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PubMed2006

Differences in clinical severity between genotype A and genotype B human metapneumovirus infection in children.

The clinical spectrum of 69 episodes of metapneumovirus pediatric infection (55 episodes caused by genotype A and 14 episodes caused by genotype B) was analyzed. Diagnosis of pneumonia was more common and the illness severity index (determined on the basis of need for hospitalization, oxygen saturation <90%, and intensive care unit stay) was higher for patients with metapneumovirus genotype A infection.

Child, Preschool↗
PubMed1996

Relationship of genotype to phenotype in fibroblast-derived transmitochondrial cell lines carrying the 3243 mutation associated with the MELAS encephalomyopathy: shift towards mutant genotype and role of mtDNA copy number.

Transmitochondrial cell lines were isolated by fusing mtDNA-less rho degrees 206 cells with enucleated fibroblasts derived from four members of a pedigree carrying in their muscle varying proportions of the mutation at position 3243 in the tRNA(Leu(UUR)) gene associated with the MELAS encephalomyopathy. The mitochondrial transformants derived from an asymptomatic individual were all homoplasmic for wild-type mtDNA. The proportion of wild-type transformants derived from clinically affected members of the pedigree appeared to decrease in correspondence with an increase in severity of the clinical symptoms of the cell donor. Furthermore, the average proportion of wild-type mtDNA in the transformants derived from each member of the pedigree was very similar to that found in mtDNA from the fibroblasts of that individual, suggesting that the distribution of genotypes in the transformants reflected fairly closely that in the fibroblasts. The genotype and phenotype of ten transformants derived from one severely affected individual were investigated during continuous culture up to 17-24 weeks after the transformation step. Six heteroplasmic clones showed a progressive increase in the proportion of mutant mtDNA, whereas the mitochondrial genotype remained constant in four clones apparently homoplasmic for wild-type mtDNA or nearly homoplasmic for mutant mtDNA. An analysis of the rate of repopulation of rho degrees 206 cells with fibroblast-derived mtDNA revealed a large variability among different transformants, with the full re-establishment of the control ratio of mtDNA to nuclear DNA being observed between approximately 6 weeks and more than 22 weeks after the transformation step. An increase in rate of O2 consumption generally accompanied the increase in mtDNA copy number of the transformants, pointing to the important role of the mtDNA copy number in determining the phenotype of a cell. The observation that a very small amount of wild-type mtDNA (2 to 5% of the control level), coexisting with strongly predominant mutant mtDNA, conferred upon the transformants a substantial respiratory capacity (50% or more) and the evidence of proportionality between O2 consumption rate and mtDNA copy number, which occurred at widely different mutant to wild-type mtDNA ratios, strongly suggest a contribution of the mutant mtDNA to the cell respiratory competence.

Cell Line↗
PubMed1996

Hepatitis B virus (HBV)/hepatitis D virus (HDV) coinfection in outbreaks of acute hepatitis in the Peruvian Amazon basin: the roles of HDV genotype III and HBV genotype F.

Recurring outbreaks of acute hepatitis have been a significant cause of morbidity and mortality among Peruvian military personnel stationed in the Amazon Basin region of Peru. The role of hepatitis B virus (HBV) and hepatitis D virus (HDV) infection was investigated as the possible cause of acute hepatitis among 88 military patients stationed at four different jungle outposts during 1992-1993. Analysis of serum markers indicated that 95% (84/88) had evidence of acute HBV infection; 64% (54/84) were also infected with HDV. Genetic analysis of PCR-amplified HDV and HBV fragments showed exclusively HDV genotype III and HBV genotype F. Furthermore, HDV RNA sequences were similar among patients from the same outpost but different from those at other jungle locations. The data suggested focal sources of HDV infection in the jungle environment of the outposts and, further, confirmed the unique association of HDV genotype III with severe cases of human disease in northern South America.

Acute Disease↗
PubMed2000

Angiotensin-converting enzyme DD genotype, angiotensin type 1 receptor CC genotype, and hyperhomocysteinemia increase first-trimester fetal-loss susceptibility.

