Methods of predicting ancestral virus sequences and uses thereof
Methods are described for predicting ancestral sequences for viruses or portions thereof. Also described are predicted ancestral sequences for adeno-associated virus (AAV) capsid polypeptides. The disclosure also provides methods of gene transfer and methods of vaccinating subjects by administering a target antigen operably linked to the AAV capsid polypeptides.
1. An adeno-associated virus (AAV) capsid polypeptide having a variant of the amino acid sequence of SEQ ID NO: 23, wherein the variant has the amino acid sequence of SEQ ID NO:23 with at least one amino acid substitution selected from Arg168Lys, Ala205Ser, Gly266Ala, Lys311Arg, Gln411Glu, Thr460Glu, Thr493Ala, Asn562Ser, Glu576Gln, Ala587Ser, and Asp609Asn.
2. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO:23 with four amino acid substitutions, wherein the four substitutions are Lys311Arg, Gln411Glu, Thr493Ala, and Glu576Gln.
3. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO:23 with four amino acid substitutions, wherein the four substitutions are Arg168Lys, Ala205Ser, Thr460Glu, and Glu576Gln.
4. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO: 23 with four amino acid substitutions, wherein the four substitutions are Ala205Ser, Gln411Glu, Thr460Glu, and Asn562Ser.
5. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO: 23 with five amino acid substitutions, wherein the five substitutions are Lys311Arg, Gln411Glu, Thr460Glu, Asn562Ser, and Ala587Ser.
6. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO: 23 with six amino acid substitutions, wherein the six substitutions are Arg168Lys, Ala205Ser, Gly266Ala, Lys311Arg, Thr460Glu, and Asp609Asn.
7. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO:23 with seven amino acid substitutions, wherein the seven substitutions are Arg168Lys, Gln411Glu, Thr493Ala, Asn562Ser, Glu576Gln, Ala587Ser, and Asp609Asn.
8. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO:23 with seven amino acid substitutions, wherein the seven substitutions are Arg168Lys, Ala205Ser, Gln411Glu, Thr493Ala, Asn562Ser, Ala587Ser, and Asp609Asn.
9. The AAV capsid polypeptide of claim 1 , having the variant of amino acid sequence of SEQ ID NO: 23 with nine amino acid substitutions, wherein the nine substitutions are Arg168Lys, Gly266Ala, Lys311Arg, Gln411Glu, Thr493Ala, Asn562Ser, Glu576Gln, Ala587Ser, and Asp609Asn.
10. The AAV capsid polypeptide of claim 1 , wherein the AAV capsid polypeptide is purified.
11. A nucleic acid molecule encoding the AAV capsid polypeptide of claim 1 .
12. A vector comprising a nucleic acid molecule encoding the AAV capsid polypeptide of claim 1 .
13. An isolated host cell comprising a nucleic acid molecule encoding the AAV capsid polypeptide of claim 1 .
14. A purified virus particle comprising the AAV capsid polypeptide of claim 1 .
15. A pharmaceutical composition comprising a purified virus particle comprising the AAV capsid polypeptide of claim 1 in a pharmaceutically acceptable excipient.