Multiple reiteration of a 40-bp nucleotide sequence in the inverted terminal repeat of the genome of a canine adenovirus

Molecular characterization of a bovine adenovirus type 7 (Bovine Atadenovirus F) strain isolated from a systemically infected calf in Germany

Bovine adenovirus 7 (BAdV-7) is an unclassified member of the genus Atadenovirus with a worldwide distribution and has been reported to induce clinical disease of varying severity in infected cattle, ranging from asymptomatic infections to severe enteric or respiratory disease. In this study, we used next-generation sequencing to obtain the first complete genome sequence of a European strain of BadV-7, from pooled spleen and liver tissue obtained from a deceased newborn Limousin calf. Histopathological analysis and electron microscopy showing systemic lesions in multiple organs with intranuclear amphophilic inclusions observed in endothelial cells in multiple peripheral tissues. Virus isolation was readily achieved from tissue homogenate using bovine esophagus cells (KOP-R), a strategy which should facilitate future in vitro or in vivo BAdV-7 studies. Phylogenetic analysis of available genome sequences of BAdV-7 showed that the newly identified strain groups most closely with a recent BAdV-7 strain, SD18-74, from the USA, confirming that this newly identified strain is a member of the Atadenovirus genus. The fiber gene was found to be highly conserved within BAdV-7 strains but was highly divergent in comparison to Ovine adenovirus 7 (OAdV-7) (39.56% aa sequence identity). Furthermore, we report a variable region of multiple tandem repeats between the coding regions of E4.1 and RH5 genes. In summary, the presented pathological and molecular characterization of this case suggests that further research into the worldwide molecular epidemiology and disease burden of BAdV-7 is warranted.

Immunogenicity of a new, inactivated canine adenovirus type 2 vaccine for dogs

PURPOSE

We constructed a new canine adenovirus type 2 (CAV-2) vaccine candidate using the recently isolated Korean CAV-2 strain; we termed the vaccine APQA1701-40P and evaluated its safety and immunogenicity in dogs.

MATERIALS AND METHODS

To generate the anti-CAV-2 vaccine, APQA1701 was passaged 40 times in MDCK cells growing in medium containing 5 mM urea and the virus was inactivated using 0.05% (volume per volume) formaldehyde. Two vaccines were prepared by blending inactivated APQA1701-40P with two different adjuvants; both were intramuscularly injected (twice) into guinea pigs. The safety and immunogenicity of the Cabopol-adjuvanted vaccine were evaluated in seronegative dogs. The humoral responses elicited were measured using an indirect enzyme-linked immunosorbent assay (I-ELISA), and via a virus neutralization assay (VNA).

RESULTS

The new, inactivated CAV-2 vaccine strain, APQA1701-40P, lacked six amino acids of the E1b-19K protein. In guinea pigs, the Cabopol-adjuvanted vaccine afforded a slightly higher VNA titer and I-ELISA absorbance than an IMS gel-adjuvanted vaccine 4 weeks post-vaccination (p>0.05). Dogs inoculated with the former vaccine developed a significantly higher immune titer than non-vaccinated dogs.

CONCLUSION

The Cabopol-adjuvanted, inactivated CAV-2 vaccine was safe and induced a high VNA titer in dogs.

Sequential circulation of canine adenoviruses 1 and 2 in captive wild carnivores, France

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Two canine adenoviruses (CAdVs) were found to circulate sequentially in captive wild carnivores in France.

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CAdV-1 caused the death of a Eurasian wolf (Canis lupus lupus) with gross lesions and histopathological changes compatible with infectious canine hepatitis.

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CAdV-2 was subsequently found to circulate subclinically in other carnivores of the same zoological park.

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Analysis of the full-length genome of the wolf CAdV-1 strain showed a high genetic relatedness with an Italian strain detected in the same species.

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Future studies are needed to assess the CAdV ecology in endangered wild carnivores.

Scarce data are currently available about the ecology of canine adenoviruses (CAdVs) in wild carnivores. In this paper, the consecutive circulation of CAdV-1 and CAdV-2 in wild carnivores maintained in a French zoological park is reported. A fatal CAdV-1 infection was observed in a Eurasian wolf (Canis lupus lupus), which displayed gross lesions, histopathological changes and immunohistochemical findings suggestive of CAdV-1 infection. The virus was isolated on cell cultures and its genome was determined through next-generation sequencing, resulting genetically related to a recent Italian CAdV-1 strain detected in an Italian wolf. Subsequently, subclinical circulation of CAdV-2 was demonstrated by molecular methods in wild carnivores maintained in the same zoological park, some of which had been previously vaccinated with a CAdV-2 vaccine. Virus detection at a long distance from vaccination and by unvaccinated animals was suggestive of infection by a CAdV-2 field strain, although no data are available about the extent and duration of shedding of CAdV-2 modified-live virus in wild or domestic carnivores. The present paper provides new insights into the CAdV ecology in wildlife, although future studies are needed to fully understand the pathogenic potential of both CAdVs especially in endangered carnivore species.

