# Patent

## Title
Cloned genomes of infectious hepatitis C viruses and uses thereof

## Abstract

The present invention discloses nucleic acid sequences which encode infectious hepatitis C viruses and the use of these sequences, and polypeptides encoded by all or part of these sequences, in the development of vaccines and diagnostics for HCV and in the development of screening assays for the identification of antiviral agents for HCV.

## Background
This application is a divisional of U.S. Ser. No. 09/014,416 filed Jan. 27, 1998 now U.S. Pat. No. 6,153,421, which claims the benefit of U.S. Provisional Application No. 60/053,062 filed Jul. 18, 1997


FIELD OF INVENTION
The present invention relates to molecular approaches to the production of nucleic acid sequences which comprise the genome of infectious hepatitis C viruses. In particular, the invention provides nucleic acid sequences which comprise the genomes of infectious hepatitis C viruses of genotype 1a and 1b strains. The invention therefore relates to the use of these sequences, and polypeptides encoded by all or part of these sequences, in the development of vaccines and diagnostic assays for HCV and in the development of screening assays for the identification of antiviral agents for HCV.
BACKGROUND OF INVENTION
Hepatitis C virus (HCV) has a positive-sense single-strand RNA genome and is a member of the virus family Flaviviridae (Choo et al., 1991; Rice, 1996). As for all positive-stranded RNA viruses, the genome of HCV functions as mRNA from which all viral proteins necessary for propagation are translated.
The viral genome of HCV is approximately 9600 nucleotides (nts) and consists of a highly conserved 5′ untranslated region (UTR), a single long open reading frame (ORF) of approximately 9,000 nts and a complex 3′ UTR. The 5′ UTR contains an internal ribosomal entry site (Tsukiyama-Kohara et al., 1992; Honda et al., 1996). The 3′ UTR consists of a short variable region, a polypyrimidine tract of variable length and, at the 3′ end, a highly conserved region of approximately 100 nts (Kolykhalov et al., 1996; Tanaka et al., 1995; Tanaka et al., 1996; Yamada et al., 1996). The last 46 nucleotides of this conserved region were predicted to form a stable stem-loop structure thought to be critical for viral replication (Blight and Rice, 1997; Ito and Lai, 1997; Tsuchihara et al., 1997). The ORF encodes a large polypeptide precursor that is cleaved into at least 10 proteins by host and viral proteinases (Rice, 1996). The predicted envelope proteins contain several conserved N-linked glycosylation sites and cysteine residues (Okamoto et al., 1992a). The NS3 gene encodes a serine protease and an RNA helicase and the NS5B gene encodes an RNA-dependent RNA polymerase.
Globally, six major HCV genotypes (genotypes 1–6) and multiple subtypes (a, b, c, etc.) have been identified (Bukh et al., 1993; Simmonds et al., 1993). The most divergent HCV isolates differ from each other by more than 30% over the entire genome (Okamoto et al., 1992a) and HCV circulates in an infected individual as a quasispecies of closely related genomes (Bukh et al., 1995; Farci et al., 1997).
At present, more than 80% of individuals infected with HCV become chronically infected and these chronically infected individuals have a relatively high risk of developing chronic hepatitis, liver cirrhosis and hepatocellular carcinoma (Hoofnagle, 1997). In the U.S., HCV genotypes 1a and 1b constitute the majority of infections while in many other areas, especially in Europe and Japan, genotype 1b predominates.
The only effective therapy for chronic hepatitis C, interferon (IFN), induces a sustained response in less than 25% of treated patients (Fried and Hoofnagle, 1995). Consequently, HCV is currently the most common cause of end stage liver failure and the reason for about 30% of liver transplants performed in the U.S. (Hoofnagle, 1997). In addition, a number of recent studies suggested that the severity of liver disease and the outcome of therapy may be genotype-dependent (reviewed in Bukh et al., 1997). In particular, these studies suggested that infection with HCV genotype 1b was associated with more severe liver disease (Brechot, 1997) and a poorer response to IFN therapy (Fried and Hoofnagle, 1995). As a result of the inability to develop a universally effective therapy against HCV infection, it is estimated that there are still more than 25,000 new infections yearly in the U.S. (Alter 1997) Moreover, since there is no vaccine for HCV, HCV remains a serious public health problem.
However, despite the intense interest in the development of vaccines and therapies for HCV, progress has been hindered by the absence of a useful cell culture system and the lack of any small animal model for laboratory study. For example, while replication of HCV in several cell lines has been reported, such observations have turned out not to be highly reproducible. In addition, the chimpanzee is the only animal model, other than man, for this disease. Consequently, HCV has been able to be studied only by using clinical materials obtained from patients or experimentally infected chimpanzees (an animal model whose availability is very limited).
However, several researchers have recently reported the construction of infectious cDNA clones of HCV, the identification of which would permit a more effective search for susceptible cell lines and facilitate molecular analysis of the viral genes and their function. For example, Dash et al., (1997) and Yoo et al., (1995) reported that RNA transcripts from cDNA clones of HCV-1 (genotype 1a) and HCV-N (genotype 1b), respectively, resulted in viral replication after transfection into human hepatoma cell lines. Unfortunately, the viability of these clones was not tested in vivo and concerns were raised about the infectivity of these cDNA clones in vitro (Fausto, 1997). In addition, both clones did not contain the terminal 98 conserved nucleotides at the very 3′ end of the UTR.
Kolykhalov et al., (1997) and Yanagi et al. (1997) reported the derivation from HCV strain H77 (which is genotype 1a) of cDNA clones of HCV that are infectious for chimpanzees. However, while these infectious clones will aid in studying HCV replication and pathogenesis and will provide an important tool for development of in vitro replication and propagation systems, it is important to have infectious clones of more than one genotype given the extensive genetic heterogeneity of HCV and the potential impact of such heterogeneity on the development of effective therapies and vaccines for HCV.
SUMMARY OF THE INVENTION
The present invention relates to nucleic acid sequences which comprise the genome of infectious hepatitis C viruses and in particular, nucleic acid sequences which comprise the genome of infectious hepatitis C viruses of genotype 1a and 1b strains. It is therefore an object of the invention to provide nucleic acid sequences which encode infectious hepatitis C viruses. Such nucleic acid sequences are referred to throughout the application as “infectious nucleic acid sequences”.
For the purposes of this application, nucleic acid sequence refers to RNA, DNA, cDNA or any variant thereof capable of directing host organism synthesis of a hepatitis C virus polypeptide. It is understood that nucleic acid sequence encompasses nucleic acid sequences, which due to degeneracy, encode the same polypeptide sequence as the nucleic acid sequences described herein.
The invention also relates to the use of the infectious nucleic acid sequences to produce chimeric genomes consisting of portions of the open reading frames of infectious nucleic acid sequences of other genotypes (including, but not limited to, genotypes 1, 2, 3, 4, 5 and 6) and subtypes (including, but not limited to, subtypes 1a, 1b, 2a, 2b, 2c, 3a 4a–4f, 5a and 6a) of HCV. For example infectious nucleic acid sequence of the 1a and 1b strains H77 and HC-J4, respectively, described herein can be used to produce chimeras with sequences from the genomes of other strains of HCV from different genotypes or subtypes. Nucleic acid sequences which comprise sequence from the open-reading frames of 2 or more HCV genotypes or subtypes are designated “chimeric nucleic acid sequences”.
The invention further relates to mutations of the infectious nucleic acid sequences of the invention where mutation includes, but is not limited to, point mutations, deletions and insertions. In one embodiment, a gene or fragment thereof can be deleted to determine the effect of the deleted gene or genes on the properties of the encoded virus such as its virulence and its ability to replicate. In an alternative embodiment, a mutation may be introduced into the infectious nucleic acid sequences to examine the effect of the mutation on the properties of the virus in the host cell.
The invention also relates to the introduction of mutations or deletions into the infectious nucleic acid sequences in order to produce an attenuated hepatitis C virus suitable for vaccine development.
The invention further relates to the use of the infectious nucleic acid sequences to produce attenuated viruses via passage in vitro or in vivo of the viruses produced by transfection of a host cell with the infectious nucleic acid sequence.
The present invention also relates to the use of the nucleic acid sequences of the invention or fragments thereof in the production of polypeptides where “nucleic acid sequences of the invention” refers to infectious nucleic acid sequences, mutations of infectious nucleic acid sequences, chimeric nucleic acid sequences and sequences which comprise the genome of attenuated viruses produced from the infectious nucleic acid sequences of the invention. The polypeptides of the invention, especially structural polypeptides, can serve as immunogens in the development of vaccines or as antigens in the development of diagnostic assays for detecting the presence of HCV in biological samples.
The invention therefore also relates to vaccines for use in immunizing mammals especially humans against hepatitis C. In one embodiment, the vaccine comprises one or more polypeptides made from a nucleic acid sequence of the invention or fragment thereof. In a second embodiment, the vaccine comprises a hepatitis C virus produced by transfection of host cells with the nucleic acid sequences of the invention.
The present invention therefore relates to methods for preventing hepatitis C in a mammal. In one embodiment the method comprises administering to a mammal a polypeptide or polypeptides encoded by a nucleic acid sequence of the invention in an amount effective to induce protective immunity to hepatitis C. In another embodiment, the method of prevention comprises administering to a mammal a hepatitis C virus of the invention in an amount effective to induce protective immunity against hepatitis C.
In yet another embodiment, the method of protection comprises administering to a mammal a nucleic acid sequence of the invention or a fragment thereof in an amount effective to induce protective immunity against hepatitis C.
The invention also relates to hepatitis C viruses produced by host cells transfected with the nucleic acid sequences of the present invention.
The invention therefore also provides pharmaceutical compositions comprising the nucleic acid sequences of the invention and/or their encoded hepatitis C viruses. The invention further provides pharmaceutical compositions comprising polypeptides encoded by the nucleic acid sequences of the invention or fragments thereof. The pharmaceutical compositions of the invention may be used prophylactically or therapeutically.
The invention also relates to antibodies to the hepatitis C viruses of the invention or their encoded polypeptides and to pharmaceutical compositions comprising these antibodies.
The present invention further relates to polypeptides encoded by the nucleic acid sequences of the invention fragments thereof. In one embodiment, said polypeptide or polypeptides are fully or partially purified from hepatitis C virus produced by cells transfected with nucleic acid sequence of the invention. In another embodiment, the polypeptide or polypeptides are produced recombinantly from a fragment of the nucleic acid sequences of the invention. In yet another embodiment, the polypeptides are chemically synthesized.
The invention also relates to the use of the nucleic acid sequences of the invention to identify cell lines capable of supporting the replication of HCV in vitro.
The invention further relates to the use of the nucleic acid sequences of the invention or their encoded proteases (e.g. NS3 protease) to develop screening assays to identify antiviral agents for HCV.



