# Patent

## Title
PCR primer set for detecting hepatitis B virus, method for detecting hepatitis B using the primer set, and hepatitis B virus detection kit including the primer set

## Abstract

Provided are a primer set selected from the group consisting of primers having nucleotide sequences as set forth in SEQ ID NOS: 1–40, a method for detecting hepatitis B virus by polymerase chain reaction (PCR) using the primer set, and a hepatitis B virus detection kit including the primer set.

## Background
BACKGROUND OF THE INVENTION
This application claims priority from Korean Patent Application No. 2003-56432, filed on Aug. 14, 2003, in the Korean Intellectual Property Office, the disclosure of which is incorporated herein in its entirety by reference.
1. Field of the Invention
The present invention relates to a primer set selected from the group consisting of primers having nucleotide sequences as set forth in SEQ ID NOS: 1 through 40, a method for detecting hepatitis B virus in which PCR is performed using the primer set, and a hepatitis B virus detection kit including the primer set.
2. Description of the Related Art
Hepatitis B is a representative virus infectious disease prevalent worldwide. It is one of common infectious diseases, ranking ninth as a cause of death. More than 300 millions of the global population is chronic hepatitis B virus carriers. Therefore, chronic hepatitis, hepatocirrhosis, liver cancer, and the like cause a million of death per a year. In this country, it is known that about 5-10% of the entire population is hepatitis B virus carriers.
Hepatitis B virus (HBV) is a virus that is consisted of viral proteins including three antigen proteins, HBsAg, HBcAg, and HBeAg. HBV DNA is protected by a protein structure called as core antigen (HBcAg) and a core is enveloped with an envelope protein known as surface antigen or S antigen (HBsAg).
As detection methods for hepatitis B, there have been widely used liver function tests that quantify T protein, albumin, T bilirubin, sGOT, sGPT, r-GPT, or alkaline phosphatase (ALP), serological detection of HBsAg and HBeAg using enzyme immunoassay, and the like. However, these methods are effective in detecting advanced hepatitis B but have problems such as difficulty of early diagnosis and low reliability.
Therefore, recently, there have been widely used a hybrid capture assay, a branched DNA assay, and a genetic assay based on polymerase chain reaction (PCR). In particular, the PCR-based genetic assay is preferred because it has high sensitivity and rapidity, and a pharmacological action against hepatitis B can be understood by observing the degree of proliferation of HBV.
PCR is a technique in which when a primer set binds to complementary strands of target nucleic acid sequence, a gene between the two primer binding sites is amplified to more than several hundreds of thousands of copies within a short time. PCR is well known in the pertinent art. In PCR, two nucleic acid primers complementary to corresponding strands of a target nucleic acid sequence are annealed to denatured strands of the target nucleic acid sequence under hybridization conditions, and then DNA polymerase, which is normally thermal stable, initiates extension at the ends of the hybridized primers to obtain DNA double strands. The above procedure is repeated to multiply the target nucleic acid sequence. When the nucleic acid primers are not hybridized with the target nucleic acid sequence, no amplified PCR products are obtained. In this case, the PCR primers serve as hybridization probes.
The PCR products thus amplified can be detected by observing labeled nucleotides in amplified strands using labeled primers. The labeled primers may be primers labeled with radioactive substance, fluorescent dye, digoxygenin, horseradish peroxidase, alkaline phosphatase, acridium ester, biotin, and jack bean urease, but are not limited thereto. PCR products obtained using non-labeled primers can be detected by visualization with dye after gel electrophoresis.
However, with respect to diagnosis of hepatitis B based on these PCR techniques, there may arise problems in that a long gene amplification time of 2-3 hours is required, false positive or false negative results may be yielded, and accurate diagnosis is difficult due to the presence of different genotypes. Therefore, to increase the diagnostic accuracy for hepatitis B, detection methods using both PCR and hybridization have been suggested. However, these detection methods also require an excessively long detection time and are costly.
SUMMARY OF THE INVENTION
The present invention provides a primer set for detecting hepatitis B virus rapidly and accurately, a method for detecting hepatitis B virus by PCR using the primer set, and a hepatitis B virus detection kit including the primer set.
According to an aspect of the present invention, there is provided a PCR set selected from the group consisting of the following primer sets: (a) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:1 and a primer having a nucleotide sequence as set forth in SEQ ID NO:2; (b) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:1 and a primer having a nucleotide sequence as set forth in SEQ ID NO:3; (c) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:5; (d) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:6; (e) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:7; (f) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:8 and the primer having the nucleotide sequence as set forth in SEQ ID NO:7; (g) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:9 and a primer having a nucleotide sequence as set forth in SEQ ID NO:10; (h) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:11 and a primer having a nucleotide sequence as set forth in SEQ ID NO:12; (i) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:13 and a primer having a nucleotide sequence as set forth in SEQ ID NO:14; (j) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:15 and a primer having a nucleotide sequence as set forth in SEQ ID NO:16; (k) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:17 and a primer having a nucleotide sequence as set forth in SEQ ID NO:18; (l) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:19 and a primer having a nucleotide sequence as set forth in SEQ ID NO:20; (m) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:21 and a primer having a nucleotide sequence as set forth in SEQ ID NO:22; (n) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:23 and a primer having a nucleotide sequence as set forth in SEQ ID NO:24; (o) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID-NO:25 and a primer having a nucleotide sequence as set forth in SEQ ID NO:26; (p) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:27 and a primer having a nucleotide sequence as set forth in SEQ ID NO:28; (q) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:29 and a primer having a nucleotide sequence as set forth in SEQ ID NO:30; (r) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:31 and a primer having a nucleotide sequence as set forth in SEQ ID NO:32; (s) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:33 and a primer having a nucleotide sequence as set forth in SEQ ID NO:34; (t) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:35 and a primer having a nucleotide sequence as set forth in SEQ ID NO:36; (u) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:37 and a primer having a nucleotide sequence as set forth in SEQ ID NO:38; and (v) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:39 and a primer having a nucleotide sequence as set forth in SEQ ID NO:40.
According to another aspect of the present invention, there is provided a method for detecting hepatitis B virus, which includes amplifying a nucleic acid sample obtained from an organism by PCR using the primer set.
According to another aspect of the present invention, there is provided a hepatitis B virus detection kit including the primer set.



