The DQA1*0104 allele is carried by DRB1*1001- and DRB1*1401-positive haplotypes in Caucasians, Africans and Orientals

Abstract: The DQA1*0104 allele is known to differ from DQA1*0101 by a single nucleotide in the sequenced part of the first exon. DQA1*0104 has a guanine in the second position of the second expressed codon, whereas DQA1*0101 and all other sequenced DQA1 alleles have an adenine in that position, changing aspartic acid to glycine. The DQA1*0104 allele was originally described in African Americans with the DRB1*12, DRB3*0101, DQA1*0104, DQB1*0501, DRB1*12, DRB3*0202, DQA1*0104, DQB1*0605 or DRB1*14, DQA1*0104, DQB1*0503 haplotypes. When developing DQA1 typing by PCR amplification with sequence-specific primers (PCR-SSP), we observed that all DR10- and DR14-positive samples carried the DQA1*0104 allele, wheres all DRB1*01 -positive DNAs carried the closely related DQA1*0101 allele. In the present study, samples representing the major ethnic groups with DR-DQ haplotypes known to carry the DQA1*0104 allele or the very similar DQA1*0101 allele were investigated by Taq I RFLP analysis, PCR-SSP typing and nucleotide sequencing. The DQA1*0104 allele was found to differ from DQA1*0101 not only in the second expressed codon, but also by a productive mutation in the signal peptide. All investigated DRB1*1001 -(n = 24) and DRB1*1401 -positive (n = 25) haplotypes, defined by homozygosity or association, of Caucasian, African or Oriental origin carried the DQA1*0104 allele, whereas the DQA1*0101 allele was found on all DRB1*01 -positive (n = 32) haplotypes. These findings demonstrate that in the assignment of HLA class II alleles, polymorphism outside the second exon sometimes must be considered. The maintenance of the DQA1*0104 allele on a few distinct haplotypes indicates that the allele is old and might also be compatible with a functional difference between the DQA1*0101 and DQA1*0104 alleles.     

DNA polymerase gene locus of <Emphasis Type="Italic">Cercopithecine herpesvirus 1</Emphasis> is a suitable target for specific and rapid identification of viral infection by PCR technology

The family Herpesviridae comprises at least 100 herpesviruses. Numerous human and animal pathogenic herpesviruses have been identified so far, including Cercopithecine herpesvirus 1 (CeHV-1). This virus is a member of the subfamily Alphaherpesvirinae and is the most hazardous herpesvirus to man. CeHV-1 is also known as B-virus or monkey B virus and as Herpesvirus simiae. In order to gain more genetic information, the viral DNA polymerase (DPOL) gene was identified using polymerase chain reaction (PCR) and DNA nucleotide sequence analysis. The deduced amino acid sequence contains the motifs and signatures that are typical for the B-family of DPOLs. The DPOL gene of CeHV-1 was found to be a suitable target for the specific and rapid identification of the Cercopithecine herpesvirus 1 infection by PCR technology. Comparative analysis of the DNA sequences of the DPOL gene loci of CeHV-1, Human herpesvirus 1 and 2 (HHV-1 and HHV-2), and other herpesviruses was carried out for determination of unique genomic regions of the individual DPOL genes. A primer set of 12 primers was used for screening the DNA of CeHV-1, HHV-1, and HHV-2 by detailed PCR. It was found that six out of twelve primer combinations are able to detect specifically the CeHV-1 genome without cross reactivity with the genome of HHV-1 and/or HHV-2. The specificity of the individual amplified DNA fragments was confirmed by DNA nucleotide sequence analysis. The results of these studies indicate that the six primer combinations of the specific CeHV-1 DPOL primer set is the method of choice for a rapid, precise and specific identification of a CeHV-1 infection by PCR. Due to the fact that this specific CeHV-1 DPOL primer set does not amplify any DNAs of HHV-1 or HHV-2 genome this technology is stressing and can be successfully used unlimited and more credible in all laboratories with PCR technical facility routinely for detection of a CeHV-1 infection in vivo or in vitro.The GenBank Accession No. of the sequence of DNA polymerase gene of Cercopithecine herpesvirus 1 (CeHV-1) reported in this study is AY568415, DPOL protein ID AAT67222; nuclear phosphoprotein ID AAT67223     