Complications of pregnancy have been found to be related with thrombophilic polymorphisms that explain about 30% of obstetric complications. We evaluated the angiotensin converting enzyme (ACE) and the angiotensin type 1 receptor (AT1R) gene polymorphisms in the renin-angiotensin system (RAS) as possible risk factors for fetal loss. Fifty-nine women with a history of three or more first-trimester fetal losses and 70 healthy women with a history of normal pregnancies were enrolled in this study. Thrombophilic factors, ACE insertion/deletion (I/D) and AT1R A1166C polymorphisms, prothrombin G20210A and factor V Leiden mutations were analyzed. At univariate and multivariate analysis, a significant association between ACE DD and AT1R CC genotype and fetal loss was observed. The effect of the ACE DD genotype on the risk of fetal loss was higher in AT1R C allele carriers. The prevalence of hyperhomocysteinemia (Hcy) (defined as baseline plasma levels higher than the 95% percentile; cut-off, 10.5 micromol/l per l) was significantly higher in women with fetal loss, and an association between Hcy and fetal loss was detected. All patients showed normal antithrombin, protein C, protein S, and plasminogen activator inhibitor-1 (PAI-1) values. The presence of one risk factor not associated with others was found in 33 out of 59 patients (56%); ACE DD genotype was the most prevalent risk factor. Our results identify new possible predictive markers for fetal loss in RAS polymorphisms and Hcy. Large-scale studies are warranted to attribute clinical relevance to these polymorphisms as risk factors for complicated pregnancies.

Adult↗
PubMed2000

Characterization of the glutathione S-transferase GSTT1 deletion: discrimination of all genotypes by polymerase chain reaction indicates a trimodular genotype-phenotype correlation.

Glutathione S-transferase theta enzyme activity involved in the metabolism of toxic compounds is absent in approximately 20% of Caucasians due to a homozygous deletion of GSTT1 (*0/0). Because the exact manner of the GSTT1 deletion was unknown, current genotyping of GSTT1 was limited to detect the presence versus complete absence of the gene by a GSTT1-specific polymerase chain reaction (PCR). Thus, heterozygous (*A/0) and homozygous (*A/A) samples could not be discriminated. We have characterized the boundaries of the deletion of the human glutathione S-transferase theta (GSTT1) gene: PCR mapping and sequencing revealed a 54251 bp fragment including GSTT1 to be deleted from chromosome 22, most likely by a homologous recombination event between two highly homologous sequence stretches that flank GSTT1. Based on the knowledge of the GSTT1*0 region, a PCR assay was devised for unambiguous discrimination of homozygously deleted (*0/0), heterozygously (*A/0) and homozygously GSTT1 carrying (*A/A) individuals. Genotyping of 180 samples of a Caucasian population revealed that the deletion consists of one defined allele, whose distribution in the population fits the Hardy-Weinberg equilibrium with observed 20% *0/0, 46% *A/0 and 34% *A/A individuals. The number of GSTT1*A alleles detected by this procedure correlated highly significant with the enzyme activity in erythrocytes. Genotype-phenotype comparisons demonstrated a codominant type of inheritance by a gene-dose effect: samples with two active alleles expressed a statistically significant higher enzymatic activity compared to those with one null allele (P < 0.0001, ANOVA).

Base Sequence↗
PubMed2002

Hepatitis C flare due to superinfection by genotype 4 in an HCV genotype 1b chronic carrier.

We report here on a patient affected by chronic hepatitis C who developed acute hepatitis C virus (HCV) superinfection with replacement of genotype 1b by genotype 4. The history revealed no risk factors for a new exposure to HCV, with the exception of colonoscopy with mucosal biopsy performed about 3 months before. This report underlines the absence of an effective immune-mediated cross-protection against different HCV genotypes. Moreover, the possible relationship between HCV infection and colonoscopy points out the importance of strict adherence to international guidelines for disinfection and cleaning of invasive diagnostic tools for all subjects examined, including HCV chronic carriers.

