Sequence Analysis of the Left End of Fowl Adenovirus Genomes

Analysis of Fowl Adenovirus 4 Transcriptome by De Novo ORF Prediction Based on Corrected Nanopore Full-Length cDNA Sequencing Data

The transcriptome of fowl adenovirus has not been comprehensively revealed. Here, we attempted to analyze the fowl adenovirus 4 (FAdV-4) transcriptome by deep sequencing. RNA samples were extracted from chicken LMH cells at 12, 18 or 26 h post-FAdV-4 infection, and subjected to Illumina strand-specific RNA-seq or nanopore full-length PCR-cDNA sequencing. After removing the reads of host cells, the data of FAdV-4 nanopore full-length cDNAs (transcripts) were corrected with reads from the Illumina RNA-seq, mapped to the viral genome and then used to predict viral open reading frames (ORFs). Other than 42 known ORFs, 39 novel ORFs were annotated to the FAdV-4 genome. Different from human adenovirus 5, one FAdV-4 ORF was often encoded by several transcripts, and more FAdV-4 ORFs were located on two exons. With these data, 18 major transcription start sites and 15 major transcription termination sites were defined, implying 18 viral promoters and 15 polyadenylation signals. The temporal cascade of viral gene transcription was observed in FAdV-4-infected cells, with six promoters possessing considerable activity in the early phase. Unexpectedly, four promoters, instead of one major late promoter, were engaged in the transcription of the viral genus-common genes on the forward strand. The clarification of the FAdV-4 transcriptome laid a solid foundation for the study of viral gene function, virulence and virus evolution, and it would help construct FAdV-4 as a gene transfer vehicle. The strategy of de novo ORF prediction could be used to parse the transcriptome of other novel adenoviruses.

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.

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.

Complete genome sequence of fowl adenovirus-8b UPM04217 isolate associated with the inclusion body hepatitis disease in commercial broiler chickens in Malaysia reveals intermediate evolution

The main aim of our study was to explore the genome sequence of the inclusion body hepatitis associated Fowl adenovirus serotype 8b (FAdV-8b) UPM04217 and to study its genomic organisation. The nucleotide sequence of the whole genome of FAdV-8b UPM04217 was determined by using the 454 Pyrosequencing platform and the Sanger sequencing method. The complete genome was found to be 44,059 bp long with 57.9% G + C content and shared 97.5% genome identity with the reference FAdV-E genome (HG isolate). Interestingly, the genome analysis using ORF Finder, Glimmer3 and FGENESV predicted a total of 39 open reading frames (ORFs) compared to the FAdV-E HG that possessed 46 ORFs. Fourteen ORFs located within the central genomic region and 16 ORFs located within the left and right ends of the genome were assigned as being the high protein-coding regions. The fusion of the small ORFs at the right end terminal specifically in ORF22 and ORF33 could be the result of gene truncation in the FAdV-E HG. The frame shift mutation in ORF25 and other mutations in ORF13 and ORF17 might have lead to the emergence of genes that could have different functions. Besides, one of the minor capsid components, pVI, in FAdV-8b UPM04217 shared the highest similarity of 93% with that of FAdV-D, while only 47% similarity was found with FAdV-E. From the gene arrangement layout of the FAdV genome, FAdV-8b UPM04217 showed intermediate evolution between the FAdV-E HG and the FAdV-D although it was apparently more similar to the FAdV-E HG.

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.

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.

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.

Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4

We present, to our knowledge, the first complete genome sequence of a waterfowl aviadenovirus, goose adenovirus (GoAdV) strain P29, and an analysis of its genetic content in comparison with five published aviadenovirus genome sequences. Of the 35 genes predicted to encode functional proteins, the central region of the genome contains 19 (IVa2 to fiber-2) that were inherited from the ancestor of all known adenoviruses. Of the remaining genes, nine have orthologues only in aviadenoviruses and seven lack orthologues in any adenovirus. We also obtained limited sequence data for a pathogenic GoAdV strain D1036/08. Phylogenetic analyses placed the two GoAdV strains monophyletically in the genus Aviadenovirus. We propose designating strains P29 and D1036/08 as GoAdV-4 and GoAdV-5, respectively.

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.

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

In this study we determined and analyzed the complete nucleotide sequence of the genome of a fowl adenovirus serotype 8 (FAdV-8) isolate and examined its pathogenicity in chickens. The full genome of FAdV-8 was 44,055 nucleotides in length with a similar organization to that of FAdV-1 and FAdV-9 genomes. No regions homologous to early regions E1, E3 and E4 of mastadenoviruses were recognized. Along with FAdV-9, FAdV-8 has only one fiber gene and with regard to sequence composition and genome organization, FAdV-8 is closer to FAdV-9 than to FAdV-1. Moreover, our findings suggest that FAdV-1 of species Fowl adenovirus A as the current type species despite its historical priority is not representative of the genus Aviadenovirus, and that FAdV-8 or FAdV-9 in species Fowl adenovirus E and Fowl adenovirus D, respectively, would be more suitable for that designation. Additionally, pathogenicity of FAdV-8 was studied in specific pathogen free chickens following oral and intramuscular inoculations. Despite lack of clinical signs and pathological changes virus was found in tissues and cloacal swabs of all birds with the highest viral copy numbers present in the cecal tonsils. The highest virus titers in the feces for orally and intramuscularly inoculated chickens were recorded at days 10 and 3 post-infection, respectively.

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.