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PubMed2002

Localized distribution of human papillomavirus genotypes in the uterine cervix.

INTRODUCTION: The localization and distribution of single or multiple HPV genotypes in the uterine cervix has not been studied thus far. The present study was undertaken to determine whether single or multiple HPV genotypes detected in cervical smears originate from a single (dysplastic) area, or from different areas (dysplastic or normal) of the uterine cervix. METHODS: Of eight patients with moderate or severe dysplasia, 31 colposcopically guided biopsies of different dysplastic lesions of the uterine cervix, as well as of normal epithelium were investigated. A highly sensitive, broad spectrum, short fragment polymerase chain reaction (SPF-10 PCR) HPV detection method in combination with a line probe assay (LiPA) for simultaneous genotyping was used. RESULTS: In the uterine cervix of four of the eight patients, multiple HPV genotypes were detected. These multiple HPV genotypes were detected in different biopsies as well as within a single biopsy. In three patients, all with carcinoma in situ or microinvasive carcinoma, only a single HPV genotype, HPV 16, was found all over the cervix including in the normal epithelium. CONCLUSION: Different HPV genotypes can be detected in different dysplastic lesions as well as within single lesions, especially in patients with severe dysplasia. The severity of the lesion may possibly have a relation with the distribution of the HPV genotypes. The low number of patients and biopsies does not allow definite conclusions. However, the impact of these findings on the outcome of screening and vaccination programs remains to be elucidated.

Adult↗
PubMed2002

[Genotyping study of hepatitis B virus in its intrauterine transmission].

OBJECTIVE: To study the characteristics of intrauterine transmission of hepatitis B virus (HBV) of different genotypes from mother to the newborn babies. METHODS: One hundred and thirty-five HBsAg-positive pregnant women from 3 hospitals in Guangzhou municipality and their 139 newborn babies were enrolled in this study. Peripheral blood samples were collected from both the mothers before delivery and the neonates within 3 d after birth, and during the follow-up survey, sampling was also performed in some of the newborn babies. Nested-PCR was employed for the amplification of the S region of HBV genome, the product of which was subjected to digestion with restriction endonuclease to compare the restriction fragments length polymorphism (RFLP) to determine the HBV genotype. Direct sequence analysis was conducted and the results compared with the sequences available in Genebank. RESULTS: HBV infection occurred in 7 (5.0%) neonates through intrauterine transmission, among whom 3 were identified as being infected with C genotype, 3 with B genotype and 1 with D genotype, all identical to the genotypes afflicting their mothers. All of the 7 mothers and the babies were asymptomatic. CONCLUSION: C and B genotypes are predominant in intrauterine transmission of HBV in Guangzhou, and base mutation, rather than mutation at the endonuclease digestion site, may take place during intrauterine transmission due to impact of the immune system. The genotyping results, however, can not help make prognostic assessment of the infected babies.

DNA, Viral↗
PubMedDate not supplied

Clinical characteristics and gB genotype of cytomegalovirus infection in Japan.

To investigate the role of cytomegalovirus (CMV) gB genotypes, we examined the relationship between gB genotypes and clinical features in 19 patients with CMV infection. We analyzed 9 immunocompetent patients (1A) and 5 patients (1B) with various basic disorders in the symptomatic group. Five patients were enrolled in the asymptomatic group (2). To investigate gB genotypes, PCR was performed with oligonucleotide primers using clinical specimens and PCR products were digested with HinfI and RsaI We determined the PCR genotype by using restriction fragment length polymorphism (RFLP) analysis patterns. In the symptomatic group (1A and 1B), all clinical specimens were identified as gB genotype 1. In the asymptomatic group (2), only 2 specimens were identified as gB genotype 3. The distribution of CMV gB genotypes in clinical specimens was as follows: gB 1-17 out of 19 (89.5%) and gB 3-2 out of 19 (10.5%). Our data revealed that gB genotype 3 CMV did not show symptomatic infection.

Adolescent↗
PubMed2003

[Relationship between the genotypes of hepatitis B virus and the severity of liver diseases].

