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Evaluation of direct metagenomics and target enriched approaches for high-throughput sequencing of field rabies viruses

Abstract

Introduction

High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).

Material and Methods

The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.

Results

Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.

Conclusion

Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.

Open access
Evaluation of long-term antibody response and cross-serotype reaction in ducks immunised with recombinant Riemerella anatipestifer outer membrane protein A and CpG ODN

Abstract

Introduction

Riemerella anatipestifer (RA) infections can lead to high mortality in ducklings. Inactivated vaccines against RA are commercially available, but they fail to provide cross-protection against various serotypes. We have previously demonstrated that a subunit vaccine containing recombinant outer membrane protein A (rOmpA) antigen of serotype 2 formulated with CpG oligodeoxynucleotides (ODN) as the adjuvant was able to stimulate both humoral and cellular immunities.

Material and Methods

In the present study, thirty healthy 7-day-old Pekin ducks were randomly assigned to three equal treatment groups: rOmpA-vaccinated, rOmpA + CpG-vaccinated, and control. Vaccine was injected intramuscularly and a booster dose of the same vaccine was given two weeks after primary immunisation. The long-term antibody response and cross-serotype reaction of this vaccine were evaluated in ducks.

Results

Compared to ducks immunised with rOmpA alone, ducks immunised with rOmpA + CpG ODN had significantly (p < 0.05) increased serum antibody titre from two weeks until nine months after primary immunisation. In addition, expression of cytokines including interferon (IFN)-α, IFN-γ, interleukin (IL)-6, and IL-12 was significantly (p < 0.05) enhanced in PBMC of ducks immunised with rOmpA + CpG ODN two weeks after primary immunisation. Antibodies from ducks immunised with the rOmpA + CpG ODN vaccine could also detect RA serotypes 1 and 6 in Western blot analysis.

Conclusion

Combination of rOmpA and CpG ODN could be a feasible strategy for developing a subunit RA vaccine with long term and broader-ranging protection.

Open access
First description of histopathological lesions associated with a fatal infection of moose (Alces alces) with the liver fluke Parafasciolopsis fasciolaemorpha Ejsmont, 1932

Abstract

Introduction

Parafasciolopsis fasciolaemorpha is a liver fluke typically parasitising moose in Central and Eastern Europe. The aim of our studies was to describe a case of fatal moose parafasciolopsosis, with special emphasis on the histopathological changes caused in the liver tissue by around 10,000 flukes.

Material and Methods

A male moose, found dead in Polesie National Park, eastern Poland, was subjected to parasitological necropsy. Macroscopic and histopathological examination of the liver was performed.

Results

Over 10,000 flukes identified as P. fasciolaemorpha were isolated from the liver parenchyma. Histopathological examination of the liver revealed the presence of multiple cavities, which were filled with flukes and cellular detritus and encysted with a layered capsule of connective tissue. Extensive liver fibrosis with signs of incomplete septal cirrhosis was also observed.

Conclusion

Parafasciolopsosis with accompanying diarrhoea was the most probable reason for the moose’s death. However, it is possible that most moose are able to survive extremely intensive P. fasciolaemorpha infection by formation of extensive fibrosis, which isolates flukes from the liver parenchyma and therefore retards the failure of the organ. To the best of our knowledge, this is the first histopathological description of changes in the liver of a moose infected with P. fasciolaemorpha.

Open access
Potential role of different fish species as vectors of koi herpesvirus (CyHV-3) infection

Abstract

Introduction

Koi herpesvirus (KHV) has infected farmed common carp in Poland clinically and asymptomatically since 2004. The role of non-carp species as vectors of virus transmission is well known except for in the case of KHV. The aim was to better understand this virus’ infection and transmission pathways in common carp, looking at the potential vector role of fishes kept with them.

