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PubMed2005

Rapid detection and characterisation of infectious bronchitis virus (IBV) from New Zealand using RT-PCR and sequence analysis.

AIMS: To develop a reverse transcriptase-polymerase chain reaction (RT-PCR) assay to detect infectious bronchitis virus (IBV) from commercially-raised poultry in New Zealand and compare results with those from virus isolation. To characterise the IBV isolates using sequence analysis. METHODS: Pooled tissue samples (trachea, kidney, caecal tonsils and cloacal swabs) from 164 broiler and 53 layer flocks located throughout New Zealand were collected in transport medium containing antibiotics. Tissues were homogenised and the resultant supernatant used directly in a RT-PCR assay, and also inoculated into the allantoic cavity of 10-day-old embryonated eggs for virus isolation. Primers for the RT-PCR were selected from an area close to the N-terminus of the S1 (spike) gene and bracketed the hypervariable region 1 (HVR 1). The RT-PCR amplimers were sequenced from both termini, and alignment was constructed and analysed. RESULTS: From the 217 field samples that were subjected to RT-PCR, 42 (19%) were positive. Twenty-nine (69%) of these RT-PCR-positive, and none of the RT-PCR-negative, samples yielded virus by isolation in chicken embryos. A phylogenetic tree constructed from these amplimers, that spanned the HVR of the S1 gene, revealed the IBV isolates clustered into two demarcated groups which had <60% homology. It is likely that the isolates of one group were derived from the live attenuated vaccine commonly used in New Zealand. CONCLUSIONS: The RT-PCR assay exhibited higher sensitivity than virus isolation and could be used for rapid diagnosis of IBV in the field. The prevalence of IBV appears to be surprisingly high in New Zealand although the use of pooled samples in the study did not allow accurate calculation of the prevalence in birds. Sequence analysis of a hypervariable region from the S1 gene was informative for the differentiation of closely-related strains.

Animals↗
PubMedDate not supplied

Molecular characterization of Spanish infectious bursal disease virus field isolates.

Nine Spanish isolates of infectious bursal disease virus (IBDV) were characterized and classified after reverse transcriptase-polymerase chain reaction of a 248-bp fragment of the VP2 gene hypervariable region and restriction fragment length polymorphism (RFLP). The restriction endonucleases (REs) used were BstNI, Sad, SspI, TaqI, DraI, and StyI. Sequencing of the amplified product and further comparison of these sequences with published sequence data from other IBDV strains were also performed. Very virulent and classic strains were identified. None of the strains identified had molecular characteristics similar to that of the American variant strains. Four very virulent strains (VG-248, 5939, 6145, and 7333) were digested by the TaqI, SspI, and StyI enzymes. The sequences of these strains were closely related to other European and Japanese very virulent IBDV (vvIBDV) strains. Strains VG-311, VG-262, and VG-208 were digested by the BstNI and Sad REs and were classified as classic strains. Strains VG-276 and VG-313 had unique RFLP patterns. VG-276 exhibited the SspI RE site, which has been reported as a characteristic of vvIBDV strains, whereas the VG-313 strain exhibited a Sad and StyI RE site indicative of the classic IBDV Edgar and 52-70 strains. However, nucleotide sequence analysis of the amplified hypervariable region strain VG-276 revealed a higher identity with the classic strains STC, 52/70, and 9109 IBDV strains, whereas strain VG-313 exhibited a higher identity with the vvIBDV strains.

Animals↗
PubMed1991

Single mutations in a gene for a tail fiber component of an Escherichia coli phage can cause an extension from a protein to a carbohydrate as a receptor.

