Unique features of fowl adenovirus 9 gene transcription

High Phenotypic Variation between an In Vitro-Passaged Fowl Adenovirus Serotype 1 (FAdV-1) and Its Virulent Progenitor Strain despite Almost Complete Sequence Identity of the Whole Genomes

Adenoviral gizzard erosion is an emerging disease with negative impact on health and production of chickens. In this study, we compared in vitro and in vivo characteristics of a fowl adenovirus serotype 1 (FAdV-1), attenuated by 53 consecutive passages in primary chicken embryo liver (CEL) cell cultures (11/7127-AT), with the virulent strain (11/7127-VT). Whole genome analysis revealed near-complete sequence identity between the strains. However, a length polymorphism in a non-coding adenine repeat sequence (11/7127-AT: 11 instead of 9) immediately downstream of the hexon open reading frame was revealed. One-step growth kinetics showed delayed multiplication of 11/7127-AT together with significantly lower titers in cell culture (up to 4 log₁₀ difference), indicating reduced replication efficiency in vitro. In vivo pathogenicity and immunogenicity were determined in day-old specific pathogen-free layer chicks inoculated orally with the respective viruses. In contrast to birds infected with 11/7127-VT, birds infected with 11/7127-AT did not exhibit body weight loss or severe pathological lesions in the gizzard. Virus detection rates, viral load in organs and virus excretion were significantly lower in birds inoculated with 11/7127-AT. Throughout the experimental period, these birds did not develop measurable neutralizing antibodies, prevalent in birds in response to 11/7127-VT infection. Differences in pathogenicity between the virulent FAdV-1 and the attenuated strain could not be correlated to prominently discriminate genomic features. We conclude that differential in vitro growth profiles indicate that attenuation is linked to modulation of viral replication during interaction of the virus with the host cells. Thus, hosts would be unable to prevent the rapid replication of virulent FAdV leading to severe tissue damage, a phenomenon broadly applicable to further FAdV serotypes, considering the substantial intra-serotype virulence differences of FAdVs and the variation of diseases.

Downregulation of Cell Surface Major Histocompatibility Complex Class I Expression Is Mediated by the Left-End Transcription Unit of Fowl Adenovirus 9

Major histocompatibility complex class I (MHC-I) molecules play a critical role in the host’s antiviral response by presenting virus-derived antigenic peptides to cytotoxic T lymphocytes (CTLs), enabling the clearance of virus-infected cells. Human adenoviruses evade CTL-mediated cell lysis, in part, by interfering directly with the MHC-I antigen presentation pathway through the expression of E3-19K, which binds both MHC-I and the transporter associated with antigen processing protein and sequestering MHC-I within the endoplasmic reticulum. Fowl adenoviruses have no homologues of E3-19K. Here, we show that representative virus isolates of the species Fowl aviadenovirus C, Fowl aviadenovirus D, and Fowl aviadenovirus E downregulate the cell surface expression of MHC-I in chicken hepatoma cells, resulting in 71%, 11%, and 14% of the baseline expression level, respectively, at 12 h post-infection. Furthermore, this work reports that FAdV-9 downregulates cell surface MHC-I through a minimum of two separate mechanisms—a lysosomal-independent mechanism that requires the presence of the fowl adenovirus early 1 (FE1) transcription unit located within the left terminal genomic region between nts 1 and 6131 and a lysosomal-dependent mechanism that does not require the presence of FE1. These results establish a new functional role for the FE1 transcription unit in immune evasion. These studies provide important new information about the immune evasion of FAdVs and will enhance our understanding of the pathogenesis of inclusion body hepatitis and advance the progress made in next-generation FAdV-based vectors.

