Cellular heterogeneity in red and melanized focal muscle changes in farmed Atlantic salmon (Salmo salar) visualized by spatial transcriptomics.

Spatial transcriptomics is a technique that provides insight into gene expression profiles in tissue sections while retaining structural information. We have employed this method to study the pathological conditions related to red and melanized focal changes in farmed Atlantic salmon (Salmo salar). Our findings support a model where similar molecular mechanisms are involved in both red and melanized filet discolorations and genes associated with several relevant pathways show distinct expression patterns in both sample types. Interestingly, there appears to be significant cellular heterogeneity in the foci investigated when looking at gene expression patterns. Some of the genes that show differential spatial expression are involved in cellular processes such as hypoxia and immune responses, providing new insight into the nature of muscle melanization in Atlantic salmon.

Infectious salmon anaemia virus-molecular biology and pathogenesis of the infection.

Aquaculture has a long history in many parts of the world, but it is still young at an industrial scale. Marine fish farming in open nets of a single fish species at high densities compared to their wild compatriots opens a plethora of possible infections. Infectious salmon anaemia (ISA) is an example of disease that surfaced after large-scale farming of Atlantic salmon (Salmo salar) appeared. Here, a review of the molecular biology of the ISA virus (ISAV) with emphasis on its pathogenicity is presented. The avirulent HPR0 variant of ISAV has resisted propagation in cell cultures, which has restricted the ability to perform in vivo experiments with this variant. The transition from avirulent HPR0 to virulent HPRΔ has not been methodically studied under controlled experimental conditions, and the triggers of the transition from avirulent to virulent forms have not been mapped. Genetic segment reassortment, recombination and mutations are important mechanisms in ISAV evolution, and for the development of virulence. In the 25 years since the ISAV was identified, large amounts of sequence data have been collected for epidemiologic and transmission studies, however, the lack of good experimental models for HPR0 make the risk evaluation of the presence of this avirulent, ubiquitous variant uncertain. This review summarizes the current knowledge related to molecular biology and pathogenicity of this important aquatic orthomyxovirus.

Infectious pancreatic necrosis virus (IPNV) serotype Sp is prevalent in Turkish rainbow trout farms.

Infectious pancreatic necrosis virus (IPNV) is a common pathogen of rainbow trout (Oncorhynchus mykiss) in Turkey. We found that 455 of 1,676 sample pools tested were IPNV positive. Positive samples were found in all geographical regions where sampling was conducted. Sequence and phylogenetic analyses of VP2 from 30 isolates representing all regions showed that the viruses were highly similar in sequence and grouped within Genogroup 5 (serotype Sp-A2). No correlations between sequences, sampling sites or geographical origins were identified. Although clinical disease was evident in several farms, analyses of the amino acid sequence of VP2 showed that all virus strains harboured the P217 T221 motif, assumed to be associated with low virulence. We conclude that IPNV is prevalent in Turkish rainbow trout farms and that the viruses are very homogenous and likely to be of European origin. Frequent exchange of eggs and live fish within the farming industry may explain the homogeneity of the IPNV.

Companion Animals as a Source of Viruses for Human Beings and Food Production Animals.

Companion animals comprise a wide variety of species, including dogs, cats, horses, ferrets, guinea pigs, reptiles, birds and ornamental fish, as well as food production animal species, such as domestic pigs, kept as companion animals. Despite their prominent place in human society, little is known about the role of companion animals as sources of viruses for people and food production animals. Therefore, we reviewed the literature for accounts of infections of companion animals by zoonotic viruses and viruses of food production animals, and prioritized these viruses in terms of human health and economic importance. In total, 138 virus species reportedly capable of infecting companion animals were of concern for human and food production animal health: 59 of these viruses were infectious for human beings, 135 were infectious for food production mammals and birds, and 22 were infectious for food production fishes. Viruses of highest concern for human health included hantaviruses, Tahyna virus, rabies virus, West Nile virus, tick-borne encephalitis virus, Crimean-Congo haemorrhagic fever virus, Aichi virus, European bat lyssavirus, hepatitis E virus, cowpox virus, G5 rotavirus, influenza A virus and lymphocytic choriomeningitis virus. Viruses of highest concern for food production mammals and birds included bluetongue virus, African swine fever virus, foot-and-mouth disease virus, lumpy skin disease virus, Rift Valley fever virus, porcine circovirus, classical swine fever virus, equine herpesvirus 9, peste des petits ruminants virus and equine infectious anaemia virus. Viruses of highest concern for food production fishes included cyprinid herpesvirus 3 (koi herpesvirus), viral haemorrhagic septicaemia virus and infectious pancreatic necrosis virus. Of particular concern as sources of zoonotic or food production animal viruses were domestic carnivores, rodents and food production animals kept as companion animals. The current list of viruses provides an objective basis for more in-depth analysis of the risk of companion animals as sources of viruses for human and food production animal health.