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.

Complete sequence and organization of the human adenovirus serotype 46 genome

Out of 51 human adenoviral serotypes recognized to date, 32 of them belong to species D. Members of species D adenoviruses are commonly isolated from immune suppressed patients (organ transplant) and patients suffering from AIDS. The role of species D adenoviruses in pathogenesis is currently unclear. To derive new insights into the genetic content and evolution of species D adenoviruses and as a first step towards development of human adenovirus serotype 46 (Ad46) as vector, the complete nucleotide sequence of the virus was determined. The size of the genome is 35,178 bp in length with a G+C content of 56.9%. All the early and late region genes are present in the expected locations of the genome. The deduced amino acid sequences of all late region genes, with the exception of fiber, exhibited high degree of homology with the corresponding proteins of other adenoviruses. The deduced amino acid sequences of early regions E1, E3 and E4 showed a high degree of homology with the corresponding proteins of adenoviruses belonging to species D and less homology with the corresponding proteins of adenoviruses of other species. The homologues of Ad5 E3 region genes encoding 12.5K, gp19K, 10.4K, 14.5K and 14.7K are conserved in the genome of Ad46. However, the E3 region of Ad46 lacks genes encoding 6.7K and adenovirus death protein (ADP) but contains two additional open reading frames with a coding capacity of 433 and 281 amino acids. The fiber protein of Ad46 is 200 amino acids smaller than the fiber protein of Ad5 and contains only 10 pseudo-repeats in the shaft region. To facilitate the manipulation of the genome, the complete genome of Ad46 was cloned into a single bacterial plasmid. Following transfection into E1 complementing cell lines, the virus was recovered demonstrating the feasibility of viral genome manipulation for generation of recombinant viruses.

The long repeat region is dispensable for fowl adenovirus replication in vitro

Two regions containing tandemly repeated sequences are present in the fowl adenovirus 9 (FAdV-9) genome. The longer repeat region (TR-2) is composed of 13 contiguous 135-bp-long direct repeats, the function of which is unknown. An infectious FAdV-9 genomic clone, constructed by homologous recombination in Escherichia coli, was used for engineering of recombinant viruses. The enhanced green fluorescence protein (EGFP) coding sequence was cloned in both rightward and leftward orientations so as to replace TR-2. Replication-competent recombinant FAdVs were recovered, demonstrating that TR-2 was dispensable for FAdV-9 propagation in vitro. The expression of EGFP in infected cells was demonstrated by fluorescence microscopy, immunoprecipitation, and RT-PCR.

Novel human gene transfer vectors: evaluation of wild-type and recombinant animal adenoviruses in human-derived cells

Major disadvantages of human adenovirus (hAd) vectors in gene therapy include preexisting or induced immune responses, and possible coreplication of recombinant hAd in the presence of wild-type hAds. These disadvantages may be overcome by using nonhuman, animal adenoviruses (aAds). We evaluated four different aAds for their potential use as viral vectors. The canine adenovirus type 2 (CAV2) and bovine adenovirus type 3 (BAV3) appeared to be suitable systems, as they infect human cells. CAV2, but not BAV3, caused cytotoxicity, and only limited (CAV2) or no (BAV3) production of infectious virus particles was observed after infection of human cell lines. CAV2 showed higher expression of endogenous genes than did BAV3 in the tested human cells. No interference between hAd and CAV2 or BAV3, such as recombination of DNA or cross-activation of virus replication, was observed in up to five passages in double-infected human cells. Transfection of cloned genomic CAV2 or BAV3 DNA into appropriate permissive cell lines rescued infectious virus. Furthermore, we produced a recombinant E1-deleted BAV3, and showed that it could infect and express a reporter gene in various human cell types. The goal was to construct and evaluate recombinant (E1-deleted) animal adenoviruses (aAds) as new vector systems for human gene therapy. The rationale for developing aAds for human use is the potential higher safety and efficiency, as compared with human adenoviruses (hAds). Coreplication and recombination with preexisting hAds should not be possible owing to lack of homology, and preexisting immunity in the general population should be limited. Of the four aAds we evaluated, BAV3 appeared to be the best candidate. It infects human cells without showing growth or cytotoxic effects, viral gene expression was barely detectable, and no trans-activation of either virus was detected in coinfections with hAd5. Rescue of virus in permissive cells, from plasmids containing the CAV2 or BAV3 genome, confirmed our approach. Furthermore, an E1-deleted recombinant BAV3 was constructed and shown to transduce and express the lacZ reporter gene in human cells.