OBJECTIVE: To investigate the relationship between different genotypes of hepatitis B virus (HBV) and the severity of liver diseases. METHODS: The S nucleotide sequences of HBV strains isolated from plasma samples of 284 patients were detected and compared. Among them, 87 patients were HBV asymptomatic carriers (ASC), 157 chronic hepatitis B (CHB), 22 liver cirrhosis (LC), and 18 hepatocellular carcinoma (HCC). RESULTS: Genotypes B and C were predominant, with a 26.1% proportion and a 63.2% proportion respectively. The percentage of genotypes B and C in patients with ASC, CHB, LC, and HCC were significantly different (x(2)=15.09, P<0.001). Compared with genotype B, genotype C was more common in patients with CHB and HCC (59.6% vs 43.2%, chi(2)=10.87, P<0.001; 7.7% vs 1.4%, x(2)=7.41, P<0.001), but in patients with LC there was no different (7.7% vs 8.1%, chi(2)=1.29, P>0.05). CONCLUSION: This study suggests that genotype B and C are predominant. And genotype C may induce more severe the liver inflammation than genotype B may do.

Adult↗
PubMedDate not supplied

BB genotype of the vitamin D receptor gene polymorphism postpones parathyroidectomy in hemodialysis patients.

BACKGROUND: Bsml vitamin D receptor (VDR) gene polymorphism has been reported to influence the progression of secondary hyperparathyroidism but it is not known how much the genetic background contributes to the need for parathyroidectomy (PTx). We investigated the influence of VDR gene polymorphism on PTx in patients with different dialysis vintage. METHODS: We studied 121 parathyroidectomized HD patients ("PTx " group). Patients who had required early parathyroidectomy ("early PTx" group) or late parathyroidectomy ("late PTx" group) were analyzed separately. The cut-off point between these two groups was 89 months (mean time on hemodialysis (HD) before parathyroidectomy). Serum intact parathyroid hormone, calcium, phosphorus and alkaline phosphatase were measured. Bsml genotypes were analyzed by polymerase chain reaction. Statistical analysis was done with univariant analysis of variance (ANOVA) to compare the genotype groups and general factorial ANOVA, entering time on HD as the dependent variable, with genotype, sex, age and chronic renal failure (CRF) etiology as factors. As a control group for the association studies we determined genotypic frequencies in 162 HD patients ("total HD" group), and in a healthy control population of 120 individuals ("healthy" group), tested by contingency table analysis and the chi-square test. RESULTS: No significant differences were found between the genotypes except for the time on HD. General factorial ANOVA showed that the adjusted means of the time on HD were significantly different for the various genotypes (p = 0.015). The BB genotype was significantly less frequent in the "early PTx " group than in the "total HD" and "late PTx" groups. CONCLUSIONS: Individuals with the BB genotype can remain longer on HD before they need parathyroidectomy.

Adult↗
PubMed2003

[Hepatitis B virus genotypes and the heterogeneity of its polymerase gene].

OBJECTIVE: To study the heterogeneity of polymerase gene (P gene) within hepatitis B virus (HBV) genotypes based on a systematic analysis of 202 HBV P genes, providing some useful references for further studies on the relationship among HBV genotypes, P gene mutations, replication and nucleoside analogues drug-resistance. METHODS: 202 HBV complete sequences containing P genes were obtained from GenBank and were analysed using computer softwares. RESULTS: There were some genotype-related characteristics of HBV P genes. As reverse transcriptase domain was concerned, there were more amino acid divergences in genotype C and D compared with these in genotype A. There were also amino acid substitutions in the A-F conserved regions of the reverse transcriptase domain within and between HBV genotypes. CONCLUSIONS: There are divergences of P genes and amino acids within and between HBV genotypes, which should be considered when amino acid changes are analyzed whether they are proposed to be drug-resistance mutations or the results from quasispecies-selected. Moreover, these divergences may affect the antiviral effect of nucleoside analogues on HBV with different genotypes.

Amino Acid Sequence↗
PubMed2002

Geographical distribution of hepatitis C virus genotypes in India.

