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.     

Phylogenetic character mapping of RADES Probing,a new marker for exploring the clonal evolution of expressed coding sequences in Trypanosoma cruzi,the agent of Chagas disease

We have tested a new genetic marker, RADES Probing (RADES-P), on a standard sample of 19 laboratory-cloned stocks of Trypanosoma cruzi, the agent of Chagas disease. This set of stocks, fully characterized using multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA (RAPD), is representative of this parasite’s main genetic subdivisions. RADES-P consists in hybridizing RAPD profiles with probes composed of the products of random amplified differentially expressed sequences (RADES). The profiles thus obtained uncover only expressed coding sequences that are as well present on RAPD gels. Direct visual examination and the banding record show that these RADES-P profiles are different of, and not redundant with, both RAPD and RADES patterns obtained on the same set of stocks with the same primers. Phylogenetic character mapping (PCM) of the RADES-P polymorphism fairly confirms the known population structure and phylogenetic diversity of T. cruzi. This suggests that the impact of clonal evolution on T. cruzi has been predominant enough over the long term to carve the polymorphism of all types of DNA sequences, including polymorphisms of expressed coding sequences, although these sequences are subject to natural selection.     

Consistent treatment of length variants in the human mtDNA control region: a reappraisal

In forensic science, as well as in molecular anthropology and medical genetics, human mitochondrial DNA (mtDNA) variation is being recorded by aligning mtDNA sequences to the revised Cambridge reference sequence (rCRS). This task is straightforward for the vast majority of nucleotide positions but appears to be difficult for some short sequence stretches, namely, in regions displaying length variation. Earlier guidelines for imposing a unique alignment relied on binary alignment to a standard sequence (the rCRS) and used additional priority rules for resolving ambiguities. It turns out, however, that these rules have not been applied rigorously and led to inconsistent nomenclature. There is no way to adapt the priority rules in a reasonable way because binary alignment to a standard sequence is bound to produce artificial alignments that may place sequences separated by a single mutation at mismatch distance larger than 1. To remedy the situation, we propose a phylogenetic approach for multiple alignment and resulting notation.     

2010年安徽省蚊虫标本分离到基因Ⅰ型流行性乙型脑炎病毒

目的在安徽省不同地区开展流行性乙型脑炎病毒(JEV)病原学调查,了解当地JEV的基因型别及分子特征。方法 2010年8月在安徽省阜阳、淮南、安庆市的3个标本采集点使用诱蚊灯采集蚊虫标本,通过组织培养法分离病毒,并对病毒分离物进行血清学和分子生物学鉴定;利用生物信息学技术对新分离病毒的序列进行分析,完成同源性和系统发生分析。结果采集到3属3种共计7651只蚊虫标本,通过组织培养技术分离得到11株病毒分离物,鉴定结果显示均为基因Ⅰ型JEV。安徽省JEV新分离株与基因Ⅰ型JEV的同源性最高,核苷酸同源性为96.8%～99.5%,氨基酸同源性为97.8%～100%。结论在安徽省首次分离到基因Ⅰ型JEV,与我国上海市及浙江省JEV分离株进化关系较近。     

华东地区散发性戊型肝炎病毒系统进化分析

目的 了解华东地区散发性戊型肝炎病毒(HEV)的系统进化特征.方法 2005-2008年收集华东地区14家二级或三级医院413份散发戊型肝炎患者血清,应用巢式RT-PCR方法检测HEVRNA并测序.参照GenBank相关序列,分析各序列之间的同源性,并构建进化树.结果 413例患者的男女性别比为1.75:1,40～69岁患者居多(61.5%).413份患者血清有140份分离出HEV RNA,阳性分离率为34%.所有分离的140份病毒株均属于HEV Ⅳ型,与Ⅰ、Ⅱ、Ⅲ和Ⅳ型参考病毒株的核苷酸同源性分别为77.9%～88.3%、80.8%～90.6%、73.4%～85.2%和91.0%～95.4%.结论 基因Ⅳ型HEV是引起华东地区散发性戊型肝炎的优势病毒株,其起源和进化等问题仍需进一步研究.     

