The invention provides for the early detection, diagnostic, and prognostic assays and assay kits for breast cancer and other cancers, based upon the detection of human endogenous retroviruses (HERVs) as cancer biomarkers.

The present disclosure relates to a method of detecting and quantifying a virus-of-interest from human viral shed in a community, including: concentrating viral material from a wastewater sample to form a viral nucleic acid material; measuring an amount of a virus-of-interest nucleic acid in the viral nucleic acid material to obtain a first amount; measuring an amount of a marker or bacteriophage nucleic acid in the viral nucleic acid material to obtain a second amount; and forming a ratio of the first amount to the second amount to estimate a level of virus-of-interest from human viral shed within a community. In embodiments, methods for quantifying, monitoring, and/or identifying virus-of-interest such as SARS-CoV-2 are also disclosed.

The present disclosure provides methods for rapidly assaying the titer of an RNA viral vector such as a lentiviral vector. The method can be used to quickly evaluate the titer of intermediate products in various steps of a lentiviral vector production process.

An in vitro or ex vivo method for determining the risk of complication in a patient, including a step of measuring the expression of C3AR1 in a biological sample from the patient.

Provided are methods of detecting replication competent retrovirus in a sample containing a cell transduced with a viral vector particle encoding a recombinant and/or heterologous molecule, e.g., heterologous gene product. The methods may include assessing transcription of one or more target genes, such as viral genes, that are expressed in a retrovirus but not expressed in the viral vector particle. Replication competent retrovirus may be determined to be present if the levels of RNA of the one or more target genes is higher than a reference value, which can be measured directly or indirectly, including from a positive control sample containing RNA from the respective target gene at a known level and/or at or above the limit of detection of the assay.

The inventive technology includes novel systems, method and compositions for the identification and classification of host-derived RNA biomarkers produced in response to an infection.

The present invention relates to novel strains of pig that are highly suitable for xenotransplantation. The first novel pig strain lacks functional porcine endogenous retroviruses so is suitable as a donor for tissue and/or cell xenotransplantation into a human recipient. These pigs can also be used as a foundation pig for further manipulation, for example, by gene editing of xenoantigens to produce a second novel strain of pig that is not only free of infectious porcine retroviruses but is also free of the main xenoantigens responsible for hyperacute organ rejection. These pigs can be used for whole organ, tissue and/or cell transplantation into a human recipient. The present invention also relates to methods for selecting pigs that lack infectious porcine endogenous retroviruses, and their use for tissue and/or cell xenotransplantation into humans, and to methods of gene editing of xenoantigens of the selected pigs to further enhance the immunological quality of the donor organs, tissues and/or cells to avoid xenotransplant rejection.

The invention is directed to methods of assessing the safety of therapeutic compounds and therapeutic genetic manipulations, including integrating gene therapy vectors and genome editing. In particular, the invention provides a method, wherein the oncogenic potential of therapeutic compounds and therapeutic genetic manipulations, including integrating gene therapy vectors and genome editing, is determined by determining the percentage of differentiation blocked hematopoietic progenitor cells.

The subject invention pertains to materials and methods for detecting, preventing and treating retroviral infections in humans and other animals susceptible to infection by retrovirus. It has been discovered that FIV can be transmitted from cats to humans and that the FIV can infect human cells in vivo and that antibodies generated by the infected person cross-react with HIV antigens. Thus, the methods and compositions of the subject invention can be used to detect, prevent and treat FIV infection in humans and other non-feline animals that are susceptible to FIV infection. The methods and compositions of the invention can also be used to prevent and treat infection by HIV in humans.

Compositions, methods and kits for detecting Chikungunya virus (CHIKV) nucleic acids are for detecting very low levels of the viral nucleic acids using nucleic acid amplification. The kit includes a first primer up to 100 bases long and includes a target-complementary 3′ terminal sequence of 15-48 contiguous bases. The first primer optionally may include a first primer 5′ sequence (i.e., an upstream sequence) that is not complementary to CHIKV nucleic acids.