A recent perspective on fiber and hexon genes proteins analyses of fowl adenovirus toward virus infectivity-A review

Fowl adenovirus (FAdV) is a double-stranded DNA virus with a non-enveloped structure comprising three major proteins known as hexon, penton, and fiber. Molecular analysis which emphasizes on hexon and fiber proteins is currently the major focus of curiosity for FAdV antigenicity and pathogenicity. Recently, disease outbreaks associated with FAdV infections such as inclusion body hepatitis, hepatitis hydropericardium syndrome, and gizzard erosion, were commonly reported and continue to increase worldwide. Studies on the virulence gene of the virus were intensively conducted to provide a better understanding on the role of these major capsid proteins in the development of a safe and effective vaccine against the disease in the poultry industry. This paper highlights the variations of the fiber and hexon genes, their importance in genotypes and serotypes differentiation, and infectivity between FAdV strains. It appears that the L1 loop of hexon and the knob of fiber genes are the infectivity markers for FAdV infection. The fiber-2 protein plays a major role in FAdV pathogenicity than the hexon protein, while the fiber-1 protein is important for viral replication and assembly, regardless of virulence capability instead of infectivity. The hexon protein plays a major role in virus infectivity and tissue tropism. These findings could further enhance the knowledge of FAdV strains’ classification and evolution, diagnosis, and strategies to prevent and control FAdV infection and outbreaks in chicken farms.

Characterization of a fowl adenovirus 9 (FAdV-9) early promoter and its application in generating dual expression FAdV-9s

The CMV immediate early promoter from the EGFP expression plasmid pEGFP-N1 was replaced with the very left end of the fowl adenovirus 9 (FAdV-9) genome (ntds 73-574) to demonstrate and delineate the promoter function of this sequence. Expression of an EGFP ORF which replaced ORF1 and ORF2 demonstrated that the native promoter can drive down stream foreign gene expression. Replacement of ORF1 and ORF2 with a bicistronic cassette, incorporating a 493 bp IRES from an Ontario strain of avian encephalomyelitis virus (AEV) separating an EGFP ORF and mCherry ORF allowed for expression of both ORFs from a recombinant FAdV. These results provide an additional platform for multivalent vaccines development based on a native FAdV-9 promoter and an avian virus IRES.

The first complete genome sequence and pathogenicity characterization of fowl adenovirus 11 from chickens with inclusion body hepatitis in Pakistan

Inclusion body hepatitis (IBH), hydropericardium syndrome, and gizzard erosion associated with fowl adenovirus (FAdV) infections are reported globally and resulted in significant poultry industry economic losses. In 2018, severe IBH appeared in Pakistan in a 17-week-old layer flock. Subsequently, a FAdV-11 strain (designated as PKFAd18) was isolated from liver samples and identified based on phylogenetic analyses of the serotype-specific L1 region of the capsid hexon gene. There is no complete genome sequence of the Pakistani FAdV-11. This study successfully sequenced the complete genome of PKFAd18. The full genome of PKFAd18 contains 43 840 base pairs (bp) with a G + C content of 53.9 %, which is comparable to other FAdV serotypes. Similar to other FAdV-11 strains, PKFAd18 has only one fiber, while FAdV-1 and FAdV-4 have two fibers. Notably, PKFAd18 showed unique characteristics compared to other FAdV-11 strains. A natural large genomic deletion (1215 bp) appeared in tandem repeat region two, relative to the ON-NP2 strain. Phylogenetic analyses of the PKFAd18 penton gene showed higher homology with FAdV-9, highlighting potential natural recombination between FAdV-11 and FAdV-9. Moreover, the pathogenicity of PKFAd18 studied in specific-pathogen-free chickens showed that PKFAd18 is capable of inducing severe IBH and could be responsible for IBH in Pakistan. Thus, the first complete genome of FAdV-11 in Pakistan was sequenced in this study, which enriches the diversity of knowledge about FAdV-11 and is useful for developing diagnostics and vaccines for IBH induced by FAdV-11 in Pakistan.

