16S rRNA基因高变区V4和V3−V4及测序深度对油藏细菌菌群分析的影响

【背景】16S rRNA基因测序是当前研究微生物群落组成及其分布的重要手段。【目的】揭示16S rRNA基因高变区V4 (515-806)和V3-V4 (338-806)及测序深度(1-2万条和10万条)对油藏微生物细菌群落组成和多样性分析的影响。【方法】所用油水样细菌16SrRNA基因拷贝数为(6.51±0.56)×108/L,16SrRNA基因V4区测序使用IlluminaMiSeqPE250测序平台,V3-V4区测序使用MiSeqPE300测序平台。【结果】测序深度达到1-2万条时,V4和V3-V4区测序文库覆盖率均达到99.6%以上,且具有较好的可重复性;V4区测序深度为1-2万和10万时,菌群α多样性指数受测序深度影响不显著;与V4区测序相比,同样测序深度(1-2万)下,V3-V4区测序获得的菌群α多样性指数有所降低。V4测序1-2万与10万获得的菌群中几乎未出现显著性差异微生物类群;同样测序深度(1-2万)下,V4与V3-V4测序相比,优势微生物类群Epsilonproteobacteria(51.37%:64.23%)和Deltaproteobacteria (17.96%:11.40%)相对丰度表现出显著差异。【结论】测序深度达到一定水平,增加测序深度会一定程度上影响菌群α多样性指数,对菌群β多样性分析的影响十分有限;同一测序深度下,V4区与V3-V4区测序获得的细菌菌群α多样性指数明显不同,部分优势微生物类群的相对丰度值之间具有显著性差异。鉴于测序读长的提升和测序成本降低,与V4区测序相比,V3-V4区测序在更低的测序深度下文库覆盖率更高,可提供更多用于反映物种亲缘关系的16S rRNA碱基信息,本文认为V3-V4区测序可作为当下菌群分析的首选区域。     

猎豹(Acinonyx jubatus)肠道微生物多样性及其性别差异研究

[目的]探讨猎豹（Acinonyx jubatus）肠道微生物多样性特征。[方法]通过采集新鲜粪便样品,对9只健康成年野生猎豹（4只雄性,5只雌性）的肠道微生物16S rRNA基因V3-V4区进行高通量测序,对猎豹肠道微生物多样性进行研究。[结果]测序共获得肠道微生物16S rRNA基因V3-V4区有效序列599349条,序列平均长度405 bp。通过以97%的序列相似性进行分类,共获得操作分类单元（OTU） 268个。经序列比对和分类鉴定,这些OTU都属于细菌域,包括10个门,21个纲,35个目,72个科,144个属。其中,丰度最高的5个细菌门是厚壁菌门（Firmicutes,平均占OTU总数的42.29%%）、放线菌门（Actinobacteria,31.54%）、梭杆菌门（Fusobacteroidetes,16.66%）、变形菌门（Proteobacteria,5.30%）和拟杆菌门（Bacteroidetes,4.19%）。拟杆菌门的丰度较低是猎豹肠道微生物的主要特征。丰度最高的5个科依次是红蝽杆菌科（Coriobacteriaceae,31.28%）、消化链球菌科（Peptostreptococcaceae,平均占17.66%）,梭杆菌科（Fusobacteriaceae,15.46%）、毛螺菌科（Lachnospiraceae,12.40%）、梭菌科I（Clostridiaceae_I,6.93%）等。丰度最高的5个属依次是柯林斯氏菌属（Collinsella,30.16%）、梭杆菌属（Fusobacterium,15.46%）、艰难梭菌属（Peptoclostridium,11.46%）、Blautia属（8.28%）和狭窄梭菌属1（Clostridium_sensu_stricto_1,6.39%）。约有2.32%的OTU没有归类到属。群落alpha多样性分析结果显示,猎豹肠道微生物群落Shannon指数为2.93-4.41,Simpson指数为0.72-0.91。通过依据性别进行分组,对雌雄两组之间的alpha多样性比较表明,雄性组的物种和Shannon指数略高于雌性组。Beta多样性分析表明,雌雄两组之间的差异高于各组内部不同个体之间的差异。然而,聚类分析显示,相同性别的猎豹的肠道微生物并没有聚在一起。[结论]本文通过高通量测序技术研究了猎豹肠道微生物多样性特征和性别差异,为猎豹的保护、救护饲养和消化生理学研究提供了基础数据。     

