# US 2020/0399323 A1 · Recombinant adenoviruses and uses thereof > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2020/0399323 A1 - Document ID: US20200399323A1 - Status: Published application - Kind: A1 - Application number: 16/772,045 - Filed: 2018-12-11 - Published: 2020-12-24 - Earliest claimed: 2017-12-11 - Assignees: Beth Israel Deaconess Medical Center, Inc. - Applicants: Beth Israel Deaconess Medical Center, Inc. - Inventors: Dan H. BAROUCH; Peter ABBINK; Mark Justin IAMPIETRO; Menzo J. E. HAVENGA - Web page: https://patentgrep.com/patent/US20200399323A1 ## CPC - C07K 14/075: Adenoviridae - C12N 15/86: Viral vectors - A61K 31/7088: Compounds having three or more nucleosides or nucleotides - A61K 35/761: Adenovirus - A61K 39/0011: {Cancer antigens} - A61K 39/12: Viral antigens - A61K 39/235: Adenoviridae - C07K 14/005: from viruses - C07K 14/5425: {IL-9} - C12N 7/00: Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00) - C12N 15/861: Adenoviral vectors - A61K 2039/5256: {expressing foreign proteins} - C12N 2710/10321: Viruses as such, e.g. new isolates, mutants or their genomic sequences - C12N 2710/10334: Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein - C12N 2710/10343: viral genome or elements thereof as genetic vector - C12N 2740/15034: Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein - C12N 2740/16034: Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein - C12N 2770/24134: Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) ## Abstract Featured are recombinant adenoviruses and vectors thereof. In particular, the adenoviruses are simian (rhesus) adenoviruses having a low seroprevalence and high immunogenicity (when expressing, e.g., an antigenic polypeptide) relative to other adenoviruses and vectors thereof. Also featured are methods for producing the adenoviruses and methods of treatment of diseases by administering the adenoviral vector(s) to a subject (e.g., a human). ## Claims ### Claim 1 An isolated polynucleotide or complement thereof comprising a nucleotide sequence encoding a hexon protein, wherein the nucleotide sequence encoding the hexon protein has at least 93% sequence identity over the entire sequence of any one of SEQ ID NOs: 55, 58, 59, 61, 62, 64, 65, and 67. ### Claim 2 (depends on 1) The isolated polynucleotide or complement thereof of claim 1, wherein the nucleotide sequence encoding the hexon protein has at least 94%, 95%, 96%, 97%, 98%, 99%, and 100% sequence identity over the entire sequence of any one of SEQ ID NOs: 55, 58, 59, 61, 62, 64, 65, and 67. ### Claim 3 (depends on 1, 2) The isolated polynucleotide or complement thereof of claim 1 or 2, wherein the hexon protein comprises an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 159, 162, 163, 165, 166, 168, 169, and 171. ### Claim 4 (depends on 3) The isolated polynucleotide or complement thereof of claim 3, wherein the amino acid sequence of the hexon protein comprises one or more amino acid substitutions, deletions, or insertions between amino acids 120 to 170, amino acids 220 to 270, or amino acids 380 to 430 of SEQ ID NO: 159, 162, 163, 165, 166, 168, 169, or 171. ### Claim 5 (depends on 1, 2, 3, 4) The isolated polynucleotide or complement thereof of any one of claims 1 to 4, further comprising a nucleotide sequence encoding at least one fiber protein, wherein the nucleotide sequence encoding the at least one fiber protein has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 6 (depends on 5) The isolated polynucleotide or complement thereof of claim 5, further comprising a nucleotide sequence encoding at least two fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 7 (depends on 5, 6) The isolated polynucleotide or complement thereof of claim 5 or 6, further comprising a nucleotide sequence encoding at least three fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the sequence of any one of SEQ ID NOs: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 8 (depends on 1, 2, 3, 4, 5, 6, 7) The isolated polynucleotide or complement thereof of any one of claims 1 to 7, further comprising a nucleotide sequence encoding a penton protein, wherein the nucleotide sequence encoding the penton protein has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 107, 110, 111, 113, 114, 116, 117, and 119. ### Claim 9 (depends on 1, 2, 3, 4, 5, 6, 7, 8) The isolated polynucleotide or complement thereof of any one of claims 1 to 8, wherein the nucleotide sequence has at least 90% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 5, 6, 8, 9, 11, 12, and 14. ### Claim 10 (depends on 9) The isolated polynucleotide or complement thereof of claim 9, wherein the nucleotide sequence has at least 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 5, 6, 8, 9, 11, 12, and 14. ### Claim 11 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) The isolated polynucleotide or complement thereof of any one of claims 1 to 10, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 226, 227, 236-243, 246-249, 252-255, and 262-263. ### Claim 12 An isolated polynucleotide or complement thereof comprising a nucleotide sequence encoding a hexon protein, wherein the nucleotide sequence encoding the hexon protein has 99% or greater sequence identity over the entire nucleic acid sequence of SEQ ID NO: 56. ### Claim 13 (depends on 12) The isolated polynucleotide or complement thereof of claim 12, wherein the nucleotide sequence encoding the hexon protein has 100% sequence identity to the entire