Ten novel HLA-DRB1 alleles and one novel DRB3 allele

Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the variants are single-nucleotide substitutions, four resulting in an amino acid change (DRB1*1145, *1148, *0828 and *1514) and four with silent substitutions (DRB1*040504, *130103, *160502 and DRB3*020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and one allele alters three nucleotides and two amino acids.     

Seven new HLA-B alleles associated with antigens in the B7 CREG

This paper describes seven novel HLA-B alleles. Five of these new alleles contain polymorphic motifs previously reported in HLA-B alleles, suggesting an origin resultant from a gene conversion mechanism. B*0723 contains a polymorphism previously unreported in class I HLA molecules. B*4105 contains a nucleotide substitution previously unreported in class I HLA molecules, which encodes a protein sequence previously reported only in HLA-C locus alleles.     

藏汉民族线粒体基因组全序列的比较研究

目的 以藏汉民族线粒体基因组全序列为基础,进行Haplogroup构建和系统发生分析,在全序列水平上比较核苷酸的变异,阐释可能的变异机制和蕴含的生物学意义.方法 采用Applied Biosystems 3730DNA自动测序仪分别对40名藏族和50名汉族的标本进行线粒体DNA序列测定,应用phredPhrap 16.0软件进行全序列拼接,并以rCRS(revised Cambridge Reference Sequence)为标准与测定序列进行比对分析;根据MTTO-MAP的标准,通过Network方法进行Haplogroup构建和系统发生的分析,并结合其它方法对产生的数据进行深入解读.结果 数据分析结果显示:在系统发生上,藏汉民族90个线粒体DNA序列归类到13个Haplogroups,除M9以外,其它各Haplogroup出现频率之间比较差异无统计学意义;通过两个民族的线粒体DNA全序列比对,发现21个分布频率有统计学意义的变异位点,其中的5个为新变异位点;另外,对D-Loop区的5个突变位点进行了单倍型构建,90个标本可分为2种Supertype,发现在藏汉民族之间Supertypel和Supertype 2的分布频率均有统计学意义.结论 藏汉民族在种族起源和系统发生上具有较近的母系遗传关系;在全序列有统计学意义的位点究竟是适应性或者中性选择,抑或是一种病理性突变尚需深入的探讨.     

Grandparental genotyping enhances exome variant interpretation

Trio exome sequencing is a powerful tool in the molecular investigation of monogenic disorders and provides an incremental diagnostic yield over proband‐only sequencing, mainly due to the rapid identification of de novo disease‐causing variants. However, heterozygous variants inherited from unaffected parents may be inadvertently dismissed, although multiple explanations are available for such scenarios including mosaicism in the parent, incomplete penetrance, imprinting, or skewed X‐inactivation. We report three probands, in which a pathogenic or likely pathogenic variant was identified upon exome sequencing, yet was inherited from an unaffected parent. Segregation of the variants (in NOTCH1, PHF6, and SOX10) in the grandparent generation revealed that the variant was de novo in each case. Additionally, one proband had skewed X‐inactivation. We discuss the possible genetic mechanism in each case, and urge caution in data interpretation of exome sequencing data. We illustrate the utility of expanding segregation studies to the grandparent generation and demonstrate the impact on exome interpretation strategies, by showing that objective genotype data can overcome subjective parental report of lack of symptoms.     

