Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus

Discovery of the first sea turtle adenovirus and turtle associated circoviruses

Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host-virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host-virus interactions.

Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer

We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.

Adenoviruses in Avian Hosts: Recent Discoveries Shed New Light on Adenovirus Diversity and Evolution

While adenoviruses cause infections in a wide range of vertebrates, members of the genus Atadenovirus, Siadenovirus, and Aviadenovirus predominantly infect avian hosts. Several recent studies on avian adenoviruses have encouraged us to re-visit previously proposed adenovirus evolutionary concepts. Complete genomes and partial DNA polymerase sequences of avian adenoviruses were extracted from NCBI and analysed using various software. Genomic analyses and constructed phylogenetic trees identified the atadenovirus origin from an Australian native passerine bird in contrast to the previously established reptilian origin. In addition, we demonstrated that the theories on higher AT content in atadenoviruses are no longer accurate and cannot be considered as a species demarcation criterion for the genus Atadenovirus. Phylogenetic reconstruction further emphasised the need to reconsider siadenovirus origin, and we recommend extended studies on avian adenoviruses in wild birds to provide finer evolutionary resolution.

Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia

Little is known about the diversity of adenoviruses in wild birds and how they have evolved and are maintained in complex ecosystems. In this study, 409 samples were collected from woodland birds caught for banding (droppings), birds submitted to a wildlife hospital (droppings and tissues), silver gulls (droppings or tissues), and feral pigeons (Columbia livia; oral, cloacal swabs, or tissues) from the Greater Sydney area in NSW, Australia. Additional samples were from native pigeons and doves (swabs) presented to the Healesville Sanctuary, VIC, Australia. Samples were screened for adenovirus DNA using degenerate primers and polymerase chain reaction. Adenovirus sequences were detected in eighty-three samples representing thirty-five novel amino acid sequences. Fourteen novel sequences were atadenoviruses, seven were aviadenoviruses, twelve were siadenoviruses, and one was a mastadenovirus. Sequences from passerine birds were predominately found to form a single lineage within the atadenoviruses, a second lineage in the siadenoviruses, and a third smaller aviadenovirus lineage. These viruses appeared to have co-evolved with a diverse group of woodland birds that share similar habitat. Evidence for host/virus co-evolution in some viruses and a wide host range in others was observed. A high prevalence of adenovirus infection was found in rainbow lorikeets (Trichoglossus haematodus), galahs (Eolophus roseicapilla), and sulphur-crested cockatoos (Cacatua galerita). Sequences were either identical to or mapped to already established lineages in the Aviadenovirus, Siadenovirus, and Atadenovirus genera, suggesting a possible origin of the psittacine adenoviruses in ancestral Australian psittacine birds. The sequences of passerine and psittacine origin provided insight into diversity and structure of the Atadenovirus genus and demonstrated for the first-time viruses of passerine origin in the Aviadenovirus genus. Four unrelated adenovirus sequences were found in silver gull samples (Chroicocephalus novaehollandiae), including one of pigeon origin, suggesting environmental virus exposure. Three pigeon adenovirus types were detected in feral pigeons and infection prevalence was high. Evidence for host switching between invasive species and native species and native species and invasive species was documented. A variant of a murine adenovirus was detected in kidney tissue from two bird species suggesting mouse to bird transmission.

The complete genome sequence of bearded dragon adenovirus 1 harbors three genes encoding proteins of the C-type lectin-like domain superfamily

Bearded dragon adenovirus 1 (BDAdV-1), also known as agamid adenovirus 1, has been described worldwide as a prevalent infectious agent of the inland bearded dragon (Pogona vitticeps), the most common squamate exotic pet reptile. Previous limited sequence data of the adenoviral DNA polymerase and hexon genes indicated that BDAdV-1 is a member of genus Atadenovirus family Adenoviridae. Atadenoviruses infect ruminants, marsupials, testudine reptiles and birds, yet the genus has been shown to be of squamate reptile origin. Here, we report a screening survey along with the complete genome sequence of BDAdV-1, derived directly from the sample of a deceased juvenile dragon showing central nervous system signs prior to passing. The BDAdV-1 genome is 35,276 bp and contains 32 putative genes. Its genome organization is characteristic of the members of genus Atadenovirus, however, a divergent LH3 gene indicates structural interactions of different nature compared to other genus members such as snake adenovirus 1. We identified five novel open reading frames (ORFs), three of which encode proteins of the C-type lectin-like domain (CTLD) superfamily. ORF3 has a CTLD group II-like domain architecture displaying structural similarity with natural killer cell surface receptors and with an alphaherpesviral virulence factor gene for neurotropism, UL45. ORF4 and 6 are extremely long compared to typical adenoviral right-end genes and possibly encode members of the CTLD superfamily with novel, previously undescribed domain architectures. BDAdV-1 is the hitherto most divergent member of genus Atadenovirus providing new insights on adenoviral diversity, evolution and pathogenesis.