BRIEF DESCRIPTION OF THE DRAWINGS
The above and other features and advantages of the present invention will become more apparent by describing in detail exemplary embodiments thereof with reference to the attached drawings in which:
FIG. 1 schematically illustrates the genome sequence of hepatitis B virus (HBV) including target nucleotide sequences for PCR primer sets according to the present invention and the positions of the HBV genome sequence binding with primers of SEQ ID NOS: 1 through 8 according to the present invention;
FIG. 2 illustrates a branch diagram of genotypes A-F of HBV and 90% or more homology regions of each genotype selected as candidate regions for primers to design PCR primer sets according to the present invention;
FIG. 3 illustrates Interaction Plot-Data Means for Concentration for each primer according to the present invention after 40 cycles of PCR at 95° C. for 20 seconds, 58° C. for 30 seconds, and 72° C. for 40 seconds, using MJResearch PTC-100 machine;
FIGS. 4A and 4B are graphs that illustrate respectively the concentration of PCR products versus annealing temperature and the concentration of PCR products versus extension temperature, in a two-step PCR analysis using primers of the present invention; and FIG. 4C is a comparative graph that illustrates the concentration of PCR products versus annealing temperature in a typical three-step PCR analysis and a two-step PCR analysis using primers of the present invention;
FIG. 5 schematically illustrates a top view and a sectional view (FIG. 5A) and a bottom view (FIG. 5B) of a microchip used in the present invention;
FIG. 6 illustrates results of 2% TAE agarose gel electrophoresis for PCR products after a two-step PCR on a microchip using primers according to the present invention;
FIG. 7A is a comparative graph that illustrates a PCR time required for almost same DNA concentration in the present invention and a conventional technique, and FIG. 7B is an enlarged view that illustrates only the concentration values of FIG. 7A; and
FIG. 8 illustrates diagnostic results for 100 Korean persons based on molecular weight marker after electrophoresis using hepatitis detection kits according to the present invention and a conventional technique.



