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(12) United States Patent (10) Patent No.: US 7,790,366 B1 Houghton Et Al

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(12) United States Patent (10) Patent No.: US 7,790,366 B1 Houghton Et Al US007790366B1 (12) United States Patent (10) Patent No.: US 7,790,366 B1 Houghton et al. (45) Date of Patent: *Sep. 7, 2010 (54) NANBV DIAGNOSTICS AND VACCINES 4,683, 195 A 7, 1987 Mullis et al. ................... 435/6 4,683.202 A 7, 1987 Mullis et al. ............... 435,912 (75) Inventors: Michael Houghton, Danville, CA (US); 4,702,909. A 10/1987 Villarejos et al. .............. 435/5 GeorgeQui-Lim Kuo, Choo, San El Francisco, Cerrito, CA CA (US); (US) 4,707.439 A * 1 1/1987 Seto .............................. 435/5 4,722,897 A * 2/1988 Soeda et al. ............... 435/69.1 (73) Assignee: Novartis Vaccines and Diagnostics, 4,769,326 A * 9/1988 Rutter ....................... 435.68.1 Inc., Emeryville, CA (US) 4,870,026 A * 9/1989 Wands ........................ 436,538 (*) Notice: Subject to any disclaimer, the term of this 4,891.313 A 1/1990 Berger et al. ............... 435/7.94 patent is extended or adjusted under 35 5,077, 193 A 12, 1991 Mishiro et al. ................. 435/5 U.S.C. 154(b) by 0 days. 5,101,024 A * 3/1992 Kudo et al. .............. 536,23.53 5,106,726 A 4/1992 Wang ............................ 435/5 This patent is Subject to a terminal dis- 5, 191,064 A 3/1993 Arima et al. ................ 530/324 claimer. 5,218,099 A 6/1993 Reyes et al. .............. 536,23.72 5,268,278 A * 12/1993 Canosi et al. .............. 435/69.7 (21) Appl. No.: 08/441,443 5,310,893 A * 5/1994 Erlich et al. ............. 536, 24.31 (22) Filed: May 15, 1995 5,372,928 A 12/1994 Miyamura 5,436,126 A 7/1995 Wang ............................ 435/5 Related U.S. Application Data (60) Division of application No. 08/307,273, filed on Sep. 16, 1994, now Pat. No. 6,074,816, which is a division of application No. 08/103,961, filed on Aug. 9, 1993, (Continued) now Pat. No. 5,350,671, which is a continuation of FOREIGN PATENT DOCUMENTS application No. 07/456,637, filed on Dec. 21, 1989, now abandoned, which is a continuation-in-part of AU 89.10967 11, 1989 application No. 07/355,002, filed on May 18, 1989, now abandoned, which is a continuation-in-part of application No. 07/341,334, filed on Apr. 20, 1989, now abandoned, which is a continuation-in-part of (Continued) application No. PCT/US88/04125, filed on Nov. 18, 1988, and a continuation-in-part of application No. OTHER PUBLICATIONS 07/325,338, filed on Mar. 17, 1989, now abandone which is a continuation-in-part of application N Prince et al. 1984 Lancet Nov. 10. p. 1071, Nov. 10, 1984.* 07/271,450, filed on Nov. 14, 1988, now abandone which is a continuation-in-part of application N (Continued) 07/263,584, filed on Oct. 26, 1988, now abandone Primary Examiner Mary K Zeman which is a continuation-in-part of application N (74) Attorney, Agent, or Firm—Alisa Harbin; Otis Littlefield 07/191,263, filed on May 6, 1988, now abandone which is a continuation-in-part of application N (57) ABSTRACT 07/161,072, filed on Feb. 26, 1988, now abandone which is a continuation-in-part of application N 07/139,886, filed on Dec. 30, 1987, now abandone A family of cDNA sequences derived from hepatitis C virus which is a continuation-in-part of application No. (HCV) are provided. These sequences encode antigens which 07/122,714, filed on Nov. 18, 1987, now abandoned. react immunologically with antibodies present in individuals with non-A non-B hepatitis (NANBH), but which are absent (51) Int. Cl. from individuals infected with hepatitis A virus, or hepatitis B A6 IK 39/00 (2006.01) virus, and also are absent in control individuals. The HCV (52) U.S. Cl. ........................... 435/5: 435/7.1:435/69.1; cDNA sequences lack Substantial homology to the sequences 435/320.1; 436/501:536/23.1:536/24.1 of hepatitis delta virus (HDV) and HBV. A comparison of the (58) Field of Classification Search ..................... 435/5, sequences of amino acids encoded in the HCV cDNA with the 435/6, 7.1, 810,948,975; 424/89, 86; 536/24.5, sequences of Flaviviruses indicates that HCV may be related 536/23.1, 23.72, 24.3, 24.32, 24.33: 514/44; to the Flaviviruses. 436/501, 63, 94,811, 820 See application file for complete search history. The HCV cDNA sequences and the polypeptides encoded therein are useful as reagents for the detection and therapy of (56) References Cited HCV. The reagents provided in the invention are also useful U.S. PATENT DOCUMENTS for the isolation of NANBH agent(s), for the propagation of these agents in tissue culture, and for the screening of antiviral 4,395,395 A 7/1983 Tabor et al. .................... 