Attenuation of human respiratory syncytial virus by genome scale codon-pair deoptimization

Patent metadata

Field	Value
Publication number	US-12054749-B2
Application number	US-202217831259-A
Country	US
Kind code	B2
Filing date	Jun 2, 2022
Priority date	Feb 8, 2013
Publication date	Aug 6, 2024
Grant date	Aug 6, 2024

Abstract

Described herein are RSV polynucleotide sequences that make use of multiple codons that are containing silent nucleotide substitutions engineered in multiple locations in the genome, wherein the substitutions introduce a numerous synonymous codons into the genome. Due to the large number of defects involved, the attenuated viruses disclosed herein provide a means of producing attenuated, live vaccines against RSV.

First claim

What is claimed:

1. A recombinant polynucleotide comprising a recombinant nucleotide sequence encoding respiratory syncytial virus (RSV) proteins NS1, NS2, or both,
wherein the codon pair bias of the recombinant nucleotide sequence encoding NS1 is reduced by at least 0.05 compared to a wildtype RSV for a corresponding nucleotide sequence encoding the RSV protein, or
wherein the codon pair bias of the recombinant nucleotide sequence encoding NS2 is reduced by at least 0.05 compared to a wildtype RSV for a corresponding nucleotide sequence encoding the RSV protein, or

both.

2. The recombinant polynucleotide of claim 1 , wherein the recombinant nucleotide sequence encodes a RSV NS1 amino acid sequence, RSV NS2 amino acid sequence, or both, that is the same as the corresponding wildtype RSV amino acid sequence, or a RSV NS1 amino acid sequence, RSV NS2 amino acid sequence, or both with up to four amino acid substitutions, additions, or deletions compared to the corresponding wildtype RSV amino acid sequence.

3. The recombinant polynucleotide of claim 1 , wherein the recombinant nucleotide sequence encoding the RSV NS 1 protein is from about 75% to about 95% identical to the corresponding nucleotide sequence of SEQ ID NO: 1, or the recombinant nucleotide sequence encoding the RSV NS 2 protein is from about 75% to about 95% identical to the corresponding nucleotide sequence of SEQ ID NO: 1, or both.

4. The recombinant polynucleotide of claim 1 , wherein the protein is NS1 and the recombinant nucleotide sequence encoding the RSV NS 1 protein is from about 75% to about 95% identical to the corresponding nucleotide sequence of the wildtype virus.

5. The recombinant polynucleotide of claim 4 , wherein the recombinant nucleotide sequence encoding the RSV NS1 protein is about 87% identical to the corresponding sequence of the wildtype virus.

6. The recombinant polynucleotide of claim 1 , wherein the recombinant nucleotide sequence encoding the RSV NS1 protein is from about 75% to about 95% identical to nucleotides 99 to 518 of SEQ ID NO: 5.

7. The recombinant polynucleotide of claim 6 , wherein the recombinant nucleotide sequence encoding the RSV NS1 protein has the sequence of nucleotides 99 to 518 of SEQ ID NO: 5.

8. The recombinant polynucleotide of claim 1 , wherein the protein is NS2 and the recombinant nucleotide sequence encoding the RSV NS2 protein is from about 75% to about 95% identical to the corresponding nucleotide sequence of the wildtype virus.

9. The recombinant polynucleotide of claim 8 , wherein the recombinant nucleotide sequence encoding the RSV NS2 protein is about 88% identical to the corresponding sequence of the wildtype virus.

10. The recombinant polynucleotide of claim 9 , wherein the recombinant nucleotide sequence encoding the RSV NS2 protein is from about 75% to about 95% identical to nucleotides 628 to 1002 of SEQ ID NO: 5.

11. The recombinant polynucleotide of claim 10 , wherein the recombinant nucleotide sequence encoding the RSV NS2 protein has the sequence of nucleotides 628 to 1002 of SEQ ID NO: 5.

12. A recombinant genome or antigenome comprising the recombinant polynucleotide of claim 1 .

13. A method of producing a recombinant virus, comprising expressing the recombinant genome or antigenome of claim 12 in a cell.

14. A recombinant virus having the recombinant genome or antigenome of claim 12 .

15. The recombinant virus of 14, wherein the recombinant genome or antigenome is modified to include a previously characterized RSV mutation or deletion.

16. A composition comprising the recombinant virus of claim 14 and a physiologically acceptable carrier and/or adjuvant.

17. A method of producing an immune response to a viral protein, comprising administering the recombinant virus of claim 14 to an animal.

18. The method of claim 17 , wherein the recombinant virus is administered via injection, aerosol delivery, nasal spray, nasal droplets, oral inoculation, or topical application.

19. The method of claim 17 , wherein the animal is a mammal.

20. The method of claim 19 , wherein the mammal is a human.

Assignees

• The Us Secretary Department Of Health & Human Services
• Univ New York State Res Found

Inventors

• Collins Peter L
• Le Nouen Cyril
• Brock Linda G
• Buchholz Ursula J
• Dinapoli Joshua Marc
• Mueller Steffen
• Wimmer Eckard

Classifications

• C12N2760/00062

  by genetic engineering · CPC title

• C12N2760/00034

  Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein · CPC title

• C12N2760/00021

  Viruses as such, e.g. new isolates, mutants or their genomic sequences · CPC title

• C07K14/005

  from viruses · CPC title

• A61K2039/55

  characterised by the host/recipient, e.g. newborn with maternal antibodies · CPC title