The T-even type Escherichia coli phage Ox2 recognizes the outer membrane protein OmpA as a receptor. This recognition is accomplished by the 266 residue protein 38, which is located at the free ends of the virion's long tail fibers. Host-range mutants had been isolated in three consecutive steps: Ox2----Ox2h5----Ox2h10----Ox2h12, with Ox2h12 recognizing the outer membrane protein OmpC efficiently and having lost some affinity for OmpA. Protein 38 consists, in comparison with these proteins of other phages, of two constant and one contiguous array of four hypervariable regions; the alterations leading to Ox2h12 were all found within the latter area. Starting with Ox2h12, further host-range mutants could be isolated on strains resistant to the respective phage: Ox2h12----h12h1----h12h1.1----h12h1.11----h12 h1.111. It was found that Ox2h12h1.1 (and a derivative of Ox2h10, h10h4) probably uses, instead of OmpA or OmpC, yet another outer membrane protein, designated OmpX. Ox2h12h1.11 was obtained on a strain lacking OmpA, -C and -X. This phage could not grow on a mutant of E. coli B, possessing a lipopolysaccharide (LPS) with a defective core oligosaccharide; Ox2h12h1.111 was obtained from this strain. It turned out that the latter two mutants used LPS as a receptor, most likely via its glucose residues. Selection for resistance to them in E. coli B (ompA+, ompC-, ompX-) yielded exclusively LPS mutants, and in another strain, possessing OmpA, C and X, the majority of resistant mutants were of this type. Isolated LPS inactivated the mutant phages very well and was inactive towards Ox2h12. By recombining the genes of mutant phages into the genome of parental phages it could be shown that the phenotypes were associated with gene 38. All mutant alterations (mostly single amino acid substitutions) were found within the hypervariable regions of protein 38. In particular, a substitution leading to Ox2h12h1.11 (Arg170----Ser) had occurred at the same site that led to Ox2h10 (His170----Arg), which binds to OmpC in addition to OmpA. It is concluded that not only can protein 38 gain the ability to switch from a protein to a carbohydrate as a receptor but can do so using the same domain of the polypeptide.

Bacterial Outer Membrane Proteins↗
PubMed1993

Evidence for cobinding of self- and allopeptides to human class II major histocompatibility antigen DR1 by energy transfer.

Purified human class II major histocompatibility antigen HLA-DR1 was subjected to high-performance gel filtration with fluorescence detection to investigate simultaneous binding of two classes of peptides: the N-terminally fluoresceinated allopeptides fluorescein isothiocyanate (FITC)-conjugated DR1 beta-(66-78) and FITC-conjugated DR3 beta-(66-78), derived from the third hypervariable region of the beta chain of DR1 and DR3, respectively, and the DR1-associated self-peptide SP3, carrying the fluorophor 7-amino-4-methyl-coumarin-3-acetic acid (AMCA) at the N terminus. By analyzing the dimer-associated fluorescence signals, we measured an interpeptide energy transfer AMCA-->FITC that proved to be peptide-specific: it did not occur after replacement of the allopeptide by the DR1-restricted peptide IM-(18-29) from influenza matrix protein, whereas it was restored by SP3, due to the high homology of SP3 and allopeptide. Transfer analyses with truncated AMCA-SP3 and AMCA-IM-(18-29) are consistent with Leu-3 being a common anchor residue of both peptides that allows an interaction with the hydrophobic specifity pocket around Ala-37 of the alpha 1 domain. This interaction is mirrored by the intrinsic fluorescence of neighboring Trp-43: we found the protein-peptide transfer Trp(DR1)-->AMCA with AMCA-SP3 but with none of the allopeptides. Since each energy transfer affords close proximity of two fluorophors, the following picture emerges: self- or foreign peptides bind to the DR1 binding cleft by occupation of previously described specificity pockets. Simultaneously, allopeptides of the third hypervariable region or homologous peptides may occupy a cryptic binding site by displacing the beta 1-helix that normally lines the binding groove. Thus, the described complexes raise additional possibilities for the molecular basis of auto- or alloreactivity.

Amino Acid Sequence↗
PubMed1992

HLA-DR peptide-induced alloreactive T cell lines reveal an HLA-DR sequence that can be both "dominant" and "cryptic": evidence for allele-specific processing.

Previously, we reported on a T cell line, ThoU6, which we obtained through stimulation of DPw3+ cells with a synthetic "DR3 peptide" with a sequence identical to the third hypervariable region of the DRB1*0301 chain. This T cell line recognizes both the synthetic peptide presented by DPw3 as well as DR3+ DPw3+ stimulator cells. This implies that the synthetic DR3 peptide has a natural counterpart in DR3-positive cells. Here we describe the recognition pattern of another T cell line that was sensitized with the same synthetic DR3 peptide. This T cell line, BieU6, shows both HLA-DRw13/Dw18 (self)-restricted recognition of the synthetic DR3 peptide and allorecognition towards DR13/Dw19, a molecule which is highly homologous to Dw18, in the absence of synthetic peptide. These results suggest that the epitope formed by the Dw18 molecule plus the synthetic DR3 peptide and recognized by T cell line BieU6 mimics the Dw19 molecule. The potential role for a Dw19-specific peptide is discussed. The inability of T cell line BieU6 to recognize Dw18+ DR3+ cells indicates that, in this case, the synthetic DR3 peptide is "cryptic", i.e. does not have a natural counterpart that is effectively presented to T cells. Mapping of the shortest peptides recognized by T cell lines ThoU6 and BieU6 indicate that these sequences are fully overlapping. We, therefore, suggest that the antigen-presenting molecules, HLA-DPw3 and HLA-Dw18, differ in their accessibility for self peptides derived from the third hypervariable region of DR molecules. These observations may be explained by allele-specific processing.