Molecular cloning and restriction enzyme mapping of avian adenovirus type 8 DNA

Avian adenovirus (AAV) type 8 was cultured in an avian hepatoma cell line designated CH-SAH and the viral DNA extracted and purified. Restriction enzyme analysis of viral DNA using the endonucleases ApaI, EcoRI, HindIII, KpnI, NotI, SpeI, StuI and XbaI was carried out, and fragments representing the entire genome were cloned. According to the restriction enzyme fragments, the size of the AAV type 8 genome was calculated to be 44.7 kb. Subcloning of viral DNA fragments and hybridization studies using selected viral DNA fragments facilitated the construction of the physical map of AAV type 8 DNA.

Sequence analysis of putative pVIII, E3 and fibre regions of porcine adenovirus type 3

Sequence analysis of a region of the genome of porcine adenovirus type 3 from map unit 79.5 to map unit 92 was performed. Homology studies revealed genes coding for the hexon-associated protein pVIII on the left and for the fibre protein on the right of the sequenced region. By analogy with the genomic organization of other adenoviruses, the 1179 bp sequence between the pVIII and fibre open reading frames, extending from map unit 81.3 to map unit 84.7, was identified as the equivalent of the E3 region of human adenoviruses. The deduced amino acid sequence of one of the three open reading frames of the putative E3 region showed homology with the 13.3K E3 protein of canine adenovirus type 2. The primary structure of the putative fibre protein was similar to that described for human adenovirus types 2 and 5, with a 14 pseudorepeat motif in the shaft region of the fibre. A 742 bp tandem repeat starting in the middle of the fibre gene and extending beyond the termination codon of this gene was observed.

Molecular cloning and physical mapping of porcine adenovirus types 1 and 2

The 25R strain of porcine adenovirus type 1 (PAV-1) and the A47 strain of PAV-2 were propagated in ST cells, and DNA was extracted from the infected cells by a modified Hirt method. The DNA of each virus was digested by each of nine restriction endonucleases, and restriction enzyme fragments representing the entire genome were cloned. The genomic size of each virus was approximately 33 kb. Physical maps for the nine restriction endonucleases were constructed from the results of double digestion and Southern blot hybridization experiments, and oriented with respect to the PAV-3 genome. PAV-1 and PAV-2 were found to be related genetically to PAV-3, and there was a closer relationship between PAV-1 and PAV-3 than between PAV-1 and PAV-2 or between PAV-2 and PAV-3.

Sequence analysis of putative E3 and fiber genomic regions of two strains of canine adenovirus type 1

The nucleotide sequences of the genomes of two strains of canine adenovirus, type 1 (Glaxo and CLL) have been determined within the region spanning approximately 0.80-0.91 map unit. Homology comparisons with other adenoviral DNAs indicate that this region contains part of the hexon-associated protein (pVIII) precursor gene on the left, and a 57-kDa fiber-encoding gene on the right. In both viral strains, the sequences of these genes are identical. Accepting the generally highly conserved nature of the genetic organization of adenoviral genomes, the 1136-bp sequence between them would include the canine equivalent of the human adenoviral E3 region. In the Glaxo strain, which is nonattenuated, this sequence contains only two R-strand open reading frames capable of coding for polypeptides of 60 residues or more. One of these appears to code for a transmembrane glycoprotein of 194 amino acid residues. Neither ORF, however, shows significant homology with any other known adenoviral DNA or protein sequence. The corresponding region in the attenuated strain CLL is almost identical with that of the Glaxo, but with a 325-bp deletion resulting in a fusion of the two ORFs. It seems, therefore, that neither ORF is essential for viral replication in vitro, since the CLL strain replicates just as efficiently as the Glaxo. The suggestion is made that the attenuation of the CLL strain may be related to the nonfunctionality of its E3 gene product(s).

Early region 4 sequence and biological comparison of two isolates of mouse adenovirus type 1

The DNA sequence of 88-100 map units of mouse adenovirus type 1 (MAV-1) was determined. One translational open reading frame showed 48% sequence similarity to a human adenovirus type 2 early region 4 protein. Based on the protein similarity, genome location, and transcriptional polarity, we concluded that this region of MAV-1 corresponds to early region 4. A 241-bp sequence consisting of 10 imperfect direct repeats with sequence similarity to minisatellite DNA was found in this region. Two virus isolates with different passage histories were examined and were found to have a sequence polymorphism within this region. The two viruses were compared for growth in cell culture and mice and small quantitative differences were observed only in vivo.