BRIEF DESCRIPTION OF FIGURES
FIG. 1 shows a strategy for constructing full-length cDNA clones of HCV strain H77. The long PCR products amplified with H1 and H9417R primers were cloned directly into pGEM-9zf(−) after digestion with Not I and Xba I (pH211 and pHSO1). Next, the 3′ UTR was cloned into both pH211 and pH501 after digestion with Afl II and Xba I (pH21 and pH50). pH21 was tested for infectivity in a chimpanzee. To improve the efficiency of cloning, we constructed a cassette vector with consensus 5′ and 3′ termini of H77. This cassette vector (pCV) was obtained by cutting out the BamHI fragment (nts 1358–7530 of the H77 genome) from pH50, followed by religation. Finally, the long PCR products of H77 amplified with primers H1 and H9417R(H product) or primers A1 and H9417R (A product) were cloned into pCV after digestion with Age I and Afl II or with Pin AI and Bfr I. The latter procedure yielded multiple complete cDNA clones of strain H77 of HCV.
FIG. 2 shows the results of gel electrophoresis of long RT-PCR amplicons of the entire ORF of H77 and the transcription mixture of the infectious clone of H77. The complete ORF was amplified by long RT-PCR with the primers H1 or A1 and H9417R from 105 GE of H77. A total of 10 μg of the consensus chimeric clone (pCV-H77C) linearized with Xba I was transcribed in a 100 μl reaction with T7 RNA polymerase. Five μl of the transcription mixture was analyzed by gel electrophoresis and the remainder of the mixture was injected into a chimpanzee. Lane 1, molecular weight marker; lane 2, products amplified with primers H1 and H9417R; lane 3, products amplified with primers A1 and H9417R; lane 4, transcription mixture containing the RNA transcripts and linearized clone pCV-H77C (12.5 kb).
FIG. 3 is a diagram of the genome organization of HCV strain H77 and the genetic heterogeneity of individual full-length clones compared with the consensus sequence of H77. Solid lines represent aa changes. Dashed lines represent silent mutations. A * in pH21 represents a point mutation at nt 58 in the 5′ UTR. In the ORF, the consensus chimeric clone pCV-H77C had 11 nt differences [at positions 1625 (C→T), 2709 (T→C), 3380 (A→G), 3710 (C→T), 3914 (G→A), 4463 (T→C), 5058 (C→T), 5834 (C→T), 6734 (T→C), 7154 (C→T), and 7202 (T→C)] and one aa change (F→L at aa 790) compared with the consensus sequence of H77. This clone was infectious. Clone pH21 and pCV-H11 had 19 nts (7 aa) and 64 nts (21 aa) differences respectively, compared with the consensus sequence of H77. These two clones were not infectious. A single point mutation in the 3′ UTR at nucleotide 9406 (G→A) introduced to create an Afl II cleavage site is not shown.
FIGS. 4A–4F show the complete nucleotide (SEQ ID NO:2) of a H77C clone produced according to the present invention and FIGS. 4G–4H show the amino acid (SEQ ID NO:1) encoded by the H77C clone.
FIG. 5 shows an agarose gel of long RT-PCR amplicons and transcription mixtures. Lanes 1 and 4: Molecular weight marker (Lambda/HindIII digest). Lanes 2 and 3: RT-PCR amplicons of the entire ORF of HC-J4. Lane 5: pCV-H77C transcription control (Yanagi et al., 1997). Lanes 6, 7, and 8: 1/40 of each transcription mixture of pCV-J4L2S, pCV-J4L4S and pCV-J4L6S, respectively, which was injected into the chimpanzee.
FIG. 6 shows the strategy utilized for the construction of full-length cDNA clones of HCV strain HC-J4. The long PCR products were cloned as two separate fragments (L and S) into a cassette vector (pCV) with fixed 5′ and 3′ termini of HCV (Yanagi et al., 1997). Full-length cDNA clones of HC-J4 were obtained by inserting the L fragment from three pCV-J4L clones into three identical pCV-J4S9 clones after digestion with PinAI (isoschizomer of AgeI) and BfrI (isoschizomer of AflII).
FIGS. 7A through 7D shows amino acid positions with a quasispecies of HC-J4 in the acute phase plasma pool obtained from an experimentally infected chimpanzee. Cons-p9: consensus amino acid sequence deduced from analysis of nine L fragments and nine S fragments (see FIG. 6). Cons-D: consensus sequence derived from direct sequencing of the PCR product. A, B, C: groups of similar viral species. Dot: amino acid identical to that in Cons-p 9. Capital letter: amino acid different from that in Cons-p9. Cons-F: composite consensus amino acid sequence combining Cons-p9 and Cons-D. Boxed amino acid: different from that in Cons-F. Shaded amino acid: different from that in all species A sequences. An *: defective ORF due to a nucleotide deletion (clone L1, aa 1097) or insertion (clone L7, aa 2770). Diagonal lines: fragments used to construct the infectious clone.
FIG. 8 shows comparisons (percent difference) of nucleotide (nts. 156–8935) and predicted amino acid sequences (aa 1–2864) of L clones (species A, B, and C, this study), HC-J4/91 (Okamoto et al., 1992b) and HC-J4/83 (Okamoto et al., 1992b). Differences among species A sequences and among species B sequences are shaded.
FIG. 9 shows UPGMA (“unweighted pair group method with arithmetic mean”) trees of HC-J4/91 (Okamoto et al., 1992b), HC-J4/83 (Okamoto et al., 1992b), two prototype strains of genotype 1b (HCV-J, Kato et al., 1990; HCV-BK, Takamizawa et al., 1991), and L clones (this study)
FIG. 10 shows the alignment of the HVR 1 SEQ ID NOS:28, 30, 32, 34, 36–38, 41, 43 and 45 and HVR2 SEQ ID NOS: 29, 31, 33, 35, 39, 40, 42, 44 and 46 amino acid sequences of the E2 sequences of nine L clones of HC-J4 (species A, B, and C) obtained from an early acute phase plasma pool of an experimentally infected chimpanzee compared with the sequences of eight clones (HC-J4/91-20 through HC-J4/91-27, Okamoto et al., 1992b) derived from the inoculum. Dot: an amino acid identical to that in the top line. Capital letters: amino acid different from that in the top line.
FIG. 11 shows the alignment of the 5′ UTR and the 3′ UTR sequences of infectious clones of genotype 1a pCV-H77C) and 1b (pCV-J4L6S). 5′ UTR for HC-J4 is SEQ ID NO:47, 5′ UTR for pCV-J4L6S is SEQ ID NO:48, 5′ UTR for pCV-H77C is SEQ ID NO: 49, 3′ UTR-3′ variable region for HC-J4 is SEQ ID NO 50 and 53, 3′ UTR-3′ variable region for pCV-J4L6S is SEQ ID NO:51 and 54, 3′ UTR-3′ variable region for pCV-H77C is SEQ ID NO:52 and 54; 3′ UTR-3′ conserved region for H77, pCV-J4L6S and pCV-H77C is SEQ ID NO 55. Top line: consensus sequence of the indicated strain. Dot: identity with consensus sequence. Capital letter: different from the consensus sequence. Dash: deletion. Underlined: PinAI and BfrI cleavage site. Numbering corresponds to the HCV sequence of pCV-J4L6S.
FIG. 12 shows a comparison of individual full-length cDNA clones of the ORF of HCV strain HC-J4 with the consensus sequence (see FIG. 7). Solid lines: amino acid changes. Dashed lines: silent mutations. Clone pCv-J4L6S was infectious in vivo whereas clones pCV-J4L2S and pCV-J4L4S were not.
FIG. 13 shows biochemical (ALT levels) and PCR analyses of a chimpanzee following percutaneous intrahepatic transfection with RNA transcripts of the infectious clone of pCV-J4L2S, pCV-J4L4S and pCV-J4L6S. The ALT serum enzyme levels were measured in units per liter (u/l). For the PCR analysis, “HCV RNA” represented by an open rectangle indicates a serum sample that was negative for HCV after nested PCR; “HCV RNA” represented by a closed rectangle indicates that the serum sample was positive for HCV and HCV GE titer on the right-hand y-axis represents genome equivalents.
FIGS. 14A–14F show the nucleotide sequence of the infectious clone of genotype 1b strain HC-J4 (SEQ ID NO:4) FIGS. 14G–14H show the amino acid (SEQ ID NO:3) encoded by the HC-J4 clone.
FIG. 15 shows the strategy for constructing a chimeric HCV clone designated pH77CV-J4 which contains the nonstructural region of the infectious clone of genotype 1a strain H77 and the structural region of the infectious clone of genotype 1b strain HC-J4.
FIGS. 16A–16F show the nucleotide sequence of the chimeric 1a/1b clone pH77CV-J4 (SEQ ID NO:6) of FIG. 15 and FIGS. 16G–16H show the amino acid sequence encoded by the chimeric 1a/1b (SEQ ID NO:5).
FIGS. 17A and 17B show the sequence of the 3′ untranslated region remaining in various 3′ deletion mutants of the 1a infectious clone pCV-H77C, (pCV-H77C has SEQ ID NOS:56, 57 and 58; pCV-H77C (−98X) has SEQ ID NO:59; pCV-H77C (−42X) has SEQ ID NO:60; pCV-H77C (X-52) has SEQ ID NO:61; pCV-H77C(X) has SEQ ID NO:62; pCV-H77C(+49X) has SEQ ID NO:63; pCV-H77C (VR-24) has SEQ ID NO:64; and pCV-H77C (−U/UC) has SEQ ID NO:65). and the strategy utilized in constructing each 3′ deletion mutant (FIGS. 17C–17G).



