Polyomavirus neutralizing antibodies

1. An isolated antibody or antigen binding fragment thereof comprising: (i) a heavy chain variable region that comprises (a) a HCDR1 (CDR-Complementarity Determining Region) of SEQ ID NO: 9, (b) a HCDR2 of SEQ ID NO:10, (c) a HCDR3 of SEQ ID NO:11 and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:25, (e) a LCDR2 of SEQ ID NO:26, and (f) a LCDR3 of SEQ ID NO:27;

(ii) a heavy chain variable region that comprises (a) a HCDR1 of SEQ ID NO:41, (b) a HCDR2 of SEQ ID NO:42, (c) a HCDR3 of SEQ ID NO:43; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:57, (e) a LCDR2 of SEQ ID NO:58, and (f) a LCDR3 of SEQ ID NO:59;

(iii) a heavy chain variable region that comprises (a) a HCDR1 of SEQ ID NO:73, (b) a HCDR2 of SEQ ID NO:74, (c) a HCDR3 of SEQ ID NO:75; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:89, (e) a LCDR2 of SEQ ID NO:90, and (f) a LCDR3 of SEQ ID NO:91;

(iv) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:105, (b) a HCDR2 of SEQ ID NO:106, (c) a HCDR3 of SEQ ID NO:107; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:121, (e) a LCDR2 of SEQ ID NO:122, and (f) a LCDR3 of SEQ ID NO:123;

(v) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:137, (b) a HCDR2 of SEQ ID NO:138, (c) a HCDR3 of SEQ ID NO:139; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:153, (e) a LCDR2 of SEQ ID NO:154, and (f) a LCDR3 of SEQ ID NO:155;

(vi) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:169, (b) a HCDR2 of SEQ ID NO:170, (c) a HCDR3 of SEQ ID NO:171; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:185, (e) a LCDR2 of SEQ ID NO:186, and (f) a LCDR3 of SEQ ID NO:187;

(vii) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:201, (b) a HCDR2 of SEQ ID NO: 202, (c) a HCDR3 of SEQ ID NO:203; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:217, (e) a LCDR2 of SEQ ID NO:218, and (f) a LCDR3 of SEQ ID NO:219;

(viii) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:233, (b) a HCDR2 of SEQ ID NO:234, (c) a HCDR3 of SEQ ID NO:235; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:249, (e) a LCDR2 of SEQ ID NO:250, and (f) a LCDR3 of SEQ ID NO:251; or

(ix) a heavy chain variable region that comprises: (a) a HCDR1 of SEQ ID NO:265, (b) a HCDR2 of SEQ ID NO: 266, (c) a HCDR3 of SEQ ID NO:267; and a light chain variable region that comprises: (d) a LCDR1 of SEQ ID NO:281, (e) a LCDR2 of SEQ ID NO:282, and (f) a LCDR3 of SEQ ID NO: 283.

2. The antibody or antigen binding fragment thereof of claim 1 , wherein one or two amino acids within a CDR have been modified.

3. The antibody or antigen binding fragment thereof of claim 1 , wherein the antibody or antigen binding fragment thereof retains at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identity compared to a corresponding human germline sequence of either the variable heavy chain region or the variable light chain region.

4. The antibody or antigen binding fragment thereof of claim 1 , wherein the antibody or antigen binding fragment thereof is a monoclonal antibody, a human antibody, a single chain antibody (scFv) or an antibody fragment.

5. An isolated antibody or antigen binding fragment thereof, wherein said antibody or antigen binding fragment thereof comprises:

(i) a heavy chain variable region (vH) that comprises SEQ ID NO:18, and a light chain variable region (vL) that comprises SEQ ID NO: 34;

(ii) a heavy chain variable region (vH) that comprises SEQ ID NO: 50, and a light chain variable region (vL) that comprises SEQ ID NO: 66;

(iii) a heavy chain variable region (vH) that comprises SEQ ID NO: 82, and a light chain variable region (vL) that comprises SEQ ID NO:98;

(iv) a heavy chain variable region (vH) that comprises SEQ ID NO:114, and a light chain variable region (vL) that comprises SEQ ID NO:130;

(v) a heavy chain variable region (vH) that comprises SEQ ID NO:146, and a light chain variable region (vL) that comprises SEQ ID NO:162;

(vi) a heavy chain variable region (vH) that comprises SEQ ID NO:178, and a light chain variable region (vL) that comprises SEQ ID NO:194;

(vii) a heavy chain variable region (vH) that comprises SEQ ID NO:210, and a light chain variable region (vL) that comprises SEQ ID NO:226;

(viii) a heavy chain variable region (vH) that comprises SEQ ID NO: 242, and a light chain variable region (vL) that comprises SEQ ID NO:258; or

(ix) a heavy chain variable region (vH) that comprises SEQ ID NO:274, and a light chain variable region (vL) that comprises SEQ ID NO:290.