nucleic acid sequence of SEQ ID NO: 56. ### Claim 14 (depends on 12, 13) The isolated polynucleotide or complement thereof of claim 12 or 13, further comprising a nucleotide sequence encoding at least one fiber protein, wherein the nucleotide sequence encoding the fiber protein has at least 90%, 92%, 95%, 97%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 19 and 42. ### Claim 15 (depends on 12, 13, 14) The isolated polynucleotide or complement thereof of any one of claims 12 to 14, further comprising a nucleotide sequence encoding at least two fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of SEQ ID NOs: 19 and 42. ### Claim 16 (depends on 12, 13, 14, 15) The isolated polynucleotide or complement thereof of any one of claims 12 to 15, further comprising a nucleotide sequence encoding a penton protein, wherein the nucleotide sequence encoding the penton protein has at least 90%, 92%, 95%, 97%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of SEQ ID NO: 108. ### Claim 17 (depends on 12, 13, 14, 15, 16) The isolated polynucleotide or complement thereof of any one of claims 12 to 16, wherein the nucleotide sequence has at least 98% sequence identity over the entire nucleic acid sequence of SEQ ID NO: 3. ### Claim 18 (depends on 17) The isolated polynucleotide or complement thereof of claim 17, wherein the nucleotide sequence comprises the sequence of SEQ ID NO: 3. ### Claim 19 (depends on 12, 13, 14, 15, 16, 17, 18) The isolated polynucleotide or complement thereof of any one of claims 12 to 18, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 228-233. ### Claim 20 An isolated polynucleotide or complement thereof comprising a nucleotide sequence encoding three adenoviral fiber proteins. ### Claim 21 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein at least one of the adenoviral fiber proteins comprises an amino acid sequence having at least 85% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 121, 122, 124, 125, 127-132, 134-143, 145, 147, 149-151, and 153-157. ### Claim 22 (depends on 21) The isolated polynucleotide or complement thereof of claim 21, wherein at least two of the adenoviral fiber proteins comprise an amino acid sequence having at least 85% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 121, 122, 124, 125, 127-132, 134-143, 145, 147, 149-151, and 153-157. ### Claim 23 (depends on 22) The isolated polynucleotide or complement thereof of claim 22, wherein the three adenoviral fiber proteins comprise an amino acid sequence having at least 85% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 121, 122, 124, 125, 127-132, 134-143, 145, 147, 149-151, and 153-157. ### Claim 24 (depends on 20, 21, 22) The isolated polynucleotide or complement thereof of any one of claims 20 to 22, wherein at least one, at least two, or all three of the adenoviral fiber proteins comprise an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 121, 122, 124, 125, 127-132, 134-143, 145, 147, 149-151, and 153-157. ### Claim 25 (depends on 20, 21, 22, 23, 24) The isolated polynucleotide or complement thereof of any one of claims 20 to 24, wherein each of the fiber proteins comprises a different amino acid sequence. ### Claim 26 (depends on 20, 21, 22, 23, 24) The isolated polynucleotide or complement thereof of any one of claims 20 to 24, wherein two or three of the fiber proteins comprise the same amino acid sequence. ### Claim 27 (depends on 20, 21, 22, 23, 24) The isolated polynucleotide or complement thereof of any one of claims 20 to 24, wherein the three fiber proteins encoded by the polynucleotide: (i) have the amino acid sequences of SEQ ID NOs: 121, 122, and 145, respectively; (ii) have the amino acid sequences of SEQ ID NOs: 124, 125, and 147, respectively; (iii) have the amino acid sequences of SEQ ID NOs: 127, 128, and 149, respectively; (iv) have the amino acid sequences of SEQ ID NOs: 129, 130, and 150, respectively; (v) have the amino acid sequences of SEQ ID NOs: 131, 132, and 151, respectively; (vi) have the amino acid sequences of SEQ ID NOs: 134, 135, and 153, respectively; (vii) have the amino acid sequences of SEQ ID NOs: 136, 137, and 154, respectively; (viii) have the amino acid sequences of SEQ ID NOs: 138, 139, and 155, respectively; (ix) have the amino acid sequences of SEQ ID NOs: 140, 141, and 156, respectively; or (x) have the amino acid sequences of SEQ ID NOs: 142, 143, and 157, respectively. ### Claim 28 (depends on 20, 21, 22, 23, 24, 25, 26, 27) The isolated polynucleotide or complement thereof of any one of claims 20 to 27, wherein the nucleotide sequence further encodes a hexon protein comprising an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 159, 161, 163-165, and 167-171. ### Claim 29 (depends on 20, 21, 22, 23, 24, 25, 26, 27, 28) The isolated polynucleotide or complement thereof of any one of claims 20 to 28, wherein the nucleotide sequence further encodes a penton protein comprising an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 211, 213, 215-217, and 219-223. ### Claim 30 (depends on 20, 21, 22, 23, 24, 25, 26, 27, 28, 29) The isolated polynucleotide or complement thereof of any one of claims 20 to 29, wherein the nucleotide sequence has at least 90% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 4, 6-8, and 10-14. ### Claim 31 (depends on 30) The isolated polynucleotide or complement thereof of claim 30, wherein the nucleotide sequence has at least 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 4, 