Of the seven deletion mutants shown, two (pCV-H77C(−98X) and (−42X)) have been constructed and tested for infectivity in chimpanzees (see FIGS. 17A and 17C) and the other six are to be constructed and tested for infectivity as described in FIGS. 17D–17G.
FIGS. 18A and 18B show biochemical (ALT levels), PCR(HCV RNA and HCV GE titer), serological (anti-HCV) and histopathological (FIG. 18B only) analyses of chimpanzees 1494 (FIG. 18A) and 1530 (FIG. 18B) following transfection with the infectious cDNA clone pCV-H77C.
The ALT serum enzyme levels were measured in units per ml (u/l). For the PCR analysis, “HCV RNA” represented by an open rectangle indicates a serum sample that was negative for HCV after nested PCR; “HCV RNA” represented by a closed rectangle indicates that the serum sample was positive for HCV; and HCV GE titer on the right-hand y-axis represents genome equivalents.
The bar marked “anti-HCV” indicates samples that were positive for anti-HCV antibodies as determined by commercial assays. The histopathology scores in FIG. 18B correspond to no histopathology (◯), mild hepatitis (⊖) and moderate to severe hepatitis (●).
DESCRIPTION OF THE INVENTION
The present invention relates to nucleic acid sequences which comprise the genome of an infectious hepatitis C virus. More specifically, the invention relates to nucleic acid sequences which encode infectious hepatitis C viruses of genotype 1a and 1b strains. In one embodiment, the infectious nucleic acid sequence of the invention has the sequence shown in FIGS. 4A–4F of this application. In another embodiment, the infectious nucleic acid sequence has the sequence shown in FIGS. 14A–14F and is contained in a plasmid construct deposited with the American Type Culture Collection (ATCC) on Jan. 26, 1998 and having ATCC accession number 209596.
The invention also relates to “chimeric nucleic acid sequences” where the chimeric nucleic acid sequences consist of open-reading frame sequences taken from infectious nucleic acid sequences of hepatitis C viruses of different genotypes or subtypes.
In one embodiment, the chimeric nucleic acid sequence consists of sequence from the genome of an HCV strain belonging to one genotype or subtype which encodes structural polypeptides and sequence of an HCV strain belonging to another genotype strain or subtype which encodes nonstructural polypeptides. Such chimeras can be produced by standard techniques of restriction digestion, PCR amplification and subcloning known to those of ordinary skill in the art.
In a preferred embodiment, the sequence encoding nonstructural polypeptides is from an infectious nucleic acid sequence encoding a genotype 1a strain where the construction of a chimeric 1a/1b nucleic acid sequence is described in Example 9 and the chimeric 1a/1b nucleic acid sequence is shown in FIGS. 16A–16F. It is believed that the construction of such chimeric nucleic acid sequences will be of importance in studying the growth and virulence properties of hepatitis C virus and in the production of hepatitis C viruses suitable to confer protection against multiple genotypes of HCV. For example, one might produce a “multivalent” vaccine by putting epitopes from several genotypes or subtypes into one clone. Alternatively one might replace just a single gene from an infectious sequence with the corresponding gene from the genomic sequence of a strain from another genotype or subtype or create a chimeric gene which contains portions of a gene from two genotypes or subtypes. Examples of genes which could be replaced or which could be made chimeric, include, but are not limited to, the E1, E2 and NS4 genes.
The invention further relates to mutations of the infectious nucleic acid sequences where “mutations” includes, but is not limited to, point mutations, deletions and insertions. Of course, one of ordinary skill in the art would recognize that the size of the insertions would be limited by the ability of the resultant nucleic acid sequence to be properly packaged within the virion. Such mutation could be produced by techniques known to those of skill in the art such as site-directed mutagenesis, fusion PCR, and restriction digestion followed by religation.
In one embodiment, mutagenesis might be undertaken to determine sequences that are important for viral properties such as replication or virulence. For example, one may introduce a mutation into the infectious nucleic acid sequence which eliminates the cleavage site between the NS4A and NS4B polypeptides to examine the effects on viral replication and processing of the polypeptide. Alternatively, one or more of the 3 amino acids encoded by the infectious 1b nucleic acid sequence shown in FIGS. 14A–14F which differ from the HC-J4 consensus sequence may be back mutated to the corresponding amino acid in the HC-J4 consensus sequence to determine the importance of these three amino acid changes to infectivity or virulence. In yet another embodiment, one or more of the amino acids from the noninfectious 1b clones pCV-J4L2S and pCV-J4L4S which differ from the consensus sequence may be introduced into the infectious 1b sequence shown in FIGS. 14A–14F.
In yet another example, one may delete all or part of a gene or of the 5′ or 3′ nontranslated region contained in an infectious nucleic acid sequence and then transfect a host cell (animal or cell culture) with the mutated sequence and measure viral replication in the host by methods known in the art such as RT-PCR. Preferred genes include, but are not limited to, the P7, NS4B and NS5A genes. Of course, those of ordinary skill in the art will understand that deletion of part of a gene, preferably the central portion of the gene, may be preferable to deletion of the entire gene in order to conserve the cleavage site boundaries which exist between proteins in the HCV polyprotein and which are necessary for proper processing of the polyprotein.
In the alternative, if the transfection is into a host animal such as a chimpanzee, one can monitor the virulence phenotype of the virus produced by transfection of the mutated infectious nucleic acid sequence by methods known in the art such as measurement of liver enzyme levels (alanine aminotransferase (ALT) or isocitrate dehydrogenase (ICD)) or by histopathology of liver biopsies. Thus, mutations of the infectious nucleic acid sequences may be useful in the production of attenuated HCV strains suitable for vaccine use.
The invention also relates to the use of the infectious nucleic acid sequences of the present invention to produce attenuated viral strains via passage in vitro or in vivo of the virus produced by transfection with the infectious nucleic acid sequences.
The present invention therefore relates to the use of the nucleic acid sequences of the invention to identify cell lines capable of supporting the replication of HCV.
In particular, it is contemplated that the mutations of the infectious nucleic acid sequences of the invention and the production of chimeric sequences as discussed above may be useful in identifying sequences critical for cell culture adaptation of HCV and hence, may be useful in identifying cell lines capable of supporting HCV replication.
Transfection of tissue culture cells with the nucleic acid sequences of the invention may be done by methods of transfection known in the art such as electroporation, precipitation with DEAE-Dextran or calcium phosphate or liposomes.
In one such embodiment, the method comprises the growing of animal cells, especially human cells, in vitro and transfecting the cells with the nucleic acid of the invention, then determining if the cells show indicia of HCV infection. Such indicia include the detection of viral antigens in the cell, for example, by immunofluorescent procedures well known in the art; the detection of viral polypeptides by Western blotting using antibodies specific therefor; and the detection of newly transcribed viral RNA within the cells via methods such as RT-PCR. The presence of live, infectious virus particles following such tests may also be shown by injection of cell culture medium or cell lysates into healthy, susceptible animals, with subsequent exhibition of the symptoms of HCV infection.
Suitable cells or cell lines for culturing HCV include, but are not limited to, lymphocyte and hepatocyte cell lines known in the art.
Alternatively, primary hepatocytes can be cultured, and then infected with HCV; or, the hepatocyte cultures could be derived from the livers of infected chimpanzees. In addition, various immortalization methods known to those of ordinary skill in the art can be used to obtain cell-lines derived from hepatocyte cultures. For example, primary hepatocyte cultures may be fused to a variety of cells to maintain stability.
The present invention further relates to the in vitro and in vivo production of hepatitis C viruses from the nucleic acid sequences of the invention.
In one embodiment, the sequences of the invention can be inserted into an expression vector that functions in eukaryotic cells. Eukaryotic expression vectors suitable for producing high efficiency gene transfer in vivo are well known to those of ordinary skill in the art and include, but are not limited to, plasmids, vaccinia viruses, retroviruses, adenoviruses and adeno-associated viruses.
In another embodiment, the sequences contained in the recombinant expression vector can be transcribed in vitro by methods known to those of ordinary skill in the art in order to produce RNA transcripts which encode the hepatitis C viruses of the invention. The hepatitis C viruses of the invention may then be produced by transfecting cells by methods known to those of ordinary skill in the art with either the in vitro transcription mixture containing the RNA transcripts (see Example 4) or with the recombinant expression vectors containing the nucleic acid sequences described herein.
The present invention also relates to the construction of cassette vectors useful in the cloning of viral genomes wherein said vectors comprise a nucleic acid sequence to be cloned, and said vector reading in the correct phase for the expression of the viral nucleic acid to be cloned. Such a cassette vector will, of course, also possess a promoter sequence, advantageously placed upstream of the sequence to be expressed. Cassette vectors according to the present invention are constructed according to the procedure described in FIG. 1, for example, starting with plasmid pCv. Of course, the DNA to be inserted into said cassette vector can be derived from any virus, advantageously from HCV, and most advantageously from the H77 strain of HCV. The nucleic acid to be inserted according to the present invention can, for example, contain one or more open reading frames of the virus, for example, HCV. The cassette vectors of the present invention may also contain, optionally, one or more expressible marker genes for expression as an indication of successful transfection and expression of the nucleic acid sequences of the vector. To insure expression, the cassette vectors of the present invention will contain a promoter sequence for binding of the appropriate cellular RNA polymerase, which will depend on the cell into which the vector has been introduced. For example, if the host cell is a bacterial cell, then said promoter will be a bacterial promoter sequence to which the bacterial RNA polymerases will bind.
The hepatitis C viruses produced from the sequences of the invention may be purified or partially purified from the transfected cells by methods known to those of ordinary skill in the art. In a preferred embodiment, the viruses are partially purified prior to their use as immunogens in the pharmaceutical compositions and vaccines of the present invention.
The present invention therefore relates to the use of the hepatitis C viruses produced from the nucleic acid sequences of the invention as immunogens in live or killed (e.g., formalin inactivated) vaccines to prevent hepatitis C in a mammal.
In an alternative embodiment, the immunogen of the present invention may be an infectious nucleic acid sequence, a chimeric nucleic acid sequence, or a mutated infectious nucleic acid sequence which encodes a hepatitis C virus. Where the sequence is a cDNA sequence, the cDNAs and their RNA transcripts may be used to transfect a mammal by direct injection into the liver tissue of the mammal as described in the Examples.
Alternatively, direct gene transfer may be accomplished via administration of a eukaryotic expression vector containing a nucleic acid sequence of the invention.
In yet another embodiment, the immunogen may be a polypeptide encoded by the nucleic acid sequences of the invention. The present invention therefore also relates to polypeptides produced from the nucleic acid sequences of the invention or fragments thereof. In one embodiment, polypeptides of the present invention can be recombinantly produced by synthesis from the nucleic acid sequences of the invention or isolated fragments thereof, and purified, or partially purified, from transfected cells using methods already known in the art. In an alternative embodiment, the polypeptides may be purified or partially purified from viral particles produced via transfection of a host cell with the nucleic acid sequences of the invention. Such polypeptides might, for example, include either capsid or envelope polypeptides prepared from the sequences of the present invention.
When used as immunogens, the nucleic acid sequences of the invention, or the polypeptides or viruses produced therefrom, are preferably partially purified prior to use as immunogens in pharmaceutical compositions and vaccines of the present invention. When used as a vaccine, the sequences and the polypeptide and virus products thereof, can be administered alone or in a suitable diluent, including, but not limited to, water, saline, or some type of buffered medium. The vaccine according to the present invention may be administered to an animal, especially a mammal, and most especially a human, by a variety of routes, including, but not limited to, intradermally, intramuscularly, subcutaneously, or in any combination thereof.
Suitable amounts of material to administer for prophylactic and therapeutic purposes will vary depending on the route selected and the immunogen (nucleic acid, virus, polypeptide) administered. One skilled in the art will appreciate that the amounts to be administered for any particular treatment protocol can be readily determined without undue experimentation. The vaccines of the present invention may be administered once or periodically until a suitable titer of anti-HCV antibodies appear in the blood. For an immunogen consisting of a nucleic acid sequence, a suitable amount of nucleic acid sequence to be used for prophylactic purposes might be expected to fall in the range of from about 100 μg to about 5 mg and most preferably in the range of from about 500 μg to about 2 mg. For a polypeptide, a suitable amount to use for prophylactic purposes is preferably 100 ng to 100 μg and for a virus 102 to 106 infectious doses. Such administration will, of course, occur prior to any sign of HCV infection.
A vaccine of the present invention may be employed in such forms as capsules, liquid solutions, suspensions or elixirs for oral administration, or sterile liquid forms such as solutions or suspensions. Any inert carrier is preferably used, such as saline or phosphate-buffered saline, or any such carrier in which the HCV of the present invention can be suitably suspended. The vaccines may be in the form of single dose preparations or in multi-dose flasks which can be utilized for mass-vaccination programs of both animals and humans. For purposes of using the vaccines of the present invention reference is made to Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., Osol (Ed.) (1980); and New Trends and Developments in Vaccines, Voller et al. (Eds.), University Park Press, Baltimore, Md. (1978), both of which provide much useful information for preparing and using vaccines. Of course, the polypeptides of the present invention, when used as vaccines, can include, as part of the composition or emulsion, a suitable adjuvant, such as alum (or aluminum hydroxide) when humans are to be vaccinated, to further stimulate production of antibodies by immune cells. When nucleic acids or viruses are used for vaccination purposes, other specific adjuvants such as CpG motifs (Krieg, A. K. et al. (1995) and (1996)), may prove useful.