HCV isolates from around the world show substantial nucleotide sequence variability throughout the viral genome. Based on the identification of these genome differences various genotypes and subtypes have been described from different geographical regions. They have been tentatively classified into six major genotypes and more than 30 subtypes, but new subtypes are continually being discovered. In recent years, substantial evidence has emerged indicating that typing and subtyping for HCV is clinically important. The present study aims at determining and comparing the prevalence of different genotypes from different parts of India (North, South, East and West). A total of 153 samples representing different regions have been genotyped in our lab. Our studies document a high prevalence of genotype 3 (> 76%) and very low prevalence of genotype 2 (< 2%), as a whole. However, genotype 3a has been found to be the highest (50%) with a decreased frequency of approximately 25% in the case of 3b, approximately 14% in 1b and approximately 10% in 1a, whereas a minimal number (approximately 4%) of genotype 4 has been found only in Southern and Western India.

Genotype↗
PubMed2004

[Establishing a new genotyping method of hepatitis B virus by polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) to analysis on S region and its application].

OBJECTIVE: To establish a new polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method of genotyping HBV using Mbo I, BsTN I, BsmA I, Hpa II and investigate the relationship between genotype and clinical spectrum of hepatitis B. METHODS: 124 full-genomic HBV sequences and 13 S-genomic sequences were analyzed, genotype specific regions were identified by the restriction enzymes Mbo I, BsTN I, BsmA I, Hpa II. And 176 samples from different kinds of hepatitis B were genotyped by this method. Five samples had been randomly selected and directly sequenced their S gene, to assess the accuracy. RESULTS: In 176 serum samples of patients with hepatitis B from Guizhou area, genotype B and C were found in 56.8% and 43.2% respectively. The proportions of genotype B and C in ASC were 40.0% and 15.7% (chi-square = 12.16, P < 0.005); and they were 31.6% and 14.0% in CHB (chi-square = 7.88, P < 0.005). CONCLUSION: Genotyping HBV, based on S gene RFLP seems to be highly sensitive, differential and accurate and could be used in large-scale surveys. HBV genotype B and C are existed in Guizhou area.

Genotype↗
PubMed2004

[Effects comparison of lamivudine therapy for hepatitis B virus genotypes B and C].

OBJECTIVE: To determine the lamivudine response of HBV genotypes in patients with HBV DNA positive chronic hepatitis. METHODS: Clinical data from 235 patients in the original trial were analyzed. RESULTS: 135 patients received lamivudine and 100 patients as controls. Almost all patients had HBV genotypes B or C. Antiviral response were 92.9% and 75.9% in lamivudine-treated patients (chi-square = 6.628, P < 0.05) and 9.8% and 8.5% in untreated controls (P > 0.05) with HBV genotype B and C, respectively. The incidences of lamivudine-induced mutation in YMDD motif were 3.6% and 16.5% in HBV genotype B and C, respectively (chi-square = 5.508, P < 0.01). We identified HBV genotype B, elevated pretreatment alanine aminotransferase (ALT) levels, and low pretreatment HBV DNA levels as independent factors associated with antiviral response. CONCLUSION: HBV genotype B was associated with a higher rate of lamivudine-induced HBV DNA clearance and lower rate of lamivudine-induced YMDD mutation compared with genotype C. HBV genotypes may be an important determinant of lamivudine therapy of chronic hepatitis B.

Adult↗
PubMed2004

Association of estrogen receptor-alpha and vitamin D receptor genotypes with therapeutic response to calcium in postmenopausal Chinese women.

