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( 12 ) United States Patent US010023845B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 023 ,845 B2 Wimmer et al . ( 45 ) Date of Patent: Jul. 17, 2018 ( 54 ) METHODS OF MAKING MODIFIED VIRAL ( 58 ) Field of Classification Search GENOMES None See application file for complete search history . (71 ) Applicant: The Research Foundation for The State University of New York , Albany , (56 ) References Cited NY (US ) U . S . PATENT DOCUMENTS ( 72 ) Inventors: Eckard Wimmer , East Setauket , NY 6 ,696 ,289 B1 2 /2004 Bae et al. (US ) ; Steve Skiena , Setauket , NY (US ) ; 2004 / 0097439 A95 /2004 Nicolas et al . Steffen Mueller , Kings Point, NY (US ) ; 2004 /0209241 A1 10 / 2004 Hermanson et al . Bruce Futcher , Stony Brook , NY (US ) ; 2008 /0118530 A1 5 / 2008 Kew et al . Dimitris Papamichail , Pennington , NJ (US ) ; John Robert Coleman , Blauvelt , FOREIGN PATENT DOCUMENTS NY (US ) ; Jeronimo Cello , Port WO 2002 /095363 A2 11 /2002 Jefferson , NY (US ) WO 2006 /042156 A2 4 / 2006 ( 73 ) Assignee : The Research Foundation for The OTHER PUBLICATIONS State University of New York , Albany , NY (US ) Cheng , L . et al. , “ Absence of Effect of Varying Thr- Leu Codon Pairs on Protein Synthesis in a T7 System ” , Biochem (2001 ) , vol . 40 , pp . 6102- 6106 ( * ) Notice : Subject to any disclaimer , the term of this Cohen , B . et al. , “ Natural Selection and Algorithmic Design of patent is extended or adjusted under 35 mRNA ” , B JCB (2003 ) , vol. 10 , pp . 3 - 4 . U . S . C . 154 ( b ) by 0 days . Doma, M . et al. , “ Endonucleolytic Cleave of Euraryotic mRNAS with Stalls and Translation Elongation ” , Nature ( 2006 ) , vol. 440 , pp . (21 ) Appl. No. : 15 /258 ,584 561- 564 . Garcia -Sastre , A . et al. , "Genetic Manipulation of Negative - Strand RNA Virus Genomes" , Annu . Rev . Microbio . ( 1993 ) , vol. 47 , pp . (22 ) Filed : Sep . 7 , 2016 765 - 790 . Greve, J . et al. , “ The Major Human Rhinovirus Receptor is ICAM (65 ) Prior Publication Data 1 ” , Cell ( 1989 ) , vol. 56 , pp . 839 -847 . US 2017 /0067030 A1 Mar. 9 , 2017 Gustafsson , C . et al ., " Codon Bias and Heterologous Protein Expression ” , Trends in Biotechnology ( 2004 ) , vol. 22 : 7 , pp . 346 353 . Johansen , L . et al. , “ The RNA Encompassing the Internal Ribosome Related U . S . Application Data Entry in the Poliovirus 5 ' Nontranslated Region Enhances the (62 ) Division of application No . 12 / 594 , 173, filed as Encapsidation of Genomic RNA ” , Virology ( 2000 ) , vol . 273 , pp . 391 - 399 . application No. PCT /US2008 / 058952 on Mar. 31 , Luytjes, W . et al . , “ Amplification , Expression , and Packaging of a 2008 , now Pat . No. 9 ,476 ,032 . Foreign Gene by Influenza Virus ” , Cell ( 1989 ) , vol. 59 , pp . 1107 1113 . McKnight , K . , “ The Human Rhinovirus Internal Cis -acting repli (60 ) Provisional application No. 61 / 068 ,666 , filed on Mar. cation element (cre ) Exhibits Disparate Properties among Stereo 7 , 2008 , provisional application No . 60 / 909, 389 , filed types" , Arch Virol . (2003 ) , vol. 148 , pp . 2397 - 2418 . on Mar. 30 , 2007 . Palease , P . et al. , Orthomyxoviridae: The Viruses and Their Repli cation , Ch . 47 , pp . 