When the nucleic acids, viruses and polypeptides of the present invention are used as vaccines or inocula, they will normally exist as physically discrete units suitable as a unitary dosage for animals, especially mammals, and most especially humans, wherein each unit will contain a predetermined quantity of active material calculated to produce the desired immunogenic effect in association with the required diluent. The dose of said vaccine or inoculum according to the present invention is administered at least once. In order to increase the antibody level, a second or booster dose may be administered at some time after the initial dose. The need for, and timing of, such booster dose will, of course, be determined within the sound judgment of the administrator of such vaccine or inoculum and according to sound principles well known in the art. For example, such booster dose could reasonably be expected to be advantageous at some time between about 2 weeks to about 6 months following the initial vaccination. Subsequent doses may be administered as indicated.
The nucleic acid sequences, viruses and polypeptides of the present invention can also be administered for purposes of therapy, where a mammal, especially a primate, and most especially a human, is already infected, as shown by well known diagnostic measures. When the nucleic acid sequences, viruses or polypeptides of the present invention are used for such therapeutic purposes, much of the same criteria will apply as when it is used as a vaccine, except that inoculation will occur post-infection. Thus, when the nucleic acid sequences, viruses or polypeptides of the present invention are used as therapeutic agents in the treatment of infection, the therapeutic agent comprises a pharmaceutical composition containing a sufficient amount of said nucleic acid sequences, viruses or polypeptides so as to elicit a therapeutically effective response in the organism to be treated. Of course, the amount of pharmaceutical composition to be administered will, as for vaccines, vary depending on the immunogen contained therein (nucleic acid, polypeptide, virus) and on the route of administration.
The therapeutic agent according to the present invention can thus be administered by, subcutaneous, intramuscular or intradermal routes. One skilled in the art will certainly appreciate that the amounts to be administered for any particular treatment protocol can be readily determined without undue experimentation. Of course, the actual amounts will vary depending on the route of administration as well as the sex, age, and clinical status of the subject which, in the case of human patients, is to be determined with the sound judgment of the clinician.
The therapeutic agent of the present invention can be employed in such forms as capsules, liquid solutions, suspensions or elixirs, or sterile liquid forms such as solutions or suspensions. Any inert carrier is preferably used, such as saline, phosphate-buffered saline, or any such carrier in which the HCV of the present invention can be suitably suspended. The therapeutic agents may be in the form of single dose preparations or in the multi-dose flasks which can be utilized for mass-treatment programs of both animals and humans. Of course, when the nucleic acid sequences, viruses or polypeptides of the present invention are used as therapeutic agents they may be administered as a single dose or as a series of doses, depending on the situation as determined by the person conducting the treatment.
The nucleic acids, polypeptides and viruses of the present invention can also be utilized in the production of antibodies against HCV. The term “antibody” is herein used to refer to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules. Examples of antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and portions of an immunoglobulin molecule, including those portions known in the art as Fab, F(ab′)2 and F(v) as well as chimeric antibody molecules.
Thus, the polypeptides, viruses and nucleic acid sequences of the present invention can be used in the generation of antibodies that immunoreact (i.e., specific binding between an antigenic determinant-containing molecule and a molecule containing an antibody combining site such as a whole antibody molecule or an active portion thereof) with antigenic determinants on the surface of hepatitis C virus particles.
The present invention therefore also relates to antibodies produced following immunization with the nucleic acid sequences, viruses or polypeptides of the present invention. These antibodies are typically produced by immunizing a mammal with an immunogen or vaccine to induce antibody molecules having immunospecificity for polypeptides or viruses produced in response to infection with the nucleic acid sequences of the present invention. When used in generating such antibodies, the nucleic acid sequences, viruses, or polypeptides of the present invention may be linked to some type of carrier molecule. The resulting antibody molecules are then collected from said mammal. Antibodies produced according to the present invention have the unique advantage of being generated in response to authentic, functional polypeptides produced according to the actual cloned HCV genome.
The antibody molecules of the present invention may be polyclonal or monoclonal. Monoclonal antibodies are readily produced by methods well known in the art. Portions of immunoglobin molecules, such as Fabs, as well as chimeric antibodies, may also be produced by methods well known to those of ordinary skill in the art of generating such antibodies.
The antibodies according to the present invention may also be contained in blood plasma, serum, hybridoma supernatants, and the like. Alternatively, the antibody of the present invention is isolated to the extent desired by well known techniques such as, for example, using DEAE Sephadex. The antibodies produced according to the present invention may be further purified so as to obtain specific classes or subclasses of antibody such as IgM, IgG, IgA, and the like. Antibodies of the IgG class are preferred for purposes of passive protection.
The antibodies of the present invention are useful in the prevention and treatment of diseases caused by hepatitis C virus in animals, especially mammals, and most especially humans.
In providing the antibodies of the present invention to a recipient mammal, preferably a human, the dosage of administered antibodies will vary depending on such factors as the mammal's age, weight, height, sex, general medical condition, previous medical history, and the like.
In general, it will be advantageous to provide the recipient mammal with a dosage of antibodies in the range of from about 1 mg/kg body weight to about 10 mg/kg body weight of the mammal, although a lower or higher dose may be administered if found desirable. Such antibodies will normally be administered by intravenous or intramuscular route as an inoculum. The antibodies of the present invention are intended to be provided to the recipient subject in an amount sufficient to prevent, lessen or attenuate the severity, extent or duration of any existing infection.
The antibodies prepared by use of the nucleic acid sequences, viruses or polypeptides of the present invention are also highly useful for diagnostic purposes. For example, the antibodies can be used as in vitro diagnostic agents to test for the presence of HCV in biological samples taken from animals, especially humans. Such assays include, but are not limited to, radioimmunoassays, EIA, fluorescence, Western blot analysis and ELISAs. In one such embodiment, the biological sample is contacted with antibodies of the present invention and a labeled second antibody is used to detect the presence of HCV to which the antibodies are bound.
Such assays may be, for example, a direct protocol (where the labeled first antibody is immunoreactive with the antigen, such as, for example, a polypeptide on the surface of the virus), an indirect protocol (where a labeled second antibody is reactive with the first antibody), a competitive protocol (such as would involve the addition of a labeled antigen), or a sandwich protocol (where both labeled and unlabeled antibody are used), as well as other protocols well known and described in the art.
In one embodiment, an immunoassay method would utilize an antibody specific for HCV envelope determinants and would further comprise the steps of contacting a biological sample with the HCV-specific antibody and then detecting the presence of HCV material in the test sample using one of the types of assay protocols as described above. Polypeptides and antibodies produced according to the present invention may also be supplied in the form of a kit, either present in vials as purified material, or present in compositions and suspended in suitable diluents as previously described.
In a preferred embodiment, such a diagnostic test kit for detection of HCV antigens in a test sample comprises in combination a series of containers, each container a reagent needed for such assay. Thus, one such container would contain a specific amount of HCV-specific antibody as already described, a second container would contain a diluent for suspension of the sample to be tested, a third container would contain a positive control and an additional container would contain a negative control. An additional container could contain a blank.
For all prophylactic, therapeutic and diagnostic uses, the antibodies of the invention and other reagents, plus appropriate devices and accessories, may be provided in the form of a kit so as to facilitate ready availability and ease of use.
The present invention also relates to the use of nucleic acid sequences and polypeptides of the present invention to screen potential antiviral agents for antiviral activity against HCV. Such screening methods are known by those of skill in the art. Generally, the antiviral agents are tested at a variety of concentrations, for their effect on preventing viral replication in cell culture systems which support viral replication, and then for an inhibition of infectivity or of viral pathogenicity (and a low level of toxicity) in an animal model system.
In one embodiment, animal cells (especially human cells) transfected with the nucleic acid sequences of the invention are cultured in vitro and the cells are treated with a candidate antiviral agent (a chemical, peptide etc.) for antiviral activity by adding the candidate agent to the medium. The treated cells are then exposed, possibly under transfecting or fusing conditions known in the art, to the nucleic acid sequences of the present invention. A sufficient period of time would then be allowed to pass for infection to occur, following which the presence or absence of viral replication would be determined versus untreated control cells by methods known to those of ordinary skill in the art. Such methods include, but are not limited to, the detection of viral antigens in the cell, for example, by immunofluorescent procedures well known in the art; the detection of viral polypeptides by Western blotting using antibodies specific therefor; the detection of newly transcribed viral RNA within the cells by RT-PCR; and the detection of the presence of live, infectious virus particles by injection of cell culture medium or cell lysates into healthy, susceptible animals, with subsequent exhibition of the symptoms of HCV infection. A comparison of results obtained for control cells (treated only with nucleic acid sequence) with those obtained for treated cells (nucleic acid sequence and antiviral agent) would indicate, the degree, if any, of antiviral activity of the candidate antiviral agent. Of course, one of ordinary skill in the art would readily understand that such cells can be treated with the candidate antiviral agent either before or after exposure to the nucleic acid sequence of the present invention so as to determine what stage, or stages, of viral infection and replication said agent is effective against.
In an alternative embodiment, a protease such as NS3 protease produced from a nucleic acid sequence of the invention may be used to screen for protease inhibitors which may act as antiviral agents. The structural and nonstructural regions of the HCV genome, including nucleotide and amino acid locations, have been determined, for example, as depicted in Houghton, M. (1996), FIG. 1; and Major, M. E. et al. (1997), Table 1.
Such above-mentioned protease inhibitors may take the form of chemical compounds or peptides which mimic the known cleavage sites of the protease and may be screened using methods known to those of skill in the art (Houghton, M. (1996) and Major, M. E. et al. (1997)). For example, a substrate may be employed which mimics the protease's natural substrate, but which provides a detectable signal (e.g. by fluorimetric or calorimetric methods) when cleaved. This substrate is then incubated with the protease and the candidate protease inhibitor under conditions of suitable pH, temperature etc. to detect protease activity. The proteolytic activities of the protease in the presence or absence of the candidate inhibitor are then determined.
In yet another embodiment, a candidate antiviral agent (such as a protease inhibitor) may be directly assayed in vivo for antiviral activity by administering the candidate antiviral agent to a chimpanzee transfected with a nucleic acid sequence of the invention and then measuring viral replication in vivo via methods such as RT-PCR. Of course, the chimpanzee may be treated with the candidate agent either before or after transfection with the infectious nucleic acid sequence so as to determine what stage, or stages, of viral infection and replication the agent is effective against.
The invention also provides that the nucleic acid sequences, viruses and polypeptides of the invention may be supplied in the form of a kit, alone or in the form of a pharmaceutical composition.
All scientific publication and/or patents cited herein are specifically incorporated by reference. The following examples illustrate various aspects of the invention but are in no way intended to limit the scope thereof.
EXAMPLES
Materials and Methods For Examples 1–4
Collection of Virus
Hepatitis C virus was collected and used as a source for the RNA used in generating the cDNA clones according to the present invention. Plasma containing strain H77 of HCV was obtained from a patient in the acute phase of transfusion-associated non-A, non-B hepatitis (Feinstone et al (1981)). Strain H77 belongs to genotype 1a of HCV (Ogata et al (1991), Inchauspe et al (1991)). The consensus sequence for most of its genome has been determined (Kolyakov et al (1996), Ogata et al (1991), Inchauspe et al (1991) and Farci et al (1996)).
RNA Purification
Viral RNA was collected and purified by conventional means. In general, total RNA from 10 μl of H77 plasma was extracted with the TRIzol system (GIBCO BRL). The RNA pellet was resuspended in 100 μl of 10 mM dithiothreitol (DTT) with 5% (vol/vol) RNasin (20–40 units/μl) (available from Promega) and 10 μl aliquots were stored at −80° C. In subsequent experiments RT-PCR was performed on RNA equivalent to 1 μl of H77 plasma, which contained an estimated 105 genome equivalents (GE) of HCV (Yanagi et al (1996)).
Primers used in the RT-PCR process were deduced from the genomic sequences of strain H77 according to procedures already known in the art (see above) or else were determined specifically for use herein. The primers generated for this purpose are listed in Table 1.







