 has instead been associated with a decline in livestock production of water buffaloes. The aim of this study was to develop a qualitative PCR assay that allows the discrimination of BuHV-1, BoHV-1 and BoHV-5. The alignment of homologous genes identified specific nucleotide sequences of BuHV- 1, BoHV-1 and BoHV-5. The design of the primers and the optimization of the PCR assay were focused on the target sequences located on the portions of gD, gE and gG genes. This assay involved the use of three different PCR end-points: the PCR of a portion of the gD gene identified only the presence of BoHV-1; the PCR of a portion of the gE gene confirmed the presence of both BoHV-5 and BuHV-1; the PCR of a portion of the gG gene discriminated between BoHV-5 and BuHV-1, as the amplification product was observed only for BoHV-5. This qualitative PCR assay allowed the differentiation of BoHV-1 and BoHV-5 infections both in cattle and water buffaloes and heterologous BuHV-1 infections in bovine. [ABSTRACT FROM AUTHOR]

Simple Summary: The sustained-release moxidectin formulation of Afilaria SR is labelled to prevent Dirofilaria immitis infection in dogs for a period of six months. An observational—in field multicentric study was design to evaluate the tolerability and the long-term prevention of Afilaria SR in Italy. A total of 583 dogs were recruited from 2018 to 2021, receiving the drug annually and monitored by veterinary practitioners after each administration. Antigenic tests were performed 210, 365, 730, and 1095 days after the administration of the drug. None of the enrolled dogs was detected as positive, since it was possible to establish that 100% of protection was achieved. Afilaria SR was well tolerated since only the 13% of dogs demonstrated mild reaction in the injection site and only two dogs out of 583 demonstrated anaphylactoid or angioneurotic reactions. These data support the high prevention rate against Dirofilaria immitis disease in all enrolled dogs and indicate the high safety profile of the product, considering the low number and the low grade of side effects. The sustained-release moxidectin formulation Afilaria SR is a relatively new product and has been labelled to prevent Dirofilaria immitis infection in dogs for a six months-period. An observational, in field multicentric study was performed, aiming to evaluate the tolerability and the long-term prevention of Afilaria SR in Italy, a country where filariasis is endemic. The study was designed to include not less than 300 dogs, older than 6 months, of any breed. Side effects were recorded by veterinarians and antigenic tests were performed after 210, 365, 730, and 1095 days after the administration of the drug. A total of 583 dogs were recruited from 2018 to 2021 and all of them were negative with respect to antigenic tests at all time points, indicating that 100% of protection was achieved. Ranking of adverse reactions and correlation to patient features were analyzed using descriptive statistics and χ2 square test, respectively. Afilaria SR was well tolerated: 13% of dogs experienced mild reactions and only two dogs out of 583 (0.3%) demonstrated anaphylactoid/angioneurotic reactions, resolved administering corticosteroids. These data support that Afilaria SR prevented Dirofilaria immitis disease in all enrolled dogs and the low number and the low grade of side effects indicate the high safety profile of the product. [ABSTRACT FROM AUTHOR]

Of 263 patients in Tuscany, Italy, from whom ticks were removed during July 2005-May 2007, five showed signs of tick-borne lymphadenopathy. Of the ticks, 17 were Dermacentor marginatus; 6 (35.3%) [...]

Abstract Background Flavivirus is a highly heterogeneous viral genus that includes important human pathogens and several viral strains with unknown zoonotic potential. Mosquito-borne flaviviruses have been isolated and characterized in Northern Italy: West Nile virus and Usutu virus were detected in mosquitoes and in different host species and recent studies provided evidence about the circulation of “insect Flavivirus” strains. Methods In order to clarify the diffusion and the distribution of the mosquito-transmitted flaviviruses in Italy, we analyzed Culex and Ochlerotatus mosquitoes collected in 2009 and 2010 in an area divided evenly between hills and plains and where the landscape is dominated by mixed agricultural patches, rice fields, deciduous tree forests, and urban environments. Each mosquito pool was tested for the presence of Flavivirus strains and we characterized positive samples by genetic sequencing. Results Positive mosquito pools revealed low infection prevalence, but suggested a continuous circulation of both Usutu virus and insect Flavivirus. Interestingly, phylogenetic analyses based on NS5 gene partial sequences showed a closer relationship among new Usutu virus strains from Piedmont and the reference sequences from the Eastern Europe, with respect to Italian samples characterized so far. Moreover, NS5 gene phylogeny suggested that mosquito flaviviruses found in Italy could belong to different lineages. Conclusions Our results contribute to a wider point of view on the heterogeneity of viruses infecting mosquitoes suggesting a taxonomical revision of the Mosquito-borne Flavivirus group.