6-8, and 10-14. ### Claim 32 (depends on 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31) The isolated polynucleotide or complement thereof of any one of claims 20 to 31, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 226, 227, 234, 235, 240-247, and 250-263. ### Claim 33 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32) A recombinant vector comprising the isolated polynucleotide or complement thereof of any one of claims 1 to 32. ### Claim 34 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33) A recombinant adenovirus comprising the isolated polynucleotide or complement thereof of any one of claims 1 to 32 or the recombinant vector of claim 33. ### Claim 35 (depends on 34) The recombinant adenovirus of claim 34, wherein the isolated polynucleotide or complement thereof comprises a deletion in or of the E1, E2, and/or E3 region. ### Claim 36 (depends on 34, 35) The recombinant adenovirus of claim 34 or 35, wherein the recombinant virus is a replication-defective virus. ### Claim 37 (depends on 34, 35, 36) The recombinant adenovirus of any one of claims 34 to 36, wherein the recombinant adenovirus binds a sialic acid receptor. ### Claim 38 (depends on 34, 35, 36, 37) The recombinant adenovirus of any one of claims 34 to 37, further comprising a heterologous nucleotide sequence encoding an antigenic or therapeutic gene product of interest or fragment thereof. ### Claim 39 (depends on 38) The recombinant adenovirus of claim 38, wherein the antigenic gene product or fragment thereof, comprises a bacterial protein or fragment thereof; a viral protein or fragment thereof; a parasitic protein or fragment thereof; or a fungal protein or fragment thereof. ### Claim 40 (depends on 39) The recombinant adenovirus of claim 39, wherein the bacterial protein or fragment thereof, is from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 41 (depends on 39) The recombinant adenovirus of claim 39, wherein the viral protein or fragment thereof, is from a viral family selected from the group consisting of Retroviridae, Flaviviridae, Arenaviridae, Bunyaviridae, Filoviridae, Togaviridae, Poxviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Rhabdoviridae, Paramyxoviridae, Picornaviridae, Hepadnaviridae, Papillomaviridae, Parvoviridae, Astroviridae, Polyomaviridae, Calciviridae, and Reoviridae. ### Claim 42 (depends on 39, 41) The recombinant adenovirus of claim 39 or 41, wherein the viral protein or fragment thereof, is from human immunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 43 (depends on 42) The recombinant adenovirus of claim 42, wherein the viral protein or fragment thereof, from HIV is Gag, Pol, Env, Nef, Tat, Rev, Vif, Vpr, or Vpu. ### Claim 44 (depends on 39, 41) The recombinant adenovirus of claim 39, 41, or 42, wherein the viral protein or fragment thereof, is an envelope glycoprotein or fragment thereof. ### Claim 45 (depends on 39) The recombinant adenovirus of claim 39, wherein the parasitic protein or fragment thereof, is from Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 46 (depends on 39) The recombinant adenovirus of claim 39, wherein the fungal protein or fragment thereof, is from Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 47 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46) A method of treating a subject having a disease, the method comprising administering the isolated polynucleotide or complement thereof of any one of claims 1 to 32, the recombinant vector of claim 33, or the recombinant adenovirus of any one of claims 34 to 46 to the subject. ### Claim 48 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46) A method of inducing an immune response in a subject comprising administering the isolated polynucleotide or complement thereof of any one of claims 1 to 32, the recombinant vector of claim 33, or the recombinant adenovirus of any one of claims 34 to 46 to the subject. ### Claim 49 (depends on 47, 48) The method of claim 47 or 48, wherein the polynucleotide comprises an antigenic gene product or fragment thereof, that promotes an immune response in the subject against an infective agent. ### Claim 50 (depends on 49) The method of claim 49, wherein the immune response comprises a decrease in expression of interleukin-9 (IL9) relative to a reference level, such as a level of IL9 in an untreated subject. ### Claim 51 (depends on 49, 50) The method of claim 49 or 50, wherein the antigenic gene product or fragment thereof, comprises a bacterial protein or fragment thereof, a viral protein or fragment thereof, a parasitic protein or fragment thereof, or a fungal protein or fragment thereof. ### Claim 52 (depends on 51) The method of claim 51, wherein the bacterial protein or fragment thereof, is from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 53 (depends on 51) The method of claim 51, wherein the viral protein or fragment thereof, is from a viral family selected from the group consisting of Retroviridae, Flaviviridae, Arenaviridae, Bunyaviridae, Filoviridae, Togaviridae, Poxviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Rhabdoviridae, Paramyxoviridae, Picornaviridae, Hepadnaviridae, Papillomaviridae, Parvoviridae, Astroviridae, Polyomaviridae, Calciviridae, and Reoviridae. ### Claim 54 (depends on 51, 53) The method of claim 51 or 53, wherein the viral protein or fragment thereof, is from human immunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 55 (depends on 54) The method of claim 54, wherein the