WO2017021471A1 - Procédés d'amplification et de séquençage du génome d'un virus de l'hépatite c - Google Patents

Procédés d'amplification et de séquençage du génome d'un virus de l'hépatite c Download PDF

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WO2017021471A1
WO2017021471A1 PCT/EP2016/068589 EP2016068589W WO2017021471A1 WO 2017021471 A1 WO2017021471 A1 WO 2017021471A1 EP 2016068589 W EP2016068589 W EP 2016068589W WO 2017021471 A1 WO2017021471 A1 WO 2017021471A1
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hepatitis
virus
dna
sequencing
full
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PCT/EP2016/068589
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WO2017021471A8 (fr
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Sylvie Jacqueline Henriette LARRAT
Pauline TREMEAUX
Elodie SANTONI
Marie-Ange THELU
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Universite Grenoble Alpes
Centre Hospitalier Universitaire De Grenoble
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/706—Specific hybridization probes for hepatitis
    • C12Q1/707—Specific hybridization probes for hepatitis non-A, non-B Hepatitis, excluding hepatitis D
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms

Definitions

  • the present invention relates to methods for amplifying and sequencing the full-length genome of a hepatitis C virus.
  • the present invention also relates to primers and kits for amplifying and sequencing the full-length genome of a hepatitis C virus.
  • Chronic hepatitis C is a major disease caused by the hepatitis C virus (HCV) and responsible for more than 350000 deaths a year through an evolution of liver fibrosis to cirrhosis or hepatocellular carcinoma. Nevertheless, it is a curable disease.
  • New standards of care are based on drugs targeting the non-structural proteins of HCV.
  • DAAs directly acting antivirals
  • SVR sustained virological response
  • Available DAAs differ in their activity against HCV genotypes and even subtypes.
  • HCV whole genome sequencing is the most accurate and reliable method.
  • viral RNA is converted in vitro into cDNA by reverse transcription and, then, cDNA is amplified by PCR to produce a DNA template.
  • cDNA is amplified by PCR to produce a DNA template.
  • HCV whole genome Due to its size (over 9 kb), its high GC content (over 58%), its high degree of variability and its secondary structures, HCV whole genome is difficult to amplify, and published techniques were either restricted to a single genotype - if not a single subtype (Tellier et al., Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes. J Clin Microbiol. 1996; 34(12):3085-81; Fan et al., Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples. Biochem Biophys Res Commun.
  • genotyping is primarily achieved by the sequencing of PCR-amplified portions of the viral genome obtained from a patient sample, followed by phylogenetic analysis. However, this approach increases the risk of errors and is not appropriate for genotyping recombinant forms of HCV.
  • One of the aims of the invention is to provide a method for amplifying the full-length HCV genome with a single PCR reaction, without a prior knowledge of its genotype.
  • Another aim of the invention is to provide a reliable method for sequencing the full- length HCV genome.
  • Another aim of the invention is to provide a method of detecting genotypes and/or subtypes of hepatitis C virus in a biological sample containing one genotype and/or subtype or in a biological sample containing a mix of different genotypes and/or subtypes.
  • Another aim of the invention is to provide primers, couples of primers and kits allowing amplification of the full-length HCV genome.
  • the invention relates to a method of amplifying the full-length genome of a hepatitis C virus of any genotype comprising:
  • primers being respectively complementary to two sequences located at the two extremities of said cDNA, said two sequences being distant from each other by at least 9 kb, and
  • the present invention is based on the unexpected observation made by the Inventors that the full-length genome of different genotypes and/or subtypes of hepatitis C virus can be amplified by a single PCR reaction with one couple of primers, without prior knowledge of the genotype of the hepatitis C virus.
  • full-length genome (or “genome”) as used herein is defined as the collective gene set carried by a viral particle of hepatitis C virus. This collective gene set can be carried by RNA, cDNA or DNA material.
  • full-length genome refers to the complete sequence or a near full-length sequence of the viral nucleic acid.