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a PCR set selected from the group consisting of the following primer sets: (a) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:1 and a primer having a nucleotide sequence as set forth in SEQ ID NO:2; (b) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:1 and a primer having a nucleotide sequence as set forth in SEQ ID NO:3; (c) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:5; (d) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:6; (e) a primer set including the primer having the nucleotide sequence as set forth in SEQ ID NO:4 and a primer having a nucleotide sequence as set forth in SEQ ID NO:7; (f) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:8 and the primer having the nucleotide sequence as set forth in SEQ ID NO:7; (g) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:9 and a primer having a nucleotide sequence as set forth in SEQ ID NO:10; (h) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:11 and a primer having a nucleotide sequence as set forth in SEQ ID NO:12; (i) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:13 and a primer having a nucleotide sequence as set forth in SEQ ID NO:14; (j) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:15 and a primer having a nucleotide sequence as set forth in SEQ ID NO:16; (k) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:17 and a primer having a nucleotide sequence as set forth in SEQ ID NO:18; (l) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:19 and a primer having a nucleotide sequence as set forth in SEQ ID NO:20; (m) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:21 and a primer having a nucleotide sequence as set forth in SEQ ID NO:22; (n) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:23 and a primer having a nucleotide sequence as set forth in SEQ ID NO:24; (o) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:25 and a primer having a nucleotide sequence as set forth in SEQ ID NO:26; (p) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:27 and a primer having a nucleotide sequence as set forth in SEQ ID NO:28; (q) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:29 and a primer having a nucleotide sequence as set forth in SEQ ID NO:30; (r) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:31 and a primer having a nucleotide sequence as set forth in SEQ ID NO:32; (s) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:33 and a primer having a nucleotide sequence as set forth in SEQ ID NO:34; (t) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:35 and a primer having a nucleotide sequence as set forth in SEQ ID NO:36; (u) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:37 and a primer having a nucleotide sequence as set forth in SEQ ID NO:38; and (v) a primer set including a primer having a nucleotide sequence as set forth in SEQ ID NO:39 and a primer having a nucleotide sequence as set forth in SEQ ID NO:40.
The present invention also provides a method for detecting hepatitis B virus, which includes amplifying a nucleic acid sample obtained from an organism by PCR using the primer set.
The PCR may be a two-step PCR including a denaturation step and an annealing and extension step and may be performed for 30 minutes or less.
The PCR may be performed on a micro PCR chip using 0.2-1 μM of each primer and 0.01 pg to 1 μg of a template DNA.
The micro PCR chip may include a silicon wafer, a surface of which is formed
The PCR may be performed under conditions of denaturation at 86-97° C. for 1-30 seconds and annealing and extension at 60-70° C. for 6-30 seconds with a PCR chamber made by silicon lithography and the other surface is formed with a heater for heating the PCR chamber; and a glass wafer having an inlet and an outlet.
The present invention also provides a hepatitis B virus detection kit including the primer set.
To facilitate understanding of the invention, a number of terms are defined below. The term “nucleic acid” refers to a molecule in which the 3′-end of pentose in one nucleotide is linked to the 5′-end of adjacent pentose via phosphodiester bond and nucleotide residues are presented as a specific sequence, i.e., linear sequence.
The term “target nucleic acid” or “nucleic acid target” refers to a specific nucleic acid sequence of interest. Therefore, “target” may be present in another nucleic acid molecule or large nucleic acid molecule. As used herein, preferably, the term “target” refers to a sequence of two or more nucleotides in a gene of hepatitis B virus (HBV).
The term “nucleic acid primer” refers to an oligonucleotide or polynucleotide used in a method of the present invention. The oligonucleotide may also be used as an amplification primer for PCR. However, as used herein, the amplification primer is called as simply “primer”. Here, the oligonucleotide or polynucleotide may include a modified bond such as phosphorothioate bond.
A target DNA for the PCR primer sets according to the present invention is a genetic fragment that contains few genetic variations in the core of HBV. Therefore, diagnostic accuracy is excellent and diagnosis for different genotypes such as genotypes A, B, C, D, E, and F is possible. In addition, accuracy and reproducibility of diagnosis are excellent in a rapid PCR machine that takes 30 minutes or less as well as in a PCR machine that takes generally 2-3 hours.
FIG. 1 schematically illustrates a genome sequence of HBV including target nucleotide sequences for PCR primer sets according to the present invention and the positions of the HBV genome sequence binding with primers of SEQ ID NOS: 1 through 8 according to the present invention. Although not shown, primers of SEQ ID NOS: 9-12 and 23-26 are attached to a surface gene region of HBV gene and primers of SEQ ID NOS: 13-22 and 27-36 are attached to an x gene region of the HBV gene.
