CN104263851A - Hepatitis C virus genetic typing chip and typing method - Google Patents

Hepatitis C virus genetic typing chip and typing method Download PDF

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CN104263851A
CN104263851A CN201410336476.2A CN201410336476A CN104263851A CN 104263851 A CN104263851 A CN 104263851A CN 201410336476 A CN201410336476 A CN 201410336476A CN 104263851 A CN104263851 A CN 104263851A
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周有良
胡春凌
王海涛
陈�峰
汪朝晖
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Abstract

The invention discloses a hepatitis C virus genetic typing chip and typing method. The hepatitis C virus genetic typing chip comprises a chip carrier, an amplification primer and a probe nucleotide segment loaded on the chip carrier. The nucleotide sequences of the primer and the probe are shown as SEQ ID No:1 and SEQ ID No:8. According to epidemic conditions of the hepatitis C virus (HCV) and aiming at six subtypes of the HCV, including 1a, 1b, 2a, 3a and 3b, a nucleic acid liquid phase chip detection method capable of typing at the same time is established. A novel detection method is provided for clinical typing detection of hepatitis C and molecular epidemiological investigation; and references are provided for selection of anti-virus treatment plans.

Description

HCV gene typing chip and classifying method
Technical field
The invention belongs to biology field, especially relate to a kind of HCV gene typing chip and classifying method.
Background technology
Hepatitis C virus (Hepatitis C Virus, HCV) is the main arch-criminal causing NANB-PTH, and global infection rate is up to 3%.After HCV infection, about have 50% ~ 80% to transfer chronic infection to, and have and nearly 20% ~ 30% can develop into liver cirrhosis and liver cancer after 20 ~ 30 years after infection.The health and lives of HCV infection serious threat people, causes huge society, economy and medical burden, is a serious social public health problem.
HCV genome is height heterogeneity, at least can be divided into 6 genotype (HCV1 ~ 6 type), have more than 100 gene hypotype.Accurate discriminating HCV hypotype, for better understanding HCV virus evolution, inquiring into the route of transmission of virus, selecting clinical treatment, judging change of illness state, evaluation antiviral therapy effect, and vaccine to be prepared etc. and had very important significance.
Summary of the invention
An object of the present invention is that design is a kind of can simultaneously to the nucleic acid liquid-phase chip of HCV gene typing, and described chip comprises chip carrier, amplimer and be carried on the probe nucleotide fragment of chip carrier; The nucleotide sequence of described primer and probe is as shown in SEQ ID NO:1 to SEQ ID NO:8.
Another object of the present invention is to provide a kind of use the nucleic acid liquid-phase chip of somatotype simultaneously can carry out the method for somatotype to hepatitis c virus gene, the step that described method adopts is:
A) magnetic carboxylic fluorescent encoding microsphere bag is by nucleic acid probe;
B) to set up for template with the gene standard substance plasmid synthesized and optimize hepatitis C virus nucleic acid liquid-phase chip genotyping detection method;
C) extract sample rna, reverse transcription becomes cDNA, carries out hepatitis C virus nucleic acid liquid-phase chip somatotype.
The present invention is according to the popularity of hepatitis C virus (HCV), for six kinds of hypotypes of HCV, comprise 1a, 1b, 2a, 3a, 3b and 6a, set up the nucleic acid liquid phase chip detecting method of somatotype while of energy, a kind of new detection method can be provided, for the selection of antiviral therapy scheme provides reference frame for the detection of hepatitis C clinical classification, Molecule Epidemiology Investigation etc.
Accompanying drawing explanation
Figure 1 shows that foundation and the optimization experiment result schematic diagram of hepatitis C virus (6a hypotype) nucleic acid liquid-phase chip genotyping detection method.
Figure 2 shows that hepatitis C virus (1b hypotype) nucleic acid liquid-phase chip genotyping detection method sensitivity experiment result schematic diagram.
Figure 3 shows that the specificity experiments result schematic diagram of hepatitis C virus nucleic acid liquid-phase chip genotyping detection method.
Figure 4 shows that hepatitis C virus nucleic acid liquid-phase chip genotyping detection method detects simulation polyinfection sample experiments result schematic diagram.
Embodiment
Below in conjunction with specific embodiments and the drawings, the present invention is described in further detail.
Material
1.1.1 Specimen origin year December in September, 2012 to 2013 is in hospital of the Chinese People's Liberation Army 100 and Suzhou City the 5th the People's Hospital's health check-up, outpatient service and healthy population 38 example of being in hospital and HCV positive resistance patient 55 example (41 examples be chronic hepatitis, 14 examples be liver cirrhosis), the Case definition of the basis for estimation 2008 " the third type Case definition WS2013 " of whose anti-HCV and HCV RNA positive patient lesion degree.Wherein, the male sex be 59 example, women be 34 example, the age be 34-57 year, average 48.3 years old.All samples all adopt venous blood 2ml, separation of serum ,-70 DEG C of preservations.