viral protein or fragment thereof, from HIV is Gag, Pol, Env, Nef, Tat, Rev, Vif, Vpr, or Vpu. ### Claim 56 (depends on 51, 53, 54, 55) The method of any one of claims 51 and 53 to 55, wherein the viral protein or fragment thereof, is an envelope glycoprotein or fragment thereof. ### Claim 57 (depends on 51) The method of claim 51, wherein the parasitic protein or fragment thereof, is from Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 58 (depends on 51) The method of claim 51, wherein the fungal protein or fragment thereof, is from Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 59 (depends on 49) The method of claim 49, wherein the infective agent is a bacterium, a virus, a parasite, or a fungus. ### Claim 60 (depends on 59) The method of claim 59, wherein the bacterium is Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 61 (depends on 59) The method of claim 59, wherein the virus is a retrovirus, flavivirus, arenavirus, bunyavirus, filovirus, togavirus, poxvirus, herpesvirus, orthomyxovirus, coronavirus, rhabdovirus, paramyxovirus, picornavirus, hepadnavirus, papillomavirus, parvovirus, astrovirus, polyomavirus, calicivirus, or reovirus. ### Claim 62 (depends on 61) The method of claim 61, wherein the retrovirus is human immunodeficiency virus (HIV). ### Claim 63 (depends on 59) The method of claim 59, wherein the virus is human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 64 (depends on 59) The method of claim 59, wherein the parasite is Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 65 (depends on 59) The method of claim 59, wherein the fungus is Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 66 (depends on 47) The method of claim 47, wherein the disease is acquired immune deficiency syndrome (AIDS), cancer, tuberculosis, leprosy, typhoid fever, pneumonia, meningitis, staphylococcal scalded skin syndrome (SSSS), Ritter's disease, tularemia (rabbit fever), brucellosis, Glanders disease, bubonic plague, septicemic plague, pneumonic plague, diphtheria, pertussis (whooping cough), tetanus, anthrax, hepatitis, smallpox, monkeypox, measles, mumps, rubella, chicken pox, polio, rabies, Japanese encephalitis, herpes, mononucleosis, influenza, Ebola virus disease, hemorrhagic fever, yellow fever, Zika fever, Marburg virus disease, toxoplasmosis, malaria, trypanosomiasis, legionellosis, aspergillosis, blastomycosis, candidiasis (thrush), coccidioidomycosis, cryptococcosis, histoplasmosis, paracoccidioidomycosis, sporotrichosis, or sinus-orbital zygomycosis. ### Claim 67 (depends on 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66) The method of any one of claims 47 to 66, wherein the subject is human. ### Claim 68 (depends on 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67) The method of any one of claims 47 to 67, wherein the recombinant adenovirus, recombinant vector, or isolated polynucleotide is administered intramuscularly, intravenously, intradermally, percutaneously, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctivally, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularly, orally, topically, locally, by inhalation, by injection, by infusion, by continuous infusion, by localized perfusion bathing target cells directly, by catheter, by lavage, by gavage, in cremes, or in lipid compositions. ### Claim 69 (depends on 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68) The method of any one of claims 47 to 68, wherein the recombinant adenovirus, recombinant vector, or isolated polynucleotide is administered as a pharmaceutical composition comprising a pharmaceutically acceptable carrier. ### Claim 70 (depends on 69) The method of claim 69, wherein the subject is administered at least one dose of the pharmaceutical composition. ### Claim 71 (depends on 70) The method of claim 70, wherein the subject is administered at least two doses of the pharmaceutical composition. ### Claim 72 (depends on 71) The method of claim 71, wherein the pharmaceutical composition is administered to the subject as part of a prime-boost regimen, comprising a priming step followed by a boosting step. ### Claim 73 (depends on 72) The method of claim 72, wherein the prime-boost regimen is a homologous prime-boost regimen, wherein the priming step and the boosting step comprises administration of the pharmaceutical composition. ### Claim 74 (depends on 72) The method of claim 72, wherein the prime-boost regimen is a heterologous prime-boost regimen, wherein the priming step comprises administration of the pharmaceutical composition. ### Claim 75 (depends on 74) The method of claim 74, wherein the boosting step comprises administration of a second, different pharmaceutical composition, wherein optionally the second pharmaceutical composition comprises a second recombinant adenovirus, a recombinant vector, a polynucleotide, or a polypeptide. ### Claim 76 (depends on 75) The method of claim 75, wherein the second pharmaceutical composition comprises a RhAd vector or a HuAd vector. ### Claim 77 (depends on 76) The method of claim 76, wherein the RhAd vector is a RhAd51 vector, a RhAd52 vector, or a RhAd53 vector. ### Claim 78 (depends on 76) The method of claim 76, wherein the HuAd vector is a HuAd5 vector. ### Claim 79 (depends on 72) The method of claim 72, wherein the prime-boost regimen is a heterologous prime-boost regimen, wherein the boosting step comprises administration of the pharmaceutical composition. ### Claim 80 (depends on 79) The method of claim 