常州地区首例cisAB血型基因特征分析及家系调查

目的 研究1例ABO亚型及基因特征。 方法 采用试管法对家系3代共7例标本进行ABO血型血清学鉴定;对正反定型不一致的标本运用聚合酶链式反应序列特异性引物(polymerase chain reaction-sequence specific primer, PCR-SSP)法基因分型;并对ABO基因第6和7外显子扩增产物进行测序分析。 结果 ABO血型血清学发现7例标本中正反定型不符3例,其中2例红细胞表型为cisAB/A 或ABx,1例为cisAB/O或A2Bx;基因分型为ABO*cisAB01/A101、ABO*cisAB01/O01。ABO基因序列分析:ABO*cisAB01/A101第7外显子发生467C>T、803G>C的特征性突变,ABO*cisAB01/O01第6外显子261位缺失G,第7外显子在467C>T、803G>C存在特征性突变。测序结果均携带有ABO*cisAB01基因。 结论 ABO*cisAB01基因能导致A抗原或者B抗原的弱表达并能稳定遗传,因此应将血型血清学和分子生物学方法相结合才能准确鉴定ABO亚型。     

新型冠状病毒Alpha变异株实验室检测研究

目的 对一例新冠肺炎境外输入病例进行实验室检测,并对新型冠状病毒（severe acute respiratory syndrome coronavirus 2,SARS - CoV - 2）变异株进行鉴定,了解不同样本类型中新冠病毒的检出情况。方法 采集咽拭子、痰液、粪便、尿液和血液多种类型样本共13份,分别提取核酸,用荧光RT - PCR法检测SARS - CoV - 2。使用纳米孔MinION Mk1C测序仪,对阳性咽拭子样本进行实时SARS - CoV - 2靶向扩增全基因组测序,运用artic - ncov2019、DNAstar和Mega等软件对测定序列进行处理和分析。结果 咽拭子、痰液、粪便、血浆和尿沉渣样本中均检出SARS - CoV - 2核酸,咽拭子和血浆样本在发病的前四天均能检出,尿沉渣样本在发病当天能检出。基于纳米孔测序技术,7 h即获得SARS - CoV - 2全基因组数据,经分析显示为新冠病毒Alpha变异株。结论 本例境外输入新冠肺炎确诊病例的病原为SARS - CoV - 2 Alpha变异株,咽拭子、血浆样本和尿沉渣样本在发病早期均能检出SARS - CoV - 2核酸。     

2018—2021年北京市沙门菌血清型及喹诺酮类耐药表型和基因型分析

目的 分析2018—2021年北京市肠道门诊哨点医院分离到的沙门菌血清型及喹诺酮类药物耐药表型和耐药基因的流行情况。方法 采用玻片凝集法鉴定血清型;微量肉汤稀释法测定药物敏感性;全基因组测序数据通过与MLST和ResFinder数据库比对,查询ST型别和耐药基因。结果 228株沙门菌共检出42种血清型,51种ST型。其中肯塔基沙门菌、肠炎沙门菌和黄金海岸沙门菌等9种血清型比较常见。77株沙门菌（33.8%）对萘啶酸耐药;40株（17.5%）对环丙沙星和左氧氟沙星耐药;38株（16.7%）对吉米沙星耐药。不同血清型对喹诺酮类药物的耐药性不同。228株沙门菌共筛选出5种喹诺酮耐药基因:qnrS（23.7%）、aac(6’)-Ib-cr（8.3%）、qnrB（6.6%）、OqxAB（1.3%）和qepA（0.4%）;喹诺酮耐药决定区存在gyrA和parC的7种氨基酸突变:以parC:T57S（70.2%）最常见,其次是gyrA:D87N（14.9%）、parC:S80I（14.5%）、gyrA:S83F（14.5%）、gyrA:D87Y（7.9%）、gyrA:D87G（5.3%）和gyrA:S83Y（1.8%）。在组合突变中,以parC:S80I-gyrA:D87N-gyrA:S83F三突变,并伴随parC:T57S最多。耐药基因和突变位点在9种常见血清型中的检出率存在差异。结论 北京市沙门菌血清型及ST型种类繁多,携带喹诺酮耐药基因以qnrS、aac(6’)-Ib-cr和 qnrB为主,存在gyrA和parC多个位点突变并协同作用。应持续监测血清型和耐药性,以指导临床有针对性合理用药。