Novel pathogenic adenovirus in Timneh grey parrot (Psittacus timneh) unveils distinct lineage within Aviadenovirus

Wild birds harbour a vast diversity of adenoviruses that remain uncharacterised with respect to their genome organisation and evolutionary relatedness within complex host ecosystems. Here, we characterise a novel adenovirus type within Aviadenovirus genus associated with severe necrotising hepatitis in a captive Timneh grey parrot, tentatively named as Timneh grey parrot adenovirus 1 (TpAdV-1). The TpAdV-1 genome is 39,867 bp and encodes 46 putative genes with seven hitherto not described ones. Comparative genomics and phylogenetic analyses revealed highest nucleotide identity with psittacine adenovirus 1 and psittacine adenovirus 4 that formed a discrete monophyletic clade within Aviadenovirus lineage suggesting a deep host co-divergent lineage within Psittaciformes hosts. Several recombination breakpoints were identified within the TpAdV-1 genome, which highlighted an ancient evolutionary relationship across the genera Aviadenovirus, Mastadenovirus and Atadenovirus. This study hints towards a host-adapted sub-lineage of avian adenovirus capable of having significant host virulence in Psittaciformes birds augmented with ecological opportunity.

Characterisation of a novel aviadenovirus associated with disease in tawny frogmouths (Podargus strigoides)

Aviadenoviruses are widespread in wild birds but rarely cause disease in nature. However, when naïve species are exposed to poultry or aviaries, aviadenoviruses can lead to disease outbreaks. This study characterised a novel aviadenovirus infection in a native Australian bird, the tawny frogmouth (Podargus strigoides) during an outbreak investigation. The identified complete genome of aviadenovirus, named tawny frogmouth aviadenovirus A (TwAviAdV-A) was 41,175 bp in length containing 52 putative genes. TwAviAdV-A exhibits the common aviadenovirus genomic organisation but with a notable monophyletic subclade in the phylogeny. The TwAviAdV-A virus was hepatotrophic and the six frogmouths presented to the wildlife hospitals in South Eastern Queensland most commonly exhibited regurgitation (in four frogmouths). Three were died or euthanized, two recovered, and one showed no signs. The detection of TwAviAdV-A in frogmouths coming into care re-emphasizes the need for strict biosecurity protocols in wildlife hospitals and care facilities.

Molecular epidemiology analysis of fowl adenovirus detected from apparently healthy birds in eastern China

BACKGROUND

Fowl adenovirus is of major concern to the poultry industry worldwidely. In order to monitor the prevalent status of Fowl adenovirus in China, a total of 1920 clinical samples from apparently healthy birds in the 25 sites of poultry flocks, Slaughterhouse and living bird markets from 8 provinces in eastern China were collected and detected by PCR, sequencing, and phylogenetic analysis.

RESULTS

The epidemiological survey showed that Fowl adenoviruses were detected in living bird markets, and circulating in a variety of fowl species, including chickens, ducks, goose and pigeons. Among the 1920 clinical samples, 166 samples (8.65%) were positive in the fowl adenovirus PCR detection. In this study, totally all the 12 serotypes (serotypes of 1, 2, 3, 4, 5, 6, 7, 8A, 8B, 9, 10 and 11) fowl adenoviruses were detected, the most prevalent serotype was serotype 1. Phylogenetic analysis indicated that 166 FAdVs of 12 serotypes were divided into 5 fowl adenovirus species (Fowl aviadenovirus A, B, C, D, E).

CONCLUSIONS

In the epidemiological survey, 8.65% of the clinical samples from apparently healthy birds were positive in the fowl adenovirus PCR detection. Totally all the 12 serotypes fowl adenoviruses were detected in a variety of fowl species, which provided abundant resources for the research of fowl adenoviruses in China. The newly prevalent FAdV serotypes provides valuable information for the development of an effective control strategy for FAdV infections in fowls.

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.

