Two novel bornaviruses identified in colubrid and viperid snakes.

We present the complete genome sequences of Caribbean watersnake bornavirus (CWBV) and Mexican black-tailed rattlesnake bornavirus (MRBV), which we identified in archived raw transcriptomic read data of a Caribbean watersnake (Tretanorhinus variabilis) and a Mexican black-tailed rattlesnake (Crotalus molossus nigrescens), respectively. The genomes of CWBV and MRBV have a length of about 8,900 nucleotides and comprise the complete coding regions and the untranslated regions. The overall genomic makeup and predicted gene content is typical for members of the genus Orthobornavirus within the family Bornaviridae. Alternative splicing was detected for the L and M genes. Based on a phylogenetic analysis of all viral proteins, we consider both viruses to be members of a single novel species within the genus Orthobornavirus. Both viruses form a distinct outgroup to all currently known orthobornaviruses. Based on the novel virus genomes, we furthermore identified closely related endogenous bornavirus-like nucleoprotein sequences in transcriptomic data of veiled chameleons (Chamaeleo calyptratus) and a common lancehead (Bothrops atrox).

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus.

Snakes are capable of surviving long periods without food. In this study we characterized the microbiota of a Timber Rattlesnake (Crotalus horridus), devoid of digesta, living in the wild. Pyrosequencing-based metagenomics were used to analyze phylogenetic and metabolic profiles with the aid of the MG-RAST server. Pyrosequencing of samples taken from the stomach, small intestine and colon yielded 691696, 957756 and 700419 high quality sequence reads. Taxonomic analysis of metagenomic reads indicated Eukarya was the most predominant domain, followed by bacteria and then viruses, for all three tissues. The most predominant phylum in the domain Bacteria was Proteobacteria for the tissues examined. Functional classifications by the subsystem database showed cluster-based subsystems were most predominant (10-15 %). Almost equally predominant (10-13 %) was carbohydrate metabolism. To identify bacteria in the colon at a finer taxonomic resolution, a 16S rRNA gene clone library was created. Proteobacteria was again found to be the most predominant phylum. The present study provides a baseline for understanding the microbial ecology of snakes living in the wild.

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes.

We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii, the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna- and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.

Genetic characterization of a reptilian calicivirus (Cro1).

BACKGROUND: Vesiviruses in the family Caliciviridae infect a broad range of animal hosts including mammals, birds, fish, amphibians and reptiles. The vesivirus Cro1 strains were isolated from diseased snakes in the San Diego zoo in 1978 and reported as the first caliciviruses found in reptiles. The goal of this study was to characterize the Cro1 strain 780032I that was isolated in cell culture from a rock rattlesnake (Crotalus lepidus) in the original outbreak. RESULTS: We re-amplified the original virus stock in Vero cells, and determined its full-length genome sequence. The Cro1 genome is 8296 nucleotides (nt) in length and has a typical vesivirus organization, with three open reading frames (ORF), ORF1 (5643 nt), ORF2 (2121 nt), and ORF3 (348 nt) encoding a nonstructural polyprotein, the major capsid protein precursor, and a minor structural protein, respectively. Phylogenetic analysis of the full-length genome sequence revealed that the Cro1 virus clustered most closely with the VESV species of the genus Vesivirus, but was genetically distinct (82-83% identities with closest strains). CONCLUSIONS: This is the first description of a full-length genome sequence from a reptile calicivirus (Cro1). The availability of the Cro1 genome sequence should facilitate investigation of the molecular mechanisms involved in Cro1 virus evolution and host range.

Measuring agreement and discord among hemagglutination inhibition assays against different ophidian paramyxovirus strains in the Eastern massasauga (Sistrurus catenatus catenatus).

At present, the hemagglutination inhibition (HI) assay is the sole commercially available serologic method available to detect exposure to ophidian paramyxovirus (OPMV) in snakes. During 2006, 26 eastern massasaugas (Sistrurus catenatus catenatus) were collected, and blood was sampled to determine their OPMV status. Samples from each snake were divided into 3 aliquots and tested by using commercially available HI assays against the 4 OPMV isolates used in the 3 laboratories that offer the service. All snakes were tested for antibodies by using HI assays against the green tree python (GTP), San Lucan rattlesnake (SLR), and Aruba Island rattlesnake (AIR) isolates. Twenty-five snakes were tested for antibodies against the western diamondback rattlesnake (WDR) isolate. All samples tested against the GTP and SLR were positive (26/26), whereas 56% (14/25) of the WDR assays were positive, and none (0/26) of the AIR assays yielded a positive result. There was 100% agreement between the GTP and SLR assays, and complete disagreement between the SLR and AIR, as well as the GTP and AIR assays. Kappa statistics for the GTP-WDR, SLR-WDR, GTP-AIR, SLR-AIR, and WDR-AIR indicated that the assays had less than chance agreement. The results demonstrate that current HI assays are not reliable as a sole diagnostic assay in the eastern massasauga. Furthermore, HI assays need to be evaluated by using other parameters to determine OPMV exposure in eastern massasaugas.