Adenoviruses across the animal kingdom: a walk in the zoo

Adenoviruses (AdVs) infect representatives of numerous species from almost every major vertebrate class, albeit their incidence shows great variability. AdVs infecting birds, reptiles, and bats are the most common and diverse, whereas only one AdV has been so far isolated both from fish and amphibians. The family Adenoviridae is divided into five genera, each corresponding to an independent evolutionary lineage that supposedly coevolved with its respective vertebrate hosts. Members of genera Mastadenovirus and Aviadenovirus seem to infect exclusively mammals and birds, respectively. The genus Ichtadenovirus includes the single known AdV from fish. The majority of AdVs in the genus Atadenovirus originated from squamate reptiles (lizards and snakes), but also certain mammalian and avian AdVs are classified within this genus. The genus Siadenovirus contains the only AdV isolated from frog, along with numerous avian AdVs. In turtles, members of a sixth AdV lineage have been discovered, pending official recognition as an independent genus. The most likely scenario for AdV evolution includes long-term cospeciation with the hosts, as well as occasional switches between closely or, rarely, more distantly related hosts.

Unconventional gene arrangement and content revealed by full genome analysis of the white sturgeon adenovirus, the single member of the genus Ichtadenovirus

Adenoviruses are commonly found in members of almost every vertebrate lineage except fish and amphibians, from each of which only a single isolate is available as yet. In this work, the complete genomic sequence of a fish adenovirus, originating from the white sturgeon (Acipenser transmontanus), was determined and analyzed. Several exceptional features were observed including the longest hitherto known genome size (of 48,395 bp) and a strange location of the putative fiber genes resulting in an unconventional organization pattern. The left genome end contained four fiber-like genes, three of them in a tandem position on the r (rightward transcribed) strand, followed by a fourth one on the l strand. Rightward from these, the conserved adenoviral gene cassette, encompassing 16 family-common genes, was identified. In the right-hand part, amounting for >42% of the entire genome, the presence of 28 ORFs, with a coding capacity of larger than 50 amino acids, was revealed. Interestingly, most of these showed no similarity to any adenoviral genes except two ORFs, resembling slightly the parvoviral NS gene, homologues of which occur in certain avian adenoviruses. These specific traits, together with the results of phylogeny reconstructions, fully justified the separation of the white sturgeon adenovirus into the recently established new genus Ichtadenovirus. Targeted attempts to find additional adenoviruses in any other fish species were to no avail as yet. Thus the founding member, WSAdV-1 still remains the only representative of ichtadenoviruses.

Adenoviruses in free-ranging Australian bearded dragons (Pogona spp.)

Adenoviruses are a relatively common infection of reptiles globally and are most often reported in captive central bearded dragons (Pogona vitticeps). We report the first evidence of adenoviruses in bearded dragons in their native habitat in Australia. Oral-cloacal swabs and blood samples were collected from 48 free-ranging bearded dragons from four study populations: western bearded dragons (P. minor minor) from Western Australia (n = 4), central bearded dragons (P. vitticeps) from central Australia (n = 2) and western New South Wales (NSW) (n = 29), and coastal bearded dragons (P. barbata) from south-east Queensland (n = 13). Samples were tested for the presence of adenoviruses using a broadly reactive (pan-adenovirus) PCR and a PCR specific for agamid adenovirus-1. Agamid adenovirus-1 was detected in swabs from eight of the dragons from western NSW and one of the coastal bearded dragons. Lizard atadenovirus A was detected in one of the dragons from western NSW. Adenoviruses were not detected in any blood sample. All bearded dragons, except one, were apparently healthy and so finding these adenoviruses in these animals is consistent with bearded dragons being natural hosts for these viruses.

Detection and phylogenetic analysis of adenoviruses occurring in a single anole species

Adenoviruses (AdVs) infect a wide range of hosts, and they have undergone recent and ancient host transfers multiple times. In reptiles, AdVs have been found in many captive individuals, and have been implicated in morbidity and mortality in several species. Yet the pathogenicity, transmission, phylogenetic distribution, and source of AdVs in the environment are still unknown. We therefore chose to opportunistically sample deceased captive Anolis sagrei individuals that were collected from different populations in the Bahamas and the Cayman Islands, as well as fecal samples from one island population, to explore the disease dynamics and diversity of adenovirus infecting A. sagrei populations. We found that adenovirus infection was present in our captive colony at low prevalence (26%), and was likely not the primary cause of observed morbidity and mortality. Among the 10 individuals (out of 38 sampled) which tested positive for adenovirus, we identified four adenovirus clades, several of which are distantly related, despite the close relationships of the A. sagrei host populations. These results suggest that while adenovirus may not be highly prevalent in the wild, it is present at low levels across much of the range of A. sagrei. It may undergo frequent host switching across both deep and shallow host divergences.

Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid

Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors.