A 1-Year Quantitative Survey of Noro-, Adeno-, Human Boca-, and Hepatitis E Viruses in Raw and Secondarily Treated Sewage from Two Plants in Norway.

A study of enteric viruses in raw and treated sewage from two secondary treatment plants, which received sewage from Oslo city (plant A) and small municipalities in Hedmark county in Norway (plant B), showed high levels of noro-, adeno-, and bocavirus throughout the year. A seasonal variation was observed for adeno- and GII norovirus with higher levels during winter and bocavirus that had more positive samples during winter. The virus concentrations in raw sewage were comparable in the two plants, with medians (log10 genome copies per liter) of 6.1, 6.3, 6.0, and 4.5 for noro GI, noro GII, adeno-, and bocavirus, respectively. The level of hepatitis E virus was not determined as it was below the limit of quantification. The mean log10 virus reduction was 0.55 (plant A) and 1.44 (plant B) with the highest reduction found in the plant with longer hydraulic retention time. The adenoviruses were dominantly serotype 41, while serotype 12 appeared sporadically. Of the 102 raw and treated sewage samples that were tested, eight were positive for hepatitis E virus of which four were from treated sewage. Two of the four obtained gene sequences from hepatitis E virus originated from the rural sewage samples and showed high similarity with a genotype 3 strain of hepatitis E virus detected in local piglets. Two other hepatitis E virus sequences obtained from urban sewage samples showed high similarities with genotype 3 strains isolated from urban sewage in Spain and a human genotype 1 isolate from India. The study gives information on the levels of noroviruses in raw and treated sewage, which is valuable to risk assessment, information indicating that some infections with hepatitis E viruses in Norway have a regional origin and that human bocavirus 2 and 3 are prevalent in the Norwegian population.

The effect of vaccination, ploidy and smolt production regime on pathological melanin depositions in muscle tissue of Atlantic salmon, Salmo salar L.

The presence of melanin in muscle fillets of farmed salmon represents a considerable quality problem for the salmon industry with major economic concerns. In this study, we have examined the presence of abnormal pigmentation in vaccinated versus unvaccinated Atlantic salmon, Salmo salar L., and evaluated possible differences between diploid and triploid fish. Furthermore, the impact of the smolt production regime at ambient (4.5 °C) versus elevated temperature (16 °C) was investigated. Pigmented muscle spots were analysed for the expression of genes involved in melanization (tyrosinase gene family) and immune-related response in addition to morphological investigations. The proportion of fish with intramuscular melanin deposits was not significantly different between vaccinated and unvaccinated fish, regardless of ploidy. However, an interaction between vaccination and smolt regime was shown, where smoltification at elevated temperature after vaccination increased the number of affected individuals compared with vaccination followed by simulated natural smoltification. Furthermore, there were overall more fish with melanin spots amongst the triploids compared with their diploid counterparts. Transcription of the tyrosinase gene family confirmed an onsite melanogenesis in all pigment spots. The histological examination and the expression of the immune-related genes revealed a chronic polyphasic myopathy that was not affected by vaccination, ploidy or smolt production regime.

Multiple passage of infectious salmon anaemia virus in rainbow trout, Oncorhynchus mykiss (Walbaum), did not induce increased virus load.