Amino Acid Sequence↗
PubMed1995

The virological and histological states of anti-hepatitis C virus-positive subjects with normal liver biochemical values.

We investigated anti-hepatitis C virus (HCV) titers, HCV RNA levels in liver and serum, genetic variability in the hypervariable region of the genome, the form of the virus in the circulation, and liver histology in 21 anti-HCV-positive subjects with sustained normal liver biochemical values. Titer of anti-HCV was determined by second generation anti-HCV-passive hemagglutination assay, and HCV RNA levels were semiquantitated by reverse transcriptase polymerase chain reaction (PCR). In 19 (90%) of the 21 subjects who had a higher titer of anti-HCV (> or = 2(14)), HCV RNA was detected in both serum and liver, and histological examination showed minimal or mild chronic hepatitis in all. In the remaining 2 patients who had a lower titer of anti-HCV, HCV RNA was not detected in serum and liver, and liver histology was normal. Anti-HCV titers and HCV RNA levels in serum and liver in the 19 HCV RNA-positive subjects were compared with those levels in the 41 patients with biopsy-proven chronic hepatitis C and elevated serum aminotransferase levels as a control group. There were no significant differences in viral levels in serum and liver between the two groups. To further investigate virological differences between the two groups with regard to degree of genetic variability and the form in the circulation, we performed the PCR-single strand conformation polymorphism (PCR-SSCP) of the hypervariable region 1 and the immunoprecipitation analyses.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1995

B-cell superantigens: implications for selection of the human antibody repertoire.

For several decades, B-cell interactions with antigens were thought to occur only through a clonal activation mechanism, in which the hypervariable regions of the immunoglobulin receptor are exclusively involved in ligand binding. However, an additional mode of interaction can occur, whereby molecules, termed B-cell superantigens, can bind human B cells bearing immunoglobulin receptors of a given variable (V)-gene family. This mechanism requires contributions from regions outside the conventional hypervariable loops and results in a B-cell response of increased magnitude. Here, Moncef Zouali reviews recent in vitro and in vivo observations on human B-cell superantigens in the context of the current consensus of B-cell development, and discusses the implications of these novel concepts with respect to pathogenesis.

Antibody Diversity↗
PubMed1996

Nosocomial transmission of hepatitis C virus in haemodialysis patients.

A systematic virological follow-up of 114 haemodialysis patients treated in the same unit showed that 37, including 17 PCR positive patients, were seropositive for hepatitis C virus (HCV). Type 1b HCV was detected in 10 patients and was much more frequent in this population than in the whole population of patients treated in the hepatogastroenterology departments in southeastern France. The E1/E2 genomic region of seven type 1b HCV strains was sequenced. In four patients, a similar strain was detected in both the E1 variable region and the E2 hypervariable region (HVR1). In addition, two of these four patients were seronegative and PCR negative at the beginning of the study and had not been transfused or transplanted during this period. A phylogenetic tree was drawn which confirmed that these strains were very similar and showed that HCV was transmitted via the nosocomial pathway in this haemodialysis unit.

Adolescent↗
PubMed2005

Land, language, and loci: mtDNA in Native Americans and the genetic history of Peru.

Despite a long history of complex societies and despite extensive present-day linguistic and ethnic diversity, relatively few populations in Peru have been sampled for population genetic investigations. In order to address questions about the relationships between South American populations and about the extent of correlation between genetic distance, language, and geography in the region, mitochondrial DNA (mtDNA) hypervariable region I sequences and mtDNA haplogroup markers were examined in 33 individuals from the state of Ancash, Peru. These sequences were compared to those from 19 American Indian populations using diversity estimates, AMOVA tests, mismatch distributions, a multidimensional scaling plot, and regressions. The results show correlations between genetics, linguistics, and geographical affinities, with stronger correlations between genetics and language. Additionally, the results suggest a pattern of differential gene flow and drift in western vs. eastern South America, supporting previous mtDNA and Y chromosome investigations.