Whole-genome sequence and pathogenicity of a fowl adenovirus 5 isolated from ducks with egg drop syndrome in China

Recently, fowl adenovirus (FAdV) infection has become widespread in poultry in China and may be asymptomatic or associated with clinical and other pathological conditions. In 2017, a severe egg drop syndrome outbreak in breeder ducks (45 weeks old) occurred in eastern Shandong province in China. The egg production rate declined from 93 to 41%, finally increasing to ~80% (did not reach complete recovery). The presence of the virus was confirmed by FAdV-5 specific PCR assay, and it was designated strain WHRS. Furthermore, next-generation and Sanger sequencing of genomic fragments yielded a 45,734 bp genome. Phylogenetic analysis showed that the genomic sequence of the WHRS strain was most homologous-(99.95%) to that of the FAdV-5 17/25,702 and 14/24,408 strain, sharing 32.1~53.4% similarity with other FAdV strains in the genus Aviadenovirus. Infected duck embryos died within 3–5 dpi, but no deaths occurred in the infected ducks. Strain WHRS could cause egg drop syndrome in ducks, accompanied by clinical signs similar to those of natural infections. Overall, strain WHRS is lethal to duck embryos and causes egg drop syndrome in breeder ducks.

Tembusu virus infection in laying chickens: Evidence for a distinct genetic cluster with significant antigenic variation

Tembusu virus (TMUV) associated disease is a growing cause of egg production decrease and encephalitis in domestic waterfowl, with expanding distribution. In previous studies, TMUV isolates were phylogenetically classified into two genetic lineages and different clusters with varied pathogenicity. However, little is known about the phenotypic and virulence characteristics of cluster 3 isolates within the duck TMUV lineage. In this study, the etiological agent causing egg drop in a laying chicken farm in southern China was investigated and a TMUV was isolated from pooled tissue samples. Genome sequencing and phylogenetic analysis grouped the isolate into TMUV cluster 3 with closest relation to the mosquito-origin TMUV YN12193. Cross-neutralization testing using convalescent sera revealed significant antigenic variation between the isolate and a representative strain of cluster 2.2. The experimental infection of SPF hens confirmed the ability of the isolate to replicate in multiple tissues and led to ovary damage. Additionally, high seroconversion rates (95.83%-100%) were detected in the three flocks following retrospective investigation. Our study demonstrates the occurrence of cluster 3 TMUV infection in laying chickens and that the virus exhibits significant antigenic variation compared with cluster 2 TMUV.

Pigeon adenovirus and pigeon torque teno virus associated with acute multifocal hepatic necrosis in pigeons in Queensland, Australia

In 2018, an outbreak resulting in deaths of 28 breeding pigeons was reported north of Brisbane, Australia. The affected birds had runny nasal discharge and poor body condition. Two birds were submitted to Biosecurity Sciences Laboratory, Brisbane, for investigation. A range of diagnostic tests excluded a number of known pathogens, and no virus was isolated in cell culture. Histopathological examination revealed severe acute multifocal necrosis in the liver with eosinophilic intranuclear inclusions in hepatocytes and Kupffer cells. High-throughput sequencing (HTS) revealed full-length sequences for pigeon adenovirus 1 (PiAd-A) and pigeon torque teno virus (PTTV). This report indicates concomitant PiAd-1and PTTV infections in Australian pigeons.

Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

Birds, notably wild ducks, are reservoirs of pathogenic and zoonotic viruses such as influenza viruses and coronaviruses. In the current study, we used metagenomics to detect and characterise avian DNA and RNA viruses from wild Pacific black ducks, Chestnut teals and Grey teals collected at different time points from a single location. We characterised a likely new species of duck aviadenovirus and a novel duck gyrovirus. We also report what, to the best of our knowledge, is the first finding of an avian orthoreovirus from Pacific black ducks and a rotavirus F from Chestnut teals. Other viruses characterised from the samples from these wild ducks belong to the virus families Astroviridae, Caliciviridae and Coronaviridae. Some of the viruses may have potential cross-species transmissibility, while others indicated a wide genetic diversity of duck viruses within a genus. The study also showed evidence of potential transmission of viruses along the East Asian-Australasian Flyway; potentially facilitated by migrating shorebirds. The detection and characterisation of several avian viruses not previously described, and causing asymptomatic but potentially also symptomatic infections suggest the need for more virus surveillance studies for pathogenic and potential zoonotic viruses in wildlife reservoirs.