Whole-genome sequences of Odocoileus hemionus deer adenovirus isolates from deer, moose and elk are highly conserved and support a new species in the genus Atadenovirus

We present the first complete genome sequence of Odocoileus hemionus deer adenovirus 1 (OdAdV-1). This virus can cause sporadic haemorrhagic disease in cervids, although epizootics with high mortality have occurred in California. OdAdV-1 has been placed in the genus Atadenovirus, based on partial hexon, pVIII and fibre genes. Ten field isolates recovered from naturally infected mule deer (Odocoileus hemionus), white-tailed deer (Odocoileus virginiana) and moose (Alces alces) from Wyoming, black-tailed deer (Odocoileus hemionus columbianus) from California, and Rocky Mountain elk (Cervus elaphus nelsoni) from Colorado and Washington state were sequenced. The genome lengths ranged from 30 620 to 30 699 bp, contained the predicted proteins and gene organization typical of members of genus Atadenovirus, and had a high percentage of A/T nucleotides (66.7 %). Phylogenic analysis found that the closest ancestry was with ruminant atadenoviruses, while a divergence of the hexon, polymerase and penton base proteins of more than 15 % supports classification as a new species. Genetic global comparison between the 10 isolates found an overall 99 % identity, but greater divergence was found between those recovered from moose and elk as compared to deer, and a single variable region contained most of these differences. Our findings demonstrate that OdAdV-1 is highly conserved between 10 isolates recovered from multiple related cervid species, but genotypic differences, largely localized to a variable region, define two strains. We propose that the virus type name be changed to cervid adenovirus 1, with the species name Cervid atadenovirus A. Sequence data were used to develop molecular assays for improved detection and genotyping.

Novel bat adenoviruses with low G+C content shed new light on the evolution of adenoviruses

Bats have been reported to carry diverse adenoviruses. However, most bat adenoviruses have been identified on the basis of partial genome sequences, and knowledge on the evolution of bat adenoviruses remains limited. In this study, we isolated and characterized four novel adenoviruses from two distinct bat species, and their full-length genomes were sequenced. Sequence analysis revealed that these isolates represented three distinct species of the genus Mastadenovirus. However, all isolates had an exceptionally low G+C content and relatively short genomes compared with other known mastadenoviruses. We further analysed the relationships among the G+C content, 5'-C-phosphate-G-3' (CpG) representation and genome size in the family Adenoviridae. Our results revealed that the CpG representation in adenoviral genomes depends primarily on the level of methylation, and the genome size displayed significant positive correlations with both G+C content and CpG representation. Since ancestral adenoviruses are believed to have contained short genomes, those probably had a low G+C content, similar to the genomes of these bat strains. Our results suggest that bats are important natural reservoirs for adenoviruses and play important roles in the evolution of adenoviruses.

Hyperplastic stomatitis and esophagitis in a tortoise (Testudo graeca) associated with an adenovirus infection

A 2-year-old female, spur-thighed tortoise (Testudo graeca) was presented with poor body condition (1/5) and weakness. Fecal analysis revealed large numbers of oxyurid-like eggs, and radiographs were compatible with gastrointestinal obstruction. Despite supportive medical treatment, the animal died. At gross examination, an intestinal obstruction was confirmed. Histopathology revealed severe hyperplastic esophagitis and stomatitis with marked epithelial cytomegaly and enormous basophilic intranuclear inclusion bodies. Electron microscopy examination revealed a large number of 60-80 nm, nonenveloped, icosahedral virions arranged in crystalline arrays within nuclear inclusions of esophageal epithelial cells, morphologically compatible with adenovirus-like particles. PCR for virus identification was performed with DNA extracted from formalin-fixed, paraffin-embedded tissues. A nested, consensus pan-adenovirus PCR and sequencing analysis showed a novel adenovirus. According to phylogenetic calculations, it clustered to genus Atadenovirus in contrast with all other chelonian adenoviruses described to date. The present report details the pathologic findings associated with an adenovirus infection restricted to the upper digestive tract.

Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae) and Worm Lizards (Amphisbaenia)

Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs) in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni), nine Iberian worm lizards (Blanus cinereus), and two Iberian green lizards (Lacerta schreiberi), respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses.

Genetic and Molecular Epidemiological Characterization of a Novel Adenovirus in Antarctic Penguins Collected between 2008 and 2013

Antarctica is considered a relatively uncontaminated region with regard to the infectious diseases because of its extreme environment, and isolated geography. For the genetic characterization and molecular epidemiology of the newly found penguin adenovirus in Antarctica, entire genome sequencing and annual survey of penguin adenovirus were conducted. The entire genome sequences of penguin adenoviruses were completed for two Chinstrap penguins (Pygoscelis antarctica) and two Gentoo penguins (Pygoscelis papua). The whole genome lengths and G+C content of penguin adenoviruses were found to be 24,630-24,662 bp and 35.5-35.6%, respectively. Notably, the presence of putative sialidase gene was not identified in penguin adenoviruses by Rapid Amplification of cDNA Ends (RACE-PCR) as well as consensus specific PCR. The penguin adenoviruses were demonstrated to be a new species within the genus Siadenovirus, with a distance of 29.9-39.3% (amino acid, 32.1-47.9%) in DNA polymerase gene, and showed the closest relationship with turkey adenovirus 3 (TAdV-3) in phylogenetic analysis. During the 2008-2013 study period, the penguin adenoviruses were annually detected in 22 of 78 penguins (28.2%), and the molecular epidemiological study of the penguin adenovirus indicates a predominant infection in Chinstrap penguin population (12/30, 40%). Interestingly, the genome of penguin adenovirus could be detected in several internal samples, except the lymph node and brain. In conclusion, an analysis of the entire adenoviral genomes from Antarctic penguins was conducted, and the penguin adenoviruses, containing unique genetic character, were identified as a new species within the genus Siadenovirus. Moreover, it was annually detected in Antarctic penguins, suggesting its circulation within the penguin population.

