Identification of a novel GC-rich 113-nucleotide region to complete the circular, single-stranded DNA genome of TT virus, the first human circovirus.
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The sequence data (H. Okamoto et al., Hepatol. Res. 10:1-16, 1998) of a newly discovered single-stranded DNA virus, TT virus (TTV), showed that it did not have the terminal structure typical of a parvovirus. Elucidation of the complete genome structure was necessary to understand the nature of TTV. We obtained a 1.0-kb amplified product from serum samples of four TTV carriers by an inverted, nested long PCR targeted for nucleotides (nt) 3025 to 3739 and 1 to 216 of TTV. The sequence of a clone obtained from serum sample TA278 was compared with those registered in GenBank. The complete circular TTV genome contained a novel sequence of 113 nt (nt 3740 to 3852 [=0]) in between the known 3'- and 5'-end arms, forming a 117-nt GC-rich stretch (GC content, 90.6% at nt 3736 to 3852). We found a 36-nt stretch (nt 3816 to 3851) with an 80.6% similarity to chicken anemia virus (CAV) (nt 2237 to 2272 of M55918), a vertebrate circovirus. A putative SP-1 site was located at nt 3834 to 3839, followed by a TATA box at nt 85 to 90, the first initiation codon of a putative VP2 at nt 107 to 109, the termination codon of a putative VP1 at nt 2899 to 2901, and a poly(A) signal at nt 3073 to 3078. The arrangement was similar to that of CAV. Furthermore, several AP-2 and ATF/CREB binding sites and an NF-kappaB site were arranged around the GC-rich region in both TTV and CAV. The data suggested that TTV is circular and similar to CAV in its genomic organization, implying that TTV is the first human circovirus. (+info)
Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus.
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There are several similarities between the small, circular, single-stranded-DNA genomes of circoviruses that infect vertebrates and the nanoviruses that infect plants. We analyzed circovirus and nanovirus replication initiator protein (Rep) sequences and confirmed that an N-terminal region in circovirus Reps is similar to an equivalent region in nanovirus Reps. However, we found that the remaining C-terminal region is related to an RNA-binding protein (protein 2C), encoded by picorna-like viruses, and we concluded that the sequence encoding this region of Rep was acquired from one of these single-stranded RNA viruses, probably a calicivirus, by recombination. This is clear evidence that a DNA virus has incorporated a gene from an RNA virus, and the fact that none of these viruses code for a reverse transcriptase suggests that another agent with this capacity was involved. Circoviruses were thought to be a sister-group of nanoviruses, but our phylogenetic analyses, which take account of the recombination, indicate that circoviruses evolved from a nanovirus. A nanovirus DNA was transferred from a plant to a vertebrate. This transferred DNA included the viral origin of replication; the sequence conservation clearly indicates that it maintained the ability to replicate. In view of these properties, we conclude that the transferred DNA was a kind of virus and the transfer was a host-switch. We speculate that this host-switch occurred when a vertebrate was exposed to sap from an infected plant. All characterized caliciviruses infect vertebrates, suggesting that the host-switch happened first and that the recombination took place in a vertebrate. (+info)
Ultrastructure of porcine circovirus in persistently infected PK-15 cells.
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The ultrastructure of porcine circovirus was examined in persistently infected porcine kidney (PK)-15 cells. Virus-infected PK-15 cells had large numbers of intracytoplasmic inclusions, and a few cells had intranuclear inclusions. Intracytoplasmic inclusions were dispersed throughout the cytoplasm but were most numerous in the perinuclear cytoplasm. Inclusion were of various sizes, round to oval, and electron dense and were of two general types. Inclusions of the first type were small (0.1-0.5 microm diameter), not surrounded by trilaminar membranes, and granular with indistinct margins that blended with surrounding cytoplasm. Some contained 12+/-2-nm-diameter icosahedral virions in loose aggregates or rarely forming paracrystalline arrays. Small inclusions could be sites of viral assembly or maturation. Intracytoplasmic inclusions of the second type were larger (0.5-5.0 microm diameter) and more numerous and had abrupt margins surrounded by trilaminar membranes. They were more electron dense than small inclusions and were heterogeneous, containing various proportions of aggregated virions, electron-dense crystalline lamellae of 5 nm periodicity, and/or whorls of myelinoid membranes. Virions usually formed paracrystalline arrays and occasionally were loosely aggregated. Larger inclusions were typical of autophagolysosomes. Intranuclear inclusions were not membrane bound and were often associated with reticulated nucleoli or aggregates of heterochromatin. Some inclusions were irregularly shaped aggregates of indistinct, circular 10-12-nm-diameter viruslike particles. Others were 0.1-1.0 microm in diameter, round or ring shaped, dense, and finely granular, with sharply demarcated margins. (+info)
Electron microscopical observations of psittacine beak and feather disease in an Umbrella cockatoo (Cacatua alba).