  • the near full-length sequence refers to a sequence corresponding to at least 80%, preferably 90% of the complete sequence of the viral nucleic acid.
  • the near full-length sequence refers to a sequence corresponding to at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% of the complete sequence of the viral nucleic acid.
  • genotypes refers to groups of viruses resulting from genetic heterogeneity and divergence in HCV sequences.
  • the classification of the HCV genotypes is based on the analysis of the full-length genome. The last consensus describes 7 genotypes numbered from 1 to 7 with nucleotid sequences varying over 30% between each other.
  • subtypes correspond to genetic variations of the particular genotypes (for example, la and lb). Generally, subtypes have nucleotide sequences varying over 30% between each other.
  • genotypes such as RF_2k/lb. These recombinant forms arise in patients that are coinfected with more than one genotype and then they can be transmitted to other patients.
  • cDNA refers to "complementary DNA", a form of DNA synthesized from a RNA template by reverse transcription.
  • total nucleic acid is defined as the total genetic material extracting from a biological sample suspected to contain the genome of a hepatitis C virus.
  • Total nucleic acid can contain DNA and/or RNA molecules.
  • amplifying refers to amplification methods that require thermocycling (e.g. PCR). Amplification means increasing the relative concentration of one or more sequences in a sample at least 10-fold, relative to unamplified components of the sample.
  • PCR refers to the polymerase chain reaction. PCR involves a DNA polymerase, pairs of primers, and thermal cycling to synthesize multiple copies of two complementary strands from double strand DNA or from cDNA.
  • an excess of at least two oligonucleotide primers forward and reverse
  • the reaction mixture is submitted to a specific thermal cycling in the presence of a DNA polymerase.
  • the reaction mixture is denatured and the primers are then annealed to their respective target sequences.
  • the primers are extended with a polymerase so as to form new pairs of complementary strands.
  • the steps of denaturation, primers annealing and polymerase extension can be repeated many times and constitute one "PCR cycle" (in “two-step PCR", annealing and extension can be carried out at the same temperature).
  • the amplified segments obtained by the PCR method are, themselves, efficient templates for subsequent PCR amplifications.
  • PCR is also called “RT-PCR”, or “reverse transcription polymerase chain reaction”, when a RNA strand is reverse transcribed into its cDNA using a reverse transcriptase, and the resulting cDNA is amplified using PCR.
  • PCR is also called “LR-PCR”, or “long range PCR”, when it refers to amplification of DNA lengths (in general over 5 kb and up to 30 kb and beyond) that cannot typically be amplified using routine PCR methods or reagents.
  • the invention relates to a method of amplifying the full-length genome of a hepatitis C virus of any genotype comprising: a) mixing:
  • primers being respectively complementary to two sequences located at the two extremities of said cDNA, said two sequences being distant from each other by at least 9 kb, and
  • a single couple of primers according to the invention allows the amplification of the full- length genome of at least 2 genotypes of HCV.
  • a couple of primers of the invention allows the amplification of the full-length genome of 2, 3, 4, 5, 6 or 7 different genotypes of HCV.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV- 1.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-2.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-3.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-4.
  • a couple of primers of the invention is used for the amplification of the fuU-length genome of HCV-5.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-6.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-7.
  • a single couple of primers according to the invention allows amplification of the full- length genome of at least 2 subtypes and/or recombinant forms of HCV.
  • a couple of primers according to the invention allows amplification of the full-length genome of at least 2 subtypes of HCV selected from the group comprising: la,
  • a single couple of primers of the invention allows amplification of the full- length genome of at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different subtypes of HCV.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-la.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-lb. In an embodiment, a couple of primers of the invention is used for the amplification of the full-length genome of HCV-la and HCV-lb.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-3a.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-la, HCV-lb and HCV-3a.
  • a couple of primers of me invention is used for the amplification of the full-length genome of HCV-2k/lb.