猎豹(Acinonyx jubatus)肠道微生物多样性及其性别差异研究（英文）

【目的】探讨猎豹(Acinonyx jubatus)肠道微生物多样性特征。【方法】通过采集新鲜粪便样品,对9只健康成年野生猎豹(4只雄性,5只雌性)的肠道微生物16S rRNA基因V3–V4区进行高通量测序,对猎豹肠道微生物多样性进行研究。【结果】测序共获得肠道微生物16S rRNA基因V3–V4区有效序列599349条,序列平均长度405 bp。通过以97%的序列相似性进行分类,共获得操作分类单元(OTU)268个。经序列比对和分类鉴定,这些OTU都属于细菌域,包括10个门,21个纲,35个目,72个科,144个属。其中,丰度最高的5个细菌门是厚壁菌门(Firmicutes,平均占OTU总数的42.29%%)、放线菌门(Actinobacteria,31.54%)、梭杆菌门(Fusobacteroidetes,16.66%)、变形菌门(Proteobacteria,5.30%)和拟杆菌门(Bacteroidetes,4.19%)。拟杆菌门的丰度较低是猎豹肠道微生物的主要特征。丰度最高的5个科依次是红蝽杆菌科(Coriobacteriaceae,31.28%)、消化链球菌科(Peptostreptococcaceae,平均占17.66%),梭杆菌科(Fusobacteriaceae,15.46%)、毛螺菌科(Lachnospiraceae,12.40%)、梭菌科I(Clostridiaceae_I,6.93%)等。丰度最高的5个属依次是柯林斯氏菌属(Collinsella,30.16%)、梭杆菌属(Fusobacterium,15.46%)、艰难梭菌属(Peptoclostridium,11.46%)、Blautia属(8.28%)和狭窄梭菌属1(Clostridium_sensu_stricto_1,6.39%)。约有2.32%的OTU没有归类到属。群落alpha多样性分析结果显示,猎豹肠道微生物群落Shannon指数为2.93–4.41,Simpson指数为0.72–0.91。通过依据性别进行分组,对雌雄两组之间的alpha多样性比较表明,雄性组的物种和Shannon指数略高于雌性组。Beta多样性分析表明,雌雄两组之间的差异高于各组内部不同个体之间的差异。然而,聚类分析显示,相同性别的猎豹的肠道微生物并没有聚在一起。【结论】本文通过高通量测序技术研究了猎豹肠道微生物多样性特征和性别差异,为猎豹的保护、救护饲养和消化生理学研究提供了基础数据。     

基于16S rRNA基因高通量测序研究狞猫肠道微生物多样性（英文）

【目的】研究狞猫肠道微生物多样性特征。【方法】对7只健康成年野生狞猫(2只雄性,5只雌性;2只来自济南野生动物园,5只来自威海野生动物园)粪便微生物16S rRNA基因V3–V4区进行高通量测序,对狞猫肠道微生物多样性进行研究。【结果】7只狞猫共获得肠道微生物16S rRNA基因V3–V4区有效序列1458741条,平均208392条,序列平均长度433 bp。通过以97%的序列相似性进行分类,获得操作分类单元(OTU)平均233个。经序列比对和分类鉴定,这些OTU都属于细菌域,包括13个门,26个纲,43个目,75个科,119个属。其中,丰度最高的细菌门是厚壁菌门(Firmicutes,平均占61.7%)、放线菌门(Actinobacteria,12.42%)、拟杆菌门(Bacteroidetes,7.79%)、梭杆菌门(Fusobacteroidetes,7.79%)和变形菌门(Proteobacteria,7.53%)。丰度最高的科依次是消化链球菌科(Peptostreptococcaceae,平均占16.15%),梭菌科I(Clostridiaceae_I,14.78%),毛螺菌科(Lachnospiraceae,13.13%),红蝽杆菌科(Coriobacteriaceae,12.31%)等。丰度最高的属是柯林斯氏菌属(Collinsella,11.44%),艰难梭菌属(Peptoclostridium,10.91%),狭窄梭菌属1(Clostridium_sensu_stricto_1,10.3%),拟杆菌属(Bacteroides,7.41%),消化链球菌属(Peptostreptococcus,5.21%)等。7只狞猫的肠道微生物中有平均15.35%的OTU没有归类到属。样本间聚类分析结果表明,来自同一动物园的样本聚为一支。【结论】本文通过高通量测序技术研究了狞猫肠道微生物的组成和多样性特征,为狞猫的救护饲养和消化生理学研究提供基础数据。     