Development of a rapid technique for extraction of viral DNA/RNA for whole genome sequencing directly from clinical liver tissues

Characterisation of the entire genome of Fowl aviadenoviruses (FAdV) requires isolation and propagation of the virus in chicken embryo liver or kidney cells, a process which is not only time consuming but may occasionally fail to result in viral growth. Furthermore, in a mixed infection, isolation in cell culture may result in the loss of viral strains. In this study, we optimised a FAdV DNA extraction technique directly from affected liver tissues using kaolin hydrated aluminium silicate treatment. The whole genome of FAdV was sequenced directly from extracted DNA without any targetted PCR based enrichment. The extraction method was also tested on avian liver tissues affected with the RNA virus Avian hepatitis E virus and demonstrated to yield sequencing grade RNA. Therefore, the method described here is a simple technique which is potentially useful for the extraction of sequencing grade DNA/RNA from tissues with high fat content.

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.

Vidovszky M, Rossi JL, Vicentini F, Harrach B, L. Kaján G. Identification of two novel adenoviruses in smooth-billed ani and tropical screech owl

Avian adenoviruses (AdVs) are a very diverse group of pathogens causing diseases in poultry and wild birds. Wild birds, endangered by habitat loss and habitat fragmentation in the tropical forests, are recognised to play a role in the transmission of various AdVs. In this study, two novel, hitherto unknown AdVs were described from faecal samples of smooth-billed ani and tropical screech owl. The former was classified into genus Aviadenovirus, the latter into genus Atadenovirus, and both viruses most probably represent new AdV species as well. These results show that there is very limited information about the biodiversity of AdVs in tropical wild birds, though viruses might have a major effect on the population of their hosts or endanger even domesticated animals. Surveys like this provide new insights into the diversity, evolution, host variety, and distribution of avian AdVs.

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.

Characterization and pathogenicity of fowl adenovirus serotype 4 isolated from eastern China

BACKGROUND

Fowl adenovirus outbreaks have occurred in China since June 2015. This virus is an emerging infectious disease that causes hydropericardium syndrome and inclusion body hepatitis (HPS-IBH), resulting in significant economic loss to poultry farmers. Five fowl adenovirus (FAdV) strains (HN, AQ, AH726, JS07 and AH712) were isolated from Jiangsu and Anhui provinces.

RESULTS

Phylogenetic analysis revealed that the five isolates belonged to species C fowl adenovirus serotype 4. An 11 amino-acid deletion in ORF29, relative to an older viral isolate, JSJ13, was observed for all five strains described here. In chicken experiments, 80-100% birds died after intramuscular inoculation and displayed lesions characteristic of HPS-IBH. The viral DNA copies were further detected by hexon-probe based real-time polymerase chain reaction (PCR) in the chicken samples. The viral loads and cytokine profiles were recorded in all the organs after infections. Despite minor genetic differences, the 5 strains displayed significantly different tissue tropisms and cytokine profiles.

CONCLUSIONS

Our data enhance the current understanding some of the factors involved in the pathogenicity and genetic diversity of the FAdV serotype 4 (FAdV-4) in China. Our work provides theoretical support for the prevention and control of HPS-IBH in chickens.

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.

An emerging new fowl adenovirus genotype

In this work, we examined the diversity of fowl adenovirus (FAdV) types occurring in Hungary. From diseased chicken flocks in Eastern Hungary, 29 FAdV strains were isolated between 2011 and 2015. We performed molecular typing of the isolates based on their partial hexon sequences. The results showed that representatives from every FAdV species from A to E are present in Hungary, but compared to the findings from our previous survey, a lower number of different FAdV types were detected. Inclusion body hepatitis was always associated with FAdV-2 or -8b, gizzard erosion was caused in almost every case by FAdV-1. Numerous strains belonging to species FAdV-B were found. The complete genome sequence of a candidate new genotype strain, showing the highest divergence from the reference FAdV-5, was determined using next generation sequencing. In order to provide results compatible with the serology-based type classification, multiple genomic regions, including the major antigenic determinants, of the new isolate (strain 40440-M/2015) were compared to their counterparts in the prototype FAdV-5 (strain 340) from species FAdV-B, at both nucleotide and amino acid sequence levels. In different comparative analyses, the two strains were always found to have larger divergence between each other than any two of the most closely related FAdV serotypes. This new emerging FAdV genotype is already present in Hungary and Austria, though its exact pathological role requires further investigations. The introduction of a novel FAdV (geno)type for the classification of these strains is further supported.