  • a couple of primers of the invention is used for the amplification of the full-length genome of HCV-la, HCV-lb, HCV-3a and HCV-2k/lb.
  • the invention relates to a method as defined above, wherein said couple of primers is chosen among the group consisting in the following couples:
  • SEQ ID NO: 2 and SEQ ID NO: 7 (5NC3/NA2).
  • Forward primers are located in the S'NC non-coding region, located at the 5' end of the HCV genome.
  • Reverse primers are located in the NSSB region coding for a non- structural protein, located at the 3 ' end of the HCV genome.
  • the invention relates to a method as defined above, wherein said couple of primers is chosen among the group consisting in the following couples:
  • the invention relates to a method as defined above, wherein said couple of primers is chosen among the group consisting in the following couples:
  • the invention relates to a method as defined above, wherein said couple of primers is chosen among the group consisting in the following couples:
  • primers for amplification by PCR.
  • primer'' refers to short oligonucleotides that can be used to initiate extension of one strand of DNA.
  • the primers have a sequence that is the reverse complement of a specific region of the target DNA.
  • these primers can be mutated for modifying their target-binding properties, they can be extended with a tail-sequence for allowing nested PCR or cloning reactions (such as the primers 5NC3-M13 and NA2-M13 in table 2), they can be chemically bound to fluorescent compounds for carrying out real-time PCR reactions, or the structure of the ribose and the phosphate can be modified to improve sensibility and specificity of the primers (such as Locked Nucleic Acids, LNA).
  • the invention relates to a method as defined above, wherein said DNA polymerase has a 3' ⁇ 5* exonuclease activity and/or a 5' ⁇ 3' exonuclease activity, preferably a 3' ⁇ 5' exonuclease activity.
  • the terms "3 ' ⁇ 5' exonuclease activity” and “5 ' ⁇ 3' exonuclease activity” refer to the proofreading activities of some DNA polymerases. These proofreading activities catalyze the removal of a mononucleotide, in the 3'-5' or 5'-3' direction, at the extremity of the duplex DNA during elongation. Following base excision, the polymerase can re-insert the correct base and elongation can continue. These proofreading activities allow replication of long DNA molecules over 1,000 bp while maintaining high fidelity.
  • the invention relates to a method as defined above, wherein said DNA polymerase has a 3' ⁇ 5' exonuclease activity and/or a 5' ⁇ 3' exonuclease activity, preferably a 3' ⁇ 5' exonuclease activity, is thermostable and allows hot-start PCR.
  • hot start PCR refers to a modified form of PCR which avoids a non-specific amplification of DNA by inactivating the DNA polymerase at low temperature.
  • the DNA polymerase is active at room temperature and, when all the reaction components are put together, nonspecific primer annealing can occur due to these low temperatures. This nonspecific annealed primer can men be extended by the Taq DNA polymerase, generating nonspecific products and lowering product yields.
  • specific antibodies are used to block the DNA polymerase at annealing temperature. When the temperature rises for amplification, the specific antibodies detach from the DNA polymerase and the amplification with greater specificity starts.
  • Hot Start PCR significantly reduces nonspecific priming, the formation of primer dimers, and often, increases product yields.
  • the term "thermostable” refers to the property of some DNA polymerase to resist to high temperatures over 90°C. Use of thermostable DNA polymerases enables running the PCR at high temperature ( ⁇ 60°C and above), which facilitates high specificity of the primers and reduces the production of unspecific products, such as primer dimers.
  • DNA polymerases suitable for the method of the invention include, but are not limited to, KOD Hot StartTM (Merck), PhusionTM (New England Biolabs), Q5 High Fidelity Hot Start DNA polymeraseTM (New England Biolabs), Platinum Taq DNA Polymerase High FidelityTM (Life Technologies), Taq Platinum PCR SurjermixTM (Life Technologies), Accuprime Pfx DNA PolymeraseTM (Life Technologies), Takara LA TaqTM (Ozyme), GXL Prime Star DNA PolymeraseTM (Takara Clontech), Expand Long TemplateTM (Roche Diagnostics), Expand Long RangeTM (Roche Diagnostics) and KAPA Long RangeTM (Kapa Biosystems).