TABLE 1







Oligonucleotides used for PCR amplification of


strain H77 of HCV








Designation
Sequence (5′ → 3′)*





SEQ ID NO:7



H9261F
GGCTACAGCGGGGGGAGACATTTATCACAGC


SEQ ID NO:8


H3′X58R
TCATGCGGCTCACGGACCTTTCACAGCTAG


SEQ ID NO:9


H9282F
GTCCAAGCTTATCACAGCGTGTCTCATGCCCGGCCCCG


SEQ ID NO:10


H3′X45R
CGTCTCTAGAGGACCTTTCACAGCTAGCCGTGACTAGGG


SEQ ID NO:11


H9375F
TGAAGGTTGGGGTAAACACTCCGGCCTCTTAGGCCATT


SEQ ID NO:12


H3′X-35R
ACATGATCTGCAGAGAGGCCAGTATCAGCACTCTC


SEQ ID NO:13


H9386F
GTCCAAGCTTACGCGTAAACACTCCGGCCTCCTTAAGCCATTCCTG


SEQ ID NO:14


H3′X-38R
CGTCTCTAGACATGATCTGCAGAGAGGCCAGTATCAGCACTCTCTGC


SEQ ID NO:15


H1
TTTTTTTTGCGGCCGC GCCAGCCCCCTGAT-



GGGGGCGACACTCCACCATG


A1
ACTGTCTTCACGCAGAAAGCGTCTAGCCAT


SEQ ID NO:17


H9417R
CGTCTCTAGACAGGAAATGGCTTAAGAGGCCGGAGTGTTTACC





*HCV sequences are shown in plain text, non-HCV-specific sequences are shown in boldface and artificial cleavage sites used for cDNA cloning are underlined. The core sequence of the T7 promoter in primer H1 is shown in italics.






Primers for long RT-PCR were size-purified.

