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| 1 | Quasispecies structure,cornerstone of hepatitis B virus infection: Mass sequencing approach显示文摘Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not identical;hence,HBV is considered a viral quasispecies.Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions,which is especially important in the P and S gene overlapping regions,but is less significant in the X and preCore/Core genes.Despite this restriction,several clinically and pathologically relevant variants have been characterized along the viral genome.Next-generation sequencing(NGS)approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains.In the present review,we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus.In addition,we provide an analysis of the clinical implications of HBV variants and their study by NGS. | Francisco Rodriguez-Frias Maria Buti David Tabernero Maria Homs | 2013 | World Journal of Gastroenterology2013，19，41： | 11 |
| 2 | Quasispecies dynamics in main core epitopes of hepatitis B virus by ultra-deep-pyrosequencing显示文摘AIM:To investigate the variability of the main immunodominant motifs of hepatitis B virus(HBV) core gene by ultra-deep-pyrosequencing(UDPS).METHODS:Four samples(2 genotype A and 2 genotype D) from 4 treatment-na ve patients were assessed for baseline variability.Two additional samples from one patient(patient 4,genotype D) were selected for analysis:one sample corresponded to a 36-mo treatment-free period from baseline and the other to the time of viral breakthrough after 18 mo of lamivudine treatment.The HBV region analyzed covered amino acids 40 to 95 of the core gene,and included the two main epitopic regions,Th50-69 and B74-84.UDPS was carried out in the Genome Sequencer FLX system(454 Life Sciences,Roche).After computer filtering of UDPS data based on a Poisson statistical model,122 813 sequences were analyzed.The most conserved position detected by UDPS was analyzed by site-directed mutagenesis and evaluated in cell culture.RESULTS:Positions with highest variability rates were mainly located in the main core epitopes,confirming their role as immune-stimulating regions.In addition,the distribution of variability showed a relationship with HBV genotype.Patient 1(genotype A) presented the lowest variability rates and patient 2(genotype A) had 3 codons with variability higher than 1%.Patient 3 and 4(both genotype D) presented 5 and 8 codons with variability higher than 1%,respectively.The median baseline frequencies showed that genotype A samples had higher variability in epitopic positions than in the other positions analyzed,approaching significance(P = 0.07,sample 1 and P = 0.05,sample 2).In contrast,there were no significant differences in variability between the epitopic and other positions in genotype D cases.Interestingly,patient 1 presented a completely mutated motif from amino acid 64 to 67(E 64 LMT 67),which is commonly recognized by T helper cells.Additionally,the variability observed in all 4 patients was particularly associated with the E 64 LMT 67 motif.Codons 78 and 79 were highly conserved in all samples,in keeping with their involvement in the interaction between the HBV virion capsid and the surface antigens(HBsAg).Of note,codon 76 was even more conserved than codons 78 and 79,suggesting a possible role in HBsAg interactions or even in hepatitis B e antigen conformation.Sequential analysis of samples from patient 4(genotype D) illustrated the dynamism of the HBV quasispecies,with strong selection of one minor baseline variant coinciding with a decrease in core variability during the treatment-free and lamivudinetreated period.The drop in variability seemed to result from a 'steady state' situation of the HBV quasispecies after selection of the variant with greatest fitness.CONCLUSION:Host immune pressure seems to be the main cause of HBV core evolution.UDPS analysis is a useful technique for studying viral quasispecies. | Maria Homs Maria Buti David Tabernero Josep Quer Alex Sanchez Noelia Corral Rafael Esteban Francisco Rodriguez-Frias | 2012 | World Journal of Gastroenterology2012，18，42： | 5 |