Adult↗
PubMed2006

Analysis of human and swine hepatitis E virus (HEV) isolates of genotype 3 in Japan that are only 81-83 % similar to reported HEV isolates of the same genotype over the entire genome.

Full-length sequences were determined for a human hepatitis E virus (HEV) isolate (HE-JA04-1911) and two swine HEV isolates (swJ8-5 and swJ12-4) that belong to one of three clusters within genotype 3 in Japan and are close to Spanish isolates according to their partial sequences. The three HEV isolates were 89.7-92.9 % identical to each other, but only 80.7-83.0 % similar to 21 HEV strains of the same genotype isolated in Canada, Kyrgyzstan, the USA and Japan over their entire genome. On comparison with HEV isolates whose partial sequence is known, the HE-JA04-1911, swJ8-5 and swJ12-4 isolates segregated into a phylogenetic cluster consisting of human and swine HEV isolates in Japan and the UK, with identities of 89.8-100 % and 87.9-92.4 %, respectively. Genotype 3 HEV isolates were found to be markedly heterogeneous. The UK-isolate-like HEV strains in Japan may have originated from the UK via the importation of pigs since 1900.

Animals↗
PubMed2006

Diversity in Indian equine rotaviruses: identification of genotype G10,P6[1] and G1 strains and a new VP7 genotype (G16) strain in specimens from diarrheic foals in India.

Rotaviruses causing severe diarrhea in foals in two organized farms in northern India, during the period from 2003 to 2005, were characterized by electropherotyping, serotyping, and sequence analysis of the genes encoding the outer capsid proteins. Of 137 specimens, 47 (34.31%) were positive for rotavirus and exhibited at least five different electropherotypes (E), E1 to E5. Strains belonging to different electropherotypes exhibited either a different serotype/genotype specificity or a lack of reactivity to typing monoclonal antibodies (MAbs) used in this study. Strains belonging to E1, E2, and E5 exhibited genotype G10,P6[1], G3, and G1 specificities and accounted for 19.0, 42.9, and 9.5% of the isolates, respectively. Though they possessed G10-type VP7, the E1 strains exhibited high reactivity with the G6-specific MAb, suggesting that the uncommon combination of the outer capsid proteins altered the specificity of the conformation-dependent antigenic epitopes on VP7. E3 and E4 strains accounted for 28.6% of the isolates and were untypeable. Sequence analysis of VP7 from E4 strains (Erv92 and Erv99) revealed that they represent a new VP7 genotype, G16. The detection of unexpected bovine rotavirus-derived G10,P6[1] reassortants, G1 serotype strains, and a new genotype (G16) strain in two distant farms reveals an interesting epidemiological situation and diversity of equine rotaviruses in India.

Amino Acid Sequence↗
PubMed2003

Hepatitis B virus genotype C takes a more aggressive disease course than hepatitis B virus genotype B in hepatitis B e antigen-positive patients.

One hundred forty-six hepatitis B e antigen (HBeAg)-positive chronic hepatitis B patients were followed up for 32 +/- 13 months. All six patients with hepatocellular carcinoma had hepatitis B virus (HBV) genotype C. Disease activity was greater in patients infected by HBV genotype C than in those infected by HBV genotype B in the HBeAg-positive phase but not after HBeAg seroconversion.

Adult↗
PubMed2000

The glutathione S-transferase-mu and -theta genotypes in the etiology of prostate cancer: genotype-environment interactions with smoking.

