HCV clade and prototype sequences thereof
Inventors
Sablon, Erwin • Quint, Wim • Van Doorn, Leen-Jan
Assignees
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Publication Number
US-8124747-B2
Publication Date
2012-02-28
Expiration Date
Abstract
The current invention relates to a previously unrecognized clade of HCV genotypes as well as to diagnostic, prophylactic and therapeutic applications of nucleic acids, proteins, and antibodies to said protein, derived of or based on the newly characterized hepatitis C viruses.
Core Innovation
The disclosed invention relates to Hepatitis C virus (HCV) and identifies a new HCV clade/genotype by phylogenetic analysis of NS5B prototype sequences together with associated 5′ non-coding region prototype sequences. The new clade/genotype is defined using phylogenetic distance relative to selected reference nucleic acids, and the disclosed sequence sets include corresponding nucleic acids encoding the relevant NS5B protein sequences as well as full length complements.
The invention provides isolated nucleic acid compositions and sequence-defined nucleic acid targets characterized by containing at least one nucleotide that is different from corresponding nucleotides in an HCV nucleic acid sequence of any of clades 1 to 6, while remaining phylogenetically close to at least one specified NS5B reference nucleic acid or its complement. The nucleic acid can be DNA, cDNA, a synthetic nucleic acid, or RNA in which “T” is replaced by “U.”
The disclosed sequence sets further include specific 5′ non-coding region regions used for genotyping and are tied to downstream nucleic acid and protein-based diagnostic and detection applications. The disclosure also includes example isolates that form a separate phylogenetic branch consistent with the newly identified clade/genotype.
Claims Coverage
The provided independent claims cover two main categories: isolated HCV nucleic acids defined by phylogenetic distance to specified NS5B reference sequences with an additional nucleotide-difference constraint relative to clades 1 to 6, and isolated HCV nucleic acids selected from specific SEQ ID NO sets, including full-length complements, that distinguish subtypes between two defined groups of reference sequences. In total, the claims define two inventive features using phylogenetic distance, SEQ ID selection, and subtype differentiation, while limiting nucleic acid type to DNA, cDNA, synthetic nucleic acid, or RNA with T→U substitution.
Phylogenetically close isolated HCV nucleic acid with clade-differentiating nucleotide
An isolated nucleic acid comprising an HCV nucleic acid sequence characterized by a phylogenetic distance less than or equal to 0.328 from specified NS5B reference nucleic acids or their complements, wherein the HCV nucleic acid sequence comprises at least one nucleotide different from the corresponding nucleotide in an HCV nucleic acid sequence of any of clades 1 to 6, and wherein the nucleic acid is DNA, cDNA, a synthetic nucleic acid, or RNA with “T” replaced by “U”.
Selected SEQ ID isolated HCV nucleic acid distinguishing subtypes between reference groups
An isolated nucleic acid comprising an HCV nucleic acid sequence selected from defined SEQ ID NOs and their full length complements, wherein the sequences set forth in one reference group are a different HCV subtype than those set forth in the other reference group, and wherein the nucleic acid is DNA, cDNA, a synthetic nucleic acid, or RNA with “T” replaced by “U”.
The claim set defines sequence-specific, isolated HCV nucleic acids associated with a newly identified clade/genotype using either a phylogenetic distance criterion to specified NS5B references plus a nucleotide difference from clades 1 to 6, or explicit selection from defined SEQ ID NOs and complement forms with subtype differentiation between two groups of reference sequences.
Stated Advantages
Enables definition of a new HCV clade/genotype using phylogenetic distance relative to specified NS5B and 5′ non-coding region prototype sequences.
Provides nucleic acid sequence targets that are phylogenetically close to specified references while containing at least one nucleotide different from corresponding nucleotides in clades 1 to 6.
Supports detection and genotyping using oligonucleotide primers and probes.
Supports diagnostic kit formats with solid supports for assays such as LiPA membrane strips.
Supports protein/antibody-based immunoassays using HCV antigens and competing antibodies.
Supports use of recombinant vectors and host cells as described in the disclosure.
Documented Applications
Oligonucleotide primers and probes for detection and genotyping of the disclosed HCV sequences.
Diagnostic kits using solid supports, including LiPA membrane strips, for HCV detection and genotyping.
Immunoassays using HCV antigens and antibodies, including competing antibody binding.
Use of recombinant vectors and host cells associated with the disclosed nucleic acid and protein sequence sets.
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