79, wherein the priming step comprises administration of a second, different pharmaceutical composition, wherein optionally the second pharmaceutical composition comprises a second recombinant adenovirus, a recombinant vector, a polynucleotide, or a polypeptide. ### Claim 81 (depends on 80) The method of claim 80, wherein the second pharmaceutical composition comprises a RhAd vector or a HuAd vector. ### Claim 82 (depends on 81) The method of claim 81, wherein the RhAd vector is a RhAd51 vector, a RhAd52 vector, or a RhAd53 vector. ### Claim 83 (depends on 81) The method of claim 81, wherein the HuAd vector is a HuAd5 vector. ### Claim 84 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33) A method of producing a recombinant adenovirus comprising transfecting a cell with (a) the isolated polynucleotide or complement thereof of any one of claims 1 to 32 or (b) the recombinant vector of claim 33; culturing the cell in a suitable medium to allow replication of the polynucleotide or the vector in said cell; and harvesting the recombinant adenovirus from the cell and/or from the medium. ### Claim 85 (depends on 84) The method of claim 84, wherein the cell is a bacterial cell, a plant cell, or a mammalian cell. ### Claim 86 (depends on 85) The method of claim 85, wherein the mammalian cell is a Chinese hamster ovary (CHO) cell. ### Claim 87 (depends on 1) The isolated polynucleotide or complement thereof of claim 1, further comprising a nucleotide sequence encoding at least one fiber protein, wherein the nucleotide sequence encoding the at least one fiber protein has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 88 (depends on 87) The isolated polynucleotide or complement thereof of claim 87, further comprising a nucleotide sequence encoding at least two fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID Nos: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 89 (depends on 87) The isolated polynucleotide or complement thereof of claim 87, further comprising a nucleotide sequence encoding at least three fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the sequence of any one of SEQ ID NOs: 17, 18, 22-24, 27-29, 32-35, 38, 39, 41, 43-45, 47, 48, 50, 51, and 53. ### Claim 90 (depends on 1) The isolated polynucleotide or complement thereof of claim 1, further comprising a nucleotide sequence encoding a penton protein, wherein the nucleotide sequence encoding the penton protein has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 107, 110, 111, 113, 114, 116, 117, and 119. ### Claim 91 (depends on 1) The isolated polynucleotide or complement thereof of claim 1, wherein the nucleotide sequence has at least 90% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 5, 6, 8, 9, 11, 12, and 14. ### Claim 92 (depends on 91) The isolated polynucleotide or complement thereof of claim 91, wherein the nucleotide sequence has at least 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 5, 6, 8, 9, 11, 12, and 14. ### Claim 93 (depends on 1) The isolated polynucleotide or complement thereof of claim 1, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 226, 227, 236-243, 246-249, 252-255, and 262-263. ### Claim 94 (depends on 12) The isolated polynucleotide or complement thereof of claim 12, further comprising a nucleotide sequence encoding at least two fiber proteins, wherein each of the fiber proteins is encoded by a nucleotide sequence having at least 90%, 92%, 95%, 97%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of SEQ ID NOs: 19 and 42. ### Claim 95 (depends on 12) The isolated polynucleotide or complement thereof of claim 12, further comprising a nucleotide sequence encoding a penton protein, wherein the nucleotide sequence encoding the penton protein has at least 90%, 92%, 95%, 97%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of SEQ ID NO: 108. ### Claim 96 (depends on 12) The isolated polynucleotide or complement thereof of claim 12, wherein the nucleotide sequence has at least 98% sequence identity over the entire nucleic acid sequence of SEQ ID NO: 3. ### Claim 97 (depends on 96) The isolated polynucleotide or complement thereof of claim 96, wherein the nucleotide sequence comprises the sequence of SEQ ID NO: 3. ### Claim 98 (depends on 12) The isolated polynucleotide or complement thereof of claim 12, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 228-233. ### Claim 99 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein each of the fiber proteins comprises a different amino acid sequence. ### Claim 100 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein two or three of the fiber proteins comprise the same amino acid sequence. ### Claim 101 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein the three fiber proteins encoded by the polynucleotide: (i) have the amino acid sequences of SEQ ID NOs: 121, 122, and 145, respectively; (ii) have the amino acid sequences of SEQ ID NOs: 124, 125, and 147, respectively; (iii) have the amino acid sequences of SEQ ID NOs: 127, 128, and 149, respectively; (iv) have the amino acid sequences of SEQ ID NOs: 129, 130, and 150, respectively; (v) have the amino acid sequences of SEQ ID NOs: 131, 132, and 151, respectively; (vi) have the amino acid sequences of SEQ ID NOs: 134, 135, and 153, respectively; (vii) have the amino acid sequences of SEQ ID NOs: 136, 137, and 154, respectively; (viii) have the amino acid sequences of SEQ ID NOs: 138, 139, and 155, respectively; (ix) have the amino acid sequences of SEQ ID