It has been reported that individuals who express GSTT1, the gene coding for the theta class of the glutathione S-transferases (GSTs), have an elevated risk of prostate cancer (CaP). This result is supported by studies that show glutathione conjugation of some xenobiotics by the GSTs can produce mutagenic intermediates. However, the potential role of environmental factors in modifying the risk of CaP conferred by GSTT1 is not known. We investigated whether there was an interaction between smoking and the non-deleted genotypes of the mu (GSTM1) and theta (GSTT1) GST genes using a clinic-based study of 276 CaP cases and 499 controls. We observed no main effect of smoking (odds ratio, 0.95; confidence interval, 0.69-1.29) or GSTM1 (odds ratio, 1.00; confidence interval, 0.73-1.36) with CaP, but did observe a statistically significant main effect of GSTT1 with CaP (odds ratio, 1.61; confidence interval, 1.14-2.28) as reported previously. No interaction between smoking and GSTM1 was observed. A significant increase in the probability of having CaP was observed in men who were both smokers and carried a non-deleted GSTT1 genotype compared with men who had neither or only one of these risk factors (P = 0.049). Approximately 30.9% of CaP cases in this study could be attributed to the smoking x GSTT1 interaction. Whereas the mechanism of this interaction is not known, it is plausible that the metabolism of carcinogenic intermediates or the response to chronic inflammation associated with smoking may be modulated by the GSTT1 genotype and may modify CaP risk.

Adult↗
PubMedDate not supplied

[Detection of the genotypic heterogeneity of Ixodes persulcatus Schulze (Acari: Ixodidae) of the North-West region of Russia and characteristics of distribution of tick-borne pathogens causing Lyme disease and Ehrlichia infections in various genotypes].

The heterogeneity of the Ixodes persulcatus population in the vicinity of Saint Petersburg was estimated by using malate dehydrogenase (MDH) isoenzyme. There are six MDH genotypes carrying 3 alleles in the Ixodes persulcatus population. The prevalence of Borrelia and Ehrlichia species in the study genotypes was analyzed. There was a difference in the prevalence and intensity of infection. The greatest abundance of Borrelia was described in the genotypes to Genogroup 1 (with allele 1). Among them, heterozygous ticks were most intensively infected. Polymerase chain reaction identified species pathogenic for man. These included 3 species of Borrelia: B. afzelii, B. garinii, and B. burgdorferi sensu stricto and 2 species of Ehrlichia muris and HGE agent. The author are the first to describe HGE agent and B. burgdorfei ss encountered in Russia.

Animals↗
PubMed1994

A study on ADH2 and ALDH2 genotyping by PCR-RFLP and SSCP analyses with description of allele and genotype frequencies in Japanese, Finn and Lapp populations.

Genetic polymorphisms of the alcohol dehydrogenase ADH2 and aldehyde dehydrogenase ALDH2 genes were investigated in Japanese, Finn, and Lapp populations by using PCR-RFLP and SSCP analyses. The ALDH2 genotypes were unequivocally determined by a PCR-RFLP assay with a mismatched primer. The determination of the ADH2 genotypes, however, was found to be problematic in PCR with the reported oligonucleotide primer sets because there are high homologies among the ADHl, ADH2, and ADH3 gene sequences. The problem of the heterozygote excess in typing results obtained by using the previously reported PCR-RFLP methods was resolved by nested PCR, in which an internal primer set reamplified the ADH2 sequence selectively from a mixture of the ADH gene sequences amplified in the first PCR amplification of genomic DNA samples as templates. A newly designed primer pair with longer sequences and single 3' end mismatches was later found to achieve a predominant amplification of the ADH2 sequence in a single PCR. RFLP and SSCP analyses of PCR products with the new primer set gave results fully consistent with those by nested PCR. Thus, the ADH2 genotypes defined in this study were free from any typing errors. The ADH2 and ALDH2 allele frequencies observed in this study were found not to be biased significantly from those reported previously from Japanese populations, and these were monomorphic for Lapp and Finn populations.

Alcohol Dehydrogenase↗
PubMed1998

Evaluation of the GTI-ASP-1 platelet antigen genotyping kit for the determination of the HPA-1 genotype.

The human platelet antigen system HPA-1 is involved in most cases of neonatal alloimmune thrombocytopenia and posttransfusion purpura, and occasionally causes refractoriness to platelet transfusions. Complete concordance was obtained in genotyping for HPA-1 in all samples tested with the HPA-1 genotyping kit and a ligation-based typing method. However, the genotyping kit is less sensitive than ligation- based typing, which could be of importance when testing cells from amnionic fluid or from chorionic villi.