基于16S rRNA基因高通量测序研究狞猫肠道微生物多样性

[目的]研究狞猫肠道微生物多样性特征。[方法]对7只健康成年野生狞猫（2只雄性,5只雌性;2只来自济南野生动物园,5只来自威海野生动物园）粪便微生物16S rRNA基因V3-V4区进行高通量测序,对狞猫肠道微生物多样性进行研究。[结果] 7只狞猫共获得肠道微生物16S rRNA基因V3-V4区有效序列1458741条,平均208392条,序列平均长度433 bp。通过以97%的序列相似性进行分类,获得操作分类单元（OTU）平均 233个。经序列比对和分类鉴定,这些OTU都属于细菌域,包括13个门,26个纲,43个目,75个科,119个属。其中,丰度最高的细菌门是厚壁菌门（Firmicutes,平均占61.7%）、放线菌门（Actinobacteria,12.42%）、拟杆菌门（Bacteroidetes,7.79%）、梭杆菌门（Fusobacteroidetes,7.79%）和变形菌门（Proteobacteria,7.53%）。丰度最高的科依次是消化链球菌科（Peptostreptococcaceae,平均占16.15%）,梭菌科I（Clostridiaceae_I,14.78%）,毛螺菌科（Lachnospiraceae,13.13%）,红蝽杆菌科（Coriobacteriaceae,12.31%）等。丰度最高的属是柯林斯氏菌属（Collinsella,11.44%）,艰难梭菌属（Peptoclostridium,10.91%）,狭窄梭菌属1（Clostridium_sensu_stricto_1,10.3%）,拟杆菌属（Bacteroides,7.41%）,消化链球菌属（Peptostreptococcus,5.21%）等。7只狞猫的肠道微生物中有平均15.35%的OTU没有归类到属。样本间聚类分析结果表明,来自同一动物园的样本聚为一支。[结论]本文通过高通量测序技术研究了狞猫肠道微生物的组成和多样性特征,为狞猫的救护饲养和消化生理学研究提供基础数据。     

群落分析中的16S rRNA及其基因16S rDNA优化扩增

本文较为完整地综述了16SrRNA在细胞中的地位和作用、转录组成、其全长基因中可变区与保守区的位置、在不同种类中的拷贝数、二级结构,及其在群落研究过程中PCR扩增产生的16S rRNA的异常序列与解决方法;以期为更多的科研工作者提供可靠参考和借鉴,提高以16S rRNA为靶分子的群落研究结果的准确性和真实性。     

IgA肾病与膜性肾病患者肠道微生物菌群结构分析

【背景】越来越多的证据表明肠道失衡与免疫介导的疾病相关,但肠道菌群和免疫介导的肾脏疾病之间的关系仍不清楚。【目的】通过Illumina高通量测序方法对IgA肾病(immunoglobulin A nephropathy, IgAN)、膜性肾病(membranous nephropathy, MN)患者和健康人群的肠道菌群进行比较。【方法】回顾性选择2020年9月–2021年12月期间,在甘肃省人民医院肾内科行肾穿刺活检并诊断为IgAN及MN患者的新鲜粪便标本,分别编号为IgAN组和MN组,收集体检中心健康人群粪便标本作为健康对照组,每组样本为10例。采用高通量测序技术对粪便样本中所有细菌的16S rRNA基因V3-V4区进行DNA测序,然后进行分类操作单元(operational taxonomic units, OTU)、物种分类、α多样性、β多样性等分析,比较3组之间的肠道菌群差异。【结果】与健康对照组相比,门水平上IgAN组的变形菌门(Proteobacteria)和放线菌门(Actinobacteria)比例明显增高,分别为18%vs. 4%和18.3%vs. 5%;属水平上I...     