435.5 4,464.474. A * 8/1984 Coursaget ................... 436,513 agents for HCV. 4,659,678 A 4, 1987 Forrest et al. ............... 436,512 4,673,634 A 6, 1987 Seto .............................. 435/5 299 Claims, 168 Drawing Sheets US 7,790,366 B1 Page 2 U.S. PATENT DOCUMENTS Kroeger (Gene 1982 20:125-38) (RN84616-07-9) Abstract Only.* EP 35384 the EP equivalent of US 4769326 1981 (RN80208-71-5P) 5,856,437 A 1/1999 Miyamura Abstract Only.* 5,871,903. A 2/1999 Miyamura Peterson (European Journal of Biochemistry 1984 143(3) 507-11). 5,871,904 A 2/1999 Kashiwakuma ................ 435.5 (RN92942-24-0) Abstract Only.* 5,959,092 A 9/1999 Miyamura Arrand, et al., “Molecular Cloning of the Complete Epstein-Barr Virus Genome as a Set of Overlapping Restriction Endonuclease FOREIGN PATENT DOCUMENTS Fragments.” Nucleic Acids Res. 9(13):2999-3014 (1981). AU 36979/89 11, 1989 Baer, et al., “DNA Sequence and Expression of the B95-8 Epstein AU 58123.90 12/1990 Barr Virus Genome.” Nature 310:207-211 (1984). EP OO61974 10, 1982 Bankier, et al., “Sequence Analysis of the 17,166 Base-Pair Ecori EP O190972 A2 8, 1986 Fragment C of B95-8 Epstein-Barr Virus.” Mol. Biol. Med 1:21-45 EP O1942O7 9, 1986 (1983). EP 0263761 4f1988 Beck, et al., “Human Cytomegalovirus Encodes a Glycoprotein EP O277437 8, 1988 Homologous to MHC Class-I Antigens.” Nature 331:269-272 EP O27.9460 8, 1988 (1988). EP 88400790.7 11, 1988 Mierendorf, et al., “Gene Isolation by Screening gt11 Libraries EP 0318216 5, 1989 With Antibodies.” Methods in Enzymology, Ch. 51, 152, Berger & EP O388232 9, 1990 Kimmel (Eds), Academic Press Ltd. (1987). EP O442394 A2 8, 1991 Biggin, et al., “Transcription and DNA Sequence of the Bamhi L. EP O293.274 9, 1991 Fragment of B95-8 Epstein-Barr Virus.” EMBO.J. 3(5):1083-1090 EP O468527 A2 1, 1992 (1984). GB 22392.45 6, 1991 Billeter, et al., “Cloning of DNA Corresponding to Four Different GB 22392.45 A 6, 1991 Measles Virus Genomic Regions.” Virology 132: 147-159 (1984). GB 2212511 1, 1992 Blumberg, "Australia Antigen and Biology of Hepatitis B.” Science JP 183629, 1983 10, 1983 197:17-25 (1977). JP O2-500880 3, 1990 Bodescot, et al., "Clustered Alternative Splice Sites. In Epstein-Barr JP 5-81600 11, 1993 Virus Rnas.” Nucleic Acids Res. 15:5887 (1987). TW T7108060 7, 1992 Boss, et al., “Cloning and Sequence Analysis of the Human Major WO WO 82.00205 1, 1982 Histocompatibility Complex Gene DC-3u.” Proc. Natl. Acad. Sci. WO WO 82fO2774 8, 1982 USA 81:5199-5203 (1984). WO WO 82.03330 10, 1982 Bradley, “Research Perspectives in Posttransfusion Non-A. Non-B WO WO 87,05930 10, 1987 Hepatitis.” Infection, Immunity and Blood Transfusion, (Dodd, WO WO 88,03410 5, 1988 R.Y. & Barker, L.F. (Eds.), Alan R. Liss Inc.) pp. 81-97 (1985). WO WO 89,04669 6, 1989 Bradley, et al., “Transmission, Etiology and Pathogenesis of Viral WO WO 89,05855 A 6, 1989 Hepatitis Non-A. Non-B in Non-Human Primates.” Adv. Hepat. Res. WO WO 89.10967 11, 1989 Ch.31 pp. 268-280 (1984). WO WO90, 11089 10, 1990 Bradley, et al., “Posttransfusion Non-A. Non-B Hepatitis: WO WO90, 14436 11, 1990 Physicochemical Properties of Two Distinct Agents.” J. Infect. Dis. WO WO91f15516 10, 1991 148(2):254-265 (1983). WO WO 93.00365 1, 1993 Burrell, et al., “Expression in Escherichia coli of Hepatitis B Virus WO WO97,08310 6, 1997 DNA Sequences Cloned in Plasmid Pbr322.” Nature 279:43-47 (1979). OTHER PUBLICATIONS Chan, et al., “Serological Responses to Infection with Three Different Hilfenhaus et al. 1992 J Gen Virol 73: 1015, Jan. 1, 1992.* Types of Hepatitis C Virus.” The Lancet 338: 1391 (1991). Branch, A.D. 1998 TIBS vol. 23 p. 45-50, Feb. 1998.* Charnay, et al., “Biosynthesis of Hepatitis BVirus Surface Antigen in Wich ( Systematic and applied microbiology 1986 7:1 18-25) Escherichia coli,” Nature 286:893-895 (1980). (RN104245-31-0) Abstract Only.* Daniels, et al., “A Second Major Class of Alu Family Repeated DNA Hobart (Nature 1980 288:5787 137-141) (RN77000-19-2) Abstract Sequences in a Primate Genome.” Nucleic Acids Res. 11(21):7595 Only.* 7610 (1983). Giese (JBC 1987 262 (31) 15251-5) (RN112263-07-7)Abstract Davies (ed.), Amino Acids and Peptides, (Chapman and Hall, Lon Only.* don, 1985). Sahagan (J Immunol 1986 137:3 1066-74) (RN104491-32-9)Ab Davis, et al., “Isolation of cDNA Clones for Differentially Expressed stract Only.* Genes of the Human Parasite Schistosoma mansoni,' Proc. Natl.
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