Journal Article↗
PubMed1991

Two French genotypes of hepatitis C virus: homology of the predominant genotype with the prototype American strain.

A hepatitis C virus (HCV) cDNA covering part of the nonstructural region, NS3, was amplified from the serum of 50 out of 76 French non-A, non-B hepatitis patients by the nested polymerase chain reaction (PCR). Determination of a 407-bp sequence from four such cases revealed the presence of two different virus genotypes, F1 and F2, which exhibited 19-20% sequence divergence. F1 was represented by three of the four isolates and showed a sequence homology of about 97.5% to the prototype American HCV isolate, but of only 79% to a reported Japanese isolate. In contrast, F2 had 91.6% homology to the Japanese isolate, but only 81% homology to the prototype American HCV. PCR products from the 50 samples were hybridized with labeled F1 and F2 fragments under stringent conditions; results indicated the F1-related strain(s) as the major HCV genotype. Furthermore, a total of 1477 bp of sequence has been determined for one of the isolates belonging to the F1 category. These results will have implications for the PCR detection of HCV infection and production of HCV vaccines, especially for European countries.

Americas↗
PubMed2006

Up-regulation of fatty acid synthase promoter by hepatitis C virus core protein: genotype-3a core has a stronger effect than genotype-1b core.

BACKGROUND/AIMS: Hepatitis C virus genotype-3a (HCV-3a) is directly linked to steatosis development. We studied the effects of HCV-3a core protein on the promoter activity of fatty acid synthase (FAS), a major enzyme involved in de novo lipid synthesis. METHODS AND RESULTS: HCV-3a and -1b core genes were cloned and expressed. Using a FAS promoter-luciferase reporter, we demonstrated that both HCV-3a and -1b core proteins up-regulated the FAS promoter. However, HCV-3a core protein expression induced significantly higher FAS promoter activity than HCV-1b core. We further showed that FAS up-regulation by HCV core was dependent on transcription factor sterol response element binding protein-1. Mutational analysis showed that processing of HCV core protein of different genotypes was differentially involved in FAS promoter up-regulation. Although lipid droplet localization of HCV core protein was not important for FAS up-regulation, a specific amino acid residue (Phe(164)) within the FATG lipid droplet localization sequence of HCV-3a core protein played a major role in the stronger FAS activation by HCV-3a core. CONCLUSIONS: The stronger effect of HCV-3a core protein on FAS activation in comparison to HCV-1b core could contribute to the higher prevalence and severity of steatosis in HCV-3a infections.

Amino Acid Sequence↗
PubMed2006

Genotyping of pathogenic Acanthamoebae isolated from clinical samples in Greece--report of a clinical isolate presenting T5 genotype.

Amoebae belonging to the genus Acanthamoeba are potentially pathogenic to humans, causing mainly amoebic keratitis. Pathogenic ability of the 15 known Acanthamoeba genotypes is under investigation. We report that four out of five cases of amoebic keratitis studied in Greece, present T4 sequence type, while the remaining one presents T5 sequence type (Acanthamoeba lenticulata), which is the second most frequent genotype found among environmental samples. Thus, it is confirmed, for the first time to our knowledge, that A. lenticulata can cause keratitis. However the reason that it is under represented in clinical samples compared to environmental ones is unknown.

Acanthamoeba↗
PubMed1997

Development of a simple restriction fragment length polymorphism (RFLP) based assay for HCV genotyping and comparative analysis with genotyping and serotyping tests.

The distribution between the different hepatitis C virus genotypes and subtypes has potentially important clinical and epidemiological implications. With this view a simple restriction fragment length polymorphism (RFLP) based assay was developed to identify the three major genotypes, 1, 2 and 3 and distinguish subtype 1a from 1b. This RFLP test uses a combination of three restriction endonuclease digestions, BstN1, BstU1 and Sau3a, respectively. Comparison with a 5'UTR based assay (LiPA), showed a 98% concordance with the RFLP based assay. In addition, good concordance is shown between these data and those obtained with a serological assay based on NS4 peptides.

Antibody Specificity↗