The fowl adenovirus (Fadv-11) outbreak in Iranian broiler chicken farms: The first full genome characterization and phylogenetic analysis

Fowl adenoviruses D and E (FAdV-D and E) can cause inclusion body hepatitis (IBH) in commercial chicken flocks. Recently, IBH outbreaks have been increasingly reported in different regions of Iran, particularly in broiler farms. The present study was conducted to perform, for the first time, a complete genome characterization of a FAdV isolate from an IBH outbreak in Iran. Briefly, liver samples were collected from affected broiler flocks and following viral DNA extraction and confirming by PCR technique; one positive sample was selected from an affected flock to conduct a complete genome sequencing. The current FAdV, named "Fowl_Adenovirus_D_isolate_iran/UT-Kiaee_2018", was placed into FAdV-11 serotype (D species). According to the complete genome sequence analysis, UT-Kiaee had high homology with Chinese and Canadian FAdV. The partial sequence of the hexon gene revealed that UT-Kiaee shared 100% identity with previous Iranian FAdVs. The present study was the first to report full genome FAdV in Iran and complete the puzzle of molecular epidemiology of FAdV in Iran through determining the possible origin of Iranian FAdvs, which are the causative agents of recent IBH outbreaks in Iran.

In vitro growth kinetics and gene expression analysis of the turkey adenovirus 3, a siadenovirus

Turkey adenovirus 3 (TAdV-3) belongs to the genus Siadenovirus, family Adenoviridae. Previously, nucleotide sequencing and annotation of the Virginia avirulent strain (VAS) of TAdV-3 genome, isolated in our laboratory, indicated the presence of a total of 23 genes and open reading frames (ORFs). The goals of this study were 1) to delineate the growth kinetics of the virus using a qPCR-based infectivity assay, and 2) to determine the virus gene expression profile during the early and late phases of infection in target B lymphocytes. The one-step growth curve experiment demonstrated 3 phases of virus replication cycle: a lag phase lasted for 12-18 h post-infection (h.p.i.), in which the virus titer declined; a log phase from 18 to 120 h.p.i., in which the number of infectious virus particles increased over 20,000 folds, and a brief decline phase thereafter. Southern blot analysis indicated that the synthesis of new viral DNA started by 8 h.p.i. Gene-specific RT-PCR analysis revealed the expression of mRNAs from the 23 TAdV-3 genes/ORFs. According to the temporal transcriptional profiling of TAdV-3 genome, genes could be divided into 3 groups based on the time of transcription initiation: group 1 showed detectable levels of transcription at 2 h.p.i and included 7 genes, i.e., hyd, III, pX, pVI, II, 100 K, and 33 K; group 2 included 12 genes whose mRNAs were detected for the first time at 4 h.p.i., i.e., ORF1, IVa2, pol, pTP, pIIIa, EP, DBP, E3, U exon, IV, ORF7, and ORF8; group 3 of transcripts were detectable starting 8 h.p.i. and included only 4 genes, i.e., 52 K, 22 K, pVII, and pVIII. Our data suggest that the transcriptional kinetics of genus Siadenovirus differ from that observed in other adenoviral genera; however, a few TAdV-3 genes showed similar expression patterns to their adenoviral homologs.

Generation and characterization of a fowl adenovirus 9 dual-site expression vector

Fowl adenoviruses (FAdVs) are widely considered as excellent platforms for vaccine development and gene therapy. We improved on our right-end partial TR-2 deleted or a left-end 2.3 kb deleted vectors by developing a single, dual-site delivery vector. We demonstrated that, in addition to ORF11, the right end ORF17 is also dispensable. To further improve the capacity and flexibility of the FAdV-9 based vector system, we generated an infectious recombinant FAdV-9 dual-site expression clone lacking 1.9 kb of the left end and replaced with mCherry under the control of a native promoter, and 3.6 kb of the right-end replaced with an EGFP expression cassette. Five intermediate FAdmid clones were successfully constructed: a) pFAdV-9Δ0-2RED (mCherry replacing the left end 2.2 kb ORF0 to 2); b) pFAdV-9RED (mCherry replacing the left end 1.9 kb ORF1 to 2); c) pFAdV-9Δ17 (deletion of ORF17 and 393 bp downstream untranslated region); d) pFAdV-9GFP (EGFP expression cassette replacing the right end 3.6 kb) and e) pFAdV-9Dual (both mCherry in the left end and the EGFP expression cassette in the right end of our vector). Our novel FAdV-9 dual-site vaccine vector, produced infectious virus and expressed either one or both mCherry and EGFP.