1647 - 1689 in Fields Virology (2007 ) , vol . 2 , 5th ( 51 ) Int. Cl. Edition , David M . Knipe , PHD , Editor- In - Chief, Wolters Kluwer, C12N 7700 ( 2006 . 01 ) publisher, Philadelphia , USA . A61K 39 / 13 ( 2006 . 01) A61K 39 / 145 ( 2006 . 01 ) (Continued ) COZK 14 / 005 ( 2006 . 01 ) Primary Examiner - Nicole Kinsey White A61K 39 /00 ( 2006 .01 ) ( 74 ) Attorney , Agent, or Firm — Fox Rothschild LLP (52 ) U . S . CI. CPC . .. C12N 7700 ( 2013 .01 ) ; A61K 39/ 13 (57 ) ABSTRACT ( 2013 . 01 ) ; A61K 39 / 145 (2013 . 01 ) ; COOK This invention provides an attenuated virus which comprises 14 /005 ( 2013 .01 ) ; A61K 2039 /5254 ( 2013 .01 ) ; a modified viral genome containing nucleotide substitutions C12N 2720 /12361 (2013 .01 ) ; C12N engineered in multiple locations in the genome , wherein the 2740 / 15061 ( 2013 .01 ) ; CI2N 2760 / 16061 substitutions introduce synonymous deoptimized codons ( 2013 .01 ) ; C12N 2760 / 16121 ( 2013 .01 ) ; CI2N into the genome . The instant attenuated virus may be used in 2760 / 16134 ( 2013 .01 ) ; CI2N 2760 / 16162 a vaccine composition for inducing a protective immune ( 2013 .01 ) ; C12N 2770 /20061 (2013 . 01 ) ; CI2N response in a subject. The invention also provides a method 2770 /24161 (2013 .01 ) ; C12N 2770 / 32061 of synthesizing the instant attenuated virus. Further, this ( 2013 .01 ) ; C12N 2770 / 32621 ( 2013 .01 ) ; C12N invention further provides a method for preventing a subject 2770 / 32634 ( 2013 . 01 ) ; C12N 2770 / 32661 from becoming afflicted with a virus -associated disease (2013 .01 ) ; C12N 2770 / 32662 (2013 .01 ) ; C12N comprising administering to the subject a prophylactically 2770 / 32671 ( 2013 .01 ) ; C12N 2770 / 32721 effective dose of a vaccine composition comprising the ( 2013 .01 ) ; C12N 2770 / 32761 ( 2013 .01 ) ; C12N instant attenuated virus . 2770 / 32762 ( 2013 .01 ) 25 Claims, 18 Drawing Sheets US 10 ,023 ,845 B2 Page 2 ( 56 ) References Cited Cis -Replicating Element in the Coding Sequence of 2 Apro ” , J . Virol . ( 2001 ) , vol. 75 : 22 , pp . 10979 - 10990 . Girard , S . et al. , “ Poliovirus Induces Apoptosis in the Mouse Central OTHER PUBLICATIONS Nervous System ” , J . Virol. ( 1999 ) , vol. 73 : 7 , pp . 6066 -6072 . Park , S . et al ., “ Advances in Computational Protein Design ” , COSB Goodfellow , I . et al . , “ Identification of a Cis - Acting Replication ( 2004 ) , vol. 14 , pp . 487 -494 . Element Within the Poliovirus Coding Region ” , J . Viol . (2000 ) , vol . Paul, A . et al ., “ Internal Ribosomal Entry Site Scanning of the 74 : 10 , pp . 4590 - 4600 . Poliovirus Polyprotein : Implications for Proteolytic Processing ” , Gu, W . et al . , " Analysis of Synonymous Codon Usage in SARS Virology ( 1998 ) , vol. 250 , 241 - 253 . Coronavirus and other viruses in the Nidovirales ” , Virus Research Pelletier , J . et al . , “ Internal Intiiation of Translation of Eukaryotic ( 2004 ) , vol . 101 , pp . 155 - 161. mRNA Directed by a Sequence Derived from Poliovirus RNA ” , Gutman , G . A . , et al, “ Nonrandom Utilization of Codon Pairs in Escherichia coli” , Proc . Natl. Acad . Sci. U . S . A . ( 1989 ) , vol. 86 , pp . Nature ( 1988 ) , vol. 334 , pp . 320 - 325 . 