基于高通量测序的褐飞虱肠道微生物多样性分析

【目的】探明褐飞虱Nilaparvata lugens成虫肠道微生物群落结构和多样性。【方法】分离褐飞虱成虫完整肠道并提取总DNA,利用Illumina MiSeq(PE300)技术对其肠道细菌16S rRNA的V3-V4变异区和真菌ITS2序列进行测序,统计肠道微生物的操作分类单元(operational taxonomic unit, OTU)数量,分析其物种组成、丰度及Alpha多样性。并通过qPCR技术验证随机挑选注释到的4种肠道菌的高通量测序数据的有效性。【结果】分别获得褐飞虱成虫肠道细菌16S rRNA和真菌ITS2优质序列32 395和24 986条,根据序列相似性进行聚类分析分别获得235和128个OTUs。其中,细菌共注释到7个门, 15个纲, 26个目, 45个科和73个属;真菌共鉴定到3个门, 9个纲, 12个目, 15个科和18个属。在门分类水平上,细菌以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)为优势门类;真菌以子囊菌门(Ascomycota)为绝对优势菌门。在属分类水平上,细菌的优势属为不动杆菌属Acinetobacter以及紫单胞菌科(Porphyromonadaceae)未确定属和毛螺菌科(Lachnospiraceae)未确定属,其丰度分别为36.37%, 17.22%和15.01%;真菌的优势属为粪壳菌纲(Sordariomycetes)未确定属,丰度为95.77%。Alpha多样性分析结果显示,褐飞虱肠道细菌(真菌)的观测物种数、Chao1指数、Shannon指数和Simpson 指数分别为235(128), 262.64(165.40), 3.90(0.91)和0.62(0.75)。4种肠道菌的qPCR结果显示高通量测序数据具有较高的有效性。【结论】褐飞虱成虫肠道细菌和真菌群落整体多样性比较丰富。研究结果为从共生微生物角度解析褐飞虱的环境适应性以及开发基于微生物防治的新技术等方面提供了依据。     

高通量测序技术分析猪粪堆肥过程中微生物群落结构变化

为了解猪粪堆肥过程中微生物群落结构组成及多样性的变化,采集猪粪堆肥过程的三个代表性样品—新鲜猪粪、高温堆肥、腐熟堆肥,利用Illumina Miseq高通量测序技术对16S rRNA V4～V5可变区序列进行测序,分别获得37 009、42 470、36 713条有效序列及328、280、160个操作分类单元(OTU)。Alpha多样性分析表明,在堆肥过程中微生物群落丰富度呈现降低趋势,而多样性呈现先上升后下降趋势。随着堆肥的进行,在门水平上,厚壁菌门、拟杆菌门和软壁菌门相对丰度降低,而变形菌门和放线菌门相对丰度升高;在属水平上,Turicibacter、Terrisporobacter、Parabacteroides、Clostridium sensu stricto、Corynebacterium等来自动物肠道的微生物相对丰度明显下降,Thermopolyspora、Thermomonospora、Thermobifida、Halocella等耐热耐盐微生物成为最主要优势菌。堆肥过程不同菌群优势度的变化是微生物与堆肥中各理化因子相互作用的结果。     

云南江城和黑井盐矿沉积物未培养放线菌多样性比较

类群特异性引物的应用使得研究者可以对感兴趣的微生物类群进行针对性研究.围绕云南江城和黑井两个地区的3个盐矿样点沉积物中放线菌的多样性和群落组成,我们通过放线菌特异性引物对总DNA进行16S rRNA基因扩增,经过克隆文库构建,利用酶切并选择其中不同带型的133个克隆的16S rRNA基因插入片段进行测序.系统发育分析和统计学结果表明,两地放线菌16S rRNA基因克隆广泛分布于整个放线菌门,同时发现部分序列可能属于放线菌的新类群.分析结果还预示,江城和黑井两地盐矿虽处云南不同地域含盐区,但两地未培养放线菌物种多样性和系统发育关系均较为相似.     

线粒体DNA高变区hν1快速测序方法及应用

本研究目的是使线粒体DNAhv1区的测序更加简单、快速和准确,以利于法医学检案。将线粒体DNAhv1高变区分别用三对重叠的引物进行全序列扩增,对这三对引物的扩增产物进行测序分析。用经过大量实验反复摸索得到的稳定的实验条件,对已确定为同一母亲所生的兄弟二人的样品进行分析,结果完全一样;对待确定姐弟关系的样品进行分析,结果是认定的;操作时间较原方法缩短一半。结果表明该方法是可替代原法的快速测序法。     

Sequence Variation of the Hypervariable Region in HCV Carriers with Normal ALT Levels: A Comparison with Symptomatic Carriers

