Systems and methods are presented that allow for selection of tumor neoepitopes that are then used to generate recombinant nucleic acids that encode one or more polytopes that are optimized for proper trafficking and processing. In preferred methods, the polytopes are encoded in a plasmid and/or a viral expression system for use as a therapeutic agent.

Cancer immunotherapy is enhanced by co-expression of cancer associated or tumor-specific (neo)epitopes with co-stimulatory molecules and/or other immune activators. Where desired, treatment may be enhanced by administration of a immune checkpoint inhibitor.

Disclosed herein are methods of performing continuous directed evolution in complex biological systems, including metazoan cells. These methods include the infection of engineered, non-naturally occurring metazoan cells with engineered, non-naturally occurring DNA viruses. The generation of infectious viruses that can infect new cells depends on the evolution of a gene of interest which is driven by an error-prone adenoviral polymerase. Also disclosed herein, are the compositions of engineered, non-naturally occurring metazoan cells and engineered, non-naturally occurring DNA viruses that function as components in the continuous directed evolution methodologies.

An adenovirus comprising an E1A polypeptide comprising one or more modifications and comprising an E4orf6/7 polypeptide comprising one or more modifications is described. Compositions and kits comprising the modified adenoviruses are also described. Further described is a method of treating a proliferative disorder in a subject comprising administering to the subject an adenovirus comprising the E1A polypeptide comprising one or more modifications and comprising the E4orf6/7 polypeptide comprising one or more modifications.

The present invention relates to a cell line for producing an adenovirus having a limited autoreplication capability, and a method of preparing the same, and more particularly, to a cell line for producing an adenovirus having no autoreplication capability by expressing at least one selected from an adenoviral E1 protein and an E1A or E1B protein, and a method of preparing the same. Also, the present invention relates to the use of the cell line expressing at least one selected from the adenoviral E1 protein and the E1A or E1B protein.

The invention provides adeno-associated virus (AAV) replication (Rep) sequences. In one embodiment, the invention provides nucleotide sequences encoding a chimeric protein, wherein the encoded chimeric protein contains a wild type AAV Rep inhibitory amino acid sequence, and wherein the nucleotide sequences contain a scrambled and/or deoptimized polynucleotide sequence encoding the wild type AAV Rep inhibitory amino acid sequence. The invention provides vectors, cells, and viruses containing the invention's sequences. Also provided are methods for detecting portions of the AAV Rep inhibitory amino acid sequence, which reduce replication and/or infection and/or productive infection by viruses. The invention's compositions and methods are useful for site-specific integration and/or expression of heterologous sequences by recombinant adeno-associated virus (rAAV) vectors and by rAAV virus particles, such as hybrid viruses (e.g., Ad-AAV) comprising such vectors. The invention's compositions and methods find application in, for example, gene therapy and/or vaccines.

The invention provides a replication-deficient serotype 28 adenoviral vector characterized by comprising a portion of a serotype 45 adenoviral hexon protein and/or a portion of a serotype 45 fiber protein in place of the endogenous serotype 28 hexon and/or fiber protein.

Certain embodiments include the enhancement of effectiveness for an adenoviral cancer therapy.

The present application provides a method for producing recombinant adenovirus. The method comprises expansion of the recombinant adenovirus packaging cells from the Working Cell Bank and re-expansion of the cells after inoculation in a packed bed bioreactor in order to obtain a re-expanded recombinant adenovirus. The present application also provides the use of a packed bed bioreactor for recombinant adenovirus production.

An adenovirus comprising an E1A polypeptide comprising one or more modifications and comprising an E4orf6/7 polypeptide comprising one or more modifications is described. Compositions and kits comprising the modified adenoviruses are also described. Further described is a method of treating a proliferative disorder in a subject comprising administering to the subject an adenovirus comprising the E1A polypeptide comprising one or more modifications and comprising the E4orf6/7 polypeptide comprising one or more modifications.