1.1.2 main agents HCV-1a, 1b, 2a, 3a, 3b and 6a gene standard substance plasmid (Shanghai march forward Bioisystech Co., Ltd), magnetic carboxylic fluorescent encoding microsphere (Magnetic COOH Beads, Luminex company of the U.S., 1.25 × 10 7individual/mL), SA-PE (treptavidin, R-phycoerythrin conjugate, SA-PE, 1mg/mL, 1mL, American I nvitrogen company), Shead Fluid (Luminex company of the U.S.), PCR Master Mix (U.S. Fermentas) 1st Strand cDNA Synthesis Kit (Japanese Takara).
1.1.3 plant and instrument liquid-phase chip detection system (MAGPIX type, Luminex company of the U.S.), PCR instrument (T100 tM, Bio-Rad company of the U.S.).
1.1.4 primer and probe primer and probe are all according to the E1 gene order that Genbank delivers, and adopt Primer Primer5.0 software design to form.Primer, probe nucleotide sequence are as shown in table 1.In order to make pcr amplification product biotinylation, downstream primer 5 ' end has carried out biotin labeling.Linked reaction is carried out for the ease of probe and carboxylated micro-spheres, all probes 5 ' have carried out C6 amination and have modified, simultaneously in order to ensure the hybridization efficiency of probe and PCR primer, with the addition of 10 poly (T) at 5 ' end of probe, poly (T) can effectively reduce sterically hindered as spacerarm, is conducive to the carrying out of probe hybridization reaction.Primer and probe are by the synthesis of the precious biotechnology company limited in Dalian.
Table 1HCV liquid-phase chip somatotype detects primer and probe sequence
Note: 1, Y is degeneracy base code, represents C and T; 2, N is degeneracy base code, represents A, T, C and G.
1.2 method
1.2.1 the activation of microballoon and No. 26, nucleic acid probe coupling random selecting, No. 36, No. 43, No. 46, No. 52 and No. 62 magnetic carboxylic fluorescent encoding microspheres are used for testing, wrap by 6a, 1a, 1b, 2a, 3a and 3b hypotype probe respectively, be labeled as 26-HCV-6a, 36-HCV-1a, 43-HCV-1b, 46-HCV-2a, 52-HCV-3a and 62-HCV-3b.Process specifications with reference to Luminex company of the U.S. carries out, and microballoon consumption is the nucleic acid probe consumption that 50 μ L, 100pmol/ μ L amination is modified is 10 μ L.
1.2.2 hepatitis C virus nucleic acid liquid-phase chip genotyping detection method foundation and optimize and to set up for template with the gene standard substance plasmid of synthesis and to optimize hepatitis C virus nucleic acid liquid-phase chip genotyping detection method.
1.2.2.1PCR the gene standard substance plasmid increasing to synthesize is template, PCR reaction is carried out: PCR Master Mix (2 ×) 10 μ L, Primer HCV-E1-F0.8 μ L, Primer HCV-E1-R0.8 μ L according to following system, template 1 μ L, uses ddH 2o supplies 20 μ L.Reaction conditions is: 95 DEG C of 10min; 94 DEG C of 30s, 50 DEG C 30,72 DEG C of 40sec, 40cycles; 72 DEG C of 10min; 4 DEG C of preservations.Design primer ratio comprises: F:R=1 μM: 10 μMs (1:10), 1.25 μMs: 10 μMs (1:8), 1.67 μMs: 10 μMs (1:6), 2.5 μMs: 10 μMs (1:4), 5 μMs: 10 μMs (1:2), 10 μMs: 10 μMs (1:1).
1.2.2.2PCR the microballoon that mixes of product and conjugated probes is hybridized and liquid-phase chip detects the mixing microballoon working fluid of abundant resuspended coupling nucleic acid probe; At each sample well, add 33 μ L nucleic acid hybridization buffers, then add 10 μ L mixing microballoon working fluids, add the PCR primer of 1 μ L/3 μ L/5 μ L/7 μ L, each sample arranges 3 repetitions, adds TE and supplies volume to 50 μ L, abundant mixing, reacts: 1. 95 DEG C of sex change 5min as follows; 2. 37 DEG C of hybridization 30min.With detection of nucleic acids damping fluid, 1mg/mL SA-PE is diluted to 4 μ g/mL, every hole adds 25 μ L, hatches 5min for 37 DEG C; Add 150 μ L termination reaction liquid (37 DEG C of preheatings), sample is placed on Luminex MAGPIX and tests, the fluorescent signal value (MFI) of analytic sample.
1.2.3 the sensitivity experiment of hepatitis C virus nucleic acid liquid-phase chip genotyping detection method is according to the concentration of gene standard substance plasmid, and often kind of standard substance are diluted to 1 × 10 10copies/ μ L, then adopts 10 times of dilution methods to be diluted to 1 × 10 0copies/ μ L, it is 1 μ L that every PCR reaction adds template amount.The hepatitis C virus nucleic acid liquid-phase chip genotyping detection method adopting 1.2.2 to set up detects, the sensitivity of evaluation method.
1.2.4 the hepatitis C virus nucleic acid liquid-phase chip genotyping detection method that the specificity experiments of hepatitis C virus nucleic acid liquid-phase chip genotyping detection method adopts 1.2.2 to set up detects hepatitis A virus, hepatitis B virus, treponema pallidum, chikungunya fever virus, dengue fever virus, it is 1 μ L that every PCR reaction adds template amount, the specificity of evaluation method.