  • the invention relates to a method as defined above, wherein each primer has a size of 15 to 40 nucleotides, preferably of 20 to 40 nucleotides, more preferably of 28 to 30 nucleotides.
  • a primer of the invention has a size of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides.
  • the invention relates to a method as defined above, wherein said at least one PCR cycle is:
  • At least one PCR cycle being repeated at least 30 times, preferably at least 40 times, more preferably at least 45 times.
  • This embodiment corresponds to a "two-step PCR" in which primers annealing and extension occurs at the same temperature.
  • the invention relates to a method as defined above, wherein said at least one PCR cycle is:
  • temperature of deriaturation in step (i) of the PCR cycle can be 95.0°C, 95.1°C, 95.2°C, 95.3°C, 95.4°C, 95.5°C, 95.6°C, 95.7°C, 95.8°C, 95.9°C, 96.0°C, 96.1°C, 96.2°C, 96.3°C, 96.4°C, 96.5°C, 96.6°C, 96.7°C, 96.8°C, 96.9°C, 97.0°C, 97.1°C, 97.2°C, 97.3°C, 97.4°C, 97.5°C, 97.6°C, 97.7°C, 97.8°C, 97.9°C or 98.0°C.
  • temperature of primers annealing/ DNA extension in step (ii) of the PCR cycle can be 65.0°C, 65.1°C, 65.2°C, 65.3°C, 65.4°C, 65.5°C, 65.6°C, 65.7°C, 65.8°C, 65.9°C, 66.0°C, 66.1°C, 66.2°C, 66.3°C, 66.4°C, 66.5°C, 66.6°C, 66.7°C, 66.8°C, 66.9°C, 67.0°C, 67.1°C, 67.2°C, 67.3°C, 67.4°C, 67.5°C, 67.6°C, 67.7°C, 67.8°C, 67.9°C, 68.0°C, 68.1°C, 68.2°C, 68.3°C, 68.4°C, 68.5°C, 68.6°C, 68.7°C, 68.8°C, 68.9°C,
  • said at least one PCR cycle being repeated at least 30 times, preferably at least 40 times, more preferably at least 45 times.
  • the invention relates to a method as defined above, wherein said at least one PCR cycle is:
  • said at least one PCR cycle being repeated at least 30 times, preferably at least 40 times, more preferably at least 45 times.
  • the invention relates to a method as defined above, wherein said mixture reaction is heated once at 98°C for at least 1 minute, preferably for at least 2 minutes, just before being subjected to said at least one PCR cycle.
  • the invention relates to a method as defined above, wherein one additive is added to said reaction mixture, said additive being preferably chosen among the group consisting in dimethylsulfoxyd (DMSO), bovine serum albumin (BSA), T4 Gene 32 Protein and betaine.
  • DMSO dimethylsulfoxyd
  • BSA bovine serum albumin
  • T4 Gene 32 Protein T4 Gene 32 Protein
  • additive refers to enhancing agents that can be used to increase the yield, specificity and consistency of DNA synthesis.
  • the invention relates to a method as defined above, wherein said cDNA is obtained by reverse transcription using a primer chosen among the group consisting in: SEQ ID NO: 9 and SEQ ID NO: 10.
  • the sequences of primers used for reverse transcription are given in table 3.
  • reverse transcriptases suitable for the method of the invention include, but are not limited to, Superscript III First Strand System for RT-PCRTM (Life Technologies) and Primescript Reverse TranscriptaseTM (Ozytne).
  • the invention relates to a method as defined above, wherein said cDNA is obtained by incubating total nucleic acid of a hepatitis C virus with a reverse transcriptase for at least 40°C, preferably for at least S0°C, during at least 50 minutes.
