First record of Tetramicra brevifilum in lumpfish (Cyclopterus lumpus, L.).

A microsporidian species with 98.3-98.4% nucleotide identity to Tetramicra brevifilum (Journal of Fish Diseases, 3, 1980, 495) was diagnosed in lumpfish (Cyclopterus lumpus, L.) broodstock held at a breeding and rearing facility in western Ireland. The fish were wild-caught from the west coast of Ireland, and the first case was diagnosed one year after capture. Clinical signs included severe bloating, lethargy, exophthalmos, anorexia, white patches on the cornea and externally visible parasitic cysts on skin and fins. Necropsy revealed severe ascites, white nodules and vacuoles in all the internal organs and partial liquefaction of the skeletal muscle. On histological examination, microsporidian xenomas were observed in all internal organs, the skin, skeletal muscle, gills and the eyes. The microsporidian species was identified by molecular analysis and transmission electron microscopy. This is the first record of T. brevifilum infecting lumpfish, and the disease is considered to be of potential significance to the rising aquaculture industry of this species.

Detection of Neoparamoeba perurans by duplex quantitative Taqman real-time PCR in formalin-fixed, paraffin-embedded Atlantic salmonid gill tissues.

The development and the application of a quantitative duplex real-time PCR for the detection of Neoparamoeba perurans and the elongation factor α 1 gene (ELF) of Atlantic salmon, Salmo salar L., and rainbow trout, Oncorhynchus mykiss (Walbaum), are described. A set of primers and probe was designed to amplify a 139-bp fragment specific to the N. perurans 18S rRNA gene. The test was shown to be very sensitive, being able to detect as little as 13.4 DNA copies per µL corresponding to 0.15 fg of template DNA. In addition, the reaction that detected N. perurans was found to have a high degree of repeatability and reproducibility, to have a linear dynamic range (R(2 ) = 0.999) extending over 5 log(10) dilutions and to have a high efficiency (104%). The assay was applied to DNA samples extracted from 48 formalin-fixed, paraffin-embedded (FFPE) salmon gill tissues showing varying degrees of gill histopathology and amoebic gill disease (AGD)-type histopathology ranging from absent to severe (each scored 0-3). Neoparamoeba perurans DNA was detected in all the blocks where AGD-type histopathology was diagnosed microscopically and in 43.6% of the blocks showing signs of gill pathology. The association between parasitic load and gill histopathology and AGD-type histopathology severity was also investigated. This study also describes the development and the application of a second real-time PCR for the generic detection of Neoparamoeba spp., Page, 1987. A set of primers and probe conserved among the Neoparamoeba spp. was designed to amplify a 150-bp fragment within the 18S rRNA gene. Applied to N. perurans-negative gill tissues, the method was used to exclude the presence of other Neoparamoeba spp. in those blocks where gill pathology was observed microscopically.

Geographical distribution of salmonid alphavirus subtypes in marine farmed Atlantic salmon, Salmo salar L., in Scotland and Ireland.

Sequence data from salmonid alphavirus (SAV) strains obtained from farmed marine Atlantic salmon, Salmo salar L. , over a 20-year period between 1991 and 2011 was reviewed to examine the geographical distribution of the genetically defined SAV subtypes in twelve regions across Ireland and Scotland. Of 160 different Atlantic salmon SAV strains examined, 62 belonged to subtype 1, 28 to subtype 2, 34 to subtype 4, 35 to subtype 5 and 1 to subtype 6. SAV subtypes 1, 4 and 6 were found in Ireland, while subtypes 1, 2, 4 and 5 were found in Scotland. In the majority of regions, there was a clear clustering of subtypes, with SAV subtype 1 being the dominant subtype in Ireland overall, as well as in Argyll and Bute in Scotland. SAV subtype 2 predominated in the Shetland and Orkney Islands. The emergence in Atlantic salmon of subtype 2 strains typically associated with sleeping disease in rainbow trout in Argyll and Bute, strongly suggesting transmission of infection between these species, was noted for the first time. SAV subtype 4 was the most common subtype found in the southern Western Isles, while SAV subtype 5 predominated in the northern Western Isles and north-west mainland Scotland. No single strain was dominant on sites in the western Highlands, with a number of sites in this region in particular having more than one subtype detected in different submissions. The significance of these results in relation to aspects of the epidemiology of infection, including transmission, biosecurity and wildlife reservoirs are discussed and knowledge gaps identified.