NOs: 140, 141, and 156, respectively; or (x) have the amino acid sequences of SEQ ID NOs: 142, 143, and 157, respectively. ### Claim 102 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein the nucleotide sequence further encodes a hexon protein comprising an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 159, 161, 163-165, and 167-171. ### Claim 103 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein the nucleotide sequence further encodes a penton protein comprising an amino acid sequence having at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the amino acid sequence of any one of SEQ ID NOs: 211, 213, 215-217, and 219-223. ### Claim 104 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein the nucleotide sequence has at least 90% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 4, 6-8, and 10-14. ### Claim 105 (depends on 104) The isolated polynucleotide or complement thereof of claim 104, wherein the nucleotide sequence has at least 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 2, 4, 6-8, and 10-14. ### Claim 106 (depends on 20) The isolated polynucleotide or complement thereof of claim 20, wherein the nucleotide sequence has at least 90%, 92%, 95%, 97%, 98%, 99%, or 100% sequence identity to all or a part of the nucleic acid sequence of any one of SEQ ID NOs: 226, 227, 234, 235, 240-247, and 250-263. ### Claim 107 (depends on 1, 12) A recombinant vector comprising the isolated polynucleotide or complement thereof of any one of claims 1, 12, and 20. ### Claim 108 (depends on 1, 12) A recombinant adenovirus comprising the isolated polynucleotide or complement thereof of any one of claims 1, 12, and 20. ### Claim 109 (depends on 108) The recombinant adenovirus of claim 108, wherein the isolated polynucleotide or complement thereof comprises a deletion in or of the E1, E2, and/or E3 region. ### Claim 110 (depends on 108) The recombinant adenovirus of claim 108, wherein the recombinant virus is a replication-defective virus. ### Claim 111 (depends on 108) The recombinant adenovirus of claim 108, wherein the recombinant adenovirus binds a sialic acid receptor. ### Claim 112 (depends on 108) The recombinant adenovirus of claim 108, further comprising a heterologous nucleotide sequence encoding an antigenic or therapeutic gene product of interest or fragment thereof. ### Claim 113 (depends on 112) The recombinant adenovirus of claim 112, wherein the antigenic gene product or fragment thereof, comprises a bacterial protein or fragment thereof; a viral protein or fragment thereof; a parasitic protein or fragment thereof; or a fungal protein or fragment thereof. ### Claim 114 (depends on 113) The recombinant adenovirus of claim 113, wherein the bacterial protein or fragment thereof, is from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 115 (depends on 113) The recombinant adenovirus of claim 113, wherein the viral protein or fragment thereof, is from a viral family selected from the group consisting of Retroviridae, Flaviviridae, Arenaviridae, Bunyaviridae, Filoviridae, Togaviridae, Poxviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Rhabdoviridae, Paramyxoviridae, Picornaviridae, Hepadnaviridae, Papillomaviridae, Parvoviridae, Astroviridae, Polyomaviridae, Calciviridae, and Reoviridae. ### Claim 116 (depends on 113) The recombinant adenovirus of claim 113, wherein the viral protein or fragment thereof, is from human immunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 117 (depends on 116) The recombinant adenovirus of claim 116, wherein the viral protein or fragment thereof, from HIV is Gag, Pol, Env, Nef, Tat, Rev, Vif, Vpr, or Vpu. ### Claim 118 (depends on 113) The recombinant adenovirus of claim 113, wherein the viral protein or fragment thereof, is an envelope glycoprotein or fragment thereof. ### Claim 119 (depends on 113) The recombinant adenovirus of claim 113, wherein the parasitic protein or fragment thereof, is from Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 120 (depends on 113) The recombinant adenovirus of claim 113, wherein the fungal protein or fragment thereof, is from Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 121 (depends on 107) A recombinant adenovirus comprising the recombinant vector of claim 107. ### Claim 122 (depends on 121) The recombinant adenovirus of claim 121, wherein the isolated polynucleotide or complement thereof comprises a deletion in or of the E1, E2, and/or E3 region. ### Claim 123 (depends on 121) The recombinant adenovirus of claim 121, wherein the recombinant virus is a replication-defective virus. ### Claim 124 (depends on 121) The recombinant adenovirus of claim 121, wherein the recombinant adenovirus binds a sialic acid receptor. ### Claim 125 (depends on 121) The recombinant adenovirus of claim 121, further comprising a heterologous nucleotide sequence encoding an antigenic or therapeutic gene product of interest or fragment thereof. ### Claim 126 (depends on 125) The recombinant adenovirus of claim 125, wherein the antigenic gene product or fragment thereof, comprises a bacterial protein or fragment thereof; a viral protein or fragment thereof; a parasitic protein or fragment thereof; or a fungal protein or fragment thereof. ### Claim 127 (depends on 126) The recombinant adenovirus of claim 126, wherein the bacterial protein or fragment thereof, is from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 128 (depends on 126) The recombinant adenovirus of claim 126, wherein the