FIG. 2 illustrates a branch diagram of genotypes A-F of HBV that can be detected using the PCR primer sets according to the present invention. Such a branch diagram of genotypes is a diagram that represents genomic groups having a high sequence homology to each other and genomes of each genomic group having commonly a specific gene region absent from other genomic groups.
Hereinafter, the present invention will be described more specifically by Examples. However, the following Examples are provided only for illustrations and thus the present invention is not limited to or by them.
EXAMPLE 1
Preparation of Primers
Primers are required to be designed so that they amplify a HBV gene containing various mutant sequences and distinguishes the HBV gene from another virus gene. For this, the present inventors (1) investigated and analyzed the characteristics of HBV genome, (2) selected the regions of the HBV genome that are genetically well conserved and have few variations by environmental factors and the like as candidate regions for primers, and (3) designed primers based on the selected regions of the HBV genome.
1.1 Characterization of HBV Genome
Referring to FIG. 1, a HBV genome is a 3.2 kb in size and contains four genes, S, C, P, and X.
HBsAg encoded by the S gene has serological antigenic sites for determining serological subtypes. That is, HBsAg carries a common determinant “a” (amino acid residue: 124-147) and subtype specific determinants, “dw, dr, yw, and yr” (amino acid 122 (d=lysine and y=arginine) and amino acid 160 (w=lysine and r=arginine) for immune response against monoclonal antibody. The common determinant “a” for all subtypes of HBsAg is a main region for anti-HBs immune response and is present in the form of various mutations in HBV. In classification of genotypes of HBV, complete viral genomes are compared (8% for genotypes A-D, 14% for genotype F). The nucleotide sequence of the S gene is utilized as a standard in classifying as a new genotype [Magnius LO et al., Intervirology, 1995; 38(1-2): 24-34].
HBeAg and HBcAg encoded by the C gene have clinically important genetic polymorphisms. HBeAg is an important protein marker of HBV to be recognized by the immune system of a host cell and has genetic polymorphisms to avoid a host cell-mediated immune response. In particular, a preCore mutation that causes premature termination of preCore (called as “translation stop codon mutation”) has been well known [Li J S et al, J. Virol. 1993 September; 67(9): 5402-10 and Okamoto H. et al., J. Virol. 1990 March; 64(3): 1298-303].
HBV polymerase encoded by the P gene has reverse-transcription activity. The reverse-transcription activity is inhibited by lamivudine which is a nucleoside analog and is also used for the treatment of HIV infection. It is known that long-term drug administration induces selective mutation of a YMDD motif related to the reverse-transcription activity [Tipples G A. et al., Hepatology, 1996, September; 24(3): 714-7].
As described above, after investigating the mutation and genotypes of known HBV genome, well-conserved gene regions were selected as candidate regions for primers.
1.2 Selection of Candidate Regions for Primers
Currently known gene groups of the genotypes A-F of HBV were searched in GenBank and patent documents. The homology and mutation sites of the nucleotide sequences of these gene groups were analyzed and regions having a 90% or more homology for each genotype were selected as candidate regions for primers.
FIG. 2 illustrates a branch diagram of the genotypes A-F of HBV and selection of 90% or more homology regions for each genotype as candidate regions for primers to design PCR primer sets according to the present invention.
1.3 Design of Primers
i) Requirements of Primers for Rapid PCR
Various requirements must be satisfied to design primers for rapid PCR. PCR is based on effective variation of temperature for maximizing enzyme activity. That is, temperature and enzyme activity are main factors for PCR. In a conventional PCR, three-steps, i.e., denaturation, annealing, and extension are performed by changing the temperature.
In the present invention, to minimize a time required for polymerization by polymerase, classical annealing and extension steps were performed at the same time. Furthermore, to maintain a high polymerization yield, primers with high melting temperature (Tm) were used.
Therefore, primers of the present invention were designed so that PCR products had at least a difference of 100-200 bps. In addition, primers of the present invention were designed to satisfy the following requirements: amplification of only a specific region, creation of sufficient PCR products so that the PCR products can be used in next analysis step, no interference between the primers during PCR, high Tm, no hairpin structures, no primer self-dimers or primer pair-dimers, no more than 4 consecutive repeats of one base, no microsatellites, and no repetitive sequences. Primers were designed by HYBsimulatorTM (Advanced Gene Computing Technologies, Inc.).
ii) Selection of Primers
Detailed sequences of the designed primers were analyzed using ClustaIX software based on a 90% homology of the candidate regions for the primers.
Primers with 100% homology to the candidate regions (for example, primer 13) were selected as desired primers. On the other hand, primers that had no 100% homology to the candidate regions but were used for important amplification sites (for example, primer 14) were designed to contain degenerate bases instead of bases of nucleotide mismatch sites after sequencing.







