Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example.

Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is some debate regarding reliability of sequencing using this technology, which is important for applications beyond diagnosis such as linking lineages to outbreaks, tracking transmission pathways and pockets of circulation, or mapping specific markers. To our knowledge, no in depth analyses of the required read coverage to compensate for the error profile in Nanopore sequencing have been described. Here, we describe the validation of a protocol for whole genome sequencing of USUV using Nanopore sequencing by direct comparison to Illumina sequencing. To that point we selected brain tissue samples with high viral loads, typical for birds which died from USUV infection. We conclude that the low-cost MinION Nanopore sequencing platform can be used for characterization and tracking of Usutu virus outbreaks.

Field and laboratory findings following the large-scale use of intermediate type infectious bursal disease vaccines in Denmark.

Following a period of clinical outbreaks of very virulent infectious bursal disease virus (vvIBDV) in Denmark, the histological bursal lesion score (HBLS) was used on a national scale to screen broiler flocks vaccinated with intermediate IBD vaccines for lesions indicative of IBDV challenge. High lesion scores were detected in a high percentage of healthy and well performing flocks despite the lack of other indications of the presence of vvIBDV. RT-PCR and subsequent sequencing showed the frequent presence of H253Q and H253N IBDV strains that were genetically close to the sequence of the intermediate vaccines with a relative risk ratio of 13.0 (P < 0.0001) in intermediate vaccine A or B vaccinated flocks compared to unvaccinated flocks. The relevance of these H253Q and H253N strains was tested under experimental conditions using a protocol derived from the European Pharmacopoeia for safety of live IBD vaccines. The results confirmed the higher pathogenicity for the bursa of these strains compared to intermediate vaccines as well as the negative effect on antibody response to a Newcastle disease (ND) vaccination performed at the peak of the bursa damage. The efficacy of the ND vaccination was still 100% showing that the H253N and H253Q IBDV strains would be considered as safe vaccine viruses. In conclusion, the use of the HBLS to screen commercial broiler flocks vaccinated with intermediate IBD vaccines for the presence of vvIBDV does not seem to be a reliable method due to the frequent occurrence of H253N and H253Q strains in those flocks. For screening of IBD vaccinated flocks for the presence of vvIBDV or other field strains, the RT-PCR with subsequent sequencing seems to be most suitable.

Prevalence of histopathological intestinal lesions and enteric pathogens in Dutch commercial broilers with time.

Intestinal disease has a major impact on the broiler industry due to economic and welfare reasons. Intestinal disease might occur due to a large number of reasons varying from well-defined pathogens to non-specific enteritis and complex syndromes. However, knowledge about the nature of intestinal disease and presence of enteric viruses in the Dutch broiler industry is largely absent. Therefore, a large-scale field study, in which 98 broiler flocks from 86 farms were sampled weekly, was started to assess the prevalence of histopathological lesions in the jejunum, a number of enterotropic viruses by real-time quantitative reverse transcriptase PCR (RT-qPCR) and coccidia by lesion scoring. Histopathological lesions indicative of intestinal disease were found in all flocks examined. The pathogens investigated were chicken astrovirus (99% of flocks positive), avian nephritis virus 3 (100%), rotavirus A (95%), rotavirus D (52%), reovirus (100%), Eimeria acervulina (94%), E. maxima (49%) and E. tenella (40%). The enteric viruses were more prevalent in the first weeks of the growing period, while coccidiosis was more frequently found at 4 and 5 weeks of age. The abundant presence of the enteric viruses and enteric disorders stresses the need to elucidate the role of these viruses in intestinal disease. Furthermore, the high prevalence of coccidiosis despite the use of anticoccidials shows that the current coccidial management programmes might be insufficient in controlling this disease.

Heartworm in a mute swan (Cygnus olor).

A severely emaciated female adult mute swan (Cygnus olor) was euthanized after a period of intensive supportive care in a wild bird rehabilitation centre. Necropsy revealed severe myocardial haemorrhages in the right ventricular free wall associated with the presence of adult heartworm (Sarconema eurycerca). On histological examination, multifocal randomly scattered blood-filled cavities without endothelial or epithelial lining (migration tracts) and surrounded by necrotic debris mixed with fibrinoid deposits and a mixed inflammatory infiltrate were seen, as well as mild multifocal degeneration and necrosis of adjacent myocardial fibres. In some of the lesions, cut sections of adult female filarial nematodes revealed numerous microfilariae in their uteri. This report is the first published case of Sarconema eurycerca in a mute swan in The Netherlands.

A clinicopathological study of 52 feline epulides.

A retrospective study was performed to characterize 52 new cases of feline epulides between 1995 and 2001, with clinical and pathological results classified according to Head's histopathologic criteria for canine epulides. The incidence of the fibromatous, acanthomatous, ossifying, and giant cell epulis were respectively 57.7% (30/52), 7.7% (4/52), 5.8% (3/52), and 28.8% (15/52). Giant cell epulides presented significant differences in clinical behavior compared with the fibromatous type, including rapid growth (P < .0001), presence of ulcerative changes (P < .01), and rapid recurrence after surgery (P < .01) from which euthanasia was judged necessary in 4 cases. Fifteen giant cell epulides were additionally examined in order to characterize the lesion both histochemically and immunohistochemically and to investigate the origin of the multinucleated giant cells (MGCs). Van Gieson staining showed osteoid and woven bone formation in 11 cases. Both the MGCs and a fraction of the mononuclear cells were positive for vimentin, tartrate-resistant acid phosphatase (TRAP), a commonly accepted marker for osteoclasts, and the polyclonal antibody receptor activator of nuclear factor kappabeta (RANK), a cytokine leading to the differentiation of osteoclast progenitors into mature osteoclasts in presence of its ligand. MGCs were negative for smooth muscle actin, MIB-1, and factor VIII. The giant cell epulis may be a variant of the fibromatous and ossifying epulis in which extensive ulceration and inflammation results in increased osteoclastic activity. The osteoclast-like giant cells are most likely formed from a monocyte/macrophage-like osteoclast precursor that differentiates into osteoclasts under the influence of mononuclear osteoblast-like stromal cells.