Material and Methods

Eight species were experimentally infected with KHV by immersion in a suspension at 20°C ±1 and transferred to a tank after 45 minutes. Specimens were euthanised at intervals up to 56 days post infection (dpi) and tissue was examined for KHV DNA. Surviving infected fishes were introduced at intervals, each time into a separate tank, to naïve common carp for experimental infection. These were observed daily for symptoms, sacrificed along with controls after three months, and dissected to provide tissue samples. Also fish from 14 species collected from a farm with a history of KHV were sampled from 3 to 22 months after disease was confirmed. Organ sections from single fish were collected in a single tube.

Results

Viral DNA was detected in tench and roach samples up to 49 dpi, but in three-spined stickleback and stone maroko samples only up to 14 dpi. Transmission of KHV to naïve carp occurred after cohabitation. KHV DNA was detected in three fish species three months after the farm outbreak.

Conclusion

We confirmed that grass and Prussian carp, tench, roach, and brown bullhead can transfer the virus to naïve common carp.

Open access
Anti-CyHV-3 effect of fluorescent, tricyclic derivative of acyclovir 6-(4-MeOPh)-TACV in vitro

Abstract

Introduction

Cyprinid herpesvirus 3 (CyHV-3) is a virus infecting carp with disease symptoms of gill necrosis, fish discoloration, sunken eyes, and mortality reaching 90%. Several research groups have examined how to potentially abate the consequences of viral activity. Recently we showed that acyclovir inhibits CyHV-3 replication in vitro and in the present study we examined the anti-CyHV-3 activity of the tricyclic derivative of acyclovir 6-(4-MeOPh)-TACV (T-ACV), a fluorescent molecule known for higher lipophilicity than acyclovir, and therefore potentially better candidate for application in vivo.

Material and Methods

CCB and KF1 cell lines were incubated with T-ACV at concentrations of 0, 66.67, and 133.33 μM for three days and toxicity examined with MTT and CV assays. To investigate the antiviral activity of T-ACV, the lines were infected with CyHV-3 or mock infected and incubated for three days with the drug at concentrations of 0 or 66.67 μM. The activity of T-ACV was evaluated by plaque assay and TaqMan qPCR.

Results

T-ACV at a concentration of 66.67 μM displayed low toxicity and inhibited CyHV-3 activity by 13–29%, varying by cell line and method.

Conclusion

The low anti-CyHV-3 activity of T-ACV indicates that it would be reasonable to screen several tricyclic derivatives of acyclovir for such activity.

Open access
Current status of porcine epidemic diarrhoea (PED) in European pigs

Abstract

Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. The disease is clinically similar to other forms of porcine gastroenteritis. Pigs are the only known host of the disease, and the occurrence of PED in wild boars is unknown. The virus causes acute diarrhoea, vomiting, dehydration, and high mortality in suckling piglets reaching 100%. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The loss in the US pig industry has been estimated at almost seven million pigs. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA.

Open access
Proinflammatory cytokine changes in bronchoalveolar lavage fluid cells isolated from pigs infected solely with porcine reproductive and respiratory syndrome virus or co-infected with swine influenza virus

Abstract

Introduction

The study evaluated the patterns of local innate immune response in bronchoalveolar lavage fluid (BALF) cells of pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV) alone or co-infected with swine influenza virus (SIV).

Material and Methods

The study was performed on 26 seven-week-old pigs in three groups: PRRSV-infected (n = 11), PRRSV and SIV-infected (n = 11), and control (n = 4). BALF was collected post euthanasia at 2 and 4 dpi (three piglets per inoculated group) and at 21 dpi (all remaining pigs). Expression of IFN-α, IFN-γ, IL-1β, IL-6, IL-8, and IL-10 mRNA was quantified in BALF cells. PRRSV RNA was quantified in BALF samples using a commercial real-time RT-PCR kit.