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Psittacine beak and feather disease (PBFD) was diagnosed in an umbrella cockatoo (Cacatua alba) with severe feather dystrophy and loss. Electron microscopically, the intranuclear and intracytoplasmic inclusion bodies observed by light microscopy were composed of viral particles forming paracrystalline arrays, whorls, semicircles or concentric circles. Recovered viral particles from the skin and feather follicle tracts were icosahedral and 15 to 20 nm in diameter. (+info)
Detection of porcine circovirus from lesions of a pig with wasting disease in Japan.
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A wasting disease characterized by progressive weight loss and dyspnea has been observed in weaning pigs on a farm in Yamagata Prefecture in 1998. Histopathologic findings in an affected pig were bronchointerstitial pneumonia and intracytoplasmic clusters of basophilic inclusions in macrophages of lymph nodes, which were similar to those in pigs with postweaning multisystemic wasting syndrome (PMWS) recently reported in North America and Europe. Porcine circovirus (PCV)-like particles were observed in bronchial lymph node of the pig by electron microscopy, and PCV antigens were detected in the lesions by immunohistochemical staining. PCV DNA was also detected in the lung and tonsil by PCR, and restriction fragment length polymorphism analysis of the PCR products with HinfI showed the same type of the PCV associated with PMWS (pmws PCV). Homology of nucleotide sequences between the PCR product and corresponding regions of published pmws PCV genomes was very high. These results indicated that virus detected in this study was pmws PCV. To our knowledge, this is the first report on the presence of pmws PCV in Japan. (+info)
Multiplex PCR for detection and typing of porcine circoviruses.
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Sets of oligonucleotide primers were designed according to the sequences of the open reading frames (ORFs) ORF1 and ORF2 of the prototype nonpathogenic PK-15 strain of porcine circovirus (PCV) type 1 (PCV-1). By the PCR performed with the various primer sets, genomic DNA or RNA from other bacterial or viral pathogens of the respiratory tracts of pigs could not be amplified. A positive amplification reaction could be visualized with DNA extracted from a viral suspension containing as few as 10 viral particles per ml. No DNA fragment could be amplified from lysates of continuous porcine cell lines (PT, ST, and PFT cells) known to be negative for PCV. When tested with clinical samples from pigs, the results of the single PCR method showed nearly 93% (13 of 14 samples) correlation with histopathological and immunohistochemical findings. Interestingly, subclinical PCV infections could be detected by single PCR with clinical samples that have been submitted from animals with irrelevant cases of respiratory and/or enteric problems. On the basis of the nucleotide sequences of PCV strains (PCV-2) recently associated with outbreaks of postweaning multisystemic wasting syndrome (PWMS) in Quebec, Canada, pig farms, other primers were designed from the PCV-1 genome, and these primers failed to amplify genomic fragments specific to the ORF1 or ORF2 genes of clinical isolates associated with PWMS but amplified DNA from the PCV-1 strain. Two rapid multiplex PCR (mPCR) methods have been developed to distinguish between both genotypes of PCV. By those two mPCR methods, (i) species-specific primer pairs were used to amplify a DNA fragment of 488 bp specific for the ORF2 genes of both genotypes, whereas a 375-bp fragment was amplified from the ORF1 gene of the PCV-1 strain only, or (ii) species-specific primer pairs were used to amplify a DNA fragment of 646 bp specific for the ORF1 genes of both genotypes, whereas a 425-bp fragment was amplified from the ORF2 gene of the PCV-1 strain only. By both mPCR methods, a PCV-2 infection was demonstrated in tissues of 94.2% (33 of 35) of the sick pigs tested, in agreement with previous findings showing the close association of this new genotype of PCV with outbreaks of PMWS in Europe and North America. On the other hand, a PCV-1 infection was confirmed in only 5.7% (2 of 35) of the pigs, and confirmation of a mixed infection with PCV-2 was obtained by a single PCR with PCV-2-specific primers. (+info)
PCR detection and characterization of type-2 porcine circovirus.