Development of a quantitative real-time PCR for the detection of Tenacibaculum maritimum and its application to field samples.

The development and the application of a quantitative real-time PCR for the detection of Tenacibaculum maritimum are described. A set of primers and probe was designed to amplify a 155-bp fragment specific to the T. maritimum 16S rRNA gene. The test was shown to be very sensitive, able to detect as little as 4.8 DNA copies number µL(-1) . In addition, the assay was found to have a high degree of repeatability and reproducibility, with a linear dynamic range (R(2) = 0.999) extending over 6 log(10) dilutions and a high efficiency (100%). The assay was applied to DNA samples extracted from 48 formalin-fixed paraffin-embedded (FFPE) Atlantic salmon, Salmo salar, gill tissues showing varying degrees of gill pathology (scored 0-3) and from 26 jellyfish samples belonging to the species Phialella quadrata and Muggiaea atlantica. For each sample, the bacterial load was normalised against the level of the salmonid elongation factor alpha 1 (ELF) detected by a second real-time PCR using previously published primers and probe. Tenacibaculum maritimum DNA was detected in 89% of the blocks with no signs of gill disease as well as in 95% of the blocks with mild-to-severe gill pathology. Association between bacterial load and gill pathology severity was investigated. T. maritimum DNA was detected at low level in four of the 26 jellyfish tested.

Prospective longitudinal studies of salmonid alphavirus infections on two Atlantic salmon farms in Ireland; evidence for viral persistence.

Prospective longitudinal studies of two outbreaks of pancreas disease in Atlantic salmon (AS), Salmo salar L., in Ireland were conducted. Both outbreaks occurred during the marine phase of production, with one caused by salmonid alphavirus subtype 1 (SAV1) and the other by SAV4. In addition to screening a range of tissues by real-time reverse transcriptase polymerase chain reaction (RRT-PCR), virological, serological and histopathological examinations were performed along with partial genome sequencing and results were related to environmental and production data and farm history. On Farm 1 (marine sampling only), infection was detected within 3 weeks of smolts being placed on the farm, while on Farm 2 (freshwater and marine sampling), infection was first detected 315 days after transfer to sea. In both outbreaks, RRT-PCR signals were detected in a range of tissues including gill, heart, kidney, pancreas/pyloric caeca, brain and serum. Persistence of signal was longest in gill and heart (> or =265 days on both farms) and shortest in serum. Mortalities on the two farms varied from 10.9% to 30%. In both cases, partial genome sequence of the causative viruses were identical to SAV strains detected in previous populations of AS on each of the study farms, including populations with which the study populations overlapped in time and space.

Production of serotype C specific and serotype C/D generic monoclonal antibodies using recombinant H(C) and H(N) fragments from Clostridium botulinum neurotoxin types C(1) and D.

Sequence variability of Clostridium botulinum serotypes C and D is particularly complex. Some serotype C and D strains have unique gene structures that encode mosaic isoforms of botulinum neurotoxin (BoNT) containing components of both BoNT type C(1) (BoNT/C(1)) and BoNT type D (BoNT/D). Such sequence variability and the potential for cross neutralisation must be taken into consideration when developing serotype C and D detection and identification assays. Three fusion proteins containing either a fragment from the carboxyl-terminal domain of the heavy chain (H(C)) of BoNT/C(1) (strain 573), a fragment from the H(C) of BoNT/D (strain BVD/-3) or a fragment from the amino-terminal domain of the heavy chain (H(N)) of BoNT/C(1) (strain 573) were expressed in Escherichia coli, and administered as immunogens to mice. Monoclonal antibodies (mAbs) against the recombinant BoNT fragments were prepared by three fusions. MAbs recognising native BoNT/C(1) and BoNT/D were detected by enzyme-linked immunosorbent assay (ELISA). Nine monoclonal antibodies (mAbs) were produced, six of which recognised a BoNT fragment that is highly conserved across all serotype C and D producing strains. We conclude that these mAbs and this approach to mAb production may facilitate the development of immunological diagnostic techniques that are not constrained by the existence of mosaic isoforms for the detection and identification of serotypes C and D.