TABLE 1







Degenerate bases








Degenerate Base
Nucleotide





R
A/G


Y
C/T


M
A/C


K
G/T


S
C/G


W
A/T


B
C/G/T


D
A/G/T


H
A/C/T


V
A/C/G


N
A/C/G/T









The sequences and characteristics of the designed primers are summarized in Table 2 below.







TABLE 2







Sequences and characteristics of primers


 














Primer
Primer
Sequence
Primer
Primer
Primer
PCR product



Set No.
No.
(5′→3′)
Length (bp)
Tm(° C.)
Direction
Length (bp)

















GS01
P1
GTGGCTTTGGGGCATGGACATT
22
61.5
F
142



 



P2
CTCTAAGGCCTCCCGATACAG
21
52.4
R



 


GS02
P1
GTGGCTTTGGGGCATGGACATT
22
61.5
F
97


 



P3
TCGAATAGAAGGAAAGAAGTCAGA
24
51.3
R



 


GS03
P4
GCTTTGGGGCATGGACATTGACC
23
63.1
F
183


 



P5
GCTTGCCTGAGTGCTGTATGGTGA
24
60.1
R



 


GS04
P4
GCTTTGGGGCATGGACATTGACC
23
63.1
F
118


 



P6
AGCAGAGGCGGTGTCGAGGAGAT
23
62.2
R



 


GS05
P4
GCTTTGGGGCATGGACATTGACC
23
63.1
F
120


 



P7
AGAGCAGAGGCGGTGTCGAGGAGAT
25
64.3
R



 


GS06
P8
GGCTTTGGGGCATGGACATTGACC
24
65.8
F
121


 



P7
AGAGCAGAGGCGGTGTCGAGGAGAT
25
64.3
R



 


GS07
P9
TAGGACCCCTGCTCGTGTAA
20
60.65
F
100


 



P10
AGAAAATTGAGAGAAGTCCACCA
23
59.26
R



 


GS08
P11
TGGTGGACTTCTCTCAATTTTC
22
58.29
F
176


 



P12
GAAGATGAGGCATAGCAGCAG
21
60.13
R



 


GS09
P13
CGATCCATACTGCGGAACTC
20
60.62
F
175


 



P14
GACGGGACGTAAACAAAGGA
20
59.97
R



 


GS10
P15
GAATCCCGCGGACGAC
16
61.21
F
103


 



P16
GACCGCGTAAAGAGAGGTG
19
58.46
R



 


GS11
P17
GCGGACGACCCCTCTC
16
60.31
F
153


 



P18
GTGCAGAGGTGAAGCGAAGT
20
60.6
R



 


GS12
P19
CACCTCTCTTTACGCGGTCT
20
59.5
F
100


 



P20
CGTTCACGGTGGTCTCCAT
19
61.99
R



 


GS13
P21
GAGGCTGTAGGCATAAATTGG
21
58.73
F
100


 



P22
CTTGGAGGCTTGAACAGTGG
20
60.82
R



 


GS14
P23
TCTTTGTATTAGGAGGCTGTAGGC
24
60.16
F
154


 



P24
ATAAGGGTCAATGTCCATGC
20
57.33
R



 


GS15
P25
TAGGACCCCTKCBCGTGTTA
20

F
100


 



P26
MGAAAATTGAGAGAAGTCMACCM
23

R



 


GS16
P27
KGGTKGACTTCTCTCAATTTTC
22

F
176


 



P28
GAAGATGAGGCATAGMAGCAG
21

R



 


GS17
P29
CGATCCATACTGYRGAACTC
20

F
175


 



P30
GAYGGRACGTASACSAAGKA
20

R



 


GS18
P31
GAATCCHGCGGACGAM
16

F
103


 



P32
GWCCGCGTAAAGAGAGGYG
19

R



 


GS19
P33
GCGGACGAMCCBTCTB
16

F
153


 



P34
GTGCAGAGGTGAAGSGAAGT
20

R



 


GS20
P35
CRCCTCTCTTTACGCGGWCT
20

F
100


 



P36
CGTTCACGGTGGTYKCCAT
19

R



 


GS21
P37
GAGGCTGTAGGCATAA
21

F
100


 



P38
CTTGGAGGCKTGAAMAGT
20

R



 


GS22
P39
TSTTTGTAYTVGGAGGCTGTAGGC
24

F
154


 



P40
ATAHGKRTCAATGTCCATGC
20

R





F: forward direction, R: reverse direction






EXAMPLE 2
PCR Experiments
To minimize a difference between PCR experiments, other reagents except DNA samples were first mixed to prepare a two-fold concentrated master mixture. Then, the master mixture was mixed with the DNA samples (1:1, by volume) to obtain a PCR mixture.
The composition of the master mixture is as follows:
