Novel bat adenoviruses with an extremely large E3 gene

Bats carry diverse RNA viruses, some of which are responsible for human diseases. Compared to bat-borne RNA viruses, relatively little information is known regarding bat-borne DNA viruses. In this study, we isolated and characterized three novel bat adenoviruses (BtAdV WIV9-11) from Rhinolophus sinicus. Their genomes, which are highly similar to each other but distinct from those of previously sequenced adenoviruses (AdVs), are 37 545, 37 566 and 38 073 bp in size, respectively. An unusually large E3 gene was identified in their genomes. Phylogenetic and taxonomic analyses suggested that these isolates represent a distinct species of the genus Mastadenovirus. Cell susceptibility assays revealed a broad cell tropism for these isolates, indicating that they have a potentially wide host range. Our results expand the understanding of genetic diversity of bat AdVs.

Molecular characterization, phylogeny analysis and pathogenicity of a Muscovy duck adenovirus strain isolated in China in 2014

This study aimed to characterize a novel adenovirus (AdV) isolated from diseased Muscovy ducks in China. After the AdV was successfully propagated in duck embryo fibroblasts, the morphological and physicochemical properties of the virions were studied by electron microscopy and different tests. The results of the analyses were in conformity with AdV properties. The full genome sequence was determined and analyzed. The new isolate (named CH-GD-12-2014) shared over 91% sequence identity with duck AdV-2 representing the species Duck aviadenovirus B. The most important distinguishing feature between the two DAdV strains was the presence of a second fiber gene in the Chinese isolate. Phylogeny reconstruction confirmed the affiliation of the virus with goose and duck AdVs in the genus Aviadenovirus. Experimental infection resulted in embryo death, and intramuscular inoculation provoked morbidity and mortality among ducks and chickens.

Structure and Sialyllactose Binding of the Carboxy-Terminal Head Domain of the Fibre from a Siadenovirus, Turkey Adenovirus 3

The virulent form of turkey adenovirus 3 (TAdV-3), also known as turkey hemorrhagic enteritis virus (THEV), is an economically important poultry pathogen, while the avirulent form is used as a vaccine. TAdV-3 belongs to the genus Siadenovirus. The carboxy-terminal region of its fibre does not have significant sequence similarity to any other adenovirus fibre heads of known structure. Two amino acid sequence differences between virulent and avirulent TAdV-3 map on the fibre head: where virulent TAdV-3 contains Ile354 and Thr376, avirulent TAdV-3 contains Met354 and Met376. We determined the crystal structures of the trimeric virulent and avirulent TAdV-3 fibre head domains at 2.2 Å resolution. Each monomer contains a beta-sandwich, which, surprisingly, resembles reovirus fibre head more than other adenovirus fibres, although the ABCJ-GHID topology is conserved in all. A beta-hairpin insertion in the C-strand of each trimer subunit embraces its neighbouring monomer. The avirulent and virulent TAdV-3 fibre heads are identical apart from the exact orientation of the beta-hairpin insertion. In vitro, sialyllactose was identified as a ligand by glycan microarray analysis, nuclear magnetic resonance spectroscopy, and crystallography. Its dissociation constant was measured to be in the mM range by isothermal titration calorimetry. The ligand binds to the side of the fibre head, involving amino acids Glu392, Thr419, Val420, Lys421, Asn422, and Gly423 binding to the sialic acid group. It binds slightly more strongly to the avirulent form. We propose that, in vivo, the TAdV-3 fibre may bind a sialic acid-containing cell surface component.

Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1

Adenoviruses are non-enveloped icosahedral viruses with trimeric fibre proteins protruding from their vertices. There are five known genera, from which only Mastadenoviruses have been widely studied. Apart from studying adenovirus as a biological model system and with a view to prevent or combat viral infection, there is a major interest in using adenovirus for vaccination, cancer therapy and gene therapy purposes. Adenoviruses from the Atadenovirus genus have been isolated from squamate reptile hosts, ruminants and birds and have a characteristic gene organization and capsid morphology. The carboxy-terminal virus-distal fibre head domains are likely responsible for primary receptor recognition. We determined the high-resolution crystal structure of the Snake Adenovirus 1 (SnAdV-1) fibre head using the multi-wavelength anomalous dispersion (MAD) method. Despite the absence of significant sequence homology, this Atadenovirus fibre head has the same beta-sandwich propeller topology as other adenovirus fibre heads. However, it is about half the size, mainly due to much shorter loops connecting the beta-strands. The detailed structure of the SnAdV-1 fibre head and other animal adenovirus fibre heads, together with the future identification of their natural receptors, may lead to the development of new strategies to target adenovirus vectors to cells of interest.