Results

The three cytokines IFN-α, IFN-γ, and IL-1β presented significant expression changes in all experimental pigs. In PRRSV-infected animals IL-8 also did, but in co-infected subjects IL-6 and IL-10 were the additional upregulated cytokines. The highest number of differentially expressed genes was observed at 4 dpi, and significant differences in cytokine gene expression did not occur between the experimental groups at any other time point. The mean PRRSV load in the BALF of PRRSV-infected pigs was higher than that of co-infected pigs at each time point, having statistical significance only at 4 dpi.

Conclusion

The results of the study indicate that infection with PRRSV alone as well as with SIV interferes with innate and adaptive immune response in the infected host. They also showed that co-infection demonstrates additive effects on IL-6 and IL-10 mRNA expression levels.

Open access
Determination of steroid esters in hair of slaughter animals by liquid chromatography with tandem mass spectrometry

Abstract

Introduction

The use of growth promoters in animal husbandry to increase weight gain and efficiency of feed conversion into muscle has been banned in the European Union since 1988, and under Directive 96/23/EC, surveillance for anabolic steroid hormones is obligatory. The hormones present in animal tissues may be of endogenous origin or may result from illegal administration. Steps have been taken to determine selected steroids in the form of esters in the alternative matrix of animal hair. Their detection in biological material is direct proof of the illegal use of anabolics.

Material and Methods

The procedure for the determination of steroid esters in animal hair, based on digestion, extraction, purification, and liquid chromatography with tandem mass spectrometry was validated under the current regulations. In total, 348 samples of animal hair were examined using this method.

Results

Good recoveries and precision values (RSD) were obtained during validation. Decision limits (CCα) and detection capabilities (CCβ) were in the ranges of 2.57–4.18 μg kg−1 and 4.38–7.12 μg kg−1, respectively. The method met the criteria for confirmation techniques with respect to Commission Decision 2002/657/EC.

Conclusion

Testing for steroid esters in animal hair was introduced into the National Residue Control Programme in 2017. Steroid esters were not found in any hair samples above the CCα, which indicates that illegal use of anabolics was not confirmed.

Open access
Effects of ketosis in dairy cows on blood biochemical parameters, milk yield and composition, and digestive capacity

Abstract

Introduction

This study aimed to characterise the effects of ketosis on milk yield and composition and digestive capacity in transition dairy cows.

Material and Methods

Seven ketotic and seven healthy cows were housed in individual stalls for six days. Samples of plasma, milk, refused total mixed ration, and faeces were collected, and the blood biochemical parameters, milk yield and composition, dry matter intake, and faecal dry matter (FDM) production were determined.

Results

Compared with healthy cows, the ketotic cows had significantly higher concentrations of milk fat and citrate, but lower levels of milk protein and lactose. The cows exhibited a need for acid detergent fibre in forage and better digestion of neutral detergent fibre, starch, crude protein, and phosphorus than healthy cows, but more fat and gross energy were excreted in their faeces. Ketotic cows had higher energy-corrected milk yields and lower FDM than healthy cows.

Conclusion

Lower feed intake coinciding with the requirement to maintain high milk production is considered to be the cause of ketosis in dairy cows. Ketotic cows exhibited lower dry matter fat digestion.

Open access
Marine tetrodotoxin as a risk for human health – a review

Abstract

Tetrodotoxin (TTX) is a toxin mainly occurring naturally in contaminated puffer fish, which are a culinary delicacy in Japan. It is also detected in various marine organisms like globefish, starfish, sunfish, stars, frogs, crabs, snails, Australian blue-ringed octopuses, and bivalve molluscs. TTX is produced by marine bacteria that are consumed mainly by fish of the Tetraodontidae family and other aquatic animals. TTX poisoning through consuming marine snails has recently begun to occur over a wider geographical extent through Taiwan, China, and Europe. This neurotoxin causes food intoxication and poses an acute risk to public health. The aim of this review is to present the most recent information about TTX and its analogues with particular regard to toxicity, methods of analysis, and risk to humans of exposure.

Open access