  • the invention relates to a method as defined above, wherein said cDNA is obtained by incubating total nucleic acid of a hepatitis C virus with a. reverse transcriptase at S0°C, during 50 minutes.
  • the invention relates to a method as defined above, wherein said cDNA is obtained by incubating total nucleic acid of a hepatitis C virus with a reverse transcriptase and at least one additive chosen among T4 Gene 32 Protein and a ribonuclease inhibitor.
  • the invention relates to a method as defined above, comprising a step of extracting said total nucleic acid of a hepatitis C virus from a biological sample containing viral particles, such as blood, plasma, hepatic puncture biopsy or peripheral blood mononuclear cells (PBMC) of a patient
  • a biological sample containing viral particles such as blood, plasma, hepatic puncture biopsy or peripheral blood mononuclear cells (PBMC) of a patient
  • patient refers to an individual infected, or suspected of being infected, by a hepatitis C virus. This term includes mammals such as humans and other primates.
  • the invention relates to a method as defined above, comprising:
  • a biological sample containing viral particles such as blood, plasma, hepatic puncture biopsy or peripheral blood mononuclear cells (PBMC) of a patient
  • primers being respectively complementary to two sequences located at the two extremities of said cDNA, said two sequences being distant from each other by at least 9 kb, and
  • the invention relates to a method as defined above, wherein an amplicon of at least 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9 or 10.0 kb is obtained.
  • the invention relates to a method as defined above, wherein at least 80 % of the genome of a hepatitis C virus is amplified.
  • the invention relates to a method as defined above, wherein at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of the genome of a hepatitis C virus is amplified.
  • the invention relates to a method as defined above, wherein at least 80 % of the coding sequence of a hepatitis C virus is amplified.
  • the invention relates to a method as defined above, wherein at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of the coding sequence of a hepatitis C virus is amplified.
  • the invention relates to a method as defined above, wherein at least 80 % of the non-coding sequence of a hepatitis C virus is amplified.
  • the invention relates to a method as defined above, wherein at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% of the non- coding sequence of a hepatitis C virus is amplified.
  • the invention relates to a method of sequencing the full-length genome of a hepatitis C virus comprising:
  • the sequence of the DNA molecule obtained by PCR amplification can be determined by using any method for sequencing DNA.
  • the invention relates to the method of sequencing as defined above, wherein the double strain DNA of at least 9kb is used as a matrix for at least one reaction of nested PCR.
  • the invention relates to the method of sequencing as defined above, wherein the double strain DNA of at least 9kb is used as a matrix for at least one PCR with random primers.
  • the invention relates to a method of detecting hepatitis C virus genotypes in a biological sample of a patient suspected of containing hepatitis C viral particles, comprising:
  • DNA library refers to a collection of DNA fragments that have been physically isolated from each other.
  • a DNA library allows further analysis, and in particular sequence analysis, of each DNA fragments individually.
  • DNA library can be obtained through different means according to the purpose or to the technology. For example, DNA fragments can be cloned into vectors (such as plasmids) or captured by beads, to allow the sequencing of each fragment
  • a read alignment is carried out after step (c) to obtain consensus sequences.
  • DNA fragments, that are used to create a DNA library have an average size between 400 and 1 100 bp, preferably between 500 and 800 bp.
  • DNA fragments have an average size of 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1 000, 1 050 or 1 100 bp.
  • DNA fragments that are used to create a DNA library, have an average size of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9 kb.
  • DNA fragments that are used to create a DNA library, are the double strand DNA of at least 9 kb obtained after step a) as such.
  • the invention relates to one of the methods as defined above, comprising a step of extracting total nucleic acid of the hepatitis C virus from a biological sample of a patient containing only one genotype of hepatitis C virus.
  • the invention relates to one of the methods as defined above, comprising a step of extracting total nucleic acid of the hepatitis C virus from a biological sample of a patient containing at least two different genotypes of hepatitis C virus.
