Otus scops adenovirus: the complete genome sequence of a novel aviadenovirus discovered in a wild owl

We present the complete genome sequence of an aviadenovirus obtained by metagenomics from cloacal swabs taken from a free-living Eurasian scops owl (Otus scops, a small raptor distributed in Europe and several parts of Asia) in China. Thirty protein coding genes were predicted in this 40,239-bp-long genome, which encodes the largest fiber protein among all reported aviadenoviruses. The viral genome sequence is highly divergent, and the encoded proteins have an average of only 55% amino acid sequence identity to those of other adenoviruses. In phylogenetic analysis, the new owl virus grouped with members of the genus Aviadenovirus and formed a common clade with another owl adenovirus reported previously in Japan. This is the second complete genome sequence of an aviadenovirus discovered in owls, and its proteins have an average of 62% amino acid sequence identity to those of the previously reported owl adenovirus. Combining this result with comparative genomic analysis of all aviadenoviruses, we propose that this owl virus and the previously described Japanese owl adenovirus can be assigned to two new species in the genus Aviadenovirus. This study provides new data on the diversity of aviadenoviruses in wild birds.

Adenoviral infection in 5 red-tailed hawks and a broad-winged hawk

Adenoviral infections among raptors are best described in falcons and are characterized most commonly by necrotizing hepatitis and splenitis; only one case has been reported in a hawk. Five red-tailed hawks (Buteo jamaicensis) and a broad-winged hawk (Buteo platypterus) had an adenoviral infection based on history, histopathology, negative-stain electron microscopy, and PCR. All birds had acute onset of illness resulting in death; 3 had evidence of a concurrent bacterial infection. Microscopically, all 6 birds had solitary, pale eosinophilic-to-amphophilic, intranuclear inclusion bodies within presumed hematopoietic cells in bone marrow and macrophages in spleen. Five of the 6 birds had similar inclusions within hepatocytes and Kupffer cells. All but one bird had severe bone marrow necrosis. There was moderate splenic necrosis (3 of 6) and mild-to-marked hepatic necrosis (4 of 6). Negative-stain electron microscopy demonstrated adenoviral particles in bone marrow (5 of 6), liver (1 of 5), and/or spleen (1 of 5). PCR was positive for adenovirus in bone marrow (3 of 5), liver (1 of 3), spleen (4 of 6), and/or intestinal contents (2 of 3). Viral DNA polymerase gene sequences clustered within the Siadenovirus genus. There was 99% nucleotide identity to one another and 90% nucleotide identity with the closest related adenovirus (Harris hawk, EU715130). Our case series expands on the limited knowledge of adenoviral infections in hawks. The splenic and hepatic necrosis, and particularly the hitherto unreported bone marrow necrosis, suggest that adenoviral infection is clinically relevant and potentially fatal in hawks.

Isolation and whole-genome sequencing of a novel aviadenovirus from owls in Japan

Adenoviruses have been reported to infect a variety of birds. Here, we isolated a novel adenovirus from the liver of a dead owl chick (Bengal eagle owl; Bubo bengalensis) at a raptor-breeding facility in Japan and determined the complete genome sequence of the virus. We performed necropsies on the dead owl chicks and found that they had enlarged livers, pericardial edema, and focal necrosis of the liver tissue. Transmission electron microscopy of the liver tissue revealed a virus-like structure, appearing as paracrystalline arrays in the nucleus, and immunohistochemical staining with anti-adenovirus antibodies showed positive reactions in hepatocytes and other cells. Attempts to isolate the virus from homogenized liver tissue of a dead owl chick showed a cytopathic effect on chicken-derived cultured cells after multiple blind passages. Further, we determined the complete genome sequence of this virus and performed phylogenetic analysis, revealing that this adenovirus belongs to the genus Aviadenovirus, forming a cluster with fowl and turkey aviadenoviruses. The amino acid sequence divergence between the DNA polymerase of this virus and its closest known adenovirus relative is approximately 29%, implying that this virus can be assigned to a new species in the genus Aviadenovirus. Based on our data, this novel owl adenovirus is a likely cause of fatal infections in owls, which may threaten wild and captive owl populations. Further, this virus is unique among raptor adenoviruses in that it infects chicken-derived cultured cells, raising the importance of further investigations to evaluate interspecies transmission of this virus.

IDENTIFICATION AND CORRELATION OF A NOVEL SIADENOVIRUS IN A FLOCK OF BUDGERIGARS (MELOPSITTACUS UNDULATES) INFECTED WITH SALMONELLA TYPHIMURIUM IN THE UNITED STATES