Phylogenetic analysis of the L and HN gene of ophidian paramyxoviruses. Brief report.

Two reptilian paramyxoviruses, isolated from a neotropical rattlesnake (neotropical virus, NTV, ATCC VR-1408) and a bush viper (bush viper virus, BVV, ATCC VR- 1409), respectively, were analysed to determine their taxonomic position among other reptilian paramyxoviruses investigated previously by Ahne et al.. A 679 bp long region of the hemagglutinin-neuraminidase (HN) gene and a 627 bp long region of the large (L) gene were reverse transcribed, amplified by polymerase chain reaction (PCR), and sequenced. The deduced amino acid sequences were compared to mammalian paramyxoviruses belonging to the genera Respirovirus and Rubulavirus. The deduced amino acid sequences revealed 58.9 to 62% homology for the partial L protein and 41% to 47.1% homology for the partial HN protein. For phylogenetic analyses, a 518 bp L gene and a 352 bp HN gene fragment were used, both generating similar trees consisting of two distinct main groups, and some intermediate isolates. BVV clustered within group "b" while NTV clustered together with the intermediate ophidian paramyxovirus isolate Crot2-OH90.

Development of a reverse transcription polymerase chain reaction procedure for the detection of marine caliciviruses with potential application for nucleotide sequencing.

A reverse transcription polymerase chain reaction (RT-PCR) procedure is described for the detection of marine caliciviruses including vesicular exanthema of swine virus (VESV), San Miguel sea lion virus (SMSV), bovine Tillamook virus (BCV Bos-1) and caliciviruses (CV) isolated from dolphin (Cetacean CV), gorilla (Primate CV) and rattlesnake (Reptile CV) using primers (1F and 1R) designed from the capsid-coding region of the viral genome. These primers were compared with those described by Neill, J.D. and Seal, B.S., 1995: Development of PCR primers for specific amplification of two distinct regions of the genomes of San Miguel sea lion and vesicular exanthema of swine viruses, Mol. Cell. Probes 9, 33-38 (Hel1/Hel2), which had been designed from the 2C-like region of the calicivirus genome. Both sets proved to be extremely useful diagnostic tools for all of the known marine calicivirus serotypes with the exception of three: SMSV-8 and -12 and mink CV suggesting that these three caliciviruses may belong to a different group. Neither of the two primer sets reacted with strains of the vesicular disease viruses of foot-and-mouth disease (FMD), swine vesicular disease (SVD) or vesicular stomatitis (VS) nor with two feline caliciviruses (FCV). The 1F/1R primer set has the advantage over the Hel1/Hel2 set in that it generates a larger PCR product for nucleotide sequence investigations and so provides greater opportunity for identifying molecular differences between the viruses.

Immunoperoxidase detection of ophidian paramyxovirus in snake lung using a polyclonal antibody.

In a retrospective study of proliferative interstitial pneumonia in viperid and nonviperid snakes, formalin-fixed, paraffin-embedded lungs from 52 snakes were screened for immunohistochemical reactivity to ophidian paramyxovirus. All snakes were from zoological collections that experienced mortalities attributed to paramyxovirus infection. Of the 52 snakes, 47 had pulmonary lesions compatible with ophidian paramyxovirus infection. Histologic changes in affected lungs included hyperplasia and hypertrophy of septal and faveolar epithelial cells, loss of ciliated cells, mixed leukocytic interstitial infiltrates, fibrinonecrotic exudate in the lumen of proximal and distal faveolar compartments, and occasional epithelial syncytial cell formation or intraepithelial eosinophilic intracytoplasmic inclusions. Lungs were immunohistochemically stained for paramyxovirus antigens by utilizing rabbit polyclonal antibodies against a paramyxovirus isolate from a black mamba (Dendroaspis polyepis polyepis). Virus infection in 6 snakes was confirmed by virus isolation from frozen lung tissue. Of the 6 lungs from which paramyxovirus was isolated, 5 lungs stained positively for viral antigens utilizing antisera to the black mamba isolate. Altogether, 36 lungs stained positively for paramyxovirus antigens. There was multifocal to diffuse linear staining of the lumenal surface of faveolar epithelium, and there were multiple foci of granular cytoplasmic staining. Immunohistochemical staining of formalin-fixed lungs from snakes with proliferative interstitial pneumonia was helpful as a routine diagnostic test for substantiating a diagnosis of ophidian paramyxovirus infection.

Characterization of a reovirus isolate from a rattle snake, Crotalus viridis, with neurological dysfunction.

A virus isolate from the brain of a rattle snake with central nervous system (CNS) symptoms was identified as a reovirus. The isolate did not agglutinate pig erythrocytes and was not neutralized by antisera against avian reovirus S1133 and mammalian reovirus type 3. The cytopathic effect in Vero cells was characterized by formation of syncytial giant cells. Electrophoretic analysis of the genome revealed 10 segments of dsRNA. The isolate displayed characteristics distinct from avian and mammalian reoviruses.