The infectious salmon anaemia virus (ISAV) has not been observed to cause natural disease in farmed rainbow trout, Onchorhynchus mykiss (Walbaum), but may cause high mortality in farmed Atlantic salmon, Salmo salar L. In this study, ISAV was passaged 10 times in succession by intraperitoneal injections of serum from previous passage into naïve rainbow trout. The serum viraemia was monitored by real-time qPCR. The rainbow trout in this study became infected but did not develop ISA. No clinical signs were observed in the rainbow trout in any passage, but replication of ISAV was detected from Day 4 post-infection (p.i.). Neither increased relative virus loads nor histopathological and immunohistochemical findings consistent with ISA were observed. However, the expression of interferon type I and Mx genes were slightly up-regulated in the hearts of some individual fish at day 17 p.i. Sequencing of all open reading frames in the ISAV genome of the 10th passage revealed two nucleotide mutations, one in segment 6 coding for the haemagglutinin-esterase (HE) and one in segment 1 coding for the basic polymerase 2 (PB2). The mutation in HE resulted in an amino acid substitution T/K(312) .

Enteric viruses in inlet and outlet samples from sewage treatment plants.

Samples collected every two weeks from the inlet and outlet of three sewage treatment plants were screened for the presence of noro-, rota-, astro-, adeno-, hepatitis A- and circoviruses by (RT)-nested PCR, and for F-specific bacteriophages by isolation in Escherichia coli Famp. Plants A and B were secondary treatment plants and plant C used primary treatment. Noroviruses were detected in 43%, 53% and 24% of the inlet samples and 26%, 40% and 21% of the outlet samples from plants A, B and C, respectively. Astroviruses, rotaviruses and adenoviruses were more prevalent. Adenoviruses were detected in 96% of inlet and 94% of outlet samples, supporting the potential of these viruses as indicators of viral contamination from sewage. Hepatitis A virus and circoviruses were found only rarely. Reduction of infective viral particles during sewage treatment was evaluated using F-specific bacteriophages. The phages were reduced by, respectively, 99%, 87% and 0% in plants A, B and C, which corresponded to the observed differences in reduction of norovirus positive samples between the same plants. The study shows that the high viral load in sewage results in a discharge to the environment of a large amount of virus despite sewage treatment. On the other hand, the advantage of a more advanced treatment is demonstrated.

Expression, antigenicity and studies on cell receptor binding of the hemagglutinin of infectious salmon anemia virus.

Infectious salmon anemia (ISA) virus belongs to the proposed genus Isavirus of Orthomyxoviridae and is an emerging pathogen in Atlantic salmon (Salmo salar) farming. The hemagglutinin-esterase (HE) of ISA virus share several characteristics with the influenza virus hemagglutinin. This study reports recombinant expression of different ISA virus HE mutants in fish cell lines. Some introduced mutations, representing minimal differences in single amino acid residues, resulted in remarkable effects on expression efficiency in general and on surface expression specifically. Receptor binding assays showed that amino acid residues in the N-terminal half part are important in receptor binding, either being directly involved in the binding, or by influencing the structure of the binding site. Deletion of the putative N-glycosylation sites of the ISA virus HE, located near the transmembrane region, did not influence expression, receptor binding properties or staining by either a neutralising MAb, or salmon convalescent sera. The humoral immune response of Atlantic salmon after ISA virus infection showed weak neutralising activity and the results indicated that it was directed against HE.

Detection of enteric viruses in shellfish from the Norwegian coast.

Common blue mussels (Mytilus edulis), horse mussels (Modiolus modiolus), and flat oysters (Ostrea edulis) obtained from various harvesting and commercial production sites along the Norwegian coast were screened for the presence of norovirus by a real-time reverse transcription (RT)-nested PCR assay and for possible indicators of fecal contamination, i.e., for F-specific RNA bacteriophages (F-RNA phages) by plaque assay and for human adenoviruses and human circoviruses by nested PCR assay. The aims were to obtain relevant information for assessing the risk of transmission of enteric viruses by shellfish and to investigate the potential of various indicator viruses in routine screening. Noroviruses were detected in 6.8% of the samples, and the indicators were detected in 23.8% (F-RNA phages), 18.6% (adenoviruses), and 8.0% (circoviruses) of the samples. A seasonal variation was observed, with the exception of circoviruses, with more positive samples in the winter. A positive correlation was found between F-RNA phages and noroviruses. However, F-RNA phages were present in only 43% of the norovirus-positive samples. The results show that mussels from the Norwegian coast can constitute a risk of infection with enteric viruses and that routine testing of samples may be justified. Advantages and disadvantages of various options for screening are discussed.