Pathogenicity and complete genome sequence of a fowl adenovirus serotype 8b isolate from China

In this study, we determined and analyzed the complete nucleotide sequence of the genome of a fowl adenovirus isolate SD1356 in China and examined its pathogenicity in specific pathogen-free chick embryos and newly hatched chicks. The full genome of SD1356 was 44,454 nucleotides in length with 58.1% G + C content. Sequence alignment and phylogenetic analysis revealed that strain SD1356 was clustered together belonging to serotype 8b of fowl adenoviruses E species (FAdV-8b). No regions homologous to early regions E1, E3, and E4 of mastadenoviruses were recognized, and being very similar to the typical organization of FAdV-E genomes. All infected embryos died 4-6 d post-inoculation with visible lesions, such as hyperemic, stunting, and clubbed down, etc. Additionally, adenovirus was found in tissues or cloacal swabs of all infected birds and most of the contact uninfected controls, despite lack of clinical signs and pathological changes. Together, our study describes the genomic characteristics of an FAdV-8b strain isolated in China. The reported FAdV-8b strain SD1356 is fetal to chick embryos and possesses horizontal transmission capacity in chickens.

Hydropericardium syndrome caused by fowl adenovirus serotype 4 in replacement pullets

Hydropericardium syndrome (HPS) is one of the important emerging diseases causing huge losses to the poultry industry. It affects mainly 3- to 6-week-old broiler chickens and rarely occurs in breeding and laying flocks. Recently, an HPS case was recorded with a sudden heavy mortality in a 100-day-old laying flock. A fowl adenovirus serotype 4 (FAdV-4), named as GDMZ strain, was isolated and identified using polymerase chain reaction coupled with electron microscopy. The animal experiment showed that a mortality of 100% was recorded with hydropericardium as a conspicuous lesion throughout the course of infection. Microscopically, vacuolar changes and intranuclear inclusion bodies were observed in the liver and vacuolar changes were observed in the heart. The complete genome sequence of GDMZ strain was determined to investigate the molecular properties of GDMZ strain. The comparative analysis revealed that the novel Chinese FAdV-4 isolate contained open reading frame (ORF) 19, ORF27, and ORF48 genomic deletions. The phylogenetic analysis revealed that FAdV-4 could be divided into two major clades, of which Chinese FAdV-4 were located at a distinct clade.

Development of a TaqMan-based real-time PCR for detecting duck adenovirus 3

Recently, a novel duck adenovirus (designated as duck adenovirus 3, DAdV-3) was discovered in Muscovy ducks, China. Here, we developed a TaqMan-based real-time PCR assay (qPCR) for the detection of DAdV-3 infection. After the optimization of the qPCR conditions, the lower limit of detection for DAdV-3 infection was 40.9 copies/μl. No cross-reactivity was observed with other duck-derived pathogens. Intra- and inter-assay variability was less than 2.30%. DAdV-3 was detected in embryos and newly hatched ducklings by qPCR assay, the findings provided evidence of possible vertical transmission of DAdV-3. The developed qPCR analysis showed high specificity, sensitivity, and reproducibility, thereby indicating that it can be used in future investigations on the pathogenesis and epidemiology of DAdV-3.

Fowl Adenovirus 4 (FAdV-4)-Based Infectious Clone for Vaccine Vector Development and Viral Gene Function Studies

Fowl adenovirus 4 (FAdV-4) is associated with economically important poultry diseases. Recent studies of fully sequenced genomes of FAdV-4 isolates suggest potential genomic regions associated with virulence and amenable for manipulation and vector development. Direct manipulation of viral genomes is cumbersome, as opposed to that of infectious clones-viral genomes cloned into plasmid or cosmid vectors. In this work, we generated an infectious clone, pFAdV-4 ON1, containing the entire viral genome of a nonpathogenic FAdV-4 (ON1 isolate). pFAdV-4 ON1 was used for targeted deletion of open reading frames (ORFs) 16 and 17 and replacement with the enhanced green fluorescence protein (EGFP) expression cassette to generate recombinant viruses. These viruses were viable, and EGFP was expressed in infected cells. Their replication, however, was significantly reduced with respect to that of the wild-type virus. These observations suggest the potential utility of FAdV-4 as a vaccine vector and the importance of ORFs 16 and 17 for virus replication at wild-type levels. To our knowledge, this is the first report of an infectious clone based on the FAdV-4 genome, and our results demonstrate its utility for studies of virulence determinants and as a platform for either vaccine or gene delivery vectors.