Prevalence of neutralising antibodies against adenoviruses in lizards and snakes

Adenoviruses (AdVs) are relatively common in lizards and snakes, and several genetically distinct AdVs have been isolated in cell culture. The aims of this study were to examine serological relationships among lizard and snake AdVs and to determine the frequency of AdV infections in these species. Isolates from a boa constrictor (Boa constrictor), a corn snake (Pantherophis gutattus) and a central bearded dragon (Pogona vitticeps), and two isolates from helodermatid lizards (Heloderma horridum and H. suspectum) were used in neutralisation tests for the detection of antibodies in plasma from 263 lizards from seven families (including 12 species) and from 141 snakes from four families (including 28 species) from the USA and Europe. Most lizard and snake samples had antibodies against a range of AdV isolates, indicating that AdV infection is common among these squamates. Neutralisation tests with polyclonal antibodies raised in rabbits demonstrated serological cross-reactivity between both helodermatid lizard isolates. However, squamate plasma showed different reactions to each of these lizard isolates in neutralisation tests.

Partial characterization of new adenoviruses found in lizards

In the years 2011-2012, a consensus nested polymerase chain reaction was used for the detection of adenovirus (AdV) infection in reptiles. During this screening, three new AdVs were detected. One of these viruses was detected in three lizards from a group of green striped tree dragons (Japalura splendida). Another was detected in a green anole (Anolis carolinensis). A third virus was detected in a Jackson's chameleon (Chamaeleo jacksonii). Analysis of a portion of the DNA-dependent DNA polymerase genes of each of these viruses revealed that they all were different from one another and from all previously described reptilian AdVs. Phylogenetic analysis of the partial DNA polymerase gene sequence showed that all newly detected viruses clustered within the genus Atadenovirus. This is the first description of AdVs in these lizard species.

Molecular characterization of a lizard adenovirus reveals the first atadenovirus with two fiber genes and the first adenovirus with either one short or three long fibers per penton

Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the Atadenovirus genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (Heloderma suspectum) and Mexican beaded lizards (Heloderma horridum). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the Atadenovirus genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus.

IMPORTANCE

Here we show that a lizard adenovirus, LAdV-2, has a penton architecture never observed before. LAdV-2 expresses two fiber proteins-one short and one long. In the virion, most vertices have one short fiber, but a few of them have three long fibers attached to the same penton base. This observation raises new intriguing questions on virus structure. How can the triple fiber attach to a pentameric vertex? What determines the number and location of each vertex type in the icosahedral particle? Since fibers are responsible for primary attachment to the host, this novel architecture also suggests a novel mode of cell entry for LAdV-2. Adenoviruses have a recognized potential in nanobiomedicine, but only a few of the more than 200 types found so far in nature have been characterized in detail. Exploring the taxonomic wealth of adenoviruses should improve our chances to successfully use them as therapeutic tools.

Novel parvovirus from the worm lizard Trogonophis wiegmanni - First virus ever detected in amphisbaenian hosts

To explore the diversity of some DNA viruses in reptiles, a continuous screening is going on, in our laboratory, by PCR using different consensus primers designed for the detection of the most conserved genome regions of adeno-, herpes- and parvoviruses. The test material consists essentially of dead specimens collected randomly from private pet owners, local pet shops, or at occasional exotic pet fairs. Here we report the partial sequence of a putative novel parvovirus obtained from a dead checkerboard worm lizard (Trogonophis wiegmanni) that had been wild-caught in its native habitat. An in-house-developed PCR with consensus primers targeting the gene of the parvoviral capsid protein was used. Other PCRs, intended to detect certain large DNA viruses, remained negative. The sequence of the PCR product indicated the presence of a hitherto unknown parvovirus in the internal organs of the checkerboard worm lizard. In phylogeny reconstruction, the novel sequence clustered with the members of the Dependovirus genus of the Parvoririnae subfamily, closest to the branch of snake adeno-associated virus. Since we could not demonstrate the presence of a potential helper virus, the putative amphisbaenian parvovirus supposedly can replicate autonomously. This is the first virus infection ever detected in any members of the suborder Amphisbaenia, and only the third parvoviral sequence obtained from any reptilian host.

A novel adenovirus in Chinstrap penguins (Pygoscelis antarctica) in Antarctica

Adenoviruses (family Adenoviridae) infect various organ systems and cause diseases in a wide range of host species. In this study, we examined multiple tissues from Chinstrap penguins (Pygoscelis antarctica), collected in Antarctica during 2009 and 2010, for the presence of novel adenoviruses by PCR. Analysis of a 855-bp region of the hexon gene of a newly identified adenovirus, designated Chinstrap penguin adenovirus 1 (CSPAdV-1), showed nucleotide (amino acid) sequence identity of 71.8% (65.5%) with South Polar skua 1 (SPSAdV-1), 71% (70%) with raptor adenovirus 1 (RAdV-1), 71.4% (67.6%) with turkey adenovirus 3 (TAdV-3) and 61% (61.6%) with frog adenovirus 1 (FrAdV-1). Based on the genetic and phylogenetic analyses, CSPAdV-1 was classified as a member of the genus, Siadenovirus. Virus isolation attempts from kidney homogenates in the MDTC-RP19 (ATCC® CRL-8135™) cell line were unsuccessful. In conclusion, this study provides the first evidence of new adenovirus species in Antarctic penguins.

