中国人细小病毒B19系统发育关系研究

目的探讨在中国分布的人细小病毒B19的系统发育。方法对B19病毒阳性的23份来自中国献血者和5份B19/HIV共感染者标本,采用病毒基因组NS1-VP1-u区测序后,与Genbank下载的参考序列比对,用软件MRBAYES 3.1.2作贝叶斯推断,用在线软件RaxML作最大似然法运算,绘制进化树并分析。结果 28份来自中国的标本均属于B19-1A亚型,且呈现复系,其中来自新疆乌鲁木齐来自四川的各1例标本与非中国序列聚在一起,其他中国26份标本与来自美国的病毒株Au聚在一枝并有着很好的支持率,来自西安的2条参考序列出现在B19-1A亚型的基部。结论中国的B19病毒是多起源的,其在中国中西部地区进化速率较慢;应该积极开展不同地区B19病毒多样性的研究。     

Evaluation of mitogenome sequence concordance,heteroplasmy detection,and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.     

风疹病毒分子流行病学研究

目的 阐述风疹病毒(RV)的遗传变异规律及分子流行病学特点。方法 利用RT-PCR扩增RVE1基因，然后测序，并用DNA STAR软件包绘制系统发生树，以分析RV的分子流行病学特点。结果 测得RV JR23株E1基因的序列，与GenBank中包括3株中国株在内的不同时间、地点分离的30株病毒株一起绘制了系统发生树，比较了各株可产生HI抗体和中和抗体区的氨基酸变异情况。(1)总体上RV的核酸、氨基酸序列高度保守。中国的4株分离株遗传性质差别相对较大，其中379株和BRD株构成了不同于其他29株的基因Ⅱ型，就其遗传来源及生物学性状需进一步研究。(2)JR23株与英、美、日20世纪60年代流行株序列相近，其遗传来源可能为20世纪60年代世界流行株的中国衍生株，但具体的初始流行时间未知。结论 RV的流行有地域的差异，其分子流行病学特点与时间有关。因为人是RV的惟一宿主，所以人员的流动性，影响了RV的流行特点。     

辽宁地区汉坦病毒分离株的基因分型

目的　分离辽宁地区汉坦病毒并对分离株 (SY 13)进行基因分型 ,以查清辽宁地区汉坦病毒流行株的基因型和基因亚型。方法　采用组织细胞培养法分离汉坦病毒 ;用RT PCR法分别扩增SY 13的M片段G1、G2区和S片段 ;采用邻位相连法 ,通过DNAStar、Clustalx、Phylip等序列分析软件分别对 3个基因片段的序列与从GenBank下载的序列进行同源性分析 ,并构建种系发生树。结果　通过对 3个基因片段进行比较分析 ,SY 13与HTN型同源性较高 ,为 79.3%～ 97.0 % ;通过M片段G2区的比较分析 ,SY 13与BAO 10、BAO 14、JIANG 13、BAO 9、Q 33处于同一分支 ,同源性为 95.0 %～97.0 %。结论　辽宁地区汉坦病毒SY 13株与黑龙江地区分离株属同一亚型 ,为HTN型病毒中的H4亚型     

新蚤属9种新蚤核糖体DNA ITS2序列变化

本研究分析了新蚤属 9个种 (Neopsyllabidentatiformis,N abagaitui,N mana ,N pleskei,N siboi,N teratura ,N hongyangensis ,N specialis和N paranoma)的核糖体DNAITS2的序列变化 ,其中二齿新蚤包括两个地理种群。结果表明 ,该序列在所研究的种内相对稳定 ,在种间 ,除N abagaitui,N specialis和N paranoma间有较多的变异外 ,其他种间的变异较少甚至没有。种间的碱基替换率为 0～ 2 78%。根据碱基替换速率推算的新蚤属两次分化时间分别为 3 5～ 10百万年和 1百万年以后。结合分子和形态特征 ,可以认为N hongyangensis是N bidentatiformis的姐妹种。根据该序列得到的系统发育关系树和根据线粒体DNA16sRNA基因所得的系统发育关系树基本一致。而N siboi则出现了线粒体基因组和核基因组进化的不一致性 ,说明该种的起源值得进一步研究     