Molecular characterization of pathogenic and nonpathogenic fowl aviadenovirus serotype 11 isolates

Fowl aviadenoviruses, many of which are of importance in veterinary medicine, are classified into 5 species. In this study, a pathogenic isolate and a nonpathogenic isolate of fowl aviadenovirus serotype 11 (FAdV-11) of species Fowl aviadenovirus D were characterized. Growth rates were analyzed for the 2 isolates, showing notable differences. The complete genomic sequences of the viruses were fully determined and were analyzed. The genomes of the 2 isolates showed 98.1% sequence identity and revealed 6 nonsynonymous mutations between the Ontario isolates. Two of the 6 mutations were also found in the sequences of recently published pathogenic Chinese fowl aviadenovirus 11 isolates, suggesting potential molecular markers that could be associated with pathogenesis. Deletions were found in the L5 region within the overlapping coding sequences for the 100, 22, and 33 kDa proteins, and these were found in only the nonpathogenic isolates. This molecular pattern was identified in FAdV-9, another nonpathogenic FAdV-D species virus. Furthermore, the tandem repeat regions varied dramatically; the pathogenic isolates contained a reduced number of tandem repeats compared with the nonpathogenic isolates. Lastly, a protein produced early in infection was analyzed using bioinformatics to determine its role in disease. This study highlights several candidate molecular determinants of avian adenovirus genomes related to pathogenicity.

Complete genome sequence of a non-pathogenic strain of Fowl Adenovirus serotype 11: Minimal genomic differences between pathogenic and non-pathogenic viruses

In this study, we conducted the clinicopathological characterization of a non-pathogenic FAdV-D serotype 11 strain MX95, isolated from healthy chickens, and its entire genome was sequenced. Experiments in SPF chickens revealed that the strain is a non-pathogenic virus that did not cause death at challenge doses of 1×10⁶ TCID50. Additionally, the infection in SPF chickens caused no apparent damage in most of the organs analyzed by necropsy and histopathology, but it did cause inclusion body hepatitis; nevertheless it did not generate severe infectious clinical symptoms. The virus was detected in several chicken organs, including the lymphoid organs, by real-time polymerase chain reaction (PCR) until 42 days. The genome of FAdV-11 MX95 has a size of 44,326bp, and it encodes 36 open reading frames (ORFs). Comparative analysis of the genome indicated only 0.8% dissimilarity with a highly virulent serotype 11 that was previously reported.

Coding potential and transcript analysis of fowl adenovirus 4: insight into upstream ORFs as common sequence features in adenoviral transcripts

Recombinant fowl adenoviruses (FAdVs) have been successfully used as veterinary vaccine vectors. However, insufficient definitions of the protein-coding and non-coding regions and an incomplete understanding of virus-host interactions limit the progress of next-generation vectors. FAdVs are known to cause several diseases of poultry. Certain isolates of species FAdV-C are the aetiological agent of inclusion body hepatitis/hydropericardium syndrome (IBH/HPS). In this study, we report the complete 45667 bp genome sequence of FAdV-4 of species FAdV-C. Assessment of the protein-coding potential of FAdV-4 was carried out with the Bio-Dictionary-based Gene Finder together with an evaluation of sequence conservation among species FAdV-A and FAdV-D. On this basis, 46 potentially protein-coding ORFs were identified. Of these, 33 and 13 ORFs were assigned high and low protein-coding potential, respectively. Homologues of the ancestral adenoviral genes were, with few exceptions, assigned high protein-coding potential. ORFs that were unique to the FAdVs were differentiated into high and low protein-coding potential groups. Notable putative genes with high protein-coding capacity included the previously unreported fiber 1, hypothetical 10.3K and hypothetical 10.5K genes. Transcript analysis revealed that several of the small ORFs less than 300 nt in length that were assigned low coding potential contributed to upstream ORFs (uORFs) in important mRNAs, including the ORF22 mRNA. Subsequent analysis of the previously reported transcripts of FAdV-1, FAdV-9, human adenovirus 2 and bovine adenovirus 3 identified widespread uORFs in AdV mRNAs that have the potential to act as important translational regulatory elements.