AIM: To investigate the correlation between calcium treatment in postmenopausal women and estrogen receptor-alpha (ER-alpha) Xba I and Pvu II genotype and vitamin D receptor (VDR) Apa I genotype. METHODS: One hundred fifteen postmenopausal Chinese women of Han population were enrolled and treated with calcichew-D3 (1000 mg calcium and 400 U vitamin D3) daily for 1 year. At entry and after 1 year treatment, the bone mineral density (BMD), serum and urinary bone turnover biochemical markers were evaluated. ER-alpha and VDR genotype were analyzed using PCR-restriction fragment length polymorphism. RESULTS: After 1 year of calcium supplementation, a significant increase of BMD and a marked reduction in serum ALP and PTH levels, and a significant increase of serum 25-(OH) vitamin D level were observed (P<0.01 or P<0.05). At entry and after 1 year of treatment, no significant association was found between Xba I, Pvu II, and Apa I genotypes and BMD in L1-4, Neck, and Troch, and all bone turnover marker levels. However, the percentage of change (median, QR) in Neck BMD was significantly different in homozygous XX [-4.14 (from -6.54 to -1.34)] in comparison with Xx [1.72 (from -1.12 to 3.20)] (P<0.001) or xx [1.22 (from -1.74 to 3.06)] Xba I ER-alpha genotype (P=0.001). CONCLUSION: Women with ER-alpha Xba I genotype XX may have a higher risk of relatively fast bone mass loss in femoral neck after menopause and that they may have a poor responsiveness to calcium supplementation. The changes in BMD are not associated with ER-alpha Pvu II genotype and VDR Apa I genotype after 1 year of calcium supplementation.

Aged↗
PubMed2005

Comparison of archival plasma and formalin-fixed paraffin-embedded tissue for genotyping in hepatocellular carcinoma.

Biobanks containing formalin-fixed paraffin-embedded tissue, as well as frozen serum or plasma, are important resources for molecular epidemiologic studies. However, few studies have compared the reliability of formalin-fixed tissue samples and archival plasma samples for genotyping. We determined the genotype of four proposed genetic risk factors for hepatocellular carcinoma [hereditary hemochromatosis (HFE 63 and 282), alpha(1)-antitrypsin deficiency (AAT 342) and cystic fibrosis (CFTR 508)] on formalin-fixed tissue samples, stored for up to 25 years, from 318 patients diagnosed with hepatocellular carcinoma and on plasma or serum samples from 31 of these patients. The genotypes were analyzed by RFLP or allele-specific amplification as well as by TaqMan assays. In addition, genotyping was attempted after whole genome amplification by multiple displacement amplification (MDA). Genotyping was successful in 94% of the tissue samples and successful and identical to the tissue samples from the same subjects in 98% of the plasma/serum samples. DNA from plasma samples could be amplified >5,000-fold by MDA and genotyping after MDA gave identical results to the genotyping of the same subjects before whole genome amplification. MDA amplification of the tissue samples was not successful. In summary, archival plasma was found to be an adequate source of efficiently amplifiable DNA. MDA on plasma samples allows analysis of multiple genotypes in epidemiologic studies.

Carcinoma, Hepatocellular↗
PubMed2005

[Establishment and application of real-time fluoriescene-based metry polymerase chain reaction for hepatitis B virus genotyping].

OBJECTIVE: To explore a new method for determining hepatitis B virus (HBV) genotypes B-D with real-time fluorescence-based PCR. METHODS: The PCR primers and probes were designed according to the analysis of 143 complete HBV genomes from GenBank and on the basis of a search for genotype-specific nucleotide sequences which were conserved in the 3 HBV genotypes. Real-time fluorescence-based PCR was performed for HBV genotyping of 128 samples collected from Lanzhou. Three samples of each genotype of B, C and D were randomly selected and their S gene was sequenced for confirmation of the results of PCR-based method. RESULTS: Real-time PCR identified genotype B in 26 (20.3%), genotype C in 92 (71.9%), and genotype D in 10 (7.8%) cases. The sequencing results of the S gene of 18 PCR-produced clones were in complete consistence with those of fluorescence-based PCR. CONCLUSION: The real-time PCR method is convenient, highly sensitive, rapid and accurate, especially suitable in clinical and large-scale epidemiological studies.

Fluorometry↗
PubMedDate not supplied

Minimal sizes of cases with a susceptible genotype and minimal odds ratios among susceptible individuals in case-control studies.