cDNA Synthesis

The RNA was denatured at 65° C. for 2 min, and cDNA synthesis was performed in a 20 μl reaction volume with Superscript II reverse transcriptase (from GIBCO/BRL) at 42° C. for 1 hour using specific antisense primers as described previously (Tellier et al (1996)). The cDNA mixture was treated with RNase H and RNase Ti (GIBCO/BRL) for 20 min at 37° C.
Amplification and Cloning of the 3′ UTR
The 3′ UTR of strain H77 was amplified by PCR in two different assays. In both of these nested PCR reactions the first round of PCR was performed in a total volume of 50 μl in 1× buffer, 250 μmol of each deoxynucleoside triphosphate (dNTP; Pharmacia), 20 pmol each of external sense and antisense primers, 1 μl of the Advantage KlenTaq polymerase mix (from Clontech) and 2 μl of the final cDNA reaction mixture. In the second round of PCR, 5 μl of the first round PCR mixture was added to 45 μl of PCR mixture prepared as already described. Each round of PCR (35 cycles), which was performed in a Perkin Elmer DNA thermal cycler 480, consisted of denaturation at 94° C. for 1 min (in 1st cycle 1 min 30 sec), annealing at 60° C. for 1 min and elongation at 68° C. for 2 min. In one experiment a region from NS5B to the conserved region of the 3′ UTR was amplified with the external primers H9261F and H3′X58R, and the internal primers H9282F and H3′X45R (Table 1). In another experiment, a segment of the variable region to the very end of the 3′ UTR was amplified with the external primers H9375F and H3′X-35R, and the internal primers H9386F and H3′X-38R (Table 1, FIG. 1). Amplified products were purified with QIAquick PCR purification kit (from QIAGEN), digested with Hind III and Xba I (from Promega), purified by either gel electrophoresis or phenol/chloroform extraction, and then cloned into the multiple cloning site of plasmid PGEM-9zf(−) (Promega) or pUC19 (Pharmacia). Cloning of cDNA into the vector was performed with T4 DNA ligase (Promega) by standard procedures.
Amplification of Near Full-Length H77 Genomes by Long PCR
The reactions were performed in a total volume of 50 μl in 1× buffer, 250 μmol of each dNTP, 10 pmol each of sense and antisense primers, 1 μl of the Advantage KlenTaq polymerase mix and 2 μl of the cDNA reaction mixture (Tellier et al (1996)). A single PCR round of 35 cycles was performed in a Robocycler thermal cycler (from Stratagene), and consisted of denaturation at 99° C. for 35 sec, annealing at 67° C. for 30 sec and elongation at 6° C. for 10 min during the first 5 cycles, 11 min during the next 10 cycles, 12 min during the following 10 cycles and 13 min during the last 10 cycles. To amplify the complete ORF of HCV by long RT-PCR we used the sense primers H1 or A1 deduced from the 5′ UTR and the antisense primer H9417R deduced from the variable region of the 3′ UTR (Table 1, FIG. 1).
Construction of Full-Length H77 cDNA Clones
The long PCR products amplified with H1 and H9417R primers were cloned directly into pGEM-9zf(−) after digestion with Not I and Xba I (from Promega) (as per FIG. 1). Two clones were obtained with inserts of the expected size, pH211 and pH501. Next, the chosen 3′ UTR was cloned into both pH211 and pH501 after digestion with Afl II and Xba I (New England Biolabs). DH5α competent cells (GIBCO/BRL) were transformed and selected with LB agar plates containing 100 μg/ml ampicillin (from SIGMA). Then the selected colonies were cultured in LB liquid containing ampicillin at 30° C. for  ̃18–20 hrs (transformants containing full-length or near full-length cDNA of H77 produced a very low yield of plasmid when cultured at 37° C. or for more than 24 hrs). After small scale preparation (Wizard Plus Minipreps DNA Purification Systems, Promega) each plasmid was retransformed to select a single clone, and large scale preparation of plasmid DNA was performed with a QIAGEN plasmid Maxi kit.
Cloning of Long RT-PCR Products into a Cassette Vector
To improve the efficiency of cloning, a vector with consensus 5′ and 3′ termini of HCV strain H77 was constructed (FIG. 1). This cassette vector (pCV) was obtained by cutting out the BamHI fragment (nts 1358-7530 of the H77 genome) from pH50, followed by religation. Next, the long PCR products of H77 amplified with H1 and H9417R or A1 and H9417R primers were purified (Geneclean spin kit; BIO 101) and cloned into pCV after digestion with Age I and Afl II (New England Biolabs) or with Pin AI (isoschizomer of Age I) and Bfr I (isoschizomer of Afl II) (Boehringer Mannheim). Large scale preparations of the plasmids containing full-length cDNA of H77 were performed as described above.
Construction of H77Consensus Chimeric cDNA Clone
A full-length cDNA clone of H77 with an ORF encoding the consensus amino acid sequence was constructed by making a chimera from four of the cDNA clones obtained above. This consensus chimera, pCV-H77C, was constructed in two ligation steps by using standard molecular procedures and convenient cleavage sites and involved first a two piece ligation and then a three piece ligation. Large scale preparation of pCV-H77C was performed as already described.
In Vitro Transcription
Plasmids containing the full-length HCV cDNA were linearized with Xba I (from Promega), and purified by phenol/chloroform extraction and ethanol precipitation. A 100 μl reaction mixture containing 10 μg of linearized plasmid DNA, 1× transcription buffer, 1 mM ATP, CTP, GTP and UTP, 10 mM DTT, 4% (v/v) RNasin (20–40 units/μl) and 2 μl of T7 RNA polymerase (Promega) was incubated at 3° C. for 2 hrs. Five μl of the reaction mixture was analyzed by agarose gel electrophoresis followed by ethidium bromide staining. The transcription reaction mixture was diluted with 400 μl of ice-cold phosphate-buffered saline without calcium or magnesium, immediately frozen on dry ice and stored at −8° C. The final nucleic acid mixture was injected into chimpanzees within 24 hrs.
Intrahepatic Transfection of Chimpanzees
Laparotomy was performed and aliquots from two transcription reactions were injected into 6 sites of the exposed liver (Emerson et al (1992). Serum samples were collected weekly from chimpanzees and monitored for liver enzyme levels and anti-HCV antibodies. Weekly samples of 100 μl of serum were tested for HCV RNA in a highly sensitive nested RT-PCR assay with AmpliTaq Gold (Perkin Elmer)(Yanagi et al (1996); Bukh et al (1992)). The genome titer of HCV was estimated by testing 10-fold serial dilutions of the extracted RNA in the RT-PCR assay (Yanagi et al (1996)). The two chimpanzees used in this study were maintained under conditions that met all requirements for their use in an approved facility.
The consensus sequence of the complete ORF from HCV genomes recovered at week 2 post inoculation (p.i) was determined by direct sequencing of PCR products obtained in long RT-PCR with primers A1 and H9417R followed by nested PCR of 10 overlapping fragments. The consensus sequence of the variable region of the 3′ UTR was determined by direct sequencing of an amplicon obtained in nested RT-PCR as described above. Finally, we amplified selected regions independently by nested RT-PCR with AmpliTaq Gold.
Sequence Analysis
Both strands of DNA from PCR products, as well as plasmids, were sequenced with the ABI PRISM Dye Termination Cycle Sequencing Ready Reaction Kit using Taq DNA polymerase (Perkin Elmer) and about 100 specific sense and antisense sequence primers.
The consensus sequence of HCV strain H77 was determined in two different ways. In one approach, overlapping PCR products were directly sequenced, and amplified in nested RT-PCR from the H77 plasma sample. The sequence analyzed (nucleotides (nts) 35–9417) included the entire genome except the very 5′ and 3′ termini. In the second approach, the consensus sequence of nts 157–9384 was deduced from the sequences of 18 full-length cDNA clones.
Example 1
Variability in the Sequence of the 3′ UTR of HCV Strain H77
The heterogeneity of the 3′ UTR was analyzed by cloning and sequencing of DNA amplicons obtained in nested RT-PCR. 19 clones containing sequences of the entire variable region, the poly U-UC region and the adjacent 19 nt of the conserved region, and 65 clones containing sequences of the entire poly U-UC region and the first 63 nts of the conserved region were analyzed. This analysis confirmed that the variable region consisted of 43 nts, including two conserved termination codons (Han et al (1992)). The sequence of the variable region was highly conserved within H77 since only 3 point mutations were found among the 19 clones analyzed. A poly U-UC region was present in all 84 clones analyzed. However, its length varied from 71–141 nts. The length of the poly U region was 9–103 nts, and that of the poly UC region was 35–85 nts. The number of C residues increased towards the 3′ end of the poly UC region but the sequence of this region is not conserved. The first 63 nts of the conserved region were highly conserved among the clones analyzed, with a total of only 14 point mutations. To confirm the validity of the analysis, the 3′ UTR was reamplified directly from a full-length cDNA clone of HCV (see below) by the nested-PCR procedure with the primers in the variable region and at the very 3′ end of the HCV genome and cloned the PCR product. Eight clones had 1–7 nt deletions in the poly U region. Furthermore, although the C residues of the poly UC region were maintained, the spacing of these varied because of 1–2 nt deletions of U residues. These deletions must be artifacts introduced by PCR and such mistakes may have contributed to the heterogeneity originally observed in this region. However, the conserved region of the 3′ UTR was amplified correctly, suggesting that the deletions were due to difficulties in transcribing a highly repetitive sequence.
One of the 3′ UTR clones was selected for engineering of full-length cDNA clones of H77. This clone had the consensus variable sequence except for a single point mutation introduced to create an Afl II cleavage site, a poly U-UC stretch of 81 nts with the most commonly observed UC pattern and the consensus sequence of the complete conserved region of 101 nts, including the distal 38 nts which originated from the antisense primer used in the amplification. After linearization with Xba I, the DNA template of this clone had the authentic 3′ end.
Example 2
The Entire Open Reading Frame of H77 Amplified in One Round of Long RT-PCR
It had been previously demonstrated that a 9.25 kb fragment of the HCV genome from the 5′ UTR to the 3′ end of NS5B could be amplified from 104 GE (genome equivalents) of H77 by a single round of long RT-PCR (Tellier et al (1996a)). In the current study, by optimizing primers and cycling conditions, the entire ORF of H77 was amplified in a single round of long RT-PCR with primers from the 5′ UTR and the variable region of the 3′ UTR. In fact, 9.4 kb of the H77 genome (H product: from the very 5′ end to the variable region of the 3′ UTR) could be amplified from 105 GE or 9.3 kb (A product: from within the 5′ UTR to the variable region of the 3′ UTR) from 104 GE or 105 GE, in a single round of long RT-PCR (FIG. 2). The PCR products amplified from 105 GE of H77 were used for engineering full-length cDNA clones (see below).
Example 3
Construction of Multiple Full-Length cDNA Clones of H77 in a Single Step by Cloning of Long RT-PCR Amplicons Directly into a Cassette Vector with Fixed 5′ and 3′ Termini
Direct cloning of the long PCR products (H), which contained a 5′ T7 promoter, the authentic 5′ end, the entire ORF of H77 and a short region of the 3′ UTR, into pGEM-9zf(−) vector by Not I and Xba I digestion was first attempted. However, among the 70 clones examined all but two had inserts that were shorter than predicted. Sequence analysis identified a second Not I site in the majority of clones, which resulted in deletion of the nts past position 9221. Only two clones (pH211 and pH501) were missing the second Not I site and had the expected 5′ and 3′ sequences of the PCR product. Therefore, full-length cDNA clones (pH21 and pH50) were constructed by inserting the chosen 3′ UTR into pH211 and pH501, respectively. Sequence analysis revealed that clone pH21 had a complete full-length sequence of H77; this clone was tested for infectivity. The second clone, pH50, had one nt deletion in the ORF at position 6365; this clone was used to make a cassette vector.
The complete ORF was amplified by constructing a cassette vector with fixed 5′ and 3′ termini as an intermediate of the full-length cDNA clones. This vector (pCV) was constructed by digestion of clone pH50 with BamHI, followed by religation, to give a shortened plasmid readily distinguished from plasmids containing the full-length insert. Attempts to clone long RT-PCR products (H) into pCV by Age I and Afl II yielded only 1 of 23 clones with an insert of the expected size. In order to increase the efficiency of cloning, we repeated the procedure but used Pin A I and Bfr I instead of the respective isoschizomers Age I and Afl II. By this protocol, 24 of 31 H clones and 30 of 35 A clones had the full-length cDNA of H77 as evaluated by restriction enzyme digestion. A total of 16 clones, selected at random, were each retransformed, and individual plasmids were purified and completely sequenced.
Example 4
Demonstration of Infectious Nature of Transcripts of a cDNA Clone Representing the Consensus Sequence of Strain H77
A consensus chimera was constructed from 4 of the full-length cDNA clones with just 2 ligation steps. The final construct, pCV-H77C, had 11 nt differences from the consensus sequence of H77 in the ORF (FIG. 3). However, 10 of these nucleotide differences represented silent mutations. The chimeric clone differed from the consensus sequence at only one amino acid [L instead of F at position 790]. Among the 18 ORFs analyzed above, the F residue was found in 11 clones and the L residue in 7 clones. However, the L residue was dominant in other isolates of genotype 1a, including a first passage of H77 in a chimpanzee (Inchauspe et al (1991)).
To test the infectivity of the consensus chimeric clone of H77 intrahepatic transfection of a chimpanzee was performed. The pCV-H77C clone was linearized with Xba I and transcribed in vitro by T7 RNA polymerase (FIG. 2). The transcription mixture was next injected into 6 sites of the liver of chimpanzee 1530. The chimpanzee became infected with HCV as measured by detection of 102 GE/ml of viral genome at week 1 p.i. Furthermore, the HCV titer increased to 104 GE/ml at week 2 p.i., and reached 106 GE/ml by week 8 p.i. The viremic pattern observed in the early phase of the infection with the recombinant virus was similar to that observed in chimpanzees inoculated intravenously with strain H77 or other strains of HCV (Shimizu (1990)).
The sequence of the HCV genomes from the serum sample collected at week 2 p.i. was analyzed. The consensus sequence of nts 298–9375 of the recovered genomes was determined by direct sequencing of PCR products obtained in long RT-PCR followed by nested PCR of 10 overlapping fragments. The identity to clone pCV-H77C sequence was 100%. The consensus sequence of nts 96–291, 1328–1848, 3585–4106, 4763–5113 and 9322–9445 was determined from PCR products obtained in different nested RT-PCR assays. The identity of these sequences with pCV-H77C was also 100%. These latter regions contained 4 mutations unique to the consensus chimera, including the artificial Afl II cleavage site in the 3′ UTR. Therefore, RNA transcripts of this clone of HCV were infectious.
The infectious nature of the consensus chimera indicates that the regions of the 5′ and 3′ UTRs incorporated into the cassette vector do not destroy viability. This makes it highly advantageous to use the cassette vector to construct infectious cDNA clones of a other HCV strains when the consensus sequence for each ORF is inserted.
In addition, two complete full-length clones (dubbed pH21 and pCV-H11) constructed were not infectious, as shown by intrahepatic injection of chimpanzees with the corresponding RNA transcripts. Thus, injection of the transcription mixture into 3 sites of the exposed liver resulted in no observable HCV replication and weekly serum samples were negative for HCV RNA at weeks 1–17 p.i. in a highly sensitive nested RT-PCR assay. The cDNA template injected along with the RNA transcripts was also not detected in this assay.
Moreover, the chimpanzee remained negative for antibodies to HCV throughout the follow-up. Subsequent sequence analysis revealed that 7 of 16 additional clones were defective for polyprotein synthesis and all clones had multiple amino acid mutations compared with the consensus sequence of the parent strain. For example, clone pH21, which was not infectious, had 7 amino acid substitutions in the entire predicted polyprotein compared with the consensus sequence of H77 (FIG. 3). The most notable mutation was at position 1026, which changed L to Q, altering the cleavage site between NS2 and NS3 (Reed (1995)). Clone pCV-H11, also non-infectious, had 21 amino acid substitutions in the predicted polyprotein compared with the consensus sequence of H77 (FIG. 3). The amino acid mutation at position 564 eliminated a highly conserved C residue in the E2 protein (Okamoto (1992a)).
Example 4A
The chimpanzee of Example 4, designated 1530, was monitored out to 32 weeks p.i. for serum enzyme levels (ALT) and the presence of anti-HCV antibodies, HCV RNA, and liver histopathology. The results are shown in FIG. 18B.
A second chimp, designated 1494, was also transfected with RNA transcripts of the pCV-H77C clone and monitored out to 17 weeks p.i. for the presence of anti-HCV antibodies, HCV RNA and elevated serum enzyme levels. The results are shown in FIG. 18A.
Materials and Methods for Examples 5–10
Source Of HCV Genotype 1b
An infectious plasma pool (second chimpanzee passage) containing strain HC-J4, genotype 1b, was prepared from acute phase plasma of a chimpanzee experimentally infected with serum containing HC-J4/91 (Okamoto et al., 1992b). The HC-J4/91 sample was obtained from a first chimpanzee passage during the chronic phase of hepatitis C about 8 years after experimental infection. The consensus sequence of the entire genome, except for the very 3′ end, was determined previously for HC-J4/91 (Okamoto et al., 1992b).
Preparation Of HCV RNA
Viral RNA was extracted from 100 μl aliquots of the HC-J4 plasma pool with the TRIzol system (GIBCO BRL). The RNA pellets were each resuspended in 10 μl of 10 mM dithiothreitol (DTT) with 5% (vol/vol) RNasin (20–40 units/μl) (Promega) and stored at −8° C. or immediately used for cDNA synthesis.
Amplification and Cloning of the 3′ UTR
A region spanning from NS5B to the conserved region of the 3′ UTR was amplified in nested RT-PCR using the procedure of Yanagi et al., (1997).