Analysis of Variance↗
PubMed1993

Sequence analysis of putative structural regions of hepatitis C virus isolated from 5 Japanese patients with hepatocellular carcinoma.

The nucleotide sequences of the 5'-portion of the HCV genome, consisting of 2672 nucleotides, were determined by analysis of clones derived from 5 different patients with liver cirrhosis and hepatocellular carcinoma. Comparison of 5 genomes and 8 isolates already reported demonstrated the significant genome diversity in the structural regions. Genetic divergence was outstanding in the envelope regions (E1 and NS1/E2, > 59.7% identity) in contrast to the sequence conservation of the 5' non-coding (> 93.8% identity) or core regions (> 82.0% identity). Although hypervariable regions were found in the NS1/E2 region as reported, hydropathicity was maintained for all clones, reflecting the biological functions of these regions.

Amino Acid Sequence↗
PubMed2003

Hypervariable spacer regions are good sites for developing specific PCR-RFLP markers and PCR primers for screening actinorhizal symbionts.

While the ribosomal RNA like highly conserved genes are good molecular chronometers for establishing phylogenetic relationships, they can also be useful in securing the amplification of adjoining hyper-variable regions. These regions can then be used for developing specific PCR primers or PCR-RFL profiles to be used as molecular markers. We report here the use of ITS region of rrn operon of Frankia for developing PCR-RFL profiles capable of discriminating between closely related frankiae. We have also made use of the ITS1 region of the nuclear rrn operon of Alnus nepalensis (D Don) for designing a PCR primer for specific amplification of nuclear DNA of this tree.

Alnus↗
PubMed2003

Sequence polymorphism of the mitochondrial DNA control region in the Slovenian population.

The forensic application of mitochondrial DNA (mtDNA) typing requires large and regionally well-defined databases. To expand the database for forensic identification purposes in Slovenia, the mtDNA control region sequences of the hypervariable regions HVI and HVII were determined in a population of 129 maternally unrelated Slovenians, using a fluorescent-based capillary electrophoresis sequencing method. A total of 111 different haplotypes resulting from 124 polymorphic positions (80 polymorphic positions in HVI and 44 in HVII) were found. Of these, 101 mtDNA types were unique, 6 haplotypes were shared by 2 individuals, 1 haplotype by 3 individuals, 2 haplotypes by 4 individuals, and the most common haplotype was found in 5 individuals. The most frequent haplotypes in the Slovenian population,263(G), 315.1(C) and 263(G), 309.1(C), 315.1(C) are also the most common in other European populations. The data support the concept that these haplotypes may represent a common European mtDNA sequence types. The sequence poymorphisms were compared to the databases of west Austria and central Italy and the HVI and HVII sequence matching probabilities within and between populations were calculated. It is 1.1-4.5 times more likely to find a sequence match in a random pair of Slovenians than in a random Slovenian-Italian pair and in a random Slovenian-Austrian pair. The length heteroplasmy in the homopolymeric C-stretch regions located at nucleotide positions 16184-16193 in HVI and at positions 303-315 in HVII was observed in 17% and 8% of individuals, respectively. A statistical estimate of the results for this population showed the random match probability and the genetic diversity of 1.16% and 0.996, respectively.

Austria↗
PubMed1995

Retrospective investigation of hematopoietic chimerism after BMT by PCR amplification of hypervariable DNA regions.

We report on nine patients submitted to BMT with sex-matched donors and investigated by means of PCR amplification of the VNTRs ApoB, D1S80, DXS52, and D17S5. In all cases it was possible to detect a polymorphism able to distinguish between donor and patient cells, thus allowing us to recognize the presence of complete or mixed chimerism. In eight patients PCR analysis showed a complete chimerism during the entire follow-up. Only one of these patients relapsed, while the others are alive and without any sign of relapse 56.2 months (mean) after BMT. Mixed chimerism was detected in only one patient, who relapsed 3 months after this finding. These results confirm the usefulness of the study of PCR-amplified VNTRs in the assessment of marrow engraftment after BMT, mostly in sex-matched transplants where, in the absence of specific chromosome rearrangements, cytogenetic or FISH analysis cannot be used.

