The present invention provides compositions, kits, and method for determining the levels of expression of human polyoma or papillomavirus species and RNA transcripts. These levels can be used for the prognosis of risk of developing virally-induced cancers. The ratio (R) between early and late transcripts is indicative of HPV infections associated with higher risk of developing genital neoplasia and cancer.

The disclosure features systems and methods for measuring and diagnosing target constituents bound to labeling particles in a sample. The systems include a radiation source, a sample holder, a detector configured to obtain one or more diffraction patterns of the sample each including information corresponding to optical properties of sample constituents, and an electronic processor configured to, for each of the one or more diffraction patterns: (a) analyze the diffraction pattern to obtain amplitude information and phase information corresponding to the sample constituents; (b) identify one or more particle-bound target sample constituents based on at least one of the amplitude information and the phase information; and (c) determine an amount of at least one of the particle-bound target sample constituents in the sample based on at least one of the amplitude information and the phase information.

A method for detecting at least one systemic condition and at least one locoproximal condition within a surgical site of a subject following a surgery is disclosed. The method includes obtaining a surgical drainage fluid sample from the surgical site and a blood sample from the subject, isolating analyte-containing portions from the surgical drainage fluid sample and the blood sample, and detecting and quantifying at least a portion of the analytes within the analyte-containing portions to produce at least one assay result, wherein the at least one assay result is indicative of the at least one systemic condition and the at least one locoproximal condition within a surgical site of a subject. At least one assay result may be provided to a practitioner and used to select at least one additional treatment.

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

The invention provides methods for treating infections, disorders or diseases caused by a human papillomavirus other than HPV-16 by determining the HPV type of the patient, providing a synthetic-long-peptide based therapeutic vaccine for treatment of said patient and administering said therapeutic vaccine to said patient. The invention further provides novel immunogenic compositions and therapeutic vaccines against human papillomaviruses other than HPV-16 and uses thereof.

The disclosure relates to test kits and methods for detecting the presence of multiple human papilloma vims polynucleotides in a biological sample.

Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

A method for detecting in vitro the presence of a genome of a DNA virus or a viral derived DNA in an infected eukaryotic cell, tissue or biological fluid using Molecular Combing or other nucleic acid stretching methods together with probes, especially nucleic acid probes, having a special design. A method for monitoring in vitro the effects of anti-viral treatment by following the presence of genomic viral or viral derived DNA polynucleotides in a virus-infected cell, tissue or biological fluid. Detection of an infectious form of a virus using Molecular Combing and DNA hybridization. A kit comprising probes used to carry out these methods and a composition comprising the probes.

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.