Characterization of the infectious salmon anemia virus genomic segment that encodes the putative hemagglutinin.

The genomic segment encoding the putative hemagglutinin of infectious salmon anemia virus (ISAV) is described. Expression of the putative hemagglutinin in a salmon cell line demonstrated hemadsorptive properties of the protein for salmon erythrocytes. The polypeptide was recognized by an ISAV-specific monoclonal antibody. Nucleotide sequencing indicated the occurrence of a variable region in the hemagglutinin gene.

Detection of infectious salmon anaemia virus (ISAV) by RT-PCR after cohabitant exposure in Atlantic salmon Salmo salar.

A reverse transcription polymerase chain reaction (RT-PCR) was used to study the early phase of infectious salmon anaemia virus (ISAV) infection in Atlantic salmon Salmo salar L. The detection threshold for the RT-PCR was estimated to be 0.01 to 0.1 TCID50. A protocol that closely mimics the conditions in populations of farmed salmon was used. The major port of ISAV entry was most likely the gills, but oral entry could not be excluded. The gills and heart were RT-PCR positive 5 d post infection and there was a rapid viraemic spread of the virus after entry. Ten or more days post infection, most organs yielded RT-PCR positive samples. The viral load of the fish followed a 2-phase curve with the first maximum at approximately 15 d and a minimum around 25 d. After 25 d, there was a steady increase in viral load until all sampled organs eventually became positive. In an experiment in which the transportation of material from field to diagnostic laboratory was simulated, the transportation of whole fish was found to be optimal for the performance of RT-PCR.

Inactivation of infectious salmon anaemia virus, viral haemorrhagic septicaemia virus and infectious pancreatic necrosis virus in water using UVC irradiation.

The UVC irradiation doses necessary for a 99.9% (3-log) inactivation of 3 different fish pathogenic viruses diluted in freshwater/seawater and wastewater from a fish processing plant were determined. The results showed that both infectious salmon anaemia virus (ISAV) and viral haemorrhagic septicaemia virus (VHSV) were very sensitive to UVC irradiation, showing a 3-log reduction of infectivity in freshwater of 33 +/- 3.5 and 7.9 +/- 1.5 J m(-2), respectively, while that of infectious pancreatic necrosis virus (IPNV) was substantially higher, 1188 +/- 57 J m(-2). Using ISAV as a model, a comparison of the effect of UVC irradiation on virus isolation versus reverse transcription polymerase chain reaction (RT-PCR) showed that considerably higher UVC doses, depending on the length of the amplified product, were necessary to abolish RT-PCR detection of viral RNA.

The viral RNA 3'- and 5'-end structure and mRNA transcription of infectious salmon anaemia virus resemble those of influenza viruses.

The nucleotide sequences of the termini of two of the genomic segments of the negative strand RNA virus infectious salmon anaemia virus (ISAV) were determined. The sequence of the terminal 9 nucleotides at both ends of the viral RNAs was identical, and showed distinctive sequence homology with the conserved terminal sequences found in the orthomyxoviruses. For both ISAV genomic segments a computer-based secondary structure modelling indicated that the terminal 21-24 nucleotides were able to form self-complementary panhandle structures. Comparison with ISAV-derived mRNA sequences showed that ISAV mRNAs have heterogeneous 5'-ends, and are polyadenylated from a signal sequence 13-14 nucleotides downstream of the 5'-end terminus of the vRNA. Furthermore, the in vitro replication of ISAV was hindered by the RNA polymerase II inhibitor alpha-amanitin. These findings indicate that the mechanisms for replication of ISAV are similar to those of the orthomyxoviruses, and add to the previously reported structural similarities between ISAV and the orthomyxoviruses.

Antigenic diversity of Norwalk-like viruses: expression of the capsid protein of a genogroup I virus, distantly related to Norwalk virus.