6. The antibody or antigen binding fragment thereof of claim 5 , wherein the antigen or antigen binding fragment thereof retains at least 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% identity over either the variable light or variable heavy region.

7. The antibody or antigen binding fragment thereof of claim 5 , wherein less than 10 amino acids within the variable light or variable heavy region have been modified.

8. The antibody or antigen binding fragment thereof of claim 5 , wherein the antibody or antigen binding fragment thereof is a monoclonal antibody, a chimeric antibody, a human engineered antibody, a human antibody, a single chain antibody (scFv) or an antibody fragment.

9. A nucleic acid that encodes the antibody or antigen binding fragment thereof of claim 1 or 5 .

10. A vector comprising the nucleic acid of claim 9 .

11. A host cell comprising the vector of claim 10 .

12. A diagnostic reagent comprising the antibody or antigen binding fragment thereof of claim 1 or 5 , wherein the antibody or antigen binding fragment thereof is labeled.

13. The diagnostic reagent of claim 12 , wherein the label is selected from the group consisting of a radiolabel, a fluorophore, a chromophore, an imaging agent, and a metal ion.

14. The antibody or antigen binding fragment thereof of claim 1 or 5 wherein the antibody or antigen binding fragment thereof has reduced glycosylation or no glycosylation or is hypofucosylated.

15. A pharmaceutical composition comprising the antibody or antigen binding fragment thereof of claim 1 or 5 and a pharmaceutically acceptable carrier.

16. The pharmaceutical composition of claim 15 , wherein the pharmaceutically acceptable carrier comprises histidine or a sugar.

17. The pharmaceutical composition of claim 16 , wherein the sugar is sucrose.

18. A pharmaceutical composition comprising a plurality of antibodies or antigen binding fragments thereof of claim 1 or 5 , wherein at least 0.05%, 0.1%, 0.5%, 1%, 2%, 3%, or 5% of the antibodies in the composition have an α2,3-linked sialic acid residue.

19. A pharmaceutical composition comprising a plurality of antibodies or antigen binding fragments thereof of claim 1 or 5 , wherein none of the antibodies or antigen binding fragments thereof comprise a bisecting GlcNAc.

20. A pharmaceutical composition comprising the antibody or antigen binding fragment thereof of claim 1 or 5 , wherein the composition is a lyophilisate.

21. A method of neutralizing a BK virus or JC virus infection comprising administering via injection or infusion to a patient in need an effective amount of the antibody or antigen binding fragment thereof of claim 1 or 5 .

22. The method of claim 21 , wherein the patient in need is diagnosed with BK viruria or BK viremia.

23. The method of claim 21 , wherein the patient in need is diagnosed with JC viruria or JC viremia.

24. A method of treating or reducing the likelihood of a BK virus or JC virus associated disorder, comprising administering via injection or infusion to a patient in need an effective amount of the antibody or antigen binding fragment thereof of claim 1 or 5 , and wherein the disorder is selected from the group consisting of: nephropathy, BKVAN, hemorrhagic cystitis (HC), Progressive Multifocal Leukoencephalopathy (PML), granule cell neuronopathy (GCN), interstitial kidney disease, ureteral stenosis, vasculitis, colitis, retinitis, meningitis, and immune reconstitution inflammatory syndrome (IRIS).

25. The method of claim 24 , wherein the antibody or antigen binding fragment thereof is reconstituted prior to injection or infusion.

26. The method of claim 24 , wherein the antibody or the antigen binding fragment thereof is administered in combination with another therapeutic agent.

27. The method of claim 26 , wherein the another therapeutic agent is an additional anti-BKV or JCV antibody.

28. The method of claim 26 , wherein the another therapeutic agent is an immunosuppressive agent.

29. The method of claim 28 , wherein the immune suppressive agent is: a monophosphate dehydrogenase inhibitor, a purine synthesis inhibitor, a calcineurin inhibitor or an mTOR inhibitor.

30. The method of claim 28 , wherein the immunosuppressive agent is mycophenolate mofetil (MMF), mycophenolate sodium, azathioprine, tacrolimus, sirolimus or cyclosporine.

31. The method of claim 24 , wherein the PML is associated with the treatment of multiple sclerosis, rheumatoid arthritis, or psoriasis.

32. The method of claim 31 , wherein treatment of multiple sclerosis is with natalizumab, fingolimod, dimethyl fumarate, fumaric acid esters, or alemtuzumab.

33. The method of claim 31 , wherein the treatment of rheumatoid arthritis is with rituximab.

34. The method of claim 31 , wherein treatment of psoriasis is with efalizumab.