A flock of budgerigars (Melopsittacus undulates) was purchased from a licensed breeder and quarantined at a zoologic facility within the United States in 2016. Following 82 deaths within the flock, the remaining 66 birds were depopulated because of ongoing clinical salmonellosis despite treatment. Gross necropsy was performed on all 66 birds. Histopathologic examination was performed on 10 birds identified with gross lesions and 10 birds without. Pathologic findings were most often observed in the liver, kidney, and spleen. Lesions noted in the livers and spleens were consistent with published reports of salmonellosis in psittacine species. Multisystemic changes associated with septicemia were not noted, most likely because of antibiotic intervention before euthanasia. Of the 20 budgerigars evaluated by histopathology, six had large basophilic intranuclear inclusion bodies within tubular epithelia in a portion of the kidneys. Electronic microscopy, next-generation sequencing, Sanger sequencing, and phylogenetic analyses were used to identify and categorize the identified virus as a novel siadenovirus strain BuAdV-1 USA-IA43444-2016. The strain was 99% similar to budgerigar adenovirus 1 (BuAdV-1), previously reported in Japan, and to a psittacine adenovirus 5 recently identified in a U.S. cockatiel. Salmonella typhimurium carriers were identified via polymerase chain reaction (PCR) and bacterial culture and compared with viral carriers identified via PCR. Inclusion bodies and Salmonella detection were significant in birds with gross lesions versus those without; however, there was no correlation between budgerigars positive with siadenovirus by PCR and concurrent Salmonella infection. Identifying subclinical siadenovirus strain BuAdV-1 USA-IA43444-2016 infection in this flock significantly differs from a previous report of clinical illness in five budgerigars resulting in death caused by BuAdV-1 in Japan. S. typhimurium remains a significant pathogen in budgerigars, and zoonotic concerns prompted depopulation to mitigate the public health risks of this flock.

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.

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.

Novel siadenovirus infection in a cockatiel with chronic liver disease

A 15-year-old female cockatiel (Nymphicus hollandicus) undergoing long term management for hepatopathy died and underwent necropsy. Microscopic findings were consistent with chronic liver disease characterized by distorted hepatic architecture, fibrosis and biliary proliferation. The additional finding of large intranuclear inclusion bodies within hepatocytes and renal tubular epithelium prompted diagnostic next generation sequencing. The assembled sequences isolated from pooled kidney and liver were related to siadenoviruses. The genus Siadenovirus, within the family Adenoviridae, includes several species of viruses that pathogenically infect avian species including hemorrhagic enteritis virus of turkeys and marble spleen virus of pheasants. Siadenoviruses have previously been reported in seven psittacine species: a plum-headed parakeet (Psittacula cyanocephala), an umbrella cockatoo (Cacatua alba) budgerigars (Melopsittacus undulates), an eastern rosella (Platycercus eximius), a scarlet chested parrot (Neophema splendida), a cockatiel (Nymphicus hollandicus), and a red-crowned parakeet (Cyanoramphus novaezelandiae). This report describes a novel siadenovirus in a cockatiel that is highly identical to budgerigar adenovirus 1 and distinct from PsAdV-2 in cockatiels. We report the clinical pathologic, gross, and histopathologic findings in a cockatiel with chronic hepatitis and a novel siadenovirus, PsAdV-5. The sequencing data is presented with a phylogenetic analysis.

Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains

BACKGROUND

Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose.

METHODS

Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay.

RESULTS

The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly.

CONCLUSIONS

The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge suggest that RAdV-1 uses a different natural receptor for cell attachment than TAdV-3. Deletion of the beta-hairpin arm shows little impact on the structure and stability of the siadenovirus fibre heads.

Raptor gastroenterology

Free-living raptors are frequently presented to wildlife rehabilitation centers. Conditions affecting the gastrointestinal tract can be the primary reason for presentation. The gastrointestinal tract can also be affected secondary to debilitation from other injuries or from the stress of the rehabilitation process. A thorough understanding of the anatomy, physiology, and natural history of these species is crucial to successful treatment and rehabilitation. This article addresses raptor gastroenterology with an emphasis on conditions affecting free-living birds.

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.

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.

Partial sequence of the DNA-dependent DNA polymerase gene of fowl adenoviruses: a reference panel for a general diagnostic PCR in poultry

Adenoviruses are frequent infectious agents in different poultry species. The traditional, serological typing of new isolates by virus neutralisation tests is now in transition to be replaced by PCR and sequencing. The first PCRs, recommended for the detection of adenoviruses, had been designed to target the gene of the major capsid protein, the hexon. In birds, members of three different genera of the family Adenoviridae may occur. Accordingly, three specific hexon PCRs had to be elaborated for the detection of adenoviruses in poultry. A significantly more sensitive PCR, targeting the viral DNA-dependent DNA polymerase gene, has been described recently. This method proved to be an efficient alternative for the general detection of adenoviruses irrespective of their genus affiliation. Fowl adenoviruses (FAdVs), isolated from chicken to date, comprise twelve serotypes classified into five virus species (FAdV-A to E). The polymerase gene sequence has been determined yet only from three FAdV types representing three species. In the present work, the panel of polymerase gene sequences was completed with those of the rest of FAdVs. The newly determined sequences will facilitate the identification of new FAdV isolates as an existing species or as a putative new FAdV. Once the polymerase sequence is known, more specific PCRs for the amplification of the hexon and other genes can be designed and performed according to the preliminary species classification.

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.

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.