  • Hepatitis C virus exists as a population of distinct but closely related viral variants. These variants may display divergent replicative capacity, cell tropism, immunologic escape, and antiviral-drug resistance.
  • a patient is co-infected with 2 or more distinct HCVs with distinct genotypes.
  • a DNA library allows to separate and identify the HCV variants that are present within a sample. Therefore, it is possible to detect and identify resistance-associated variants within a sample.
  • the method of the invention can be used to detect variants that are present in low quantity, even in minority, within a sample.
  • the invention relates to one of the methods as defined above, wherein said step of sequencing is achieved using by the Sanger method or a NGS method.
  • NGS Next Generation Sequencing * * refers to the so-called methods of nucleic acid sequencing and comprises the sequencing-by-synthesis or sequencing-by- ligation platforms currently employed by IUumina, Life Technologies, Pacific Biosciences and Roche, etc.
  • Next generation sequencing methods may also include, but not be limited to, nanopore sequencing methods such as offered by Oxford Nanopore or electronic detection-based methods such as the Ion Torrent technology commercialized by Life Technologies.
  • the invention relates to the method as defined above, wherein said step of fragmenting the double strand DNA is achieved using by nebulization, by ultrasonication or by enzymatic digestion, preferably by nebulization.
  • nebulization refers to a DNA fragmentation by forcing DNA through a small hole in a nebulizer unit Generally, the size of the fragments varies accoding to the pressure of the gas used to push the DNA through the nebulizer, the speed at which the DNA solution passes through the hole, the viscosity of the solution, and the temperature.
  • sonication refers to a DNA fragmentation method by subjecting DNA to brief periods of sonication with ultrasonic frequencies.
  • enzymatic digestion refers to a DNA fragmentation method by using enzymes to digest DNA. Usually, enzymatic digestion can be achieved using restriction enzymes that cut DNA at or near specific recognition sequences (restriction sites).
  • the invention relates to a method of detecting hepatitis C virus genotypes in a biological sample of a patient suspected of containing hepatitis C viral particles, comprising:
  • step (c) analyzing the sequences obtained from step (b) by performing, preferably using a software, at least one of the following steps:
  • the invention relates to a method of detecting hepatitis C virus genotypes in a biological sample of a patient suspected of containing hepatitis C viral particles, comprising: (a) amplifying the full-length genome of a hepatitis C virus using the method as defined above to obtain a double strand DNA of at least 9 kb,
  • step (c) analyzing the sequences obtained from step (b) by performing, preferably using a software, at least one of the following steps:
  • step (d) interpreting the data obtained from step (c) by performing queries in at least one database, preferably using a software, said at least one database being preferably chosen among: a drug resistance database, a disease prognosis database and a reference database.
  • the invention relates to a primer chosen among the group consisting in: SEQ ID NO: 4 (2CH), SEQ ID NO: 6 (7er) and SEQ ID NO: 10 (3UTR1).
  • the invention relates to a couple of primers chosen among the group consisting in the following couples:
  • SEQ ID NO: 35 and SEQ ID NO: 39 (GSa-S'I-Rfi/GSaO'LIto).
  • the invention relates to a couple of primers chosen among the group consisting in the following couples:
  • the invention relates to a couple of primers chosen among the group consisting in the following couples:
  • the invention relates to a kit for the amplification of the full-length genome of a hepatitis C virus comprising:
  • the invention relates to a kit for the amplification of the full-length genome of a hepatitis C virus comprising:
  • the invention relates to a kit for the amplification of the full-length genome of a hepatitis C virus comprising:
  • the invention relates to a kit for the amplification of the full-length genome of a hepatitis C virus comprising:
  • the invention relates to a kit as defined above further comprising a reverse transcriptase.
  • the invention relates to a kit as defined above further , comprising a primer for the reverse transcription chosen among SEQ ID NO: 9 and SEQ ID NO: 10.