5xPCR buffer solution
 1.0 μl



Distilled water
1.04 μl



10 mM dNTPs
 0.1 μl



20 μM of each primer mixture
 0.2 μl



Enzyme mixture
0.16 μl










2.1: PCR on Conventional PCR Tubes
The PCR mixture prepared previously was loaded in MJRsearch PTC-100 machine and a PCR cycle of 95° C. for 20 seconds, 58° C. for 30 seconds, and 72° C. for 40 seconds was then repeated for 40 times.
To select optimal primers, PCR was performed with varying the type of primers (primers 1-5), experimental temperature (50° C., 53° C., 56° C., and 59° C.), and the concentration of MgCl2 (2.5 mM and 3.5 mM), and correlation between these experimental parameters is shown in FIG. 3.
FIG. 3 illustrates Interaction Plot-Data Means for Concentration for each primer. According to the experimental result, as compared to the primer 5 used as control (represented by red line), performance difference between other primers was insignificant.
2.2 Rapid PCR Experiments
The performance of the above PCR mixture at annealing and extension temperatures was analyzed and two-step temperature experiments for obtaining optimal PCR time were performed. The experimental results are presented in FIGS. 4A and 4B. As shown in FIGS. 4A and 4B, the primers of the present invention exhibited high amplification efficiency even at a high annealing temperature due to high Tm. The result shows that the annealing temperatures are within the extension temperature range.
Based on the above result, comparative experiments between a three-step PCR (95° C. for 20 seconds, 58° C. for 30 seconds, and 72° C. for 40 seconds) and a two-step PCR (95° C. for 20 seconds and 68° C. for 30 seconds) were performed to obtain an optimal time required for PCR and the results are shown in FIG. 4C. As shown in FIG. 4C, the two-step PCR exhibited the same pattern for the concentration of PCR products as the three-step PCR.
FIG. 4A illustrates the concentration of PCR products versus annealing temperature and FIG. 4B illustrates the concentration of PCR products versus extension temperature.
2.3 Cross Reactivity Among Viruses
Whether the primers of the present invention react with other viruses was analyzed. First, comparative analysis between known nucleotide sequences was performed using BLAST search. According to the comparative analysis results, the primers of the present invention showed 100% homology with only HBV. When PCR was performed using the following five viruses and human gDNA, no cross reactivity was observed. The experimental results for cross reactivity are summarized in Table 3 below.







TABLE 3







Experimental results for cross reactivity













Section
HIV
CMV
HPV
HSV-1
HSV-2
Human gDNA





Number of experiments (n = 9)
—
—
—
—
—
—


Sequence matching
NS
NS
NS
NS
NS
NS





HIV: Human immunodeficiency virus,


CMV: Human cytomegalovirus,


HPV: Human papiloma virus


HSV-1: Human herpes simplex virus type 1,


HSV-2: Human herpes simplex virus type 2


NS: No significant homology






2.4 Analysis of Detection Limit
The detection limit of PCR according to the present invention was analyzed using international standard HBV DNA and the results are summarized in Table 4 below.
DNA samples of the international standard HBV DNA in sera were extracted using Qiagen MinElute kit and purified. To perform PCR, a two-fold concentrated master mixture was prepared and then mixed with the DNA samples (1:1, by volume) to obtain a PCR mixture.
The composition of the master mixture is as follows:
















5xPCR buffer solution
 1.0 μl



Distilled water
1.04 μl



10 mM dNTPs
 0.1 μl



20 μM of each primer mixture
 0.2 μl



Enzyme mixture
0.16 μl










The PCR was performed as the following conditions: 91° C. for 1 second and 63° C. for 15 seconds.