viral protein or fragment thereof, is from a viral family selected from the group consisting of Retroviridae, Flaviviridae, Arenaviridae, Bunyaviridae, Filoviridae, Togaviridae, Poxviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Rhabdoviridae, Paramyxoviridae, Picornaviridae, Hepadnaviridae, Papillomaviridae, Parvoviridae, Astroviridae, Polyomaviridae, Calciviridae, and Reoviridae. ### Claim 129 (depends on 126) The recombinant adenovirus of claim 126, wherein the viral protein or fragment thereof, is from human immunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 130 (depends on 129) The recombinant adenovirus of claim 129, wherein the viral protein or fragment thereof, from HIV is Gag, Pol, Env, Nef, Tat, Rev, Vif, Vpr, or Vpu. ### Claim 131 (depends on 126) The recombinant adenovirus of claim 126, wherein the viral protein or fragment thereof, is an envelope glycoprotein or fragment thereof. ### Claim 132 (depends on 126) The recombinant adenovirus of claim 126, wherein the parasitic protein or fragment thereof, is from Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 133 (depends on 126) The recombinant adenovirus of claim 126, wherein the fungal protein or fragment thereof, is from Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 134 (depends on 1, 12) A method of treating or inducing an immune response in a subject having a disease, the method comprising administering the isolated polynucleotide or complement thereof of any one of claims 1, 12, and 20, a recombinant vector comprising the isolated polynucleotide or complement thereof, or a recombinant adenovirus comprising the isolated polynucleotide or complement thereof, to the subject. ### Claim 135 (depends on 134) The method of claim 134, wherein the polynucleotide comprises an antigenic gene product or fragment thereof, that promotes an immune response in the subject against an infective agent. ### Claim 136 (depends on 135) The method of claim 135, wherein the immune response comprises a decrease in expression of interleukin-9 (IL9) relative to a reference level, such as a level of IL9 in an untreated subject. ### Claim 137 (depends on 135) The method of claim 135, wherein the antigenic gene product or fragment thereof, comprises a bacterial protein or fragment thereof, a viral protein or fragment thereof, a parasitic protein or fragment thereof, or a fungal protein or fragment thereof. ### Claim 138 (depends on 137) The method of claim 137, wherein the bacterial protein or fragment thereof, is from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 139 (depends on 137) The method of claim 137, wherein the viral protein or fragment thereof, is from a viral family selected from the group consisting of Retroviridae, Flaviviridae, Arenaviridae, Bunyaviridae, Filoviridae, Togaviridae, Poxviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Rhabdoviridae, Paramyxoviridae, Picornaviridae, Hepadnaviridae, Papillomaviridae, Parvoviridae, Astroviridae, Polyomaviridae, Calciviridae, and Reoviridae. ### Claim 140 (depends on 137) The method of claim 137, wherein the viral protein or fragment thereof, is from human immunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 141 (depends on 140) The method of claim 140, wherein the viral protein or fragment thereof, from HIV is Gag, Pol, Env, Nef, Tat, Rev, Vif, Vpr, or Vpu. ### Claim 142 (depends on 137) The method of claim 137, wherein the viral protein or fragment thereof, is an envelope glycoprotein or fragment thereof. ### Claim 143 (depends on 137) The method of claim 137, wherein the parasitic protein or fragment thereof, is from Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 144 (depends on 137) The method of claim 137, wherein the fungal protein or fragment thereof, is from Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 145 (depends on 135) The method of claim 135, wherein the infective agent is a bacterium, a virus, a parasite, or a fungus. ### Claim 146 (depends on 145) The method of claim 145, wherein the bacterium is Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium leprae, Pseudomonas aeruginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Francisella tularensis, Brucella, Burkholderia mallei, Yersinia pestis, Corynebacterium diphtheria, Neisseria meningitidis, Bordetella pertussis, Clostridium tetani, or Bacillus anthracis. ### Claim 147 (depends on 145) The method of claim 145, wherein the virus is a retrovirus, flavivirus, arenavirus, bunyavirus, filovirus, togavirus, poxvirus, herpesvirus, orthomyxovirus, coronavirus, rhabdovirus, paramyxovirus, picornavirus, hepadnavirus, papillomavirus, parvovirus, astrovirus, polyomavirus, calicivirus, or reovirus. ### Claim 148 (depends on 147) The method of claim 147, wherein the retrovirus is human immunodeficiency virus (HIV). ### Claim 149 (depends on 145) The method of claim 145, wherein the virus is human papillomavirus (HPV), hepatitis A virus (Hep A), hepatitis B virus (HBV), hepatitis C virus (HCV), Variola major, Variola minor, monkeypox virus, measles virus, rubella virus, mumps virus, varicella zoster virus (VZV), poliovirus, rabies virus, Japanese encephalitis virus, herpes simplex virus (HSV), cytomegalovirus (CMV), rotavirus, influenza, Ebola virus, yellow fever virus, Zika virus, or Marburg virus. ### Claim 150 (depends on 145) The method of claim 145, wherein the parasite is Toxoplasma gondii, Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Trypanosoma spp., or Legionella