Establishment of an agamid cell line and isolation of adenoviruses from central bearded dragons (Pogona vitticeps)

A cell line was established from whole 6–8-week-old central bearded dragon ( Pogona vitticeps) embryos. Cells were mid-sized and showed an elongated and polymorphic form. The cell line grew in a monolayer and has been serially passaged for 17 passages at time of publication. This cell line has been used with samples from adenovirus polymerase chain reaction (PCR)-positive bearded dragons, and 2 virus isolates have been obtained so far. The isolates show a clear cytopathic effect in inoculated cells. Both virus isolates have been serially passaged on this cell line, and have been identified by PCR amplification and sequencing of a portion of the DNA-dependent DNA polymerase gene and show 100% nucleotide identity to the corresponding region of an agamid adenovirus. Electron microscopic examination of supernatant from infected cells demonstrated the presence of nonenveloped particles, with a diameter of approximately 80 nm in both virus isolates.

Whole-genome sequences of two turkey adenovirus types reveal the existence of two unknown lineages that merit the establishment of novel species within the genus Aviadenovirus

There are eight species established for aviadenoviruses: Fowl adenovirus A–E, Goose adenovirus A, Falcon adenovirus A and Turkey adenovirus B. The aim of this study was to sequence and analyse the complete genomes of turkey adenovirus 4 (TAdV-4) and TAdV-5 (strain 1277BT) in addition to almost two-thirds of the genome of another TAdV-5 strain (strain D1648). By applying next-generation sequencing, the full genomes were found to be 42 940 and 43 686 bp and the G+C content was 48.5 and 51.6 mol% for TAdV-4 and TAdV-5, respectively. One fiber gene was identified in TAdV-4, whereas two fiber genes were found in TAdV-5. The genome organization of TAdV-4 resembled that of fowl adenovirus 5 (FAdV-5), but it had ORF1C near the left end of the genome. TAdV-4 also had five 123 bp tandem repeats followed by five 33 bp tandem repeats, but they occurred before and not after ORF8, as in several fowl adenoviruses. The genome organization of TAdV-5 was almost the same as that of FAdV-1 but with a possible difference in the splicing pattern of ORF11 and ORF26. Phylogenetic analyses and G+C content showed differences that seem to merit the establishment of two new species within the genus Aviadenovirus: Turkey adenovirus C (for TAdV-4) and Turkey adenovirus D (for TAdV-5). Our analyses suggest a common evolutionary origin of TAdV-5 and FAdV-1.

Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus

Adenovirus fibre proteins play an important role in determining viral tropism. The C-terminal domain of the fibre protein from snake adenovirus type 1, a member of the Atadenovirus genus, has been expressed, purified and crystallized. Crystals were obtained belonging to space groups P2(1)2(1)2(1) (two different forms), I2(1)3 and F23. The best of these diffracted synchrotron radiation to a resolution of 1.4 Å. As the protein lacks methionines or cysteines, site-directed mutagenesis was performed to change two leucine residues to methionines. Crystals of selenomethionine-derivatized crystals of the I2(1)3 form were also obtained and a multi-wavelength anomalous dispersion data set was collected.

Phylogenetic analyses of novel squamate adenovirus sequences in wild-caught Anolis lizards

Adenovirus infection has emerged as a serious threat to the health of captive snakes and lizards (i.e., squamates), but we know relatively little about this virus' range of possible hosts, pathogenicity, modes of transmission, and sources from nature. We report the first case of adenovirus infection in the Iguanidae, a diverse family of lizards that is widely-studied and popular in captivity. We report adenovirus infections from two closely-related species of Anolis lizards (anoles) that were recently imported from wild populations in the Dominican Republic to a laboratory colony in the United States. We investigate the evolution of adenoviruses in anoles and other squamates using phylogenetic analyses of adenovirus polymerase gene sequences sampled from Anolis and a range of other vertebrate taxa. These phylogenetic analyses reveal that (1) the sequences detected from each species of Anolis are novel, and (2) adenoviruses are not necessarily host-specific and do not always follow a co-speciation model under which host and virus phylogenies are perfectly concordant. Together with the fact that the Anolis adenovirus sequences reported in our study were detected in animals that became ill and subsequently died shortly after importation while exhibiting clinical signs consistent with acute adenovirus infection, our discoveries suggest the need for renewed attention to biosecurity measures intended to prevent the spread of adenovirus both within and among species of snakes and lizards housed in captivity.