Phylogenetic analyses and molecular epidemiology of European salmonid alphaviruses (SAV) based on partial E2 and nsP3 gene nucleotide sequences.

Sequence data were generated for portions of the E2 and nsP3 genes of 48 salmonid alphaviruses from farmed Atlantic salmon (AS), Salmo salar L., and rainbow trout (RT), Oncorhynchus mykiss (Walbaum), in marine and freshwater environments, respectively, from the Republic of Ireland, Northern Ireland, England, Scotland, Norway, France, Italy and Spain between 1991 and 2007. Based on these sequences, and those of six previously published reference strains, phylogenetic trees were constructed using the parsimony method. Trees generated with both gene segments were similar. Clades corresponding to the three previously recognized subtypes were generated and in addition, two further new clades of viruses were identified. A single further strain (F96-1045) was found to be distinct from all of the other strains in the study. The percentage of nucleotide divergence within clades was generally low (0-4.8% for E2, 0-6.6% for nsP3). Interclade divergence tended to be higher (3.4-19.7% for E2, 6.5-28.1% for nsP3). Based on these results and using current SAV terminology, the two new clades and F96-1045 were termed SAV subtypes 4, 5 and 6, respectively. SAV4 contained AS strains from Ireland and Scotland, while SAV5 contained only Scottish AS strains. Recently identified SAV strains from RT in Italy and Spain were shown to belong to SAV2. In addition, marine AS strains belonging to SAV2 were identified for the first time. Analysis of the origin of several clusters of strains with identical E2 and nsP3 sequences strongly support horizontal transmission of virus between farms and aquaculture companies. Evidence in support of vertical transmission was not found.

Sequence comparison of pigeon circoviruses.

The genome sequences of eight pigeon circoviruses (PiCV) were determined and compared with four previously published sequences. The viruses compared were from the USA, five European countries, China and Australia and included PiCVs from racing, feral, ornamental and meat pigeons and a Senegal dove (Streptopelia senegalensis). The 12 PiCV genomes, ranging from 2032 to 2040 nucleotides in length, displayed similar organizations. Pairwise comparisons showed that the genome nucleotide sequence identities ranged from 85.1% to 97.8% and that the amino acid identities of the putative replication associated (Rep) and putative capsid (Cap) proteins displayed ranges of 91.5-99.1% and 73.0-99.3%, respectively. Comparative analyses identified conserved nucleotide sequences within the Rep gene and 3' intergenic regions, which would be suitable for diagnostic PCR primers, and variable amino acid sequences within the capsid proteins, which should be considered when selecting virus isolates for vaccine development.

Molecular characterization of novel circoviruses from finch and gull.

The purpose of this study was to molecularly characterize circoviruses that infect finches and gulls. Circovirus-specific DNAs were isolated using polymerase chain reaction methods from bursa of Fabricius tissues from a Gouldian finch (Chloebia gouldiae) and a herring gull (Larus argentatus) that were known to be circovirus-infected. Nucleotide sequence determination and analysis of cloned genomic DNAs showed that these circoviruses represented novel members of the genus Circovirus of the family Circoviridae, and have been tentatively named Finch circovirus (FiCV) and Gull Circovirus (GuCV). Both new circoviruses shared genome organizational features with previously characterized circoviruses, such that both contained two major, inversely-arranged open reading frames encoding the putative replication-associated and capsid proteins, and both contained a potential stem-loop and nonanucleotide motif. Phylogenetic analyses based on genome nucleotide sequences and involving the seven additional genus members indicated that FiCV and GuCV were more closely related to canary circovirus, beak and feather disease virus and pigeon circovirus, and that FiCV and canary circovirus were the most closely related avian circoviruses. Pairwise comparisons showed that the capsid proteins of FiCV and GuCV shared highest amino acid identity values with those of canary circovirus (62.0%) and pigeon circovirus (40.6%), respectively. The 5' intergenic region of GuCV was longer (207 nucleotides) and contained more direct and inverse repeated sequences than those of other circoviruses, while the 3' intergenic region of FiCV was notable in being longer (307 nucleotides) than its counterparts in other circoviruses and in containing two long repeats of 77 nucleotides.