spp. ### Claim 151 (depends on 145) The method of claim 145, wherein the fungus is Aspergillus, Blastomyces dermatitidis, Candida, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum var. capsulatum, Paracoccidioides brasiliensis, Sporothrix schenckii, Zygomycetes spp., Absidia corymbifera, Rhizomucor pusillus, or Rhizopus arrhizus. ### Claim 152 (depends on 134) The method of claim 134, wherein the disease is acquired immune deficiency syndrome (AIDS), cancer, tuberculosis, leprosy, typhoid fever, pneumonia, meningitis, staphylococcal scalded skin syndrome (SSSS), Ritter's disease, tularemia (rabbit fever), brucellosis, Glanders disease, bubonic plague, septicemic plague, pneumonic plague, diphtheria, pertussis (whooping cough), tetanus, anthrax, hepatitis, smallpox, monkeypox, measles, mumps, rubella, chicken pox, polio, rabies, Japanese encephalitis, herpes, mononucleosis, influenza, Ebola virus disease, hemorrhagic fever, yellow fever, Zika fever, Marburg virus disease, toxoplasmosis, malaria, trypanosomiasis, legionellosis, aspergillosis, blastomycosis, candidiasis (thrush), coccidioidomycosis, cryptococcosis, histoplasmosis, paracoccidioidomycosis, sporotrichosis, or sinus-orbital zygomycosis. ### Claim 153 (depends on 134) The method of claim 134, wherein the subject is human. ### Claim 154 (depends on 134) The method of claim 134, wherein the recombinant adenovirus, recombinant vector, or isolated polynucleotide is administered intramuscularly, intravenously, intradermally, percutaneously, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostatically, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, peritoneally, subcutaneously, subconjunctivally, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularly, orally, topically, locally, by inhalation, by injection, by infusion, by continuous infusion, by localized perfusion bathing target cells directly, by catheter, by lavage, by gavage, in cremes, or in lipid compositions. ### Claim 155 (depends on 134) The method of claim 134, wherein the recombinant adenovirus, recombinant vector, or isolated polynucleotide is administered as a pharmaceutical composition comprising a pharmaceutically acceptable carrier. ### Claim 156 (depends on 155) The method of claim 155, wherein the subject is administered at least one dose of the pharmaceutical composition. ### Claim 157 (depends on 156) The method of claim 156, wherein the subject is administered at least two doses of the pharmaceutical composition. ### Claim 158 (depends on 157) The method of claim 157, wherein the pharmaceutical composition is administered to the subject as part of a prime-boost regimen, comprising a priming step followed by a boosting step. ### Claim 159 (depends on 158) The method of claim 158, wherein the prime-boost regimen is a homologous prime-boost regimen, wherein the priming step and the boosting step comprises administration of the pharmaceutical composition. ### Claim 160 (depends on 158) The method of claim 158, wherein the prime-boost regimen is a heterologous prime-boost regimen, wherein the priming step comprises administration of the pharmaceutical composition. ### Claim 161 (depends on 160) The method of claim 160, wherein the boosting step comprises administration of a second, different pharmaceutical composition, wherein optionally the second pharmaceutical composition comprises a second recombinant adenovirus, a recombinant vector, a polynucleotide, or a polypeptide. ### Claim 162 (depends on 161) The method of claim 161, wherein the second pharmaceutical composition comprises a RhAd vector or a HuAd vector. ### Claim 163 (depends on 162) The method of claim 162, wherein the RhAd vector is a RhAd51 vector, a RhAd52 vector, or a RhAd53 vector. ### Claim 164 (depends on 162) The method of claim 162, wherein the HuAd vector is a HuAd5 vector. ### Claim 165 (depends on 158) The method of claim 158, wherein the prime-boost regimen is a heterologous prime-boost regimen, wherein the boosting step comprises administration of the pharmaceutical composition. ### Claim 166 (depends on 165) The method of claim 165, wherein the priming step comprises administration of a second, different pharmaceutical composition, wherein optionally the second pharmaceutical composition comprises a second recombinant adenovirus, a recombinant vector, a polynucleotide, or a polypeptide. ### Claim 167 (depends on 166) The method of claim 166, wherein the second pharmaceutical composition comprises a RhAd vector or a HuAd vector. ### Claim 168 (depends on 167) The method of claim 167, wherein the RhAd vector is a RhAd51 vector, a RhAd52 vector, or a RhAd53 vector. ### Claim 169 (depends on 167) The method of claim 167, wherein the HuAd vector is a HuAd5 vector. ### Claim 170 (depends on 1, 12) A method of producing a recombinant adenovirus comprising transfecting a cell with (a) the isolated polynucleotide or complement thereof of any one of claims 1, 12, and 20 or (b) a recombinant vector comprising the isolated polynucleotide or complement thereof; culturing the cell in a suitable medium to allow replication of the polynucleotide or the vector in said cell; and harvesting the recombinant adenovirus from the cell and/or from the medium. ### Claim 171 (depends on 170) The method of claim 170, wherein the cell is a bacterial cell, a plant cell, or a mammalian cell. ### Claim 172 (depends on 171) The method of claim 171, wherein the mammalian cell is a Chinese hamster ovary (CHO) cell.