In brief, the RNA was denatured at 65° C. for 2 minutes, and cDNA was synthesized at 42° C. for 1 hour with Superscript II reverse transcriptase (GIBCO BRL) and primer H3X58R (Table 1) in a 20 μl reaction volume. The cDNA mixture was treated with RNase H and RNase T1 (GIBCO BRL) at 37° C. for 20 minutes. The first round of PCR was performed on 2 μl of the final cDNA mixture in a total volume of 50 μl with the Advantage cDNA polymerase mix (Clontech) and external primers H9261F (Table 1) and H3′X58R (Table 1). In the second round of PCR [internal primers H9282F (Table 1) and H3′X45R (Table 1)], 5 μl of the first round PCR mixture was added to 45 μl of the PCR reaction mixture. Each round of PCR (35 cycles), was performed in a DNA thermal cycler 480 (Perkin Elmer) and consisted of denaturation at 94° C. for 1 minute (1st cycle: 1 minute 30 sec), annealing at 60° C. for 1 minute and elongation at 68° C. for 2 minutes. After purification with QIAquick PCR purification kit (QIAGEN), digestion with HindIII and XbaI (Promega), and phenol/chloroform extraction, the amplified products were cloned into pGEM-9zf(−) (Promega) (Yanagi et al., 1997).
Amplification and Cloning of the Entire ORF
A region from within the 5′ UTR to the variable region of the 3′ UTR of strain HC-J4 was amplified by long RT-PCR (FIG. 1) (Yanagi et al., 1997). The cDNA was synthesized at 42° C. for 1 hour in a 20 μl reaction volume with Superscript II reverse transcriptase and primer J4-9405R (5′-GCCTATTGGCCTGGAGTGGTTAGCTC-3′) SEQ ID NO:18, and treated with RNases as above. The cDNA mixture (2 μl) was amplified by long PCR with the Advantage cDNA polymerase mix and primers A1 (Table 1) (Bukh et al., 1992; Yanagi et al., 1997) and J4-9398R (5′AGGATGGCCTTAAGGCCTGGAGTGGTTAGCTCCCCGTTCA-3′) NO:19. Primer J4-9398R contained extra bases (bold) and an artificial AflII cleavage site (underlined). A single PCR round was performed in a Robocycler thermal cycler (Stratagene), and consisted of denaturation at 99° C. for 35 seconds, annealing at 6° C. for 30 seconds and elongation at 68° C. for 10 minutes during the first 5 cycles, 11 minutes during the next 10 cycles, 12 minutes during the following 10 cycles and 13 minutes during the last 10 cycles.
After digesting the long PCR products obtained from strain HC-J4 with PinAI (isoschizomer of AgeI) and BfrI (isoschizomer of AflII) (Boehringer Mannheim), attempts were made to clone them directly into a cassette vector (pCV), which contained the 5′ and 3′ termini of strain H77 (FIG. 1) but no full-length clones were obtained. Accordingly, to improve the efficiency of cloning, the PCR product was further digested with BglII (Boehringer Mannheim) and the two resultant genome fragments [L fragment: PinAI/BglII, nts 156–8935; S fragment: BglII/BrfI, nts 8936–9398] were separately cloned into pCV (FIG. 6).
DH5α competent cells (GIBCO BRL) were transformed and selected on LB agar plates containing 100 μg/ml ampicillin (SIGMA) and amplified in LB liquid cultures at 30° C. for 18–20 hours.
Sequence analysis of 9 plasmids containing the S fragment (miniprep samples) and 9 plasmids containing the L fragment (maxiprep samples) were performed as described previously (Yanagi et al., 1997). Three L fragments, each encoding a distinct polypeptide, were cloned into pCV-J4S9 (which contained an S fragment encoding the consensus amino acid sequence of HC-J4) to construct three chimeric full-length HCV cDNAs (pCV-J4L2S, pCV-J4L4S and pCV-J4L6S) (FIG. 6). Large scale preparation of each clone was performed as described previously with a QIAGEN plasmid Maxi kit (Yanagi et al., 1997) and the authenticity of each clone was confirmed by sequence analysis.
Sequence Analysis
Both strands of DNA were sequenced with the ABI PRISM Dye Termination Cycle Sequencing Ready Reaction Kit using Taq DNA polymerase (Perkin Elmer) and about 90 specific sense and antisense primers. Analyses of genomic sequences, including multiple sequence alignments and tree analyses, were performed with GeneWorks (Oxford Molecular Group) (Bukh et al., 1995).
The consensus sequence of strain HC-J4 was determined by direct sequencing of PCR products (nts 11–9412) and by sequence analysis of multiple cloned L and S fragments (nts 156–9371). The consensus sequence of the 3′ UTR (3′ variable region, polypyrimidine tract and the first 16 nucleotides of the conserved region) was determined by analysis of 24 cDNA clones.
Intrahepatic Transfection of a Chimpanzee with Transcribed RNA
Two in vitro transcription reactions were performed with each of the three full-length clones. In each reaction 10 μg of plasmid DNA linearized with Xba I (Promega) was transcribed in a 100 μl reaction volume with T7 RNA polymerase (Promega) at 37° C. for 2 hours as described previously (Yanagi et al., 1997). Five μl of the final reaction mixture was analyzed by agarose gel electrophoresis and ethidium bromide staining (FIG. 5). Each transcription mixture was diluted with 400 μl of ice-cold phosphate-buffered saline without calcium or magnesium and then the two aliquots from the same cDNA clone were combined, immediately frozen on dry ice and stored at −80° C. Within 24 hours after freezing the transcription mixtures were injected into the chimpanzee by percutaneous intrahepatic injection that was guided by ultrasound. Each inoculum was individually injected (5–6 sites) into a separate area of the liver to prevent complementation or recombination. The chimpanzee was maintained under conditions that met all requirements for its use in an approved facility.
Serum samples were collected weekly from the chimpanzee and monitored for liver enzyme levels and anti-HCV antibodies. Weekly samples of 100 μl of serum were tested for HCV RNA in a sensitive nested RT-PCR assay (Bukh et al., 1992, Yanagi et al., 1996) with AmpliTaq Gold DNA polymerase. The genome equivalent (GE) titer of HCV was determined by testing 10-fold serial dilutions of the extracted RNA in the RT-PCR assay (Yanagi et al., 1996) with 1 GE defined as the number of HCV genomes present in the highest dilution which was positive in the RT-nested PCR assay.
To identify which of the three clones was infectious in vivo, the NS3 region (nts 3659–4110) from the chimpanzee serum was amplified in a highly sensitive and specific nested RT-PCR assay with AmpliTaq Gold DNA polymerase and the PCR products were cloned with a TA cloning kit (Invitrogen). In addition, the consensus sequence of the nearly complete genome (nts 11–9441) was determined by direct sequencing of overlapping PCR products.
Example 5
Sequence Analysis of Infectious Plasma Pool of Strain HC-J4 Used as the Cloning Source
As an infectious cDNA clone of a genotype 1a strain of HCV had been obtained only after the ORF was engineered to encode the consensus polypeptide (Kolykhalov et al., 1997; Yanagi et al., 1997), a detailed sequence analysis of the cloning source was performed to determine the consensus sequence prior to constructing an infectious cDNA clone of a 1b genotype.
A plasma pool of strain HC-J4 was prepared from acute phase plasmapheresis units collected from a chimpanzee experimentally infected with HC-J4/91 (Okamoto et al., 1992b). This HCV pool had a PCR titer of 104–105 GE/ml and an infectivity titer of approximately 103 chimpanzee infectious doses per ml.
The heterogeneity of the 3′ UTR of strain HC-J4 was determined by analyzing 24 clones of nested RT-PCR product. The consensus sequence was identical to that previously published for HC-J4/91 (Okamoto et al., 1992b), except at position 9407 (see below). The variable region consisted of 41 nucleotides (nts. 9372–9412), including two in-frame termination codons. Furthermore, its sequence was highly conserved except at positions 9399 (19 A and 5 T clones) and 9407 (17 T and 7 A clones). The poly U-UC region varied slightly in composition and greatly in length (31–162 nucleotides). In the conserved region, the first 16 nucleotides of 22 clones were identical to those previously published for other genotype 1 strains, whereas two clones each had a single point mutation. These data suggested that the structural organization at the 3′ end of HC-J4 was similar to that of the infectious clone of a genotype 1a strain of Yanagi et al (1997).
Next, the entire ORF of HC-J4 was amplified in a single round of long RT-PCR (FIG. 5). The original plan was to clone the resulting PCR products into the PinAI and BrfI site of a HCV cassette vector (pCV), which had fixed 5′ and 3′ termini of genotype 1a (Yanagi et al., 1997) but since full-length clones were not obtained, two genome fragments (L and S) derived from the long RT-PCR products (FIG. 6) were separately subcloned into pCV.
To determine the consensus sequence of the ORF, the sequence of 9 clones each of the L fragment (pCV-J4L) and of the S fragment (pCV-J4S) was determined and quasispecies were found at 275 nucleotide (3.05%) and 78 amino acid (2.59%) positions, scattered throughout the 9030 nts (3010 aa) of the ORF (FIG. 7). Of the 161 nucleotide substitutions unique to a single clone, 71% were at the third position of the codon and 72% were silent.
Each of the nine L clones represented the near complete ORF of an individual genome. The differences among the L clones were 0.30–1.53% at the nucleotide and 0.31–1.47% at the amino acid level (FIG. 8). Two clones, L1 and L7, had a defective ORF due to a single nucleotide deletion and a single nucleotide insertion, respectively. Even though the HC-J4 plasma pool was obtained in the early acute phase, it appeared to contain at least three viral species (FIG. 9). Species A contained the L1, L2, L6, L8 and L9 clones, species B the L3, L7 and L10 clones and species C the L4 clone. Although each species A clone was unique all A clones differed from all B clones at the same 20 amino acid sites and at these positions, species C had the species A sequence at 14 positions and the species B sequence at 6 positions (FIG. 7).
Okamoto and coworkers (Okamoto et al., 1992b) previously determined the nearly complete genome consensus sequence of strain HC-J4 in acute phase serum of the first chimpanzee passage (HC-J4/83) as well as in chronic phase serum collected 8.2 years later (HC-J4/91). In addition, they determined the sequence of amino acids 379 to 413 (including HVR1) and amino acids 468 to 486 (including HVR2) of multiple individual clones (Okamoto et al., 1992b).
It was found by the present inventors that the sequences of individual genomes in the plasma pool collected from a chimpanzee inoculated with HC-J4/91 were all more closely related to HC-J4/91 than to HC-J4/83 (FIGS. 8, 9) and contained HVR amino acid sequences closely related to three of the four viral species previously found in HC-J4/91 (FIG. 10).
Thus, the data presented herein demonstrate the occurrence of the simultaneous transmission of multiple species to a single chimpanzee and clearly illustrates the difficulties in accurately determining the evolution of HCV over time since multiple species with significant changes throughout the HCV genome can be present from the onset of the infection. Accordingly, infection of chimpanzees with monoclonal viruses derived from the infectious clones described herein will make it possible to perform more detailed studies of the evolution of HCV in vivo and its importance for viral persistence and pathogenesis.
Example 6
Determination of the Consensus Sequence of HC-J4 in the Plasma Pool
The consensus sequence of nucleotides 156–9371 of HC-J4 was determined by two approaches. In one approach, the consensus sequence was deduced from 9 clones of the long RT-PCR product. In the other approach the long RT-PCR product was reamplified by PCR as overlapping fragments which were sequenced directly. The two “consensus” sequences differed at 31 (0.34k) of 9216 nucleotide positions and at 11 (0.37%) of 3010 deduced amino acid positions (FIG. 7). At all of these positions a major quasispecies of strain HC-J4 was found in the plasma pool. At 9 additional amino acid positions the cloned sequences displayed heterogeneity and the direct sequence was ambiguous (FIG. 7). Finally, it should be noted that there were multiple amino acid positions at which the consensus sequence obtained by direct sequencing was identical to that obtained by cloning and sequencing even though a major quasispecies was detected (FIG. 7).
For positions at which the two “consensus” sequences of HC-J4 differed, both amino acids were included in a composite consensus sequence (FIG. 7). However, even with this allowance, none of the 9 L clones analyzed (aa 1–2864) had the composite consensus sequence: two clones did not encode the complete polypeptide and the remaining 7 clones differed from the consensus sequence by 3–13 amino acids (FIG. 7).
Example 7
Construction of Chimeric Full-Length cDNA Clones Containing the Entire ORF Of HC-J4
The cassette vector used to clone strain H77 was used to construct an infectious cDNA clone containing the ORF of a second subtype.
In brief, three full-length cDNA clones were constructed by cloning different L fragments into the PinAI/BglII site of pCV-J4S9, the cassette vector for genotype 1a (FIG. 6), which also contained an S fragment encoding the consensus amino acid sequence of HC-J4. Therefore, although the ORF was from strain HC-J4, most of the 5′ and 3′ terminal sequences originated from strain H77. As a result, the 5′ and 3′ UTR were chimeras of genotypes 1a and 1b (FIG. 11).
The first 155 nucleotides of the 5′ UTR were from strain H77 (genotype 1a), and differed from the authentic sequence of HC-J4 (genotype 1b) at nucleotides 11, 12, 13, 34 and 35. In two clones (pCV-J4L2S, pCV-J4L6S) the rest of the 5′ UTR had the consensus sequence of HC-J4, whereas the third clone (pCV-J4L4S) had a single nucleotide insertion at position 207. In all 3 clones the first 27 nucleotides of the 3′ variable region of the 3′ UTR were identical with the consensus sequence of HC-J4. The remaining 15 nucleotides of the variable region, the poly U-UC region and the 3′ conserved region of the 3′ UTR had the same sequence as an infectious clone of strain H77 (FIG. 11).
None of the three full-length clones of HC-J4 had the ORF composite consensus sequence (FIGS. 7, 12). The pCV-J4L6S clone had only three amino acid changes: Q for R at position 231 (E1), V for A at position 937 (NS2) and T for S at position 1215 (NS3). The pCV-J4L4S clone had 7 amino acid changes, including a change at position 450 (E2) that eliminated a highly conserved N-linked glycosylation site (Okamoto et al., 1992a). Finally, the pCV-J4L2S clone had 9 amino acid changes compared with the consensus sequence of HC-J4. A change at position 304 (E1) mutated a highly conserved cysteine residue (Bukh et al., 1993; Okamoto et al., 1992a).
Example 8
Transfection of a Chimpanzee by in Vitro Transcripts of a Chimeric cDNA
The infectivity of the three chimeric HCV clones was determined by ultra-sound-guided percutaneous intrahepatic injection into the liver of a chimpanzee of the same amount of cDNA and transcription mixture for each of the clones (FIG. 5). This procedure is a less invasive procedure than the laparotomy procedure utilized by Kolykhalov et al. (1997) and Yanagi et al. (1997) and should facilitate in vivo studies of cDNA clones of HCV in chimpanzees since percutaneous procedures, unlike laparotomy, can be performed repeatedly.
As shown in FIG. 13, the chimpanzee became infected with HCV as measured by increasing titers of 102 GE/ml at week 1 p.i., 103 GE/ml at week 2 p.i. and 104–105 GE/ml during weeks 3 to 10 p.i.
The viremic pattern found in the early phase of the infection was similar to that observed for the recombinant H77 virus in chimpanzees (Bukh et al., unpublished data; Kolykhalov et al., 1997; Yanagi et al., 1997). The chimpanzee transfected in the present study was chronically infected with hepatitis G virus (HGV/GBV-C) (Bukh et al., 1998) and had a titer of 106 GE/ml at the time of HCV transfection. Although HGV/GBV-C was originally believed to be a hepatitis virus, it does not cause hepatitis in chimpanzees (Bukh et al., 1998) and may not replicate in the liver (Laskus et al., 1997). The present study demonstrated that an ongoing infection of HGV/GBV-C did not prevent acute HCV infection in the chimpanzee model.
However, to identify which of the three full-length HC-J4 clones were infectious, the NS3 region (nts. 3659–4110) of HCV genomes amplified by RT-PCR from serum samples taken from the infected chimpanzee during weeks 2 and 4 post-infection (p.i.) were cloned and sequenced. As the PCR primers were a complete match with each of the original three clones, this assay should not have preferentially amplified one virus over another. Sequence analysis of 26 and 24 clones obtained at weeks 2 and 4 p.i., respectively, demonstrated that all originated from the transcripts of pCV-J4L6S.
Moreover, the consensus sequence of PCR products of the nearly complete genome (nts. 11–9441), amplified from serum obtained during week 2 p.i., was identical to the sequence of pCV-J4L6S and there was no evidence of quasispecies. Thus, RNA transcripts of pCV-J4L6S, but not of pCV-J4L2S or pCV-J4L4S, were infectious in vivo. The data in FIG. 13 is therefore the product of the transfection of RNA transcripts of pCV-J4L6S.
In addition, the chimeric sequences of genotypes 1a and 1b in the UTRs were maintained in the infected chimpanzee. The consensus sequence of nucleotides 11–341 of the 5′ UTR and the variable region of the 3′ UTR, amplified from serum obtained during weeks 2 and 4 p.i., had the expected chimeric sequence of genotypes 1a and 1b (FIG. 11). Also three of four clones of the 3′ UTR obtained at week 2 p.i. had the chimeric sequence of the variable region, whereas a single substitution was noted in the fourth clone. However, in all four clones the poly U region was longer (2–12 nts) than expected. Also, extra C and G residues were observed in this region. For the most part, the number of C residues in the poly UC region was maintained in all clones although the spacing varied. As shown previously, variations in the number of U residues can reflect artifacts introduced during PCR amplification (Yanagi et al., 1997). The sequence of the first 19 nucleotides of the conserved region was maintained in all four clones. Thus, with the exception of the poly U-UC region, the genomic sequences recovered from the infected chimpanzee were exactly those of the chimeric infectious clone pCV-J4BL6S.
The results presented in FIG. 13 therefore demonstrate that HCV polypeptide sequences other than the consensus sequence can be infectious and that a chimeric genome containing portions of the H77 termini could produce an infectious virus. In addition, these results showed for the first time that it is possible to make infectious viruses containing 5′ and 3′ terminal sequences specific for two different subtypes of the same major genotype of HCV.
Example 9
Construction of a Chimeric 1a/1b Infectious Clone
A chimeric 1a/1b infectious clone in which the structural region of the genotype 1b infectious clone is inserted into the 1a clone of Yanagi et al. (1997) is constructed by following the protocol shown in FIG. 15. The resultant chimera contains nucleotides 156–2763 of the 1b clone described herein inserted into the 1a clone of FIGS. 4A–4F. The sequences of the primers shown in FIG. 15 which are used in constructing this chimeric clone, designated pH77CV-J4, are presented below.
1. H2751S (Cla I/Nde I) SEQ ID NO:20