OBJECTIVE: Disease risk elevation due to an environmental factor only for individuals with a susceptible genotype is a typical example of gene-environment interaction. In order to identify risk factors interacting with susceptible genotypes in case-control studies, presumptions on minimal size of cases with the susceptible genotype (S (min)) and odds ratio (OR) among the susceptible individuals (OR(susceptible)) are useful. MODEL: Proportion of exposed cases (P(1)) and OR for whole cases (OR(whole)) statistically detectable in a case-control study can be calculated in a conventional method. P(1) was assumed to be a weighted sum of the exposed among cases with the genotype (P(x)) and cases without the genotype (equal to proportion of the exposed among controls, P(0)), i.e., S P(x) + (1 - S) P0, where S is the size (proportion) of cases with the genotype. For each calculated P(1), S became the minimum (S(min)) in case of P(x) = 1. OR(susceptible) was calculated by {P(x) (1 - P(0))} / {(1 - P(x)) P(0)}. RESULTS: S(min) and OR(susceptible) were listed for the combinations of the above components. For example, a detectable P(1) was 0.638 for P(0)=0.5 in a case-control study with 200 cases (N(1)) and 200 controls (N(0)), when a error of a two-sided test was 0.05 with an 80% of power. In case of P(1)=0.638, OR(whole) was 1.77, producing S(min) = 0.277 for infinite OR(susceptible). It indicates that an environmental factor cannot be detected in case that a high-risk genotype frequency is less than 0.277. INTERPRETATION: If the size of cases with a susceptible genotype is expected to be less than S(min), case-control studies are unlikely to detect a significant OR of the environmental factor.

Case-Control Studies↗
PubMed2006

Genotypic characterization of Helicobacter pylori cagA and vacA from biopsy specimens of patients with gastroduodenal diseases.

BACKGROUND: Helicobacter pylor i infection is closely associated with gastroduodenal diseases. H. pylori infection with different vacA and cagA genotypes may result in divergent consequences. The aim of the present study was to investigate the prevalence of H. pylori infection and the correlation between cagA and vacA genotypes with the consequences of H. pylori infection in Taiwan. METHODS: Genomic DNA from 97 gastric biopsies of patients with various gastroduodenal diseases was collected, and the prevalence of H. pylori infection, cagA genotypes and vacA genotypes, was analyzed by polymerase chain reaction. In addition, the correlations between cagA and vacA genotypes and the consequences of H. pylori-infection were statistically examined. RESULTS: Our results indicated that 57.7% of this sample of patients with gastroduodenal diseases were infected with H. pylori. Prevalence of cagA(+) strain in H. pylori -infected patients was 71.4%. All of the genotypes of the cagA(+) H. pylori strains among our patients were type A. Prevalence of vacA signal region s1 and middle region m2 genotype in H. pylori- infected patients was 98.2% and 53.6%, respectively. CONCLUSIONS: Our study demonstrated that individuals infected with H. pylori strains that carried cagA gene and vacA s1/m2 genotypes were associated with the development of gastroduodenal diseases, compared to those infected with cagA(-) gene and vacA(-) H. pylori strains.

Adolescent↗
PubMed2006

[Correlation between infection of different glycoprotein B genotypes of human cytomegalovirus and human chronic periodontitis].

OBJECTIVE: To investigate the correlation between infection of different human cytomegalovirus (HCMV) glycoprotein B (gB) genotypes and human chronic periodontitis. METHODS: A nested-polymerase chain reaction (nPCR) was employed to detect HCMV gB gene in the subgingival plaque samples from 65 chronic periodontitis patients and in the gingival crevicular fluid samples from 24 periodontally healthy control. The amplification fragments of gB gene were further genotyped by restriction fragment length polymorphism (RFLP). The correlation among infection with the different HCMV genotypes and the severity of periodontal lesion were evaluated. RESULTS: In terms of teeth examined, the prevalence of HCMV (59.23%, 154/260) in the chronic periodontitis lesions was significantly higher than that of HCMV (32.29%, 31/96) in the periodontally healthy control (P < 0.01). Of the HCMV DNA positive samples from the chronic periodontitis lesions, 11.7% (18/154) was genotyped as gB I, 80.5% (124/154) as gB II, and 7.8% (12/154) as gB I and gB II co-infection, and of the HCMV DNA positive samples from the periodontal healthy control, 45.2% (14/31) was genotyped as gB I, 38.7% (12/31) as gB II, and 16.1% (5/31) as gB I and gB II co-infection. The gB II genotype was more dominant among the chronic periodontitis lesions compared with that among the periodontally healthy control (P < 0.01). In chronic periodontitis, no statistical significance could be found between infection of different HCMV gB genotypes and the different clinical parameters of CAL, PD and GI (P > 0.05). CONCLUSIONS: Subgingival infection with HCMV is closely associated with chronic periodontitis. Infection of HCMV may not correlate directly with severity of periodontitis. However, gB II may be the dominant genotype of HCMV, which is associated with the chronic periodontitis.