1.2.5 hepatitis C virus nucleic acid liquid-phase chip genotyping detection method detects simulation polyinfection sample experiments according to the concentration of gene standard substance plasmid, and often kind of standard substance are diluted to 1 × 10 7standard substance are combined by copies/ μ L, add two kinds, three kinds, four kinds, five kinds, six kinds plasmid standards in a reaction tubes simultaneously.The hepatitis C virus nucleic acid liquid-phase chip genotyping detection method adopting 1.2.2 to set up detects, and evaluation method detects the effect of polyinfection sample.
1.2.6 the clinical application of hepatitis C virus nucleic acid liquid-phase chip genotyping detection method collects normal people, hepatitis C patient blood sample, totally 93 parts, and be separated and obtain serum, extract sample rna, reverse transcription becomes cDNA.The hepatitis C virus nucleic acid liquid-phase chip genotyping detection method adopting 1.2.2 to set up and real time fluorescent PCR method detect simultaneously.Compare with clinical diagnoses, laboratory test results is analyzed, determine susceptibility, the accuracy of the hepatitis C virus nucleic acid liquid-phase chip genotyping detection method that this institute sets up.Real time fluorescent PCR method is bought business-like test kit and is detected.Simultaneously, for the hepatitis C sample of nucleic acid liquid-phase chip genotyping detection method test positive, carry out pcr amplification, PCR primer is cloned into carrier T, selects mono-clonal, identifies after the positive through PCR, deliver to Sinogenomax Co., Ltd. to check order, analyze sequencing result, judge HCV gene hypotype, analytical results and liquid-phase chip detection method compare.
1.2.7 hepatitis C virus nucleic acid liquid-phase chip genotyping detection method experimental result judging criterion really thribble according to Luminex business recommendations judging criterion and documents and materials, in conjunction with this research experiment situation, the judging criterion of hepatitis C virus nucleic acid liquid-phase chip somatotype test experience result is set as follows: (1) data validity analysis: the fluorescent signal value of blank group is not higher than 100; (2) sample to be tested analysis judges: detected result Cutoff value is set as 4 times of PCR Blank fluorescent signal value, when not higher than PCR Blank fluorescent signal value 2 times of the fluorescent signal value of 1. sample to be tested, is judged to be negative sample; During the fluorescent signal value >=Cutoff value of 2. sample to be tested, be judged to be positive sample; 3. when the 2 times≤fluorescent signal value < Cutoff value of PCR Blank fluorescent signal value, be set to, between gray area, be judged to be suspicious specimen, need to carry out repeating experiment or taking other detection methods to verify further.
2 results
The foundation of 2.1 hepatitis C virus nucleic acid liquid-phase chip genotyping detection methods and optimization experiment result are analyzed by carrying out detection to the gene standard substance plasmid of hepatitis C virus six hypotypes, determine that the optimum reaction condition of hepatitis C virus nucleic acid liquid-phase chip genotyping detection method is: F:R primer ratio is 1:10 and 1:8; PCR primer application of sample amount is 3 μ L, 5 μ L or 7 μ L.The experimentally accessibility of situation and experimental implementation, select F:R primer ratio to be 1:10, PCR primer application of sample amount is 5 μ L, 95 DEG C of sex change 5min, and 37 DEG C of hybridization 30min, SA-PE concentration is 4 μ g/mL is optimum reaction condition.Be described the foundation of detection method and optimization with 6a hypotype experimental result, Fig. 1 can find out, along with the rising of primer ratio F:R, fluorescent signal value is on a declining curve.When F:R primer ratio is 1:10 and 1:8, fluorescent signal value is higher, and background signal value is lower, obtains good experimental result.When primer ratio is for during for 1:2 and 1:1, while fluorescent signal value reduces, sample segment microballoon background signal value but raises.When primer ratio is 1:6 and 1:4, fluorescent signal value reduces not too obvious, but sample segment microballoon background signal value is also increased significantly.Along with the increase of PCR primer application of sample amount, fluorescent signal value is in raising and the trend tended to be steady.When PCR primer application of sample amount is increased to 3 μ L from 1 μ L, the amplitude that fluorescent signal value increases is maximum, and when PCR primer application of sample amount is increased to 5 μ L and 7 μ L from 3 μ L, fluorescent signal value has increase, but the amplitude increased is relatively not obvious.In sum, the optimum reaction condition of hepatitis C virus (6a hypotype) nucleic acid liquid-phase chip genotyping detection method is: F:R primer ratio is 1:10 and 1:8; PCR primer application of sample amount is 3 μ L, 5 μ L or 7 μ L.