Partial characterization of a new adenovirus lineage discovered in testudinoid turtles

In the USA and in Hungary, almost simultaneously, adenoviruses of a putative novel lineage were detected by PCR and sequencing in turtles belonging to four different species (including two subspecies) of the superfamily Testudinoidea. In the USA, partial sequence of the adenoviral DNA-dependent DNA polymerase was obtained from samples of a captive pancake tortoise (Malacochersus tornieri), four eastern box turtles (Terrapene carolina carolina) and two red-eared sliders (Trachemys scripta elegans). In Hungary, several individuals of the latter subspecies as well as some yellow-bellied sliders (T. scripta scripta) were found to harbor identical, or closely related, putative new adenoviruses. From numerous attempts to amplify any other genomic fragment by PCR, only a nested method was successful, in which a 476-bp fragment of the hexon gene could be obtained from several samples. In phylogeny reconstructions, based on either DNA polymerase or hexon partial sequences, the putative new adenoviruses formed a clade distinct from the five accepted genera of the family Adenoviridae. Three viral sub-clades corresponding to the three host genera (Malacochersus, Terrapene, Trachemys) were observed. Attempts to isolate the new adenoviruses on turtle heart (TH-1) cells were unsuccessful. Targeted PCR screening of live and dead specimens revealed a prevalence of approximately 25% in small shelter colonies of red-eared and yellow-bellied sliders in Hungary. The potential pathology of these viruses needs further investigation; clinically healthy sliders were found to shed the viral DNA in detectable amounts. Based on the phylogenetic distance, the new adenovirus lineage seems to merit the rank of a novel genus.

Genome analysis of bat adenovirus 2: indications of interspecies transmission

The genome of bat adenovirus 2 was sequenced and analyzed. It is similar in size (31,616 bp) to the genomes of bat adenovirus 3 and canine adenoviruses 1 and 2. These four viruses are monophyletic and share an identical genome organization, with one E3 gene and four E4 genes unique to this group among the mastadenoviruses. These findings suggest that canine adenoviruses may have originated by interspecies transfer of a vespertilionid bat adenovirus.

Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica

Adenoviruses have been identified in humans and a wide range of vertebrate animals, but not previously from the polar region. Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. This is the first evidence of a novel adenovirus, SPSAdV, from a large polar seabird (family Stercorariidae) in Antarctica.

Genome-based phylogeny of dsDNA viruses by a novel alignment-free method

Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification.

Viruses infecting reptiles

A large number of viruses have been described in many different reptiles. These viruses include arboviruses that primarily infect mammals or birds as well as viruses that are specific for reptiles. Interest in arboviruses infecting reptiles has mainly focused on the role reptiles may play in the epidemiology of these viruses, especially over winter. Interest in reptile specific viruses has concentrated on both their importance for reptile medicine as well as virus taxonomy and evolution. The impact of many viral infections on reptile health is not known. Koch's postulates have only been fulfilled for a limited number of reptilian viruses. As diagnostic testing becomes more sensitive, multiple infections with various viruses and other infectious agents are also being detected. In most cases the interactions between these different agents are not known. This review provides an update on viruses described in reptiles, the animal species in which they have been detected, and what is known about their taxonomic positions.

Genomic and phylogenetic analyses of murine adenovirus 2

Murine adenoviruses (MAdV) are supposedly the oldest members of the genus Mastadenovirus. Currently, there are three distinct MAdV types known with rather different tropism and pathology. Here we report and annotate the DNA sequence of the full genome of MAdV-2. It was found to consist of 35,203 bp thus being considerably larger than the genomes of the other two MAdV types. The increased size of the MAdV-2 genome is generally due to larger genes and ORFs, although some differences in the number of ORFs were observed for the early regions E1, E3 and E4. The homologue of the 19K gene of E1B from MAdV-2 codes for 330 amino acids (aa) and is almost twice as large as from other mastadenoviruses. Accordingly, only the N-terminal half (155aa) has homology to the 19K protein. A homologue of the gene of the 12.5K protein was identified in the E3 region of MAdV-2, but not in MAdV-1 or MAdV-3. The other gene of yet unknown function in the E3 region of MAdV-2 seems to be unique. The E4 region of MAdV-2 contains three ORFs. One has similarity to the 34K gene of other AdVs. Two unique ORFs in the E4 region of MAdV-2 have no homology to any of the five and six ORFs in the E4 region of MAdV-1 or MAdV-3, respectively. Phylogenetic analyses showed that the three murine AdVs have a close common ancestor. They likely formed the first branching of the lineage of mastadenoviruses, and seem to be the most ancient representatives of this genus.

Complete sequence of raptor adenovirus 1 confirms the characteristic genome organization of siadenoviruses

Currently, the family Adenoviridae contains five genera, out of which Siadenovirus is one of the two least densely populated ones. A new member representing a new species in this genus has been detected in various birds of prey. The virus, named raptor adenovirus 1 (RAdV-1), could not be isolated, probably because no appropriate permissive cell-line was available. Partial genomic sequences, obtained by PCR and suggesting that the virus is a new siadenovirus species, have been published earlier. In the present paper, determination and analysis of the complete RAdV-1 genome are reported. This is the first complete genome sequence acquired from a non-isolated adenovirus (AdV). The sole source was a mixture of the internal organs of the diseased and dead birds. Until now, the genomic organization considered characteristic to siadenoviruses had been deduced from the detailed study of only two virus species, one of which originated from birds and the other from a frog. The present analysis of RAdV-1 confirmed the genus-specific genetic content and genomic features of siadenoviruses, and a putative novel gene was found as well. In general, AdVs and most of the AdV genera are thought to be strictly host specific. In the genus Siadenovirus, however, two virus species of rather divergent (avian and amphibian) host origin were present when the genus was found. Although by now the greatest number of known siadenoviruses infect birds, the original hosts of the genus remain unknown.