3699 - 3703 . Rueckert , R . R ., “ Picomaviruses and Their Replication ” , Ch . 32 , pp . He, Y . et al ., “ Interaction of the Poliovirus Receptor with 705 -738 , in Virology ( 1985 ) , Bernard N . Fields, M . D ., Editor- in Poliovirus” , Proc . Natl. Acad . Sci . USA ( 2000 ) , vol. 97 : 1 , pp . 79 - 84 . Chief , Raven Press , publisher, New York , USA . Herold , J . et al. , “ Poliovirus Requires a Precise 5 ' End for Efficient Russell, C . et al. , “ The Genesis of a Pandemic Influenza Virus” , Cell Positive -Strand RNA Synthesis ” , J . Virol. (2001 ) , vol . 74 : 14 , vol. ( 2005 ) , pp . 368 - 371 . pp . 6394 -6400 . Savolainen , C . et al. , “Human Rhinoviruses ” , PRR ( 2003) , vol. 4 , Hoekema, A . , et al ., “ Codon Replacement in the PGK1 Gene of pp . 91 -98 . Saccharomyces cerevisiae : Experimental Approach to Study the Tian , J . et al . , " Accurate Muntiplex Gene Synthesis from Program Role of Biased Codon Usage in Gene Expression " , Mol. Cell . Biol. mable DNA Microchips” , Nature (2004 ), vol. 432, pp . 1050 - 1054 . ( 1987 ) , vol . 7 : 8 , pp . 2914 - 2924 . Ansardi, D . , et al. , " Complementation of a Poliovirus Defective Hofer , F . et al. , “ Members of the Low Density Lipoprotein Receptor Genome by a Recombinant Vaccinia Virus Which Provides Family Mediate Cell Entry of a Minor -Group Common Cold Virus ” , Poliovirus P1 Capsid Precursor in Trans” , J . Virol . ( 2003 ) , vol . 67: 6 , Proc . Natl . Acad . Sci. U . S . A . ( 1994 ) , vol. 91, pp . 1839 - 1842 . pp. 3684 - 3690 . Hoffmann , E et al ., “ A DNA transfection system for generation of Belov , G . et al. , “ The Major Apoptotic Pathway Activated and influenza : A virus from eight plasmids” , Proc . Natl . Acad . Sci. Suppressed by Poliovirus” , J . Virol. ( 2003 ) , vol. 771, pp . 45 -56 . U . S . A . ( 2000 ) , vol . 97 : 11 , pp . 6108 -6113 . Buchan , J . et al. , “ RNA Properties Help Shape Codon Pair Pref Hogle , J . M . “ Poliovirus Cell Entry : Common Structural Themes in erences in Open Reading Frames” , Nucl. Acids Res . (2006 ) , vol. Viral Cell Entry Pathways ” , Annu . Rev . Microbiol. ( 2002 ) , vol . 56 , 34 : 3 , pp . 1015 - 1027 . pp . 677 -702 . Cao , X . et al. , “ Replication of Poliovirus RNA Containing Two Vpg Holland , J . J . et al. “ Mutation Frequencies at Defined Single Codon Coding Sequences Leads to a Specific Deletion Event” , J . Virol. Sites in Vesicular Stomatitis Virus and Poliovirus Can Be Increased ( 1993 ) , vol. 67 : 9 , pp . 5572 -5578 . Only Slightly by Chemical Mutagenesis ” , J . Virol . ( 1990 ) , vol. 64 : 8 , Carlini, D . et al. , “ In Vivo Introduction of Unpreferred Synonymous pp . 3960 - 3962 . Codons Into The Drosophila Adh Gene Results in Reduced Levels Hsiao , L . L , “ A Compendium of Gene Expression in Normal of ADH Protein ” , Genetics ( 2003 ) , vol . 163 , pp . 239 - 243 . Human Tissues” , Physiol. Genomics ( 2001) , vol. 7 , pp . 97 - 104 . Cello , J. et al. , “ Chemical Synthesis of Poliovirus Cdna : Generation Irwin , B ., et al ., “ Codon Pair Utilization Biases Influence Transla of Infectious Virus in the Absence of Natural Template" , Science tional Elongation Step Times” J. Biol Chem . (1995 ) vol. 270 , pp . ( 2002
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