  • Figure 1 (a-b). Examples of LR-PCR products obtained for different genotypes and subtypes using different pangenotypic primers.
  • Figure 2 (a-h). Examples of quality scores (PHRED) according to read size for 3 samples sequenced using OSJ assay (a, b and c), 3 samples sequenced using GSJ+ assay (d, e and f) and for the two pyrosequencing failures (g and h). P8S1 was sequenced with the OSJ and P14S1 with the GSJ+.
  • Figure 3 Repartition of the PHRED scores each 500 bp across HCV genome on 6 examples. Data are presented as box plots in which 50% of the values lie within the box. The horizontal lines drawn through the middle of the boxes represent the median values. The top and bottom of each box are the 25 th and 75 th percentiles of all values. The numbering is based on the sequence of HCV strain H77 (GenBank accession no. AF009606).
  • Figure 4 Examples of sequence depth of coverage obtained for 6 samples.
  • the nucleotide numbering is based on the sequence of HCV strain H77 (GenBank accession no. AF009606).
  • Figure 5 Phylogenetic analysis of the 19 near full-length genomes obtained compared with 86 reference sequences identified by their GenBank accession numbers. Bootstrap resampling (1000 replications) support values are shown at nodes. The tree is rooted using genotype 2 sequences, and all horizontal branch lengths are drawn to a scale of nucleotide substitutions per site.
  • Figure 7 Localization of the mutations appeared during treatment on the HCV RNA polymerase NS5B structure in complex with sofosbuvir and RNA. The structure representation was generated with PyMOL based on the PDB entry 4WTG.
  • the LR-PCR also worked for a group of 5 RF_2k/lb samples (with a mean viral load of 5.5 log UI/mL), including 3 sequential samples taken from the same patient before, during and after a failed treatment with sofosbuvir and ribavirin.
  • the 21 positive LR-PCRs were sequenced in 4 runs. Two samples (one HCVlb (P8S1) and one HCV4a (P14S1)) could not be analysed because, despite a correct number of reads (8407 and 15517 respectively), reads were too short and quality too low to allow the reconstitution of a consensus sequence (see Figure 2, panel C). Consensus sequences could be achieved for 19 samples (90%). A mean number of reads/sample of 8601 (+/- 6053) was obtained.
  • PHRED scores according to reads length greatly vary between GSJ and GSJ+ runs, with a higher quality for longer reads in GSJ+ assays (see Figure 2, panels A and B). Repartition of PHRED scores all along the genome was linear in OSJ+ assay (see Figure 3). Median values of PHRED score grouped by 500 bp range were always above 20, with the exceptions of sample P13S1 between 4500 and 5000, sample P7S2 between 5500 and 6000 and sample P15S1 at the 3'extremity where quality scores fall below 20.
  • Consensus sequence covered more than 99% of the expected sequence for 15/19 samples and covered 98.8%, 97.5%, 89.8% and 77.9% for the 4 reniaining ones (see Table 4).
  • Regions of interest i.e. amino acids from 1 to 181 for NS3 gene and amino acids 1-213 for NS5A, were totally covered for all samples.
  • Concerning NS5B all sequences covered amino acids 1 to 565, except amino acids 404-409 for P15S1. Median depth of coverage ranged from 15 to 957 X (see Figure 4).
  • RAVs were found in NS3 for 3 patients (T54A + I132V for P6S1, T54S for P10S1 and D168E for P12S1) and inNS5A for 4 patients (Y93H for P7S1 and P11S1, and L31M for P13S1 and P15S1).
  • RNA extracts were extracted from 1 mL of plasma and eluted on 50
  • RT Reverse transcription
  • HCV near-complete genome was amplified in a single fragment via a LR-PCR, from 2 ⁇ L of cDNA in a total volume of 20 ⁇ , using either PrimeSTARTM GXL DNA Polymerase (Takara Clontech) or KOD XtremeTM Hot Start DNA Polymerase (Merck). The following conditions were applied: 94 °C x 2 min, (98°C x 10 s, 68°C x 9 min 25) x 45 cycles, 4°C on hold. Several primer pairs were tested for each sample. A nested PCR with internal primers or a second-round PCR with the same ones was sometimes necessary to obtain the required DNA quantities, and done following the same conditions. Primers are listed in Table 2.