The sensitivity experiment experimental result of 2.2 hepatitis C virus nucleic acid liquid-phase chip genotyping detection methods shows, the sensitivity for HCV1a, 3a and 6a hypotype nucleic acid liquid-phase chip genotyping detection method is 1 × 10 5copies/PCR; Sensitivity for HCV1b, 2a and 3b hypotype nucleic acid liquid-phase chip genotyping detection method is 1 × 10 4copies/PCR.Wherein, for 1 × 10 of HCV1a hypotype and 6a hypotype 4the detected result of copies plasmid standard sample is positioned between gray area; For 1 × 10 of HCV1a hypotype 4copies and in 1 × 10 3the detected result of copies plasmid standard sample is positioned between gray area, confirms further by other detection method.As shown in Figure 2, all the other 5 hypotype experimental results slightly for 1b hypotype sensitivity experiment result.
The specificity experiments result of 2.3 hepatitis C virus nucleic acid liquid-phase chip genotyping detection methods adopts the hepatitis C virus nucleic acid liquid-phase chip genotyping detection method set up to detect hepatitis A virus, hepatitis B virus, hepatitis C virus, treponema pallidum, chikungunya fever virus, dengue fever virus and hepatitis c virus gene standard substance plasmid, Fig. 3 experimental result shows, for hepatitis c virus gene standard substance plasmid and hepatitis c virus-like product, detected result is positive.Wherein hepatitis c virus-like product, 3 is HCV1b hypotype, and 1 is HCV1a hypotype, and 1 is HCV2a hypotype, and also having 1 is the polyinfection of HCV1b and 2a hypotype.HCV3a, 3b and 6a hypotype does not detect.For hepatitis A virus, hepatitis B virus, treponema pallidum, chikungunya fever virus and dengue fever virus sample, detected result is negative.Experimental result illustrates, the specificity of the hepatitis C virus nucleic acid liquid-phase chip genotyping detection method that this institute sets up is better., also show the detected result of HCV-002, present method accurately can detect polyinfection sample meanwhile.
2.4 hepatitis C virus nucleic acid liquid-phase chip genotyping detection methods detect simulation polyinfection sample experiments result according to the concentration of gene standard substance plasmid, and often kind of standard substance are diluted to 1 × 10 7standard substance are combined by copies/ μ L, add two kinds, three kinds, four kinds, five kinds, six kinds plasmid standards in a reaction tubes simultaneously.Adopt hepatitis C virus nucleic acid liquid-phase chip genotyping detection method to detect, the experimental result of Fig. 4 shows, the method accurately can detect any two kinds of hypotypes, any three kinds of hypotypes, any four kinds of hypotypes, any five kinds of hypotypes and six kinds of hypotype nucleic acid.This experiment adopts standard substance plasmid simulation polyinfection sample, obtains good detected result, illustrates that present method accurately can detect polyinfection sample.
The clinical application experimental result of 2.5 hepatitis C virus nucleic acid liquid-phase chip genotyping detection methods collects normal people, hepatitis C patient blood sample, totally 93 parts, is separated and obtains serum, and extract sample rna, reverse transcription becomes cDNA.The hepatitis C virus nucleic acid liquid-phase chip genotyping detection method adopting 3.2.9 to set up and real time fluorescent PCR method detect simultaneously.Laboratory test results is as shown in table 2, and the detected result of the hepatitis C virus nucleic acid liquid-phase chip genotyping detection method that this institute sets up is compared with clinical diagnoses, and susceptibility is 74.55%, and specificity is 86.84%, and diagnosis efficiency is 79.57%; Compared with real-time fluorescence RT-PCR method detected result, susceptibility is 76.47%, and specificity is 83.33%, and diagnosis efficiency is 79.57%.Real-time fluorescence RT-PCR detected result is compared with clinical diagnoses, and susceptibility is 76.36%, and specificity is 76.32%, and diagnosis efficiency is 76.34%.The detected result of nucleic acid Luminex and clinical diagnoses and real-time fluorescence RT-PCR detected result is adopted to have higher consistence.For totally 41 parts, the hepatitis C sample of nucleic acid liquid-phase chip genotyping detection method test positive, wherein, 1a hypotype is 9 examples, and 1b hypotype is 20 examples, and 2a hypotype is 2 examples, and 3b hypotype is 2 examples, and 6a hypotype is 5 examples, 1b and 2a polyinfection hypotype is 3 examples.After carrying out sequencing analysis to sample, wherein, 1a hypotype is 7 examples, and 1b hypotype is 22 examples, and 2a hypotype is 4 examples, and 3b hypotype is 2 examples, and 6a hypotype is 6 examples.Nucleic acid liquid-phase chip genotyping detection method result and sequencing detected result have higher consistence, but sequencing can only be analyzed single hypotype, not accurate enough to polyinfection sample detection result.Hepatitis C virus nucleic acid liquid-phase chip genotyping detection method is high-flux detection method, examination detection is carried out to six kinds of hypotypes by one-time detection simultaneously, relative to the real-time fluorescence RT-PCR method that can only detect an index at every turn, greatly can shorten operating time and testing amount, the somatotype that can be conducive to hepatitis C virus detects.