The gene encoding the capsid protein of a genogroup I Norwalk-like virus (NLV) (Hu/NLV/Stav/95/Nor) was cloned and expressed in insect cells using a baculovirus vector. The His-tagged recombinant capsid protein (rStav) was antigenic and immunogenic, showed an apparent molecular weight of approximately 68 kD in protein gels, and was only soluble under denaturing conditions. The amino acid sequence of the rStav protein showed 65-88% similarity to capsid protein sequences from other genogroup I NLV and was most closely related to Desert Shield virus. Norwegian recruit sera were tested for antibodies against rStav by Western blotting (rStav WB). The sera had previously been tested for antibodies against a recombinant Norwalk virus capsid protein in an ELISA (rNV ELISA). Several rNV ELISA-negative sera showed a positive response in the rStav WB, indicating that the use of antigens representing different stains may be necessary when screening sera for antibodies against genogroup I NLV.

Preliminary survey for antibodies against caprine arthritis-encephalitis virus (CAEV) using recombinant GAG proteins: studies among small ruminant populations in north-eastern Nigeria.

A total of 1000 serum samples were obtained from small ruminants in Maiduguri, Borno state, Nigeria and tested for the presence of antibodies against caprine arthritis-encephalitis virus (CAEV) using enzyme-linked immunosorbent assay (ELISA) based on p17 and p28 recombinant GAG proteins. The distribution of the sera tested was as follows: 900 serum samples collected at slaughter from 700 goats and 200 sheep in the municipal abattoir as well as 100 sera obtained from 50 each of goats and sheep in four different flocks under the semi-intensive system of animal husbandry. All the animals sampled were aged >/=2 years and had no previous contact with imported stocks. It was observed that none of the sera had antibody against CAEV. The need to impose strict quarantine as well as the practice of testing and slaughtering of positive animals imported from CAEV endemic areas into Nigeria for breeding are suggested to prevent the introduction of the disease into the country.

Immunomagnetic separation of a Norwalk-like virus (genogroup I) in artificially contaminated environmental water samples.

Rabbit polyclonal antibodies were raised against a recombinant capsid protein from a genogroup I Norwalk-like virus (NLV). Magnetic beads coated with these antibodies were used in immunomagnetic separation (IMS) of the NLV. After capture of the NLV and washing of the beads, viral RNA was heat released and detected by RT-PCR. This IMS procedure was shown to have high sensitivity for detection of homologous NLV, while capture of a genogroup II NLV was less efficient. Antigen capture was not influenced by the content of humic acids in the samples. The combination of IMS and heat release was found to be more efficient than organic extraction of RNA from water contaminated with humic acids. The efficacy and simplicity of IMS/heat release render this combination a feasible tool for the preparation of NLV RNA from environmental samples, although the antigenic diversity of NLV may be a complicating factor.

Detection of small round structured viruses in artificially contaminated water using filter adsorption and reverse transcription polymerase chain reaction.

The small round structured viruses (SRSV) are common causes of gastroenteritis worldwide. Fecally contaminated water is an important vehicle for transmission, but detection of SRSV in environmental samples has been hampered by the lack of sensitive detection methods. The present work describes the detection of SRSV in artificially contaminated deionized water and raw drinking water. SRSV-containing fecal extracts were added to water and virus was recovered by filter adsorption-elution, followed by flocculation. RNA was extracted and SRSV were detected by the use of reverse transcription polymerase chain reaction. The sensitivity of the method corresponded to a positive SRSV detection in 500 ml deionized water with an estimated concentration of 0.5-5 virus particles per ml.

Time course tissue distribution of infectious salmon anaemia virus in experimentally infected Atlantic salmon Salmo salar.

Atlantic salmon Salmo salar L. were injected intraperitoneally with infectious salmon anaemia virus (ISAV)-infective tissue homogenate to clarify the tissue distribution of ISAV in a time course study. Fish were sampled at 11 different intervals between 1 and 40 d post-infection (p.i.) and mid-kidney, head kidney, liver, spleen, intestine, gills, muscle and heart were tested for the presence of ISAV by reverse transcriptase polymerase chain reaction (RT-PCR). The results showed that during a disease outbreak, ISAV is present in most organs. It was possible to detect ISAV at all sampling times in at least 1 of the fish examined. However, for the first 8 d p.i. positive RT-PCR results were predominantly found in samples from the head kidney and mid-kidney. Fish giving positive samples after Day 13 p.i. were RT-PCR positive in most organs. These results indicated that between Days 8 to 13 p.i. considerable replication of the virus occurred, combined with wide tissue dissemination.