  • PCR products were then purified directly or from a 0.5% agarose gel using NucleoSpinTM Gel and PCR Clean-up kit (Macherey-Nagel, Hoerdt, France). DNA concentration was quantified using Quant-iTTM Pico GreenTM dsDNA Reagent (Life Technologies, St Aubin, France) and a LightCylerTM 480 instrument (Roche Diagnostics), from 1 uL of sample diluted with TE IX on 50 uL. PicoGreen® Reagent was men added in a 1:1 ratio.
  • the obtained SFF files were split by MIDs and converted to FASTQ files. Quality control (particularly, PHRED quality score profiles) was performed on each FASTQ file using the FASTQC software. Contigs were generated de novo using the VICUNA software (Broad Institute Inc.) with default parameters except for the minimum length of contigs to output which was set to 0 and the maximum percentage of divergence between read and consensus which was set to 50% (default: 8%), when the consensus output from V-FAT presented too many gaps.
  • V-FAT processed the output of VICUNA to orient and filter the raw contigs, merge them where they overlapped based on a reference alignment (the subtype-specific reference sequence for mis alignment was determined using the HCV BLAST from Los Alamos National Laboratory (with the longest contig as query) and correct frameshifts found in coding regions. As a result, V-FAT yielded a consensus full-genome assembly. This consensus was next used as a reference for reference-guided alignment with the MOSAIK software to further analyze the data, in order to obtain the depth of coverage and the PHRED quality score distribution all along the genome.
  • Phylogenetic analysis was performed after alignment of the 19 HCV whole genome sequences obtained in this study associated with 86 reference sequences.
  • the phylogenetic tree was constructed by means of the Neighbor- Joining method on conserved sites and a Jukes-Cantor substitution model using MAFFT version 7 online software. Reliability of the various inferred clades was estimated by bootstrapping (1000 replicates). Visualization of the tree and node coloring were performed by means of Archaeopteryx.

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Abstract

La présente invention concerne des procédés d'amplification et de séquençage du génome de pleine longueur du virus de l'hépatite C. La présente invention concerne également des amorces et des trousses pour l'amplification et le séquençage du génome de pleine longueur du virus de l'hépatite C.
PCT/EP2016/068589 2015-08-03 2016-08-03 Procédés d'amplification et de séquençage du génome d'un virus de l'hépatite c WO2017021471A1 (fr)

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CN110867207B (zh) * 2019-11-26 2021-07-30 北京橡鑫生物科技有限公司 验证ngs变异检测方法的评估方法及评估装置
CN112961942A (zh) * 2021-03-31 2021-06-15 广州金域医学检验中心有限公司 用于检测HCV 2a亚型耐药突变基因的扩增引物、检测方法及应用
CN113025756A (zh) * 2021-03-31 2021-06-25 广州金域医学检验中心有限公司 一种用于检测hcv 1型耐药突变基因的检测方法及应用
CN113151595A (zh) * 2021-03-31 2021-07-23 广州金域医学检验中心有限公司 用于检测hcv 6型耐药突变基因的扩增引物、检测方法及应用
CN112961942B (zh) * 2021-03-31 2024-02-02 广州金域医学检验中心有限公司 用于检测HCV 2a亚型耐药突变基因的扩增引物、检测方法及应用
CN113151595B (zh) * 2021-03-31 2024-02-06 广州金域医学检验中心有限公司 用于检测hcv 6型耐药突变基因的扩增引物、检测方法及应用
CN113025756B (zh) * 2021-03-31 2024-02-06 广州金域医学检验中心有限公司 一种用于检测hcv 1型耐药突变基因的检测方法及应用

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