TABLE 4









Micro PCR prohibit analysis












95% detection limit
50% detection limit


IU/ml
Positive (%)
(95% confidence)
(95% confidence)













100.0
100.0
18.4 IU/ml
2.9 IU/ml


50.0
100.0
(13.9-31.0)
(0-6.9)


25.0
96.2


15.0
100.0


5.0
53.8









2.5 PCR on Microchips
To investigate effects of the primers of the present invention on PCR according to a thermal transfer rate and a temperature gradient between different temperatures, PCR was carried out on micro PCR chips instead of conventional PCR tubes. The micro PCR chips used were made of silicon, and had advantages such as fast thermal transfer in reactants due to several hundreds times faster thermal conductivity than conventional PCR tubes, a fast temperature ramping rate, and maximal thermal transfer due to use of a trace of DNA samples.
FIG. 5 schematically illustrates a top view and a sectional view (FIG. 5A) and a bottom view (FIG. 5B) of a microchip used in this Example. Referring to FIGS. 5A and 5B, the microchip used in a method of the present invention includes a silicon wafer 1 and a glass wafer 2. A micro-chamber 3 for PCR made by silicon lithography is formed at a surface of the silicon wafer 1 and a micro-heater 4 for heating the micro-chamber 3 is formed at the other surface of the silicon wafer 1. The micro-heater 4 is controlled by a micro temperature sensor 7 to precisely control the PCR. The silicon wafer 1 is covered with the glass wafer 2 having a sample inlet 5 and a sample outlet 6. A sample inserted into the micro-chamber 3 formed at the silicon wafer 1 via the sample inlet 5 was heated by the micro-heater 4 to perform PCR. After the PCR, the sample was discharged out via the sample outlet 6.
To perform PCR on the micro PCR chips, the same PCR mixture as in conventional PCR tubes was prepared. Here, there was used the GS04 primer set of Table 2 which produced smaller-sized PCR products and had a high Tm. 1 μl of the PCR mixture was loaded in each of the micro PCR chips, and a PCR cycle of 91° C. for 1 second and 63° C. for 15 seconds was then repeated for 40 times. The experimental resultants were quantified using Labchip (Agilent) and amplification was identified on a 2% TAE agarose gel.
FIG. 6 shows electrophoretic results on a 2% TAE agarose gel after the amplification. Here, 106 and 104 indicate the copy numbers of HBV templates, NTC (no template control) is a negative control for PCR, and SD (standard) is a positive control for electrophoresis.
FIGS. 7A and 7B are comparative views that illustrate the concentrations of PCR products with respect to the time required for PCR in a micro PCR chip according to the present invention and in a conventional PCR machine. Referring to FIGS. 7A and 7B, a time required for obtaining 40.54 ng/μl of a PCR product on a micro PCR chip according to the present invention was only 28 minutes. This is in contrast to 90 minutes required for obtaining 40.88 ng/μl of a PCR product using a conventional PCR machine. That is, a time required for obtaining a predetermined concentration of a PCR product using the PCR technology of the present invention was only about one-third of a time required for obtaining almost the same concentration of a PCR product using a conventional PCR machine.
2.6 Rapidity and Accuracy
The rapidity and accuracy of a PCR technique of the present invention and conventional PCR kits (Comparative Example 1: Chiron (Procleix UltrioTM) and Comparative Example 2: Roche (AMPLINAT MPX)) were evaluated and the results are presented in Table 5 below.










TABLE 5







Comparative
Comparative


Section
Invention
Example 1
Example 2







Application
Screening
Blood screening
Blood screening



test


LOD value
18.4 IU/mL
6.2 IU/mL
30 copies/ml



(95%



detection



limit)


Amplification
28.3 minutes
~1 hour
~2 hours


time


Amplification
Gene
rRNA
Gene


target


(amplification and





hybridization)





LOD: Limit of detection


IU (International Unit) = 3-7 copies






2.7 Reproducibility
Reproducibility of the PCR technique according to the present invention was evaluated with respect to days and workers and the results are presented in Tables 6 and 7.







TABLE 6







Reproducibility with respect to days


(HBV templates = 106 copies/μl)









Days












Section
1 day
2 days
3 days
4 days
5 days















Number of copies
3
3
3
3
3


Mean (ng/μl)
44.1
41.2
49.7
47.9
45.7


Standard variation
6.7
1.5
2.5
1.9
4.7


Dispersion (%)
15.1
3.8
5.1
4.0
10.3
















TABLE 7







Reproducibility with respect to workers (HBV templates = 106


copies/μl)









Days












Section
1 day
2 days
3 days
4 days
5 days















Number of copies
3
3
3
3
3


Mean (ng/μl)
55.0
38.6
44.1
39.1
24.5


Standard variation
11.5
6.4
6.7
5.8
2.0


Dispersion (%)
20.9
16.6
15.1
14.8
8.3









In addition, reproducibility of PCR techniques according to the present invention and Comparative Example 1 was evaluated with respect to days and workers and the results are presented in Table 8 below.