A unique novel reptilian paramyxovirus, four atadenovirus types and a reovirus identified in a concurrent infection of a corn snake (Pantherophis guttatus) collection in Germany

In 2009, 26 clinical samples (organs and oral/cloacal swabs) from a total of 24 corn snakes (Pantherophis guttatus) from a single owner were sent to our laboratory to be tested for the presence of viruses. Paramyxoviruses (PMV), adenoviruses (AdV) and reoviruses were detected by RT-PCR, PCR and virus isolation methods. Three snakes were infected with all three viruses at the same time, while two other snakes had a double infection (PMV and reo, AdV and reo) and nine other snakes had a single infection with any of the three viruses. No viruses were detected in 10 animals. All isolated reoviruses were identical to one another and to the reptilian orthoreovirus isolate 55-02 in the partial RNA dependent RNA polymerase (RDRP) gene sequence. AdV partial polymerase sequences represented four different types, one of which was first described here: most similar to SnAdV-1, while the other three were identical to known types: SnAV-1, -2 and -3. However, the detected single PMV differed distinctly from described reptile PMV and was a new type. According to partial L gene, HN gene and U gene sequences it may be the first described representative of a third squamatid PMV cluster: "group C" within the proposed reptilian PMV genus "Ferlavirus". Nucleotide identity values for the L gene of the new PMV compared to group A viruses range between 76.5 and 80.3%, and between 80.5 and 81.2% compared to group B viruses. For the HN gene, these values were similar: 78.2-80% (A) and 79.9-80.5% (B) and somewhat lower for the U gene: 72.7-75.4% (A) and 69.7-70% (B). No reports on the prevalence of concurrent viral infection in captive snake populations have been published so far. The possibility of concurrent infection with several different viruses and subsequent consequences for animal health should be kept in mind when testing reptile samples for viruses.

Recognition and partial genome characterization by non-specific DNA amplification and PCR of a new siadenovirus species in a sample originating from Parus major, a great tit

A seemingly novel siadenovirus species was detected by PCR and sequencing in the sample of a great tit (Parus major) found dead in Hungary. Since the genus Siadenovirus has very few known members so far, further study of the virus was intriguing not only from epizootiological but also from taxonomical aspects. The sample, which had been tested in another PCR survey previously, consisted of less than 50 microl of extracted nucleic acid. To ensure sufficient target DNA for an extended study, the viral genome had to be preserved. To this end, the sample was subjected to a novel method of non-specific DNA amplification. Using the amplified DNA as target, different PCR and sequencing strategies were applied with consensus or specific primers for the study of the central genome part of the putative tit adenovirus. The sequence of supposedly one half (13,628 bp) of the genome was determined including eight full genes between the genes of the IVa2 and hexon proteins. The gene content of the viral genome fragment as well as the results of the phylogenetic analyses with different proteins confirmed the discovery of a new species in the genus Siadenovirus. This is the first report on the detection of an adenovirus in great tits. The methods, described in this work, proved suitable for the recovery of nucleic acid samples that contain irreplaceable microbial genomic DNA but are only available in limited quantities.

Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence

Turkey hemorrhagic enteritis virus (THEV) is a member of the genus Siadenovirus and causes disease in turkey poults characterized by splenomegaly, bloody diarrhoea and death. The mechanism responsible for intestinal lesion formation and mortality is not known, although there is strong evidence that it is immune-mediated. All strains of THEV are serologically indistinguishable, although there are naturally occurring avirulent strains of THEV that replicate efficiently in turkeys without the intestinal haemorrhage or mortality associated with more virulent strains. The purpose of this study was to determine which viral genes are involved in virulence. The full-length genome of an avirulent vaccine strain was sequenced and compared with the genome of a virulent field isolate from Israel that was sequenced in 1998. Comparison of the two 26.3 kb genomes revealed 49 nucleotide differences resulting in 14 putative amino acid changes within viral proteins. Sequencing of the regions surrounding the 14 missense mutations revealed variations in ORF1, E3 and the fiber (fib) knob domain in five additional strains with varying degrees of virulence. Complete sequences of these genes were determined in a total of 11 different strains of THEV. All strains had at least one missense mutation in ORF1, and all but two of the strains had one missense mutation in E3. At least one missense mutation was found in the fiber knob domain in six out of seven virulent strains. Sequence variation of ORF1, E3 and fib in strains of THEV with different phenotypes strongly indicates that these genes are the key factors affecting virulence.