公开(公告)号：US09512183B2

公开(公告)日：2016-12-06

申请号：US14114808

申请日：2012-05-02

Applicant: Stuart Campbell Ray ,  Supriya Munshaw ,  Lin Liu

Inventor： Stuart Campbell Ray ,  Supriya Munshaw ,  Lin Liu

IPC: C07K14/005 ,  C12N9/02 ,  G01N33/569 ,  A61K39/29 ,  C12N7/00 ,  A61K39/12 ,  A61K39/00

CPC classification number: A61K39/29 ,  A61K39/12 ,  A61K2039/53 ,  C07K14/005 ,  C07K16/109 ,  C12N7/00 ,  C12N9/0069 ,  C12N2770/24221 ,  C12N2770/24234 ,  G01N33/56983 ,  G01N33/5767

Abstract: Synthetic representative HCV subtypes, including a 1a and 1b genome, dubbed Bole1a and Bole1b, are provided using an inventive method of Bayesian phylogenetic tree analysis, ancestral sequence reconstruction and covariance analysis. Bole1a branches centrally among 390 full-genome sequences used in its design, a carefully curated 143 sequence full-genome dataset, and separate genomic regions including an independent set of 214 E1E2 sequences from a Baltimore cohort. Bole1a is phylogenetically representative of widely circulating strains. Full genome non-synonymous diversity comparison and 9-mer peptide coverage analysis showed that Bole1a is able to provide more coverage (94% and 78% respectively) than any other sequence in the dataset including H77, a traditional reference sequence. Bole1a also provides unsurpassed epitope coverage when compared to all known T cell epitopes.

Abstract translation: 使用贝叶斯系统发育树分析，祖先序列重建和协方差分析的发明方法提供了合成代表性的HCV亚型，包括被称为Bole1a和Bole1b的1a和1b基因组。 Bole1a在其设计中使用的390个全基因组序列中集中分布，精心策划的143个全序列全基因组数据集，以及包含来自巴尔的摩队列的214个E1E2序列的独立基因组区域。 Bole1a是系统发育代表广泛流行的菌株。 全基因组非同义词多样性比较和9聚体肽覆盖分析显示，Bole1a能够提供比包含H77（传统参考序列）的数据集中的任何其他序列更多的覆盖率（分别为94％和78％）。 当与所有已知的T细胞表位相比时，Bole1a还提供无与伦比的表位覆盖。

公开(公告)号：US20140162340A1

公开(公告)日：2014-06-12

申请号：US14114808

申请日：2012-05-02

Applicant: Stuart Campbell Ray ,  Supriya Munshaw ,  Lin Liu

Inventor： Stuart Campbell Ray ,  Supriya Munshaw ,  Lin Liu

IPC: C07K14/005 ,  C12N9/02

CPC classification number: A61K39/29 ,  A61K39/12 ,  A61K2039/53 ,  C07K14/005 ,  C07K16/109 ,  C12N7/00 ,  C12N9/0069 ,  C12N2770/24221 ,  C12N2770/24234 ,  G01N33/56983 ,  G01N33/5767

Abstract: Synthetic representative HCV subtypes, including a 1a and 1b genome, dubbed Bole1a and Bole1b, are provided using an inventive method of Bayesian phylogenetic tree analysis, ancestral sequence reconstruction and covariance analysis. Bole1a branches centrally among 390 full-genome sequences used in its design, a carefully curated 143 sequence full-genome dataset, and separate genomic regions including an independent set of 214 E1E2 sequences from a Baltimore cohort. Bole1a is phylogenetically representative of widely circulating strains. Full genome non-synonymous diversity comparison and 9-mer peptide coverage analysis showed that Bole1a is able to provide more coverage (94% and 78% respectively) than any other sequence in the dataset including H77, a traditional reference sequence. Bole1a also provides unsurpassed epitope coverage when compared to all known T cell epitopes.

Abstract translation: 使用贝叶斯系统发育树分析，祖先序列重建和协方差分析的发明方法提供了合成代表性的HCV亚型，包括被称为Bole1a和Bole1b的1a和1b基因组。 Bole1a在其设计中使用的390个全基因组序列中集中分布，精心策划的143个全序列全基因组数据集，以及包含来自巴尔的摩队列的214个E1E2序列的独立基因组区域。 Bole1a是系统发育代表广泛流行的菌株。 全基因组非同义词多样性比较和9聚体肽覆盖分析显示，Bole1a能够提供比包含H77（传统参考序列）的数据集中的任何其他序列更多的覆盖率（分别为94％和78％）。 当与所有已知的T细胞表位相比时，Bole1a还提供无与伦比的表位覆盖。