The clinical significance of the hypervariable region (HVR) in the N-terminus of the E2/NS1 region, which encodes the putative envelope glycoprotein (gp 70) of HCV, has not yet been elucidated. We studied the relation between HVR changes and elevation of the alanine aminotransaminase (ALT) level due to liver cell injury as well as the persistence of HCV infection. Three patients (carrier group) who were HCV RNA positive and had normal ALT levels for as long as five years and three patients with high ALT levels were studied. None of the six patients had a history of treatment. HCV RNA was extracted from serum obtained from each patient in 1990 and 1995. The E2/NS1 region, including HVR-1 and HVR-2, was amplified using the RT-PCR method. PCR products were cloned and nucleotide sequences were determined using the dideoxynucleotide chain termination method. No clear correlation was found between the ALT levels and the number of nucleotide substitutions in HVR-1. The number of nucleotide substitutions in HVR-1 during the five years was greater than in other regions. Furthermore, more nucleotide substitutions occurred in the 1st and 2nd codon positions of HVR-1 than in the control region, even in the carrier group. In conclusion, HVR-1 changes are probably a more important factor in persistent viral infection than liver cell injury.     

Mutational analysis of domain antibodies reveals aggregation hotspots within and near the complementarity determining regions

High-affinity antibodies are critical for numerous diagnostic and therapeutic applications, yet their utility is limited by their variable propensity to aggregate either at low concentrations for antibody fragments or high concentrations for full-length antibodies. Therefore, determining the sequence and structural features that differentiate aggregation-resistant antibodies from aggregation-prone ones is critical to improving their activity. We have investigated the molecular origins of antibody aggregation for human V(H) domain antibodies that differ only in the sequence of the loops containing their complementarity determining regions (CDRs), yet such antibodies possess dramatically different aggregation propensities in a manner not correlated with their conformational stabilities. We find the propensity of these antibodies to aggregate after being transiently unfolded is not a distributed property of the CDR loops, but can be localized to aggregation hotspots within and near the first CDR (CDR1). Moreover, we have identified a triad of charged mutations within CDR1 and a single charged mutation adjacent to CDR1 that endow the poorly soluble variant with the desirable biophysical properties of the aggregation-resistant antibody. Importantly, we find that several other charged mutations in CDR1, non-CDR loops and the antibody scaffold are incapable of preventing aggregation. We expect that our identification of aggregation hotspots that govern antibody aggregation within and proximal to CDR loops will guide the design and selection of antibodies that not only possess high affinity and conformational stability, but also extreme resistance to aggregation.     

Species‐specific PCR primers for the mitochondrial genome control region hypervariable region 1 of the reef fish Lutjanus sebae

Lutjanus sebae is an important commercial and recreational fish found throughout the Indo‐West Pacific region. Using universal primers for the mitochondrial genome control region hypervariable region 1 (HVR1), we isolated a 385‐bp fragment of HVR1 then designed specific primers near each end of this sequence in the conserved regions flanking the hypervariable region. These primers were shown to yield good quantity and quality of product and to be species specific. Of 20 L. sebae studied, there were eight segregating sites and eight haplotypes. These primers will provide a useful tool for population genetics studies, identification of larvae and eggs and for wildlife forensics.     

Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage

The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.     

The men of Nelson's navy: a comparative stable isotope dietary study of late 18th century and early 19th century servicemen from Royal Naval Hospital burial grounds at Plymouth and Gosport, England

The Guizhou snub‐nosed monkey (Rhinopithecus brelichi) is a primate species endemic to the Wuling Mountains in southern China. With a maximum of 800 wild animals, the species is endangered and one of the rarest Chinese primates. To assess the genetic diversity within R. brelichi and to analyze its genetic population structure, we collected fecal samples from the wild R. brelichi population and sequenced the hypervariable region I of the mitochondrial control region from 141 individuals. We compared our data with those from the two other Chinese snub‐nosed species (R. roxellana, R. bieti) and reconstructed their phylogenetic relationships and divergence times. With only five haplotypes and a maximum of 25 polymorphic sites, R. brelichi shows the lowest genetic diversity in terms of haplotype diversity (h), nucleotide diversity (π), and average number of pairwise nucleotide differences (Π). The most recent common ancestor of R. brelichi lived ～0.36 million years ago (Ma), thus more recently than those of R. roxellana (～0.91 Ma) and R. bieti (～1.33 Ma). Phylogenetic analysis and analysis of molecular variance revealed a clear and significant differentiation among the three Chinese snub‐nosed monkey species. Population genetic analyses (Tajima's D, Fu's F_s, and mismatch distribution) suggest a stable population size for R. brelichi. For the other two species, results point in the same direction, but population substructure possibly introduces some ambiguity. Because of the lower genetic variation, the smaller population size and the more restricted distribution, R. brelichi might be more vulnerable to environmental changes or climate oscillations than the other two Chinese snub‐nosed monkey species. Am J Phys Anthropol, 2012. © 2011 Wiley Periodicals, Inc.     