Replication of an adenovirus type 34 mutant DNA containing tandem reiterations of the inverted terminal repeat

A mutant of human adenovirus type 34 (Ad34) has been isolated which contains DNA molecules with tandem reiterations of from two to eight copies of a 131-bp sequence within the right-sided inverted terminal repetition. Terminal heterogeneity was not eliminated by repeated plaque purifications indicating that the population of DNA molecules with various numbers of reiterations could rapidly evolve from the DNA of a single virus particle. These enlarged DNA molecules were capable of replication both in vivo and in vitro. The nucleotide sequence of the mutant Ad34 inverted terminal repetitions contained most of the essential features of the Ad origin of DNA replication. These features include the ATAATATACC sequence which is present between the highly conserved bases 9-18 in all human adenoviruses, as well as the consensus sequences for the binding of nuclear factor I and nuclear factor III. However, the reiterated sequences lacked a dG appropriately placed on the template strand to serve as a potential site for internal initiation. It appears that the rapid amplification of two to eight copies of the reiterated terminal sequences does not arise from internal initiation during replication but probably from homologous recombination.

Incomplete particles of canine adenovirus type 1: occurrence and structure

Replication of canine adenovirus (CAV) type 1 in dog kidney (DK) cells has been found to generate particles containing double-stranded DNA molecules of size 6-9 kbp with protein moieties at their 5' termini. The particles formed a discrete band in CsCl gradients at a density intermediate to that of intact virions and empty capsids. Electron microscopy demonstrated that they were morphologically similar to intact virions. Restriction enzyme digests and hybridization experiments revealed the existence of DNA molecules consisting of sequences extending from left and right termini of the intact genome. The subgenomic DNAs, therefore, appear to be viral DNA with the majority (24-26 kbp) of its internal sequences deleted. Agarose gels of viral DNA isolated from DK cells infected with plaque-purified CAV revealed, in addition to the intact viral genome, one or more sharp, well-defined subgenomic DNA bands, the sizes of which varied from approximately 6 to 9 kbp among individual isolates. Incomplete particles of this sort were found in the two strains of CAV type 1 tested (Connaught ICHV and Glaxo), but not in a strain of CAV type 2 (Manhattan).

Highly sensitive and specific non-radioactive biotinylated probes for dot-blot, Southern and colony hybridizations

We describe a simple method for the incorporation of biotin into nucleic acid probes. This method has been improved and optimized to produce biotinylated DNA probes for the detection of DNA by dot-blot, Southern and colony hybridization techniques. The sensitivity of this method has been particularly improved to allow detection of DNA quantities under one femtogram. Probes prepared by this method are highly specific for target DNA even in crude bacterial lysates.

Characterization of the genome of a vaccine strain of canine adenovirus type 1

Restriction endonuclease cleavage maps have been constructed for the genome of a canine adenovirus type 1 (CAV-1) vaccine strain (CLL; Connaught Laboratories, Ltd., Willowdale, Ontario). Restriction enzyme analyses were also carried out on CAV-1 (CLL) genomes isolated from viral stocks over 8 serial passages in a dog kidney cell line (DK 6722). The right hand 20% of the genome became more heterogeneous in size with increasing passage in DK 6722 cells due to deletions up to 3-4 kb, whereas the left terminal region was stable throughout these passages. A comparative study of CAV-1(CLL) and a virulent strain of CAV-1, Glaxo, revealed that the genome of CAV-1(CLL) was the shorter, by about 480 bp, within the region covering 0.83-0.91 map units. By virtue of its location within the genome and its dispensable nature for viral growth, this region would appear to encompass a genetic sequence corresponding to the E3 region of human adenoviruses. In terms of viral attenuation, the possible importance of the observed differences between CAV-1(CLL) and CAV-1(Glaxo) is discussed.

Stability of vaccinia virus DNA during persistent infections: accumulation of left-end deletions and of tandem repeats at both ends of the viral genome and prevention by interferon

The stability of the large vaccinia virus genome (122 MDa) has been studied in long-term cultures of persistently infected Friend erythroleukemia (FEL) cells. Deletions of about 8 MDa at the left terminus of vaccinia DNA are generated at early passages, and are maintained even after 2 years of continuous cell passages. The generation of deletions is followed by a stable accumulation of tandem repeats up to 6 MDa at the left end and up to 2 MDa at the right end of vaccinia DNA. Neither translocations nor rearrangements of DNA are observed during persistent infection. A recombinational mechanism within the tandem repeats or a mechanism similar to that described for adenovirus might explain the reiteration of tandem repeats at both ends. Significantly, in persistently infected cultures continuously treated with interferon (IFN) both the deletion and the large accumulation of tandem repeats were completely blocked. We suggest that reiteration of tandem repeats at the termini of vaccinia DNA might provide signals for more efficient virus multiplication in FEL cells.