Adult↗
PubMed2006

HDV genotypes in the Western Brazilian Amazon region: A preliminary report.

In Brazil, hepatitis delta virus (HDV) is only reported in Western Amazonia, where severe cases of acute and chronic HDV hepatitis have been described. The study area was chosen in the States of Acre and Rondonia where most cases of hepatitis B virus (HBV)/HDV are reported. From December 2003 to October 2004, 40 HBsAg carriers with anti-HDV IgM were selected. An epidemiologic questionnaire, including demographic and clinical/epidemiologic variables was filled out. HDV amplification and genotyping were performed. Genotype I was detected in 22 patients (55.0%), whereas genotype III was identified in 18 (45.0%). Patients who were infected with genotype I were older (45.1 +/- 17.8 years) than patients infected with genotype III (32.8 +/- 10.9 years; P = 0.01). No symptoms were reported by 21 (52.5%) patients. Otherwise, 19 (47.5%) had symptoms (fatigue, abdominal pain, weight loss, and decompensated liver disease) that motivated them to seek medical care. Genotype III carriers were more symptomatic, but no statistical significance was achieved. Our preliminary results show that HDV genotypes I and III are present in Brazilian Amazonia and that HDV genotype III is not limited to the Amerindian population.

Adolescent↗
PubMed2006

[Analysis and state of HCV genotype 6a infection].

OBJECTIVE: To investigate the infection state of hepatitis C virus genotype 6a in China. METHODS: Three (95, 126, 150)HCV genotype 6a serum samples were identified by digesting 5'NCR with compound enzyme method. Then, HCV 5'NCR and NS5B fragments were amplified from these samples by RT-PCR assay and sequenced. The phylogenetic trees of the samples were analyzed and compared with 24 HCV complete gene sequences from GenBank. RESULTS: The sequencing reports on 5'NCR showed "CA" bases in 3 serum samples (95,126,150) were inserted into -145 site, and the sequences of 3 serum samples had the highest homology with sequence Y12083( 0.934, 0.930, and 0.926, respectively). The results of the phylogenetic trees suggested these 3 serum samples belonged to HCV genotype 6a. The sequencing reports on NS5B showed the 3 serum samples also had the highest homology with HC-J4(0.934, 0.930, and 0.926, respectively), and the results of the phylogenetic trees suggested these 3 serum samples belonged to HCV genotype 1b. To exclude the influence of amplification efficiency of primers, NS5B fragments were amplified by HCV genotype 6a specific primers and no amplification products appeared. CONCLUSION: There are different results of HCV genotype by analyzing 5'NCR and NS5B in 3 samples infected with HCV genotype 6a. It may be related with gene recombination. It suggests HCV genotype should be analyzed on more than two regions.

Base Sequence↗
PubMed1986

Allozyme genotypes of Drosophila buzzatii: feeding and oviposition preferences for microbial species, and habitat selection.

Mature, mated female D. buzzatii were given a choice of nine microbial communities actively growing on cactus homogenate in laboratory population cages, and tests were made to determine if flies of different genotypes (for seven allozyme loci) chose different microorganism species for either feeding or oviposition. Variation in feeding preferences was determined from assays of electrophoretic genotypes and the ingested microorganism species of individual flies. Oviposition preference variation was analyzed indirectly by assaying the genotypes of individuals raised from eggs laid on different microorganisms. No significant evidence was found for differences in feeding preferences among adults of different genotypes. For oviposition preferences, there were significant microorganism-genotype associations for each of seven polymorphic loci. Analyses of the total electrophoretic genotype, rather than of individual loci, showed that the genotypes of eggs laid on the same microorganism species were more similar than those laid on different species. That is, females of different genotypes show habitat selection for oviposition sites, which would facilitate the maintenance of genetic polymorphisms.

Animals↗