Comparative genotyping and phenotyping of glutathione S-transferase GSTT1

 Only limited information is available so far concerning the human glutathione S-transferase isoenzyme class theta encoded by the GSTT1 gene. The aim of the study was to characterize individuals in respect to a polymorphic deletion of the GSTT1 gene and to validate these results with the phenotypical determination of the “conjugator status” according to Hallier et al. (1993). Determination of the GSTT1 genotype was done in 40 healthy adults by using an assay based on internal standard controlled polymerase chain reaction. The GSTT1-1 phenotype was determined by measuring the erythrocyte conjugating activity towards methyl chloride using a gas chromatographic assay. Genotypically, 34 individuals out of 40 were classified as GSTT1 positive; the remainder were negative. These results could be confirmed by phenotyping in all but one case. In the present study the frequency of “non-conjugators” was 15%. Our study demonstrates the reliability of the suggested PCR assay for GSTT1 genotyping which is easier to perform than the phenotyping assay and is not affected by confounding factors. Received: 30 August 1995 / Accepted: 12 October 1995     

应用PCR—SSCP方法对VKH患者进行HLA—DR4基因多态性的研究

目的试图建立一种简单经济的ＨＬＡ－ＤＲ４基因分型的ＳＳＣＰ方法及标准图谱；期望为将来研究ＨＬＡ－ＤＲ４相关性疾病及临床诊断ＶＫＨ提供一种新的途径和方法。方法使用ＰＣＲ－ＳＳＣＰ方法对５４例ＶＫＨ患者及１０６例正常对照者进行了ＨＬＡ－ＤＲ４基因亚型的分析。结果不同的ＤＲ４基因亚型，在中性聚丙烯酰胺凝胶电泳后有不同的迁移带。结论ＳＳＣＰ方法可区分不同的ＤＲ４基因多态性，但不能准确分型。     

随机引物聚合酶链反应对耐甲氧西林金黄色葡萄球菌基因分型的研究

目的建立耐甲氧西林金黄色葡萄球菌（ＭＲＳＡ）随机引物聚合酶链反应（ＡＰ－ＰＣＲ）基因分型的方法用于；临床流行病学调查。方法优化ＡＰ－ＰＣＲ方法并与抗生素敏感谱分型法比较，评价ＡＰ－ＦＣＲ基因分型法的可靠性与分辨力；并对４９株ＭＲＳＡ进行ＡＰ－ＲＣＲ基因分型。结果４９株医院感染的ＭＲＳＡ可分为１０个ＡＰ－ＰＣＲ谱型，主要谱型为 Ａ３型，分型率 １００％；其中 ４１株 ＭＲＳＡ为流行病学相关株。结论 ＡＰ－ＰＣＲ基因分型是一种经济、快捷、可靠的分型方法；是在分子水平上对微生物感染进行病原学、发病机理及流行病学研究较理想的工具。     

Universal genotyping in tuberculosis control program, New York City, 2001-2003

In 2001, New York City implemented genotyping to its tuberculosis (TB) control activities by using IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping to type isolates from culture-positive TB patients. Results are used to identify previously unknown links among genotypically clustered patients, unidentified sites of transmission, and potential false-positive cultures. From 2001 to 2003, spoligotype and IS6110-based RFLP results were obtained for 90.7% of eligible and 93.7% of submitted isolates. Fifty-nine (2.4%) of 2,437 patient isolates had false-positive culture results, and 205 genotype clusters were identified, with 2-81 cases per cluster. Cluster investigations yielded 57 additional links and 17 additional sites of transmission. Four additional TB cases were identified as a result of case finding initiated through cluster investigations. Length of unnecessary treatment decreased among patients with false-positive cultures.     

鲍曼不动杆菌医院感染流行病学分子研究及基因分型

目的建立随机扩增多态性DNA（RAPD）基因分型方法检测鲍曼不动杆菌,了解鲍曼不动杆菌医院感染流行病学的情况,为控制院内感染提供直接可靠的参考依据。方法对2009-2010年分离的220株鲍曼不动杆菌进行统计分析其临床分布;通过抗生素敏感性试验进行抗菌谱分型;再采用PAPD基因分型方法进行分析。结果标本主要来自ICU,烧伤科,呼吸内科等。从痰液标本中分离的鲍曼不动杆菌占61.0%,其次伤口分泌物标本是占19.0%、中段尿15.6%,其它类型标本占4.4%。抗菌谱分型分为5型。220株鲍曼不动杆菌用RAPD分型共得216株,分型率98.2%（216/220）,分为8种类型：Ⅰ-Ⅷ。结论 RAPD分型技术对鲍曼不动杆菌临床分离株分型率较高;同一抗菌谱型的基因型可能不同,同一基因型的抗菌谱也可能不同。     