Genetic characterization of novel fowl aviadenovirus 4 isolates from outbreaks of hepatitis-hydropericardium syndrome in broiler chickens in China

Since May 2015, severe outbreaks of hepatitis-hydropericardium syndrome (HHS) associated with infections of fowl aviadenovirus (FAdV) have emerged in broiler chickens in several Chinese provinces. To identify the genotype and gain a better understanding of the genetic properties of the FAdV strains responsible for the recent HHS outbreaks in China, the complete genome sequences of five isolates from outbreaks of HHS in broiler chickens in five provinces were determined. The results demonstrated that a novel fowl aviadenovirus 4 (FAdV-4) genotype was epidemic in China. To investigate the molecular characteristics of these Chinese FAdV-4 isolates, their genome contents were compared with those of reported pathogenic and non-pathogenic FAdV-4 strains. The comparative analysis revealed that the novel Chinese FAdV-4 isolates contain various genomic deletions and multiple distinct amino-acid mutations in their major structural genes. Two additional putative genetic virulence markers in the fiber 2 gene were identified. These findings confirmed some of the genetic differences between the pathogenic and non-pathogenic FAdV-4 isolates. The data presented in this report will enhance the current understanding of the molecular epidemiology and genetic diversity of FAdV-4 isolates in China and will provide additional insight into the critical factors that determine the pathogenicity of FAdV-4 strains. Finally, the emergence of this novel and highly pathogenic FAdV-4 genotype emphasizes that preventive measures against FAdV-4 infections on poultry farms should be implemented in China.

Identification of a novel aviadenovirus, designated pigeon adenovirus 2 in domestic pigeons (Columba livia)

The young pigeon disease syndrome (YPDS) affects mainly young pigeons of less than one year of age and leads to crop stasis, vomitus, diarrhea, anorexia and occasionally death. This disease is internationally a major health problem because of its seasonal appearance during competitions such as homing pigeon races or exhibitions of ornamental birds. While the etiology of YPDS is still unclear, adenoviruses are frequently discussed as potential causative agents. Electron microscopy of feces from a YPDS outbreak revealed massive shedding of adenovirus-like particles. Whole genome sequencing of this sample identified a novel adenovirus tentatively named pigeon adenovirus 2 (PiAdV-2). Phylogenetic and comparative genome analysis suggest PiAdV-2 to belong to a new species within the genus Aviadenovirus, for which we propose the name Pigeon aviadenovirus B. The PiAdV-2 genome shares 54.9% nucleotide sequence identity with pigeon adenovirus 1 (PiAdV-1). In a screening of further YPDS-affected flocks two variants of PiAdV-2 (variant A and B) were detected which shared 97.6% nucleotide identity of partial polymerase sequences, but only 79.7% nucleotide identity of partial hexon sequences. The distribution of both PiAdV-2 variants was further investigated in fecal samples collected between 2008 and 2015 from healthy or YPDS-affected racing pigeons of different lofts. Independent of their health status, approximately 20% of young and 13% of adult pigeon flocks harbored PiAdV-2 variants. Birds were free of PiAdV-1 or other aviadenoviruses as determined by PCRs targeting the aviadenovirus polymerase or the PiAdV-1 fiber gene, respectively. In conclusion, there is no indication of a correlation between YPDS outbreaks and the presence of PiAdV-2 or other aviadenoviruses, arguing against an causative role in this disease complex.