Confirmation of a novel siadenovirus species detected in raptors: partial sequence and phylogenetic analysis

Partial genome characterisation of a novel adenovirus, found recently in organ samples of multiple species of dead birds of prey, was carried out by sequence analysis of PCR-amplified DNA fragments. The virus, named as raptor adenovirus 1 (RAdV-1), has originally been detected by a nested PCR method with consensus primers targeting the adenoviral DNA polymerase gene. Phylogenetic analysis with the deduced amino acid sequence of the small PCR product has implied a new siadenovirus type present in the samples. Since virus isolation attempts remained unsuccessful, further characterisation of this putative novel siadenovirus was carried out with the use of PCR on the infected organ samples. The DNA sequence of the central genome part of RAdV-1, encompassing nine full (pTP, 52K, pIIIa, III, pVII, pX, pVI, hexon, protease) and two partial (DNA polymerase and DBP) genes and exceeding 12 kb pairs in size, was determined. Phylogenetic tree reconstructions, based on several genes, unambiguously confirmed the preliminary classification of RAdV-1 as a new species within the genus Siadenovirus. Further study of RAdV-1 is of interest since it represents a rare adenovirus genus of yet undetermined host origin.

Detection of a novel bat gammaherpesvirus in Hungary

This paper describes the detection of a novel herpesvirus in a Serotine bat (Eptesicus serotinus) in Hungary. The rescued animal showed signs of icterus and anorexia and died within a day, in spite of immediate supportive therapy. Autopsy confirmed the clinical picture by the major lesions observed in the liver. Histopathology revealed vacuolar degeneration in the hepatocytes and leukocytosis in the sinusoidal lumina. By electron microscopy, hydropic degeneration and apoptotic cells with a pycnotic nucleus were found in the liver. Bacteriological examinations gave negative results. As part of a routine screening project, detection of adeno- and herpesviruses from homogenised samples of the liver, lungs and small intestines was attempted by nested polymerase chain reaction (PCR) assays. The adenovirus PCR ended with negative results. The herpesvirus PCR resulted in an amplification product of specific size. The nucleotide sequence of the amplicon was determined and analysed by homology search and phylogenetic analysis. A novel herpesvirus was identified, which seemed to be most closely related to members of the genus Rhadinovirus within the subfamily Gammaherpesvirinae. The causative role of the detected rhadinovirus in the fatal condition of the Serotine bat could not be proven, but it is most likely that reactivation from a latent infection allowed the detection of the virus by PCR.

Adenovirus of psittacine birds: investigations on isolation and development of a real-time polymerase chain reaction for specific detection

Liver samples of psittacine birds with a histological suspicion of an adenovirus infection, confirmed by electron microscopy examination, were subjected to virus isolation attempts using a heterologous cell culture system and a homologous cell culture system in the form of chicken embryo liver cells and psittacine embryo fibroblasts, respectively. Whereas isolation in chicken embryo liver cells failed, virus was isolated successfully in the psittacine embryo fibroblasts cell culture system. Molecular investigations identified the virus as a specific psittacine adenovirus (PsAdV). Additionally, on the basis of the hexon gene sequence data obtained, a real-time polymerase chain reaction (PCR) for specific detection of PsAdV was developed. To ensure an exclusive hybridization with PsAdV, selected primers were located within the variable L1 region of the hexon gene. Furthermore, the specificity of the real-time PCR was confirmed by investigation of a panel of different avian adenoviruses and unrelated DNA viruses. Using this PCR, the threshold cycle values obtained support the propagation of PsAdV in the homologous cell culture system in comparison with the chicken cell culture system. Moreover, the developed PCR represents a reliable method for specific and sensitive detection of PsAdV in clinical samples.

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

Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.

The avian neurologic examination and ancillary neurodiagnostic techniques: a review update

The purpose of this article is to guide the avian clinician in the assessment of neurologic function in birds. Physical and neurologic examinations that evaluate cranial nerves, postural reactions, and spinal reflexes identify neurologic dysfunction and the corresponding anatomic location of the lesion. Ancillary diagnostic tests, such as cerebrospinal fluid analysis, diagnostic imaging, muscle and nerve histology, and electrodiagnostics, are tools to confirm and clarify conclusions from the neurologic examination and to identify the cause of disease. Once the disease location and pathologic process have been identified, appropriate treatment and prognosis may be provided.

Phylogenetic analysis of adenovirus sequences

Members of the family Adenoviridae have been isolated from a large variety of hosts, including representatives from every major vertebrate class from fish to mammals. The high prevalence, together with the fairly conserved organization of the central part of their genomes, make the adenoviruses one of (if not the) best models for studying viral evolution on a larger time scale. Phylogenetic calculation can infer the evolutionary distance among adenovirus strains on serotype, species, and genus levels, thus helping the establishment of a correct taxonomy on the one hand, and speeding up the process of typing new isolates on the other. Initially, four major lineages corresponding to four genera were recognized. Later, the demarcation criteria of lower taxon levels, such as species or types, could also be defined with phylogenetic calculations. A limited number of possible host switches have been hypothesized and convincingly supported. Application of the web-based BLAST and MultAlin programs and the freely available PHYLIP package, along with the TreeView program, enables everyone to make correct calculations. In addition to step-by-step instruction on how to perform phylogenetic analysis, critical points where typical mistakes or misinterpretation of the results might occur will be identified and hints for their avoidance will be provided.