Isolation of Middle East Respiratory Syndrome Coronavirus from a Patient of the 2015 Korean Outbreak

During the 2015 outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) in Korea, 186 persons were infected, resulting in 38 fatalities. We isolated MERS-CoV from the oropharyngeal sample obtained from a patient of the outbreak. Cytopathic effects showing detachment and rounding of cells were observed in Vero cell cultures 3 days after inoculation of the sample. Spherical virus particles were observed by transmission electron microscopy. Full-length genome sequence of the virus isolate was obtained and phylogenetic analyses showed that it clustered with clade B of MERS-CoV.     

Analysis of rotavirus species diversity and evolution including the newly determined full-length genome sequences of rotavirus F and G

Rotaviruses are a leading cause of viral acute gastroenteritis in humans and animals. Eight different rotavirus species (A–H) have been defined based on antigenicity and nucleotide sequence identities of the VP6 gene. Here, the first complete genome sequences of rotavirus F (strain 03V0568) and G (strain 03V0567) with lengths of 18,341 and 18,186 bp, respectively, are described. Both viruses have open reading frames for rotavirus proteins VP1 to VP7 and NSP1 to NSP5 located at the 11 genome segments. Nucleotide sequence identities to other rotaviruses ranged between 29.8% (NSP1 gene) and 61.7% (VP1 gene) for rotavirus F and between 29.3% (NSP1-2 gene) and 65.9% (NSP2 gene) for rotavirus G, thus confirming their classification as separate virus species. Encoded proteins revealed remarkable sequence differences among the rotavirus species. In contrast, the non-coding 5′-terminal sequences of the genome segments are highly conserved among all rotavirus species. Different 3′-terminal consensus sequences are found between rotavirus A/D/F, rotavirus C and rotavirus B/G/H. Phylogenetic analyses indicated a separation of rotaviruses in two major clades consisting of rotavirus A/C/D/F and rotavirus B/G/H. Within these clades, rotavirus F mainly clustered with rotavirus D and rotavirus G with rotavirus B. In addition, differentiation among mammalian and avian rotavirus A strains, host-specific evolution of rotavirus B and C as well as an ancient reassortment event between avian rotavirus A and D are indicated by the phylogenetic data. These results underline the high diversity of rotaviruses as a result of a complex evolutionary history.     

Sequence and phylogenetic analyses of human rotavirus strains: Comparison of VP7 and VP81 antigenic epitopes between Tunisian and vaccine strains before national rotavirus vaccine introduction

Group A rotaviruses (RVA) are the leading cause of severe gastroenteritis in infants and young children worldwide. Due to their epidemiological complexity, it is important to compare the genetic characteristics of vaccine strains with the RVA strains circulating before the introduction of the vaccine in the Tunisian immunization program. In the present study, the nucleotide sequences of VP7 and VP8¹ (n = 31), the main targets for neutralizing antibodies, were determined. Comparison of antigenic epitopes of 11 G1P[8], 12 G2P[4], 4 G3P[8], 2 G4P[8], 1 G6P[9] and 1 G12P[8] RVA strains circulating in Tunisia from 2006 to 2011 with the RVA strains present in licensed vaccines showed that multiple amino acid differences existed in or near putative neutralizing domains of VP7 and VP8¹. The Tunisian G3 RVA strains were found to possess a potential extra N-linked glycosylation site. The Tunisian G4 RVA were closely related to the G4 vaccine strain in RotaTeq, belonging to the same lineage, but the alignment of their VP7 amino acids revealed an insertion of an asparagine residue at position 76 which is close to a glycosylation site (aa 69–71). Despite several differences detected between Tunisian and vaccine strains, which may affect binding of neutralizing antibodies, both vaccines are known to protect against the vast majority of the circulating genotypes, providing an indication of the high vaccine efficiency that can be expected in a future rotavirus immunization program.