    
    
        CGT CAT CGA TCC TCA GCG GGC ATA TGC ACT GGA CAC GGA

2. H2870R SEQ ID NO:21

        CAT GCA CCA GCT GAT ATA GCG CTT GTA ATA TG

3. H7851S SEQ ID NO:22

        TCC GTA GAG GAA GCT TGC AGC CTG ACG CCC

4. H9173 R (P-M) SEQ ID NO:23

        GTA CTT GCC ACA TAT AGC AGC CCT GCC TCC TCT G

5. H9140S (P-M) SEQ ID NO:24

        CAG AGG AGG CAG GGC TGC TAT ATG TGG CAA GTA C

6. H9417R SEQ ID NO:25

        CGT CTC TAG ACA GGA AAT GGC TTA AGA GGC CGG AGT GTT TAC C

7. J4-2271S SEQ ID NO:26

        TGC AAT TGG ACT CGA GGA GAG CGC TGT AAC TTG GAG

8. J4-2776R (Nde I) SEQ ID NO:27

        CGG TCC AAG GCA TAT GCT CGT GGT GGT AAC GCC AG

Transcripts of the chimeric 1a/1b clone (whose sequence is shown in FIGS. 16A–16F) are then produced and transfected into chimpanzees by the methods described in the Materials and Methods section herein and the transfected animals are then be subjected to biochemical (ALT levels), histopathological and PCR analyses to determine the infectivity of the chimeric clone.

    
    


Example 10
Construction of 3′ Deletion Mutants of the 1a Infectious Clone DCV-H77C
Seven constructs having various deletions in the 3′ untranslated region (UTR) of the 1a infectious clone pCV-H77C were constructed as described in FIGS. 17A–17B. The 3′ untranslated sequence remaining in each of the seven constructs following their respective deletions is shown in FIGS. 17A–17B.
Construct pCV-H77C(−98X) containing a deletion of the 3′-most 98 nucleotide sequences in the 3′-UTR was transcribed in vitro according to the methods described herein and 1 ml of the diluted transcription mixture was percutaneously transfected into the liver of a chimpanzee with the aid of ultrasound. After three weeks, the transfection was repeated. The chimpanzee was observed to be negative for hepatitis C virus replication as measured by RT-PCR assay for 5 weeks after transfection. These results demonstrate that the deleted 98 nucleotide 3′-UTR sequence was critical for production of infectious HCV and appear to contradict the reports of Dash et al. (1996) and Yoo et al. (1995) who reported that RNA transcripts from cDNA clones of HCV-1 and HCV-N lacking the terminal 98 conserved nucleotides at the very 3′ end of the 3′-UTR resulted in viral replication after transfection into human hematoma cell lines.
Transcripts of the (−42X) mutant (FIG. 17C) were also produced and transfected into a chimpanzee and transcripts of the other five deletion mutants shown in FIGS. 17D–17G) are to be produced and transfected into chimpanzees by the methods described herein. All transfected animals are to then be assayed for viral replication via RT-PCR.
Discussion
In two recent reports on transfection of chimpanzees, only those clones engineered to have the independently determined and slightly different consensus amino acid sequence of the polypeptide of strain H77 were infectious (Kolykhalov et al., 1997; Yanagi et al., 1997). Although the two infectious clones differed at four amino acid positions, these differences were represented in a major component of the quasispecies of the cloning source. In the present study, a single consensus sequence of strain HC-J4 could not be defined because the consensus sequence obtained by two different approaches (direct sequencing and sequencing of cloned products) differed at 20 amino acid positions, even though the same genomic PCR product was analyzed. The infectious clone differed at two positions from the composite amino acid consensus sequence, from the sequence of the 8 additional HC-J4 clones analyzed in this study and from published sequences of earlier passage samples. An additional amino acid differed from the composite consensus sequence but was found in two other HC-J4 clones analyzed in this study. The two non-infectious full-length clones of HC-J4 differed from the composite consensus sequence by only 7 and 9 amino acid differences. However, since these clones had the same termini as the infectious clone (except for a single nucleotide insertion in the 5′ UTR of pCV-J4L4S), one or more of these amino acid changes in each clone was apparently deleterious for the virus.
It was also found in the present study that HC-J4, like other strains of genotype 1b (Kolykhalov et al., 1996; Tanaka et al., 1996; Yamada et al., 1996), had a poly U-UC region followed by a terminal conserved element. The poly U-UC region appears to vary considerably so it was not clear whether changes in this region would have a significant effect on virus replication. On the other hand, the 3′ 98 nucleotides of the HCV genome were previously shown to be identical among other strains of genotypes 1a and 1b (Kolykhalov et al., 1996; Tanaka et al., 1996). Thus, use of the cassette vector would not alter this region except for addition of 3 nucleotides found in strain H77 between the poly UC region and the 3′ 98 conserved nucleotides.
In conclusion, an infectious clone representing a genotype 1b strain of HCV has been constructed. Thus, it has been demonstrated that it was possible to obtain an infectious clone of a second strain of HCV. In addition, it has been shown that a consensus amino acid sequence was not absolutely required for infectivity and that chimeras between the UTRs of two different genotypes could be viable.
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## Claims

1. A composition comprising a purified and isolated nucleic acid molecule, which encodes human hepatitis C virus (HCV),
wherein expression of said molecule in transfected cells results in production of virus when transfected into cells,
wherein said molecule encodes the amino acid sequence of SEQ ID NO: 3.

2. The composition of claim 1, wherein said molecule comprises the nucleic acid sequence of SEQ ID NO: 4.

3. A composition comprising a purified and isolated nucleic acid molecule, which encodes a chimeric human hepatitis C virus (HCV),
wherein expression of said molecule in transfected cells results in production of virus when transfected into cells,
wherein said molecule is producible by the process comprising, with reference to the nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 3,
replacing a nucleic acid sequence of a HCV 1b genome that encodes the structural region of hepatitis C virus of said SEQ ID NO: 3 with a nucleic acid sequence that encodes the structural region from the genome of another strain of hepatitis C virus from a different genotype or subtype, to produce said molecule.

4. A composition comprising a purified and isolated nucleic acid molecule, which encodes a chimeric human hepatitis C virus (HCV),
wherein expression of said molecule in transfected cells results in production of virus when transfected into cells,
wherein said molecule is producible by the process comprising, with reference to the nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 3,
replacing a nucleic acid sequence of a HCV 1b genome that encodes at least one HCV protein of said SEQ ID NO: 3 with a nucleic acid sequence that encodes the corresponding HCV protein from the genome of another strain of hepatitis C virus from a different genotype or subtype, to produce said molecule.

5. The composition of claim 4, wherein the HCV protein is selected from the group consisting of: NS3 protease, E1, E2 and NS4 proteins.

6. A method for inducing an immune response comprising the administration to a mammal an effective amount of the composition of claim 1, 3, or 4 to induce an immune response.

7. The method according to claim 6, wherein the composition is provided to a mammal not infected with a hepatitis C virus.

8. The method according to claim 6, wherein the composition is provided to a mammal infected with a hepatitis C virus.