Development of a polymerase chain reaction-based in vivo method in the diagnosis of subclinical pigeon circovirus infection.

This paper describes a polymerase chain reaction (PCR)-based method performed on blood samples and intestinal content to detect subclinical pigeon circovirus (PiCV) infection in live pigeons. In addition, two sets of primers (primer set 1 and 2), designed in two different regions of the viral genome, were used to provide evidence of possible differences in PCR responses. Blood and intestinal content samples were randomly collected from a total of 50 apparently healthy meat pigeons, aged 1 to 5 wk, which came from central Italy. Samples of primary lymphoid organs were also collected. Results showed a high level of PiCV infection, although clinical signs were not present. The results obtained with the two sets of primers showed that primer set 2 was able to detect a higher number of PCR-positive pigeons (45 of 50 pigeons) than primer set 1 (11 of 50 pigeons). In both cases an increase in positive results with pigeon age indicates that the major direction of transmission is likely horizontal. In these circumstances feces can play an important epidemiologic role, as supported by the consistent circovirus detection in intestinal content. The high sensitivity of this PCR test, which is able to detect very low amounts of viral DNA (5.5 x 10(-3) fg of plasmid containing the cloned PiCV genome), makes it suitable for possible application as an epidemiologic tool for identifying virus carriers for subsequent removal from lofts.

Diagnosis of duck circovirus infections by conventional and real-time polymerase chain reaction tests.

Development of the first conventional and real-time polymerase chain reaction (PCR) tests for the diagnoses of duck circovirus (DuCV) infections is described. Both tests amplified a 230 bp fragment specific to the DuCV Rep gene. Although both tests had the same detection limit (13 x 10(3) target DNA/ml) when the target DNA was diluted in water, the detection limit of the real-time test (13 x 10(4) target DNA/ml) was 10-fold less than the conventional test (13 x 10(5) target DNA/ml) when the amplifications were performed in the presence of cellular DNA. Using the conventional PCR test, DuCV DNA was detected in 85 (84%) of 101 bursa of Fabricius samples from dead or sick ducks, aged between 1 and 12 weeks, and in samples from 35 (94%) of 37 flocks. Application of the SYBR Green-based real-time PCR test to 54 selected bursa of Fabricius samples indicated that more samples were positive by real-time PCR than by conventional PCR, allowed the numbers of genome copies to be estimated and showed that some bursa of Fabricius samples contained over 10(13) genome copies/g tissue. Although DuCV infections were detected in birds aged from 1 to 12 weeks, higher virus DNA levels were detected in ducks aged older than 5 weeks than in ducks younger than 5 weeks. An in situ hybridization method for the detection of DuCV in histological samples was also developed. Additional work is required to determine the clinicopathological significance of DuCV infections.

Flow cytometric measurement of intracellular IFN-gamma induction in aged subjects before and after parenteral influenza vaccination.

Flow cytometric analysis, used to study intracellular expression of IFN-gamma in peripheral blood mononuclear cells (PBMC) from aged volunteers before and after parenteral influenza vaccination, was found capable of rapidly detecting influenza antigen induced variation of IFN-gamma expression. Although the vaccine was capable of generating a satisfactory antibody response, it did not stimulate an increase in the percentage of IFN-gamma positive cells.

Influenza A virus specific T cell immunity in humans during aging.

To study the decreasing responsiveness of the immune system during aging, influenza virus specific cellular immunity was investigated in a cohort of healthy blood donors between 18 and 70 years of age. The percentage of influenza A virus specific T cells was determined by flow cytometry and found not to change during aging. After stimulation with phorbol 12-myristate 13-acetate and ionomycin, an increase in the percentage of IFN-gamma and IL-4 producing CD8(+) T cells was observed during aging. In addition, the cytotoxic T lymphocyte (CTL) activity was investigated in two additional groups of five donors, 18-20 and 68-70 years of age. The lytic capacity of purified CD8(+) T cells, after in vitro stimulation of peripheral blood mononuclear cells with influenza A virus, seemed lower in 68- to 70-year-old donors than in 18- to 20-year-old donors. Therefore we conclude that the reduced CTL activity in the elderly is not the result of a lower frequency of virus-specific T cells, but more likely the result of impaired antigen-specific proliferation or lower lytic capacity of these cells.