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Primers for isothermal amplification of hepatitis C virus

a technology primers, which is applied in the field of primers for isothermal amplification of hepatitis c virus, can solve the problems of difficult design of specific primers capable of carrying out genotyping in the region, and the technique cannot determine the genotype of hcv gene, so as to achieve easy and rapid detection

Inactive Publication Date: 2006-02-23
HITACHI HIGH-TECH CORP
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0009] The present inventors have successfully designed primers that enable genotype-specific isothermal amplification in a core region of gene sequences belonging to HCV subtypes 1a, 1b, 2a, 2b and 3a genes. The isothermal amplification of a HCV sample using these primers results in genotype-specific amplification and thereby enables detection and genotyping of HCV subtypes 1a, 1b, 2a, 2b and 3a genes based on whether or not amplification occurs.
[0021] The detection method of the present invention can simultaneously detect two or more HCV subtypes by using two or more pairs of primers of the present invention.
[0023] The primers of the present invention enable the detection and genotyping of a HCV subtype by isothermal amplification. The present invention therefore enables easy and rapid detection (determination) and genotyping of HCV without requiring complicated temperature control as in PCR.

Problems solved by technology

It is difficult to detect HCV at initial stage of HCV infection by immunoassay using antibodies and to prevent the symptoms from becoming worse and / or the infected blood completely from contaminating into blood for transfusion.
This is probably because the HCV RNA has a complicated secondary structure as a result typically of intramolecular hydrogen bonds, a region that can be amplified by isothermal amplification is restricted, and it is very difficult to design specific primers capable of carrying out genotyping in the region.
This technique cannot determine the genotype of HCV gene although it can amplify the HCV gene.
Specifically, all the conventional HCV genotyping techniques using oligonucleotide primers require complicated temperature control in PCR and invite complicated procedures, long time and high cost for the determination and are not satisfactory.

Method used

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  • Primers for isothermal amplification of hepatitis C virus
  • Primers for isothermal amplification of hepatitis C virus
  • Primers for isothermal amplification of hepatitis C virus

Examples

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Effect test

example 1

Screening of Primers Capable of Typing HCV Subtype 1a Gene by NASBA

[0053] An optimal pair of oligonucleotide primers for genotype-specific isothermal amplification by NASBA was determined by designing sense primers and antisense primers in regions in the core region of the HCV subtype 1a gene which are capable of highly specifically typing, setting pairs of the oligonucleotide primers in various combinations and subjecting the pairs of primers to NASBA. The sense primers are oligonucleotide primers of SEQ ID NOs: 1, 24, 25, 26, 27, 28, 29, 30, 31 and 32, and the antisense primers are oligonucleotide primers of SEQ ID NOs: 11, 33, 34, 35, 36, 37, 38 and 39 listed in Table 2. Each of the antisense primer further had a sequence (AATTCTAATACGACTCACTATAGGGAGAAGG: SEQ ID NO: 45) including a T7 promoter sequence at the 5′ end.

TABLE 2SEQPrimerSequence*location**ID NORefHCV1p2015′-GAGGTCTCGTAGACCGTGCACCA-3′(23bp)2-25bp24S1HCV1p2025′-CACCATGAGCACGAATCCTA-3′(20bp)21-40bp1S2HCV1p2O35′-TCAGAT...

example 2

Screening of Primers Capable of Genotyping HCV Subtypes 1b, 2a, 2b and 3a

[0064] Optimal pairs of oligonucleotide primers for genotype-specific isothermal amplification of HCV subtypes 1b, 2a, 2b and 3a genes by NASBA were determined by the procedure of Example 1.

[0065] (1) HCV Subtype 1b Gene

[0066] Primers listed in Table 4 were designed based on the sequence of a specific region capable of typing the core region of the HCV subtype 1b gene (SEQ ID NO: 41 corresponding to 1 to 325 bp of the core region of HCV subtype 1b). Different pairs of these primers were subjected to isothermal amplification by NASBA under the same conditions as in Example 1 using, as a template, a HCV subtype 1b gene sample, and the presence or absence of, and the position of amplified product were determined by electrophoresis. In addition, the presence or absence of, and the position of amplified product by NASBA using samples of the other HCV subtypes were determined on pairs of primers which yielded the ...

example 3

Genotyping of HCV Subtypes 1a, 1b, 2a, 2b and 3a Genes by NASBA

[0076] Genotyping of HCV was carried out by isothermal amplification according to NASBA and electrophoresis by the procedure of Example 1. More specifically, the sense primers used are oligonucleotide primers corresponding to SEQ ID NOs: 1, 3, 5 and 7, and the antisense primers are oligonucleotide primers corresponding to SEQ ID NOs: 11, 12, 13 and 14 each further having a sequence including a T7 promoter sequence at the 5′ end.

[0077] A pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 2 was so designed as to yield an amplified product having a size of 217 bp as a result of the amplification of a sample HCV subtype 1a RNA. Likewise, a pair of oligonucleotide primers corresponding to SEQ ID NOs: 3 and 4, a pair of oligonucleotide primers corresponding to SEQ ID NOs: 5 and 6, and a pair of oligonucleotide primers corresponding to SEQ ID NOs: 7 and 8 were so designed as to yield amplified products having ...

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Abstract

The present application relates to primers for isothermal amplification of HCV each include at least eighteen consecutive bases corresponding to a 3′ end region of one selected from base sequences of SEQ ID NOs: 1-10, 21 and 22. The primers are specific to HCV subtypes 1a, 1b, 2a, 2b and 3a, respectively and enable genotyping of HCV by isothermal amplification.

Description

CLAIM OF PRIORITY [0001] The present application claims priority from Japanese application JP 2004-149448 filed on May 19, 2004, the content of which is hereby incorporated by reference into this application. FIELD OF THE INVENTION [0002] The present invention relates to primers for isothermal amplification of subtypes of hepatitis C virus (hereinafter briefly referred to as “HCV”), and methods for detecting or determining HCV using the primers. BACKGROUND OF THE INVENTION [0003] Chiron Corporation, Emeryville, Calif. identified the gene of HCV in 1988. The genome sequence of HCV including about 9,500 bases has been identified, and it has been revealed that HCV has a single strand RNA as its genome. HCV is often accompanied with mutation in its gene sequence, is classified as four to six subgroups based on gene sequences in regions accompanied with frequent mutation, and is further classified as, for example, subtypes 1a, 1b, 2a, 2b and 3a (P. Simmonds, et al., J. Gen Virol., 74, 66...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/70C12Q1/68C07H21/04G01N33/53C12N15/09G01N33/566G01N33/576
CPCC12Q1/707
Inventor TANABE, MAIKOUEMATSU, CHIHIRO
Owner HITACHI HIGH-TECH CORP
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