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A polymerase chain reaction (PCR) assay was developed for detecting porcine circovirus (PCV). The assay readily detected type-2 PCV (PCV-2) and type-1 PCV (PCV-1). The PCR primers were designed based on DNA sequences conserved in all reported PCV genomes. Type 1 PCV and type 2 PCV both produced 438 bp amplification products, which were easily identified and differentiated from one another by restriction fragment length polymorphism (RFLP) analysis. Porcine circovirus was detected in 55% (931/1693) of randomly tested pigs with various clinical signs and lesions, most of which were difficult to differentiate from those associated with porcine reproductive and respiratory syndrome (PRRS). The PCR products from all positive clinical samples were identified by RFLP to be only PCV-2; DNA tested by PCR was extracted directly from one or more of lung, mesenteric or mediastinal lymph nodes, and tonsil. Type 2 PCV was also detected in 6% (2/34) of DNA extracted directly from semen of randomly chosen healthy boars. Positive PCR reactions from 554 diseased pigs were characterized by RFLP and categorized into 5 different profiles (A-E), of which 82.8% were PCV-2A (456/554), 3.0% were PCV-2B (17/554), 9.9% were PCV-2C (55/554), 1.1% were PCV-2D (6/554), and 3.2% were PCV-2E (18/554). The complete genomic nucleotide sequences of PCV-2A, B, C, D, and E were determined and found to have at least 95% homology compared with one another and with all other PCV-2 found in the GenBank database. All PCV-2 had less than 76% homology with PCV-1. This PCR assay will hopefully be useful to veterinary diagnostic laboratories for routine testing and surveillance of infection with PCV-2. The RFLP profiling system might be useful for preliminary characterization and identification of PCV isolates and might also benefit studies on the molecular epidemiology of PCV. (+info)
Porcine circoviruses: a review.
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Porcine circoviruses (PCV) are small nonenveloped DNA viruses containing a unique single-stranded circular genome. Previously, no recognized link was found between PCV infection of pigs and disease, and PCV was considered a nonpathogenic agent. Over the last 5 years, a "novel" PCV, designated PCV2, has been associated with various disease syndromes in pigs, primarily postweaning multisystemic wasting syndrome (PMWS). Pigs with PMWS have a variety of clinical signs, including debility, dyspnea, palpable lymphadenopathy, diarrhea, and pallor or icterus. Lesions associated with the presence of PCV2 in a variety of cell types include lymphohistiocytic to granulomatous interstitial pneumonia, hepatitis, nephritis, myocarditis, enteritis, and pancreatitis. The lesions of PMWS have been reproduced experimentally after inoculation of piglets with PCV2 cell culture isolates, although the full expression of the disease syndrome may require the presence of other agents such as porcine parvovirus or porcine reproductive and respiratory syndrome (PRRS) virus. Recent reports have linked PCV2 to other disorders in pigs, ranging from abortion and reproductive failure to "atypical" PRRS. Available data indicate high seroprevalence of antibodies to PCV2 worldwide. The diagnosis of PCV2-associated disease is based on the direct demonstration of PCV2 antigens or nucleic acid in affected tissues. PCV2 is now regarded as an important emerging pathogen. Although vertical transmission has been documented, the epidemiology of PCV2 infections is poorly understood, as is the role of the immune response in controlling or augmenting disease. (+info)