TABLE 8





Section
Invention
Comparative Example 1







Reproducibility
(Maximum 15%,
(Maximum 44%,


based on days
mean 8%)
mean 27%)



HBV 106
HBV 103-6



copies
copies


Reproducibility
(Maximum 21%,
(Maximum 35%,


based on workers
mean 15%)
mean 21%)



HBV 106
HBV 104-6



copies
copies









2.8 Specificity
Hepatitis diagnosis was performed for 100 Korean persons using hepatitis detection kits according to the present invention and a conventional technique (Comparative Example 3: SolgentTM, a clinical diagnostic kit commercially available in the country) and the results are shown in FIG. 8.
Referring to FIG. 8, in connection with the hepatitis detection kit according to the conventional technique, bands exhibiting nonspecific reactivity were observed. On the other hand, in the hepatitis detection kit of the present invention, no bands exhibiting nonspecific reactivity were observed.
EXAMPLE 3
Clinical Test
Test subjects were classified into a patient group representing positive reactivity to HBsAg and HBV DNA (Digene) and a normal group representing negative reactivity to HBsAg and HBeAg. Clinical tests were performed in 118 subjects for the patient group and 61 subjects for the normal groups and the test results are presented in Table 9 below.
DNA samples were extracted from the sera of the subjects using Qiagen MinElute kit and purified. To perform PCR, a two-fold concentrated master mixture was prepared and then mixed with the DNA samples (1:1, by volume) to obtain a PCR mixture.
The composition of the master mixture is as follows:
















5xPCR buffer solution
 1.0 μl



Distilled water
1.04 μl



10 mM dNTPs
 0.1 μl



20 μM of each primer mixture
 0.2 μl



Enzyme mixture
0.16 μl










The PCR was performed as the following conditions: 91° C. for 1 second and 63° C. for 15 seconds.







TABLE 9







Results of clinical tests














Patient group,

Normal group,




Section
HBsAg (+)

HBsAg (−)

















Positive
TP
115
FP
1



Negative
FN
3
TN
60







TP: true positive,



FP: false positive,



TN: true negative,



FN: false negative






According to the test results, 3 persons (about 2.5%) among 118 persons of the patient group were judged false negative and 1 person (about 1.6%) among 61 persons of the normal group was judged false positive. It can be seen from the test results that the diagnostic kit of the present invention provides very accurate diagnosis for hepatitis B infection.
In addition, sensitivity, specificity, and efficiency of the diagnostic kit of the present invention are summarized in Table 10.










TABLE 10







Section
Result



















Sensitivity
97.5%



Specificity
98.4%



Efficiency
97.8%







Sensitivity: Ratio of true patients in patient group = (TP/(TP + FN)) × 100 (%)



Specificity: Ratio of true normal persons in normal group = (TN/(TN + FP)) × 100 (%)



Efficiency: Ratio of true patients and true normal persons in total group = ((TP + TN)/(TP + TN + FP + FN)) × 100 (%)






As apparent from the above description, a primer set, a method for detecting hepatitis B virus using the primer set, and a hepatitis B virus detection kit including the primer set of the present invention, enable rapid, accurate, and reproducible diagnosis of hepatitis B.
While the present invention has been particularly shown and described with reference to exemplary embodiments thereof, it will be understood by those of ordinary skill in the art that various changes in form and details may be made therein without departing from the spirit and scope of the present invention as defined by the following claims.

## Claims

1. A PCR set consisting of a primer set including a primer consisting of SEQ ID NO: 4 and a primer consisting of SEQ ID NO:6.

2. A method for detecting hepatitis B virus, which comprises amplifying a nucleic acid sample obtained from an organism by PCR using the primer set of claim 1.

3. The method of claim 2, wherein the PCR is a two-step PCR comprising a denaturation step and an annealing and extension step.

4. The method of claim 2, wherein the PCR is performed for 30 minutes or less.

5. The method of claim 2, wherein the PCR is performed on a micro PCR chip.

6. The method of claim 2, wherein the PCR is performed using 0.2-1 μM of each primer and 0.01 pg to 1 μg of a template DNA.

7. The method of claim 2, wherein the PCR is performed under conditions of denaturation at 86-97° C. for 1-30 seconds and annealing and extension at 60-70° C. for 6-30 seconds.

8. The method of claim 5, wherein the micro PCR chip comprises:
a silicon wafer, a surface of which is formed with a PCR chamber made by silicon lithography and the other surface is formed with a heater for heating the PCR chamber; and
a glass wafer having an inlet and an outlet.

9. A hepatitis B virus detection kit comprising the primer set of claim 1.