Adolescent↗
PubMed2004

The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.

Clinical Laboratory Techniques↗
PubMed1997

Genetic and antigenic heterogeneity among feline calicivirus isolates from distinct disease manifestations.

The capsid protein genes of five feline calicivirus (FCV) isolates associated with different disease manifestations were cloned and sequenced. The viruses represented two recent isolates from cats with chronic stomatitis, one recent isolate from a cat with acute stomatitis, one recent isolate each from a cat with acute respiratory symptoms and the classical limping syndrome strain FCV-2280. The amino acid sequences were compared with eight other published sequences and analyzed for their relationships. Phylogenetic analysis of the complete capsid protein sequences or of known antigenic regions of that protein (hypervariable regions A and E) did not group the isolates of different disease manifestations in distinct subclusters. Monoclonal antibodies (MAbs) generated against either a chronic stomatitis isolate or a recent isolate associated with respiratory symptoms were tested against a panel of 11 recent isolates and four "classical' FCV strains, covering all known disease associations. With those MAbs no obvious clustering with respect to disease manifestation could be seen. Four specific sera prepared in rabbits against our prototype isolates also failed to cluster those isolates according to the disease manifestations when examined in neutralization tests. From these antigenic and genetic analyses of the capsid protein the hypothesis of the existence of biotypes of FCV responsible for distinct disease manifestations could not be confirmed.

Acute Disease↗
PubMed1999

Four genotypic variants of a Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) are distinguishable by a hypervariable genomic region.

Four genotypes named SP2A, SP2B, SP2C and SP2D were obtained in vivo by infecting S. exigua larvae with limiting dilutions of the Spanish field isolate Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) of SeMNPV. The cloning of variants SP2A, SP2B and SP2C took 1, 6, and 3 passages, respectively, before the DNA profiles showed all bands in equimolar concentrations, and they remained constant for at least six further passages indicating the stability of their genotypes. The SP2D variant isolation took over ten passages and it was genetically less stable. Physical maps of their genomes were constructed for the restriction enzymes BamHI, BglII, PstI, and XbaI. The region between 8-10 m.u. was highly variable and characteristic of each cloned genotype and, hence, can be used as RFLP markers for all four genotypic variants. This region, included in the PstI-MB fragment, was cloned and sequenced showing that all the Se-SP2 variants contained a homologous region (hr) with a variable number of 98 bp sequences tandemly repeated, which were used to distinguish genotypic variants from each other. The biological activity of the genotypic variants SP2A, SP2B, and SP2C when compared in terms of LD50 and LT50, were not significantly different. However, the SP2D genotypic variant was found to be significantly less infective (higher LD50). The emergence of new genotypes in the Se-SP2 field populations is discussed.

Animals↗
PubMed2000

Diversity of hepatitis G virus within a single infected individual.

The extent of population diversity among GB virus C (GBV-C)/hepatitis G virus (HGV) within a persistently infected individual (Iw) was investigated by sequence analysis of multiple clones generated from polymerase chain reaction (PCR)-amplified products of cDNA analogous to fragments of 5' non-coding region (5'NC), envelope region 1/2 (E1/E2) and non-structural region 3 (NS3) of viral genome. Although nucleotide substitutions were more common in coding regions than in the 5'NC region, there was no region corresponding to the hypervariable region of hepatitis C virus in the E1/E2 region. Transition substitution exceeded transversion by 7 to 12-fold, and 79.4% of substitutions were synonymous. This bias against substitutions producing amino acid replacements and the use of Pfu DNA polymerase with an error rate 10 times lower than the observed frequency of substitution, suggests that most substitutions were not artefactual. This data suggests that individual genomes of HGV within an infected individual may differ from each other at 0.23-0.84% nucleotide position and at 0.42-0.61% amino acid position.

Base Sequence↗
PubMedDate not supplied

Hypervariable 'minisatellite' regions in human DNA.

The human genome contains many dispersed tandem-repetitive 'minisatellite' regions detected via a shared 10-15-base pair 'core' sequence similar to the generalized recombination signal (chi) of Escherichia coli. Many minisatellites are highly polymorphic due to allelic variation in repeat copy number in the minisatellite. A probe based on a tandem-repeat of the core sequence can detect many highly variable loci simultaneously and can provide an individual-specific DNA 'fingerprint' of general use in human genetic analysis.

Alleles↗