丙型肝炎病毒高变区1模拟表位的交叉反应性分析

研究丙型肝炎病毒(Hepatitis C virus,HCV)高变区1(Hypervariable region 1,HVR1)抗原表位的交叉反应性,获取高反应性的抗原表位.设计并合成5种HVR1模拟表位基因,构建编码HVR1模拟表位的表达载体,表达并纯化表位蛋白.ELISA法检测表位蛋白与35份HCV抗体阳性血清的交叉反应性.包装HCV假病毒(HCV pseudotype particles,HCVpp),评价表位蛋白免疫BALB/c鼠血清在假病毒感染Huh7.5细胞中的作用.结果表明,表达纯化的5种表位蛋白(P1、P2、P5、P6、P8)均可与HCV抗体阳性血清反应,阳性反应率分别为54.3%(P1)、62.9%(P2)、80%(P5)、68.6%(P6)、54.3%(P8).表位蛋白P6、P8免疫BALB/c鼠血清对HCV假病毒感染Huh7.5细胞具明显的抑制作用.结果提示,选取的HVR1模拟表位在HCV感染免疫与疫苗研制中可能具有潜在的价值.     

Primers for amplifying the hypervariable,male‐transmitted COII‐COI junction region in amblemine freshwater mussels (Bivalvia: Unionoidea: Ambleminae)

Freshwater bivalves in the superfamily Unionoidea possess distinct male (M)‐ and female (F)‐transmitted mitochondrial DNA (mtDNA). The former evolves independently of and at a significantly faster rate than the latter. Thus, population genetic and phylogenetic analyses of M sequences facilitate the generation of independent estimates of genetic variation and evolutionary relationships which are often more robust than those provided by analyses of F sequences alone. However, M mtDNA's rapid substitution rate often renders polymerase chain reaction (PCR) amplification difficult with ‘universal’ primers. Herein, we report on three pairs of PCR primers that consistently amplify the hypervariable M COII‐COI gene junction region in 25 bivalve genera (Unionoidea: Ambleminae).     

Variability or conservation of hepatitis C virus hypervariable region 1? Implications for immune responses

The hypervariable region 1 (HVR1) of the E2 protein of hepatitis C virus (HCV) is highly heterogeneous in its primary sequence and is responsible for significant inter- and intra-individual variation of the infecting virus, which may represent an important pathogenetic mechanism leading to immune escape and persistent infection. A binding site for neutralizing antibodies (Ab) has also been allegedly identified in this region. Prospective studies of serological responses to synthetic oligopeptides derived from naturally-occurring HVR1 sequences showed promiscuous recognition of HVR1 variants in most patients via binding to C-terminal amino acid residues with conserved physicochemical properties. Monoclonal antibodies generated by immunization of mice with peptides derived from natural HVR1 sequences were shown to recognize several HVR1 variants in line with evidence gathered from studies using human sera. In addition, selected mAbs were able to bind HVR1 in the context of a complete soluble form of the E2 glycoprotein, indicating recognition of correctly folded sequences, and were shown to specifically capture circulating and recombinant HCV particles, suggesting that HVR1 is expressed on intact virus particles and therefore potentially able to interact with cellular receptor(s). These findings suggest that it is possible to induce a broadly reactive clonal immune response to multiple HCV variants and that this mechanism could be used in principle to induce protective immunity for a large repertoire of HCV variants.     

Follow-Up Study of Hypervariable Region Sequences of the Hepatitis C Virus (HCV) Genome in an Infant with Delayed Anti-HCV Antibody Responses

An infant born prematurely and infected with hepatitis C virus (HCV) one month after birth was followed for 4.5 years. The patient did not produce detectable anti-HCV antibodies until two years after the onset of hepatitis. Before seroconversion, a single clone of HCV, as determined by quasispecies of the hypervariable region (HVR) of the HCV genome, was almost exclusively found in the serum. After seroconversion, however, another distinct lineage of HCV clones replaced it within half a year. As HCV infection persisted further in the presence of anti-HCV antibodies, many derivatives of both sequence lineages emerged to exhibit the typical quasispecies feature of HVR sequences. Neither seroconversion nor the changes in HVR sequences influenced the serum aminotransferase titers.