The non-essential left end region of the fowl adenovirus 9 genome is suitable for foreign gene insertion/replacement

The goals of this study were to demonstrate that a non-essential region at the left end of the fowl adenovirus 9 (FAdV-9) genome could be used to generate recombinant viruses, examine their in vitro growth characteristics and determine their ability to transduce non-avian cells. Three FAdV-9 vectors (rFAdV-9s) were generated carrying the enhanced-green fluorescent protein (EGFP) gene: FAdV-9inEGFP, FAdV-9 Delta 1-EGFP and FAdV-9 Delta 4-EGFP. FAdV-9inEGFP carried the EGFP cassette inserted into the non-essential region without deletion resulting in an increase of the genome size to 103.7% of the wild-type. FAdV-9 Delta 1-EGFP and FAdV-9 Delta 4-EGFP (rFAdV-9 Delta s) carried the EGFP cassette replacing the non-essential sequences at nucleotides 1194-2342 and 491-2782, respectively. All rFAdV-9s had wild-type growth kinetics and plaque morphology. The rFAdV-9 Delta s replicated in CH-SAH cells with the same titers as the wild-type virus. The FAdV-9inEGFP titers were approximately 1 log lower than those of rFAdV-9 Delta s and wt FAdV-9 at 36 and 48 h post-infection (h.p.i.). EGFP was expressed in avian and mammalian cells infected with rFAdV-9s. EGFP expression, based on spectrofluorometry, was significantly higher in chicken hepatoma cells infected with FAdV-9inEGFP than in those with rFAdV-9 Delta s at 18 and 24h.p.i, suggesting a functional role of some or all non-essential ORFs on foreign gene expression. This study demonstrated the suitability of the non-essential region as an insertion/replacement site for foreign genes to generate FAdV-9-based vectors that can be applied as recombinant vaccines for poultry or gene delivery vehicles for mammalian systems.

Sequence Analysis of the Left End of Fowl Adenovirus Genomes

Nucleotide sequence analysis of the left end of the genome of fowl adenoviruses (FAdV) representing species group C (FAdV-4 and -10), D (FAdV-2) and E (FAdV-8) were carried out, and the sequence data was compared to those of FAdV-1 (FAdV-A) and FAdV-9 (FAdV-D). The viruses were propagated in chicken hepatoma cell line for viral DNA isolation. Restriction endonuclease analysis was performed followed by hybridization with two DNA probes representing the left end of FAdV-9. The identified fragments were sequenced, and the generated data were compared with the GenBank database. Nucleotide sequence homology and amino acid sequence identities were high between members of the same species group, FAdV-2 and -9, and FAdV-4 and -10, whereas different degrees of variations were observed among all FAdVs. Gene arrangement and position of ORFs at the left end of FAdV genomes were largely conserved suggesting similar gene functions. All previously characterized left end ORFs in CELO virus and FAdV-9 were found in all analyzed FAdVs. However, ORF 1C was absent in FAdV-4 and -10, but additional ORFs, most likely corresponding to duplicates of ORF 14, were observed in these viruses.

DNA sequencing and analysis of the right-hand part of the genome of the unique bovine adenovirus type 10

The prototype strain of bovine adenovirus (BAdV) type 10 and four additional isolates that were indistinguishable in serum-neutralization tests have been shown to have remarkable variation in their genome size and restriction maps. In the present study, more than 40 % of the DNA sequence of the BAdV-10 isolate with the longest genome was determined. A biased base composition resulting in low (<41 %) GC content was noticed. Analysis of the genes of the DNA-binding protein, 100K, 33K, pVIII and fibre proteins, as well as early regions E3 and E4, which are encoded by the genome fragment examined, confirmed that BAdV-10 is different from the other known BAdV types regarding its phylogenetic distance and the organization of its exceptionally short E3 region, apparently containing only two genes. A comparative analysis of the E3 and E4 regions of BAdV-10 with various animal adenoviruses revealed interesting features accounting for the very short genome of BAdV-10. In the examined BAdV-10 isolate, duplicated sequences were localized in and around the fibre gene. Since BAdV-10 appears to be pathogenic to cattle and is genetically distant from the other BAdVs, we suggest that BAdV-10 is not a genuine bovine virus, but has recently switched host and is now undergoing an adaptation process in its new host. In accordance with this hypothesis, the remarkable predominance of AT-rich codons along with the variable fibre gene might be signs of adaptation.