Abstract Background A central nervous system (CNS) disease outbreak caused by small ruminant lentiviruses (SRLV) has triggered interest in Spain due to the rapid onset of clinical signs and relevant production losses. In a previous study on this outbreak, the role of LTR in tropism was unclear and env encoded sequences, likely involved in tropism, were not investigated. This study aimed to analyze heterogeneity of SRLV Env regions - TM amino terminal and SU V4, C4 and V5 segments - in order to assess virus compartmentalization in CNS. Results Eight Visna (neurologically) affected sheep of the outbreak were used. Of the 350 clones obtained after PCR amplification, 142 corresponded to CNS samples (spinal cord and choroid plexus) and the remaining to mammary gland, blood cells, bronchoalveolar lavage cells and/or lung. The diversity of the env sequences from CNS was 11.1-16.1% between animals and 0.35-11.6% within each animal, except in one animal presenting two sequence types (30% diversity) in the CNS (one grouping with those of the outbreak), indicative of CNS virus sequence heterogeneity. Outbreak sequences were of genotype A, clustering per animal and compartmentalizing in the animal tissues. No CNS specific signature patterns were found. Conclusions Bayesian approach inferences suggested that proviruses from broncoalveolar lavage cells and peripheral blood mononuclear cells represented the common ancestors (infecting viruses) in the animal and that neuroinvasion in the outbreak involved microevolution after initial infection with an A-type strain. This study demonstrates virus compartmentalization in the CNS and other body tissues in sheep presenting the neurological form of SRLV infection.

Abstract Background West Nile Virus (WNV) transmission in Italy was first reported in 1998 as an equine outbreak near the swamps of Padule di Fucecchio, Tuscany. No other cases were identified during the following decade until 2008, when horse and human outbreaks were reported in Emilia Romagna, North Italy. Since then, WNV outbreaks have occurred annually, spreading from their initial northern foci throughout the country. Following the outbreak in 1998 the Italian public health authority defined a surveillance plan to detect WNV circulation in birds, horses and mosquitoes. By applying spatial statistical analysis (spatial point pattern analysis) and models (Bayesian GLMM models) to a longitudinal dataset on the abundance of the three putative WNV vectors [Ochlerotatus caspius (Pallas 1771), Culex pipiens (Linnaeus 1758) and Culex modestus (Ficalbi 1890)] in eastern Piedmont, we quantified their abundance and distribution in space and time and generated prediction maps outlining the areas with the highest vector productivity and potential for WNV introduction and amplification. Results The highest abundance and significant spatial clusters of Oc. caspius and Cx. modestus were in proximity to rice fields, and for Cx. pipiens, in proximity to highly populated urban areas. The GLMM model showed the importance of weather conditions and environmental factors in predicting mosquito abundance. Distance from the preferential breeding sites and elevation were negatively associated with the number of collected mosquitoes. The Normalized Difference Vegetation Index (NDVI) was positively correlated with mosquito abundance in rice fields (Oc. caspius and Cx. modestus). Based on the best models, we developed prediction maps for the year 2010 outlining the areas where high abundance of vectors could favour the introduction and amplification of WNV. Conclusions Our findings provide useful information for surveillance activities aiming to identify locations where the potential for WNV introduction and local transmission are highest. Such information can be used by vector control offices to stratify control interventions in areas prone to the invasion of WNV and other mosquito-transmitted pathogens.

Abstract Background In in a typical "left-to-right" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA) method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ)-EAs to study the influence of population on the algorithm. Results The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000). Conclusions The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.

Abstract Background Phylogenetic trees are an important tool for representing evolutionary relationships among organisms. In a phylogram or chronogram, the ordering of taxa is not considered meaningful, since complete topological information is given by the branching order and length of the branches, which are represented in the root-to-node direction. We apply a novel method based on a (λ + μ)-Evolutionary Algorithm to give meaning to the order of taxa in a phylogeny. This method applies random swaps between two taxa connected to the same node, without changing the topology of the tree. The evaluation of a new tree is based on different distance matrices, representing non-phylogenetic information such as other types of genetic distance, geographic distance, or combinations of these. To test our method we use published trees of Vesicular stomatitis virus, West Nile virus and Rice yellow mottle virus. Results Best results were obtained when taxa were reordered using geographic information. Information supporting phylogeographic analysis was recovered in the optimized tree, as evidenced by clustering of geographically close samples. Improving the trees using a separate genetic distance matrix altered the ordering of taxa, but not topology, moving the longest branches to the extremities, as would be expected since they are the most divergent lineages. Improved representations of genetic and geographic relationships between samples were also obtained when merged matrices (genetic and geographic information in one matrix) were used. Conclusions Our innovative method makes phylogenetic trees easier to interpret, adding meaning to the taxon order and helping to prevent misinterpretations.