Genome analysis of four Old World monkey adenoviruses supports the proposed species classification of primate adenoviruses and reveals signs of possible homologous recombination

Within the family Adenoviridae, presently Simian mastadenovirus A is the single species approved officially for monkey adenoviruses (AdVs), whilst the establishment of six further species (Simian mastadenovirus B to Simian mastadenovirus G) has been proposed in the last few years. We examined the genetic content and phylogenetic relationships of four Old World monkey (OWM) AdV types [namely simian AdV (SAdV)-8, -11, -16 and -19] for which it had been proposed that they should be classified into different AdV species: SAdV-11 to Human mastadenovirus G, and the other three viruses into three novel species. By full genome sequencing, we identified gene contents characteristic for the genus Mastadenovirus. Among the 36 ORFs, 2 genes of different lengths, predicted to encode the adenoviral cellular attachment protein (the fibre), were found. The E3 regions contained six genes, present in every OWM AdV, but lacked the E3 19K gene, which has seemingly appeared only in the ape (hominid) AdV lineages during evolution. For the first time in SAdVs, two other exons belonging to the gene of the so-called U exon protein were also predicted. Phylogenetic calculations, based on the fibre-1 and the major capsid protein, the hexon, implied that recombination events might have happened between different AdV species. Phylogeny inference, based on the viral DNA-dependent DNA polymerase and the penton base protein, further supported the species classification proposed earlier.

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.

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.

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.

Comparison of fiber gene sequences of inclusion body hepatitis (IBH) and non-IBH strains of serotype 8 and 11 fowl adenoviruses

Fowl adenoviruses (FAdVs) are common in broiler operations, and the most frequently isolated FAdVs belong to serotypes 1, 8, and 11. Serotype 1 viruses are considered nonpathogenic. While some serotype 8 and 11 viruses cause inclusion body hepatitis (IBH), these virus serotypes can also be isolated from non-IBH cases. The fiber protein is one of the major constituents of the adenoviral capsid, involved in virus entry, and it has been implicated in the variation of virulence of FAdVs. The fiber gene sequences of four FAdV-8 and four FAdV-11 isolates from both IBH and non-IBH cases were determined and analyzed for a possible association of the fiber gene sequence in virulence. The fiber protein can be divided into tail, shaft, and head domains comprising some specific features. The conserved "RKRP" sequence motif (aa 17-aa 20) fit the consensus sequence predicted for the nuclear localization signal, while the "VYPF" motif (aa 53-aa 56), involved in the penton base interaction, was also found. Similar to mammalian adenoviruses, 17 pseudo-repeats with an average length of 16 aa were detected in the FAdV-8 fiber shaft region, while 20 pseudo-repeats with an average length of 18 aa were found in FAdV-11 fibers. There was a 144-147 nt difference between the fiber genes of the two FAdV serotypes. In the shaft region, the TLWT motif that marks the beginning of the fiber head domain of the mastadenovirus was not evident among examined FAdVs. The FAdV-11 isolates had 99.1 % aa sequence identity and 99.3 % similarity to each other, and there was no conserved aa substitution within the fibers. The FAdV-8 fiber proteins showed an overall lower, 89 % aa sequence identity and 93.4 % similarity, to each other and 22 nonsynonymous mutations were detected. Virulence markers were not detected in the analyzed fiber gene sequences of the different pathotypes of the two FAdV serotypes.

Identification and characterization of a novel adenovirus in the cloacal bursa of gulls

Several viruses of the family of Adenoviridae are associated with disease in birds. Here we report the detection of a novel adenovirus in the cloacal bursa of herring gulls (Larus argentatus) and lesser black-backed gulls (Larus fuscus) that were found dead in the Netherlands in 2001. Histopathological analysis of the cloacal bursa revealed cytomegaly and karyomegaly with basophilic intranuclear inclusions typical for adenovirus infection. The presence of an adenovirus was confirmed by electron microscopy. By random PCR in combination with deep sequencing, sequences were detected that had the best hit with known adenoviruses. Phylogenetic analysis of complete coding sequences of the hexon, penton and polymerase genes indicates that this novel virus, tentatively named Gull adenovirus, belongs to the genus Aviadenovirus. The present study demonstrates that birds of the Laridae family are infected by family-specific adenoviruses that differ from known adenoviruses in other bird species.

Genome sequences published outside of Standards in Genomic Sciences, October - November 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Genome sequences published outside of Standards in Genomic Sciences, July - October 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.