Divergent bornaviruses from Australian carpet pythons with neurological disease date the origin of extant Bornaviridae prior to the end-Cretaceous extinction

Tissue samples from Australian carpet pythons (Morelia spilota) with neurological disease were screened for viruses using next-generation sequencing. Coding complete genomes of two bornaviruses were identified with the gene order 3’-N-X-P-G-M-L, representing a transposition of the G and M genes compared to other bornaviruses and most mononegaviruses. Use of these viruses to search available vertebrate genomes enabled recognition of further endogenous bornavirus-like elements (EBLs) in diverse placental mammals, including humans. Codivergence patterns and shared integration sites revealed an ancestral laurasiatherian EBLG integration (77 million years ago [MYA]) and a previously identified afrotherian EBLG integration (83 MYA). The novel python bornaviruses clustered more closely with these EBLs than with other exogenous bornaviruses, suggesting that these viruses diverged from previously known bornaviruses prior to the end-Cretaceous (K-Pg) extinction, 66 MYA. It is possible that EBLs protected mammals from ancient bornaviral disease, providing a selective advantage in the recovery from the K-Pg extinction. A degenerate PCR primer set was developed to detect a highly conserved region of the bornaviral polymerase gene. It was used to detect 15 more genetically distinct bornaviruses from Australian pythons that represent a group that is likely to contain a number of novel species

Incremental Multiple Classifier Active Learning for Concept Indexing in Images and Videos

Regular Papers: Multimedia Indexing and MiningInternational audienceActive learning with multiple classifiers has shown good performance for concept indexing in images or video shots in the case of highly imbalanced data. It involves however a large number of computations. In this paper, we propose a new incremental active learning algorithm based on multiple SVM for image and video annotation. The experimental result show that the best performance (MAP) is reached when 15-30% of the corpus is annotated and the new method can achieve almost the same precision while saving 50 to 63% of the computation time

Molecular detection of two adenoviruses associated with disease in Australian lizards

We give the first published description of the pathology and molecular findings associated with adenovirus infection in lizards in Australia. A central netted dragon (Ctenophorus nuchalis) exhibited severe necrotising hepatitis with abundant intranuclear inclusion bodies within hepatocytes and rarely within intestinal epithelial cells. Polymerase chain reaction (PCR) using pooled tissues yielded an amplicon that shared strong nucleotide identity with an agamid adenovirus (EU914203). PCR on the liver of a bearded dragon (Pogona minor minor) with illthrift, coccidiosis, nematodiasis and hepatic lipidosis yielded an amplicon with strong nucleotide identity to a helodermatid adenovirus (EU914207)

Paramyxoviruses in reptiles: A review

In 1972, an outbreak of neurorespiratory disease in a Swiss serpentarium formed the basis for the first description of a paramyxovirus isolated from a reptile. In the forty years since this outbreak, there have been over 50 published reports about reptilian paramyxoviruses from all over the world. The majority of these investigations have concerned themselves with ferlaviruses (sometimes previously referred to as ophidian paramyxoviruses, or OPMV). The biology of these viruses is reviewed and this is followed by a review of the clinical findings that are associated with ferlaviral infection and the various diagnostic tests that are used to identify infected reptiles. Recently, a second, and highly divergent, reptilian paramyxovirus, Sunshine virus, was described in Australian pythons, so it is an opportune time to reflect on the paramyxoviruses that infect reptiles

Molecular identification of three novel herpesviruses found in Australian farmed saltwater crocodiles (Crocodylus porosus) and Australian captive freshwater crocodiles (Crocodylus johnstoni)

As part of a larger investigation into three emerging disease syndromes highlighted by conjunctivitis and pharyngitis, systemic lymphoid proliferation and encephalitis, and lymphonodular skin infiltrates in farmed saltwater crocodiles (Crocodylus porosus) and one emerging syndrome of systemic lymphoid proliferation in captive freshwater crocodiles (Crocodylus johnstoni), cytopathic effects (CPE), including syncytial cell formation, were observed in primary crocodile cell lines exposed to clarified tissue homogenates from affected crocodiles. Ten cell cultures with CPE were then screened for herpesviruses using two broadly-reactive herpesvirus PCRs. Amplicons were obtained from 9 of 10 cell cultures and were sequenced. Three novel herpesviruses were discovered and the phylogenetic analysis of these viruses showed there was a 63% Bayesian posterior probability value supporting these viruses clustering with the subfamily Alphaherpesvirinae, and 100% posterior probability of clustering with a clade containing the Alphaherpesvirinae and other unassigned reptile herpesviruses. It is proposed that they are named Crocodyline herpesvirus (CrHV) 1, 2 and 3. CrHV1 and 2 were only isolated from saltwater crocodiles and CrHV3 was only isolated from freshwater crocodiles. A duplex PCR was designed that was able to detect these herpesviruses in formalin-fixed paraffin-embedded tissues, a sample type that neither of the broadly-reactive PCRs was able to detect these herpesviruses in. This work describes the isolation, molecular detection and phylogeny of these novel herpesviruses but the association that they have with the emerging disease syndromes requires further investigation

Diagnostic investigation of new disease syndromes in farmed Australian saltwater crocodiles (Crocodylus porosus) reveals associations with herpesviral infection

Since 2006, 3 new disease syndromes have emerged in farmed saltwater crocodiles (Crocodylus porosus) in the Northern Territory of Australia. We describe the syndromes through a retrospective study of laboratory findings from 187 diagnostic cases submitted to Berrimah Veterinary Laboratories between 2005 and 2014. The first syndrome was characterized by conjunctivitis and/or pharyngitis (CP), primarily in hatchlings. Herpesviruses were isolated in primary crocodile cell culture, or were detected by PCR directly from conjunctiva or pharyngeal tissue, in 21 of 39 cases of CP (54%), compared with 9 of 64 crocodiles without the syndrome (14%, p < 0.0001). Chlamydiaceae were detected by PCR in conjunctiva or pharyngeal tissue of 55% of 29 CP cases tested, and of these, 81% also contained herpesvirus. The second syndrome occurred in juveniles and growers exhibiting poor growth, and was characterized histologically by systemic lymphoid proliferation and nonsuppurative encephalitis (SLPE). Herpesviruses were isolated or detected by PCR from at least 1 internal organ in 31 of 33 SLPE cases (94%) compared with 5 of 95 crocodiles without the syndrome (5%, p < 0.0001). The third syndrome, characterized by multifocal lymphohistiocytic infiltration of the dermis (LNS), occurred in 6 harvest-sized crocodiles. Herpesviruses were isolated from at least 1 skin lesion in 4 of these 6 cases. Although our study revealed strong associations between herpesvirus and the CP and SLPE syndromes, the precise nature of the role of herpesvirus, along with the pathogenesis and epidemiology of the syndromes, requires further investigation