Claims (3)

1. a HCV gene typing chip, comprises chip carrier, amplimer and be carried on the probe nucleotide fragment of chip carrier; The nucleotide sequence of described primer and probe is as shown in SEQ ID NO:1 to SEQ ID NO:8.
2. use a method for HCV gene typing chip somatotype described in claim 1, comprise step:
A) magnetic carboxylic fluorescent encoding microsphere bag is by nucleic acid probe;
B) to set up for template with the gene standard substance plasmid synthesized and optimize hepatitis C virus nucleic acid liquid-phase chip genotyping detection method;
C) extract sample rna, reverse transcription becomes cDNA, carries out hepatitis C virus nucleic acid liquid-phase chip somatotype.
3. the method for HCV gene typing as claimed in claim 2, is characterized in that: in described primer pair, F:R primer ratio is 1:10 and 1:8.
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Citations (2)

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CN101377486A (en) * 2007-08-29 2009-03-04 中山大学达安基因股份有限公司 HCV gene typing detecting reagent kit
CN101660002A (en) * 2008-08-27 2010-03-03 中山大学达安基因股份有限公司 HCV genotyping DNA microarray chip

Patent Citations (2)

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Publication number Priority date Publication date Assignee Title
CN101377486A (en) * 2007-08-29 2009-03-04 中山大学达安基因股份有限公司 HCV gene typing detecting reagent kit
CN101660002A (en) * 2008-08-27 2010-03-03 中山大学达安基因股份有限公司 HCV genotyping DNA microarray chip

Non-Patent Citations (2)

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Title
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