| 3 | Quantitative longitudinal evaluations of hepatitis delta virus RNA and hepatitis B virus DNA shows a dynamic, complex replicative profile in chronic hepatitis B and D显示文摘 | Melanie Schaper Francisco Rodriguez-Frias Rosendo Jardi David Tabernero Maria Homs Gerardo Ruiz Josep Quer Rafael Esteban Maria Buti | 2010 | Journal of Hepatology2010，，5： | 1 |
| 4 | A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model显示文摘 | Clara Ramírez Josep Gregori Maria Buti David Tabernero Sílvia Camós Rosario Casillas Josep Quer Rafael Esteban Maria Homs Francisco Rodriguez-Frías | 2013 | Antiviral Research2013，，2： | 1 |
| 5 | Successful use of entecavir for a severe case of reactivation of hepatitis B virus following polychemotherapy containing rituximab显示文摘 | Mayra J. Sanchez Maria Buti Maria Homs Andres Palacios Francisco Rodriguez-Frias Rafael Esteban | 2009 | Journal of Hepatology2009，，6： | 1 |
| 6 | Biogas production and saccharification of Salix pretreated at different steam explosion conditions 显示文摘 | SveinJ Hom Maria M Estevez b Henrik K Nielsen | 2011 | BioresourceTechnology2011，102，17： | 1 |
| 7 | Quantitative longitudinal evaluations of hepatitis delta virus RNA and hepatitis B virus DNA shows a dynamic, complex replicative profile in chronic hepatitis B and D显示文摘 | Melanie Schaper Francisco Rodriguez-Frias Rosendo Jardi David Tabernero Maria Homs Gerardo Ruiz Josep Quer Rafael Esteban Maria Buti | 2010 | Journal of Hepatology2010，，5： | 1 |
| 8 | Analysis of hepatitis B genotype changes in chronic hepatitis B infection: Influence of antiviral therapy显示文摘 | Rosendo Jardi Francisco Rodriguez-Frias Melanie Schaper Elena Giggi David Tabernero Maria Homs Rafael Esteban Maria Buti | 2008 | Journal of Hepatology2008，，5： | 1 |
| 9 | Enhanced history matching process by incorporation of saturation logs as model selection criteria显示文摘This paper proposes a methodology for an alternative history matching process enhanced by the incorporation of a simplified binary interpretation of reservoir saturation logs(RST) as objective function. Incorporating fluids saturation logs during the history matching phase unlocks the possibility to adjust or select models that better represent the near wellbore waterfront movement, which is particularly important for uncertainty mitigation during future well interference assessments in water driven reservoirs. For the purposes of this study, a semi-synthetic open-source reservoir model was used as base case to evaluate the proposed methodology. The reservoir model represents a water driven, highly heterogenous sandstone reservoir from Namorado field in Brazil. To effectively compare the proposed methodology against the conventional methods, a commercial reservoir simulator was used in combination with a state-of-the-art benchmarking workflow based on the Big LoopTMapproach. A well-known group of binary metrics were evaluated to be used as the objective function, and the Matthew correlation coefficient(MCC) has been proved to offer the best results when using binary data from water saturation logs. History matching results obtained with the proposed methodology allowed the selection of a more reliable group of reservoir models,especially for cases with high heterogeneity. The methodology also offers additional information and understanding of sweep behaviour behind the well casing at specific production zones, thus revealing full model potential to define new wells and reservoir development opportunities. | APONTE Jesus Manuel WEBBER Robert CENTENO Maria Astrid DHAKAL Hom Nath SAYED Mohamed Hassan MALAKOOTI Reza | 2023 | Petroleum Exploration and Development2023，50，2： | 0 |
| 10 | 以饱和度测井数据为油藏模型选择标准的改进历史拟合方法显示文摘提出了一种将储集层饱和度测井数据二元简化形式作为油藏模型选择标准的改进历史拟合方法,使用半合成开源油藏模型作为基础模型对提出的方法进行评估,并与常规方法进行了比较。历史拟合阶段引入流体饱和度测井数据,有助于调整或选择能够更好地表征近井地带水驱前缘推进的模型,从而有效降低水驱油藏后续井间干扰评价的不确定性。研究表明,对含水饱和度测井数据进行二元分类时,马修斯相关系数作为分类指标的效果最佳。与常规方法相比,根据提出的方法可以选出一组更可靠的储集层(特别是强非均质性储集层)模型,选出的模型历史拟合效果更好,对近井地带含水饱和度、生产井及其不同层位含水率的拟合质量更好。 | APONTE Jesus Manuel WEBBER Robert CENTENO Maria Astrid DHAKAL Hom Nath SAYED Mohamed Hassan MALAKOOTI Reza | 2023 | 石油勘探与开发2023，50，2： | 0 |
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