Antibody response and virus tissue distribution in chickens inoculated with wild-type and recombinant fowl adenoviruses

We demonstrated that the long tandemly repeated region (TR-2) is dispensable for in vitro replication of fowl adenovirus 9 (FAdV-9). The TR-2-deleted recombinant FAdV-9 expressing the enhanced green fluorescence protein was further characterized for in vivo effects. Groups of chickens were exposed to recombinant or wild-type FAdV-9 by intramuscular injection, through the feed or drinking water and one group served as a negative control. The antibody (Ab) response, evaluated by ELISA and a plaque reduction test depended on the virus, dosage and the route of inoculation. Although the highest levels of anti-viral Ab were detected in chickens inoculated intramuscularly (i.m.) with wild-type FAdV-9, the deletion of TR-2 did not have a significant effect on the immune response. The tissue distribution of the virus was examined by the polymerase chain reaction (PCR) and was similar for both wild-type and recombinant viruses. Based on these results the TR-2 was dispensable for viral replication in vivo and did not influence virus distribution, and the recombinant FAdV-9 induced the same immune response as the wild-type virus.

Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses

BACKGROUND

The genome of the avian adenovirus Chicken Embryo Lethal Orphan (CELO) has two terminal regions without detectable homology in mammalian adenoviruses that are left without annotation in the initial analysis. Since adenoviruses have been a rich source of new insights into molecular cell biology and practical applications of CELO as gene a delivery vector are being considered, this genome appeared worth revisiting. We conducted a systematic reannotation and in-depth sequence analysis of the CELO genome.

RESULTS

We describe a strongly diverged paralogous cluster including ORF-2, ORF-12, ORF-13, and ORF-14 with an ATPase/helicase domain most likely acquired from adeno-associated parvoviruses. None of these ORFs appear to have retained ATPase/helicase function and alternative functions (e.g. modulation of gene expression during the early life-cycle) must be considered in an adenoviral context. Further, we identified a cluster of three putative type-1-transmembrane glycoproteins with IG-like domains (ORF-9, ORF-10, ORF-11) which are good candidates to substitute for the missing immunomodulatory functions of mammalian adenoviruses. ORF-16 (located directly adjacent) displays distant homology to vertebrate mono-ADP-ribosyltransferases. Members of this family are known to be involved in immuno-regulation and similiar functions during CELO life cycle can be considered for this ORF. Finally, we describe a putative triglyceride lipase (merged ORF-18/19) with additional domains, which can be expected to have specific roles during the infection of birds, since they are unique to avian adenoviruses and Marek's disease-like viruses, a group of pathogenic avian herpesviruses.

CONCLUSIONS

We could characterize most of the previously unassigned ORFs pointing to functions in host-virus interaction. The results provide new directives for rationally designed experiments.

Genetic content and evolution of adenoviruses

This review provides an update of the genetic content, phylogeny and evolution of the family Adenoviridae. An appraisal of the condition of adenovirus genomics highlights the need to ensure that public sequence information is interpreted accurately. To this end, all complete genome sequences available have been reannotated. Adenoviruses fall into four recognized genera, plus possibly a fifth, which have apparently evolved with their vertebrate hosts, but have also engaged in a number of interspecies transmission events. Genes inherited by all modern adenoviruses from their common ancestor are located centrally in the genome and are involved in replication and packaging of viral DNA and formation and structure of the virion. Additional niche-specific genes have accumulated in each lineage, mostly near the genome termini. Capture and duplication of genes in the setting of a 'leader-exon structure', which results from widespread use of splicing, appear to have been central to adenovirus evolution. The antiquity of the pre-vertebrate lineages that ultimately gave rise to the Adenoviridae is illustrated by morphological similarities between adenoviruses and bacteriophages, and by use of a protein-primed DNA replication strategy by adenoviruses, certain bacteria and bacteriophages, and linear plasmids of fungi and plants.