云南境外禽流感H5N1亚型病毒神经氨酸酶基因进化及分子结构特征分析

目的:禽流感病毒神经氨酸酶(NA)是病毒粒子重要表面抗原之一,其抗原性差异决定病毒神经氨酸酶亚型(N1-N9)的划分。NA介导病毒对敏感细胞的侵染及协助子代病毒粒子的成熟和释放,与病毒的宿主嗜性及毒力有关。方法:对2003~2009年期间采集自云南境外家禽的H5N1亚型阳性样品中病毒NA基因进行测序,并与国内外已知代表毒株进行序列比对及系统发育分析。认识云南境外禽流感H5N1亚型病毒神经氨酸酶(NA)基因分子结构特征。结果:21份代表性病毒样品NA基因核苷酸和氨基酸序列同源性介于94.3%~99.3%、93.1%~99.3%。系统发育分析表明可划分为6个不同进化(亚)分支(1、7、9、2.4、2.3.2、2.3.4),其中进化亚分支2.3.4毒株已成为当前云南境外流行的优势毒株;所有云南境外毒株NA蛋白的49-68位氨基酸均存在缺失。结论:糖基化位点存在特有变异;云南境外毒株对Oseltam ivir(达菲)类抗病毒药物可能无耐药性。     

中国卫氏并殖吸虫线粒体基因组及多地域株的系统发育分析

目的　对福建省大、小囊蚴来源的两型卫氏并殖吸虫线粒体基因组序列进行比较和系统发育分析，探寻其可能存在的与表型相关的遗传特征。方法　以在福建省南平市延平区太平镇溪蟹中分离出的两种大小不同的囊蚴（直径分别为380～420 μm和320～340 μm）分别感染犬，收集犬粪及肺部虫卵及成虫。比较两种来源虫卵大小及外形差异；抽提两型并殖吸虫成虫基因组DNA，扩增并获得线粒体全基因组序列，进行序列结构及系统发育关系分析。结果　大、小囊蚴分别感染犬后，所获得的成虫体肥厚，具口、腹吸盘，腹吸盘位于体中线稍前，可见睾丸、卵巢和卵黄腺等结构，固定后呈椭圆形，长宽比约为1.7∶1。两组卵在长、宽上均有显著性差异，大囊蚴感染后所获虫卵亦较大。两组成虫和卵形态特征及ITS2基因序列符合卫氏并殖吸虫特征。成虫线粒体基因组序列分析显示，大、小囊蚴来源的成虫线粒体基因组蛋白编码区序列基本一致，主要差异区域位于前非编码区。滑动窗口分析显示，不同地域来源的卫氏并殖吸虫线粒体基因组间，多态性最大区域位于ND4基因内。系统发育分析表明，两型并殖吸虫均聚入卫氏并殖吸虫中国地域分支，与韩国/日本株关系较近，与（东）南亚株遗传距离较远。结论　中国福建大、小囊蚴来源的两型卫氏并殖吸虫在线粒体基因组水平上遗传距离较近，未表现出明显分化，但非编码区突变和结构变化可能影响了两者在表型上的差异。此外，线粒体各编码基因的进化速率存在明显差异，提示在进行系统发育等相关研究时，应注意选择合适的分子标记。     

贵州及周边省市狂犬病病毒的分群和进化研究

目的 全面掌握贵州及周边省市狂犬病病毒(RABV)的遗传进化特征和分群特点,了解狂犬病疫苗株与流行株的分子遗传差异,为贵州狂犬病疫情的预防和控制提供指导依据.方法 搜索GenBank数据库中贵州及周边5个省市具有明确时间、地区及宿主信息的流行毒株,对其糖蛋白基因(G)全序列进行汇总,并结合本实验室获得的贵州毒株和国内现役疫苗株G序列,利用MEGA和BEAST软件分别进行系统进化和时间进化分析.结果 贵州及周边省市79株RABV均属于基因1型,9个类群的RABV流行株具有明显的地域特征,11株疫苗株分化为2个类群;RABV流行株与疫苗株G基因核苷酸和氨基酸同源性分别为0.827～0.999和0.713～0.998;贵州及周边省市RABV流行毒株的最近共同祖先(TMRCA)可追溯至150年前.结论 贵州及周边省市流行的RABV优势毒株群仍属于基因1型,但毒株经过多年流行已经出现了分化,有必要对流行毒株与疫苗株的遗传变异一致性进行深入研究.     

Evolutionary processes and environmental factors underlying the genetic diversity and lifestyles of Bacillus cereus group bacteria

Bacteria of the Bacillus cereus group are environmental Gram-positive spore-forming bacteria ubiquitously distributed. Despite the high degree of genetic similarity among the different strains, they show strong phenotypic variability, from mammal or entomopathogen strains to soil-dwelling saprophytes, and from psychrophylic to thermotolerant strains. Most of the phenotypes are linked to the presence of large plasmids that encode for diverse toxins. However, other processes, like mutation or recombination, also participate in shaping the evolution and population structure of these bacteria. Here we review different aspects of the evolution of this group.