2009-2020年我国轮状病毒腹泻流行特征和基因型变化趋势

目的 了解2009-2020年我国全人群腹泻患者中轮状病毒感染者的流行特征和基因型变化趋势,为进一步开展腹泻监测和防控提供科学依据。方法 资料来源于国家科技重大专项传染病监测技术平台信息管理系统的我国28个省份252家哨点医院腹泻症候群监测数据,采用描述性流行病学方法分析2009-2020年轮状病毒腹泻病例在不同气候带地区、人群以及时间的分布特点及A组轮状病毒腹泻病例的基因分型特征和变化趋势。结果 2009-2020年共对114 606例腹泻病例进行轮状病毒检测,轮状病毒阳性率为19.1%（21 872/114 606）,阳性病例以A组轮状病毒为主（98.2%,21 471/21 872）。轮状病毒阳性率较高的年份分别为2009年（36.9%,2 436/6 604）和2010年（30.6%,5 130/16 790）,2011-2017年在14.0%~18.0%之间变化,2018年小幅上升（20.3%,2 211/10 900）,之后两年连续下降（15.5%,2 262/14 611和9.5%,470/4 963）。男性（20.2%,13 660/67 471）的轮状病毒阳性率明显高于女性（17.4%,8 212/47 135）;＜5岁婴幼儿的轮状病毒阳性率最高（28.4%,18 261/64 300）,是成年人的4倍以上。中温带、暖温带及亚热带地区的轮状病毒阳性率于12月至次年2月达高峰,而高原寒带存在2个高峰,分别出现在11月至次年1月及5-6月。2009-2020年A组轮状病毒优势基因型由G3P［8］、G1P［8］逐步发展为G9P［8］。结论 2009-2020年我国轮状病毒感染总体呈现下降趋势,呈明显的季节性流行,各年龄组人群阳性率差异较大,儿童腹泻仍是重点关注的问题,需进一步加强轮状病毒疫苗的接种,持续开展流行特征和基因型变化的监测。     

Characterization and Phylogenetic Analysis of Brazilian Chicken Anaemia Virus

Chicken anaemia virus (CAV) was detected by a Nested-PCR assay in field samples from different regions of Brazil. The 539 bp amplified fragments of vp1 gene from 44 field samples were sequenced and 10 new nucleotide sequences of CAV were observed. These sequences were phylogenetically analysed by Mega2 using neighbour joining distance methods with 1000 bootstrap replications. Phylogenetic analysis did not show correlation between CAV pathology pattern and genetic groups. The 10 nucleotide sequences of the Brazilian samples were also analysed together with 30 sequences of CAV strains previously described from other countries. The genetic variability observed was not related to the geographical distribution. Amino acid substitutions were detected at 9 positions of the Brazilian sequences and two of them had not been observed before, ⁶⁵R replacing the Q residue and ⁹⁸F replacing Y residue. The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers AY855079 to AY855088.     

Optimum two-stage designs in case–control association studies using false discovery rate

Genetic association studies using case–control designs are often done to identify loci associated with disease susceptibility. These studies are often expensive to perform, due to a large number of genetic markers. Several types of two-stage designs are proposed and used from the point of cost effectiveness. We proposed to control the false discovery rate for multiple-testing correction in two-stage designs, using optimal sample sizes and criteria for selecting markers associated with a disease in each stage to minimize the cost of genotyping. The expected power and cost of two-stage designs were compared with those of one-stage designs, under the assumptions that the genetic markers are independent and total sample size is fixed. The results showed that the proposed two-stage procedure usually reduced the cost of genotyping by 40–60%, with a power similar to that of the one-stage designs. In addition, the sample size and selection criteria, which are optimized parameters, are defined as a function of a prior probability that marker–disease association is true. So, the effects of mis-specification of a prior probability on efficiency were also considered.Aya Kuchiba and Noriko Y. Tanaka have contributed equally to this study.     

Relationships among porcine and human P[6] rotaviruses: evidence that the different human P[6] lineages have originated from multiple interspecies transmission events

Porcine rotavirus strains (PoRVs) bearing human-like VP4 P[6] gene alleles were identified. Genetic characterization with either PCR genotyping or sequence analysis allowed to determine the VP7 specificity of the PoRVs as G3, G4, G5 and G9, and the VP6 as genogroup I, that is predictive of a subgroup I specificity. Sequence analysis of the VP8* trypsin-cleavage product of VP4 allowed PoRVs to be characterized further into genetic lineages within the P[6] genotype. Unexpectedly, the strains displayed significantly higher similarity (up to 94.6% and 92.5% at aa and nt level, respectively) to human M37-like P[6] strains (lineage I), serologically classifiable as P2A, or to the atypical Hungarian P[6] human strains (HRVs), designated as lineage V (up to 97.0% aa and 96.1% nt), than to the porcine P[6] strain Gottfried, lineage II (<85.1% aa and 82.2 nt), which is serologically classified as P2B. Interestingly, no P[6] PoRV resembling the original prototype porcine strain, Gottfried, was detected, while Japanase P[6] PoRV clustered with the atypical Japanase G1 human strain AU19. By analysis of the 10th and 11th genome segments, all the strains revealed a NSP4B genogroup (Wa-like) and a NSP5/6 gene of porcine origin. These findings strongly suggest interspecies transmission of rotavirus strains and/or genes, and may indicate the occurrence of at least 3 separate rotavirus transmission events between pigs and humans, providing convincing evidence that evolution of human rotaviruses is tightly intermingled with the evolution of animal rotaviruses.