Viruses and other bioagents are of high medical and biodefense concern and their detection at concentrations well below the threshold necessary to cause health hazards continues to be a challenge with respect to sensitivity, specificity, and selectivity. Ideally, assays for accurate and real time detection of viral agents and other bioagents would not necessitate any pre-processing of the analyte, which would make them applicable for example to bodily fluids (blood, sputum) and man-made as well as naturally occurring bodies of water (pools, rivers). We describe herein a robust biosensor that combines the sensitivity of surface acoustic waves (SAW) generated at a frequency of 325 MHz with the specificity provided by antibodies and other ligands for the detection of viral agents. In preferred embodiments, a lithium tantalate based SAW transducer with silicon dioxide waveguide sensor platform featuring three test and one reference delay lines was used to adsorb antibodies directed against Coxsackie virus B4 or the negative-stranded category A bioagent Sin Nombre virus (SNV), a member of the genus Hantavirus, family Bunyaviridae, negative-stranded RNA viruses. Rapid detection (within seconds) of increasing concentrations of viral particles was linear over a range of order of magnitude for both viruses, although the sensor was approximately 5010.sup.4-fold more sensitive for the detection of SNV. For both pathogens, the sensor's selectivity for its target was not compromised by the presence of confounding Herpes Simplex virus type 1. The biosensor was able to detect SNV at doses lower than the load of virus typically found in a human patient suffering from hantavirus cardiopulmonary syndrome (HCPS). Further, in a proof-of-principle real world application, the SAW biosensor was capable of selectively detecting SNV agents in complex solutions, such as naturally occurring bodies of water (river, sewage effluent) without analyte pre-processing.

A method of identifying stable peptides from a protein, said method comprising: obtaining a peptide from a protein; comparing a solvent-accessible surface area (SASA) of the peptide with a SASA of a corresponding peptide region within the protein; using a result of the comparison to determine whether or not the peptide is structurally stable relative to the corresponding peptide region within the protein. Also disclosed is use of the method to identify stable immunogenic epitopes of SARS-CoV-2, and methods of detecting an antibody response.

A method of diagnosing a subset of Epstein Barr Virus, Myalgic Encephalomyelitis Chronic Fatigue Syndrome (ME/CFS) patients through a multi-prong clinical/serological analysis is provided wherein Epstein Barr Virus Abortive Lytic Replication (EBV) is determined as the specific causal agent through the use of serum antibodies to EBV encoded dUTPase and serum antibodies to EBV DNA Polymerase as molecular markers. A method of treating patients diagnosed with Epstein Barr Virus Abortive Lytic Replication (EBV), Myalgic Encephalomyelitis Chronic Fatigue Syndrome (ME/CFS) with specific antiviral nucleosides is also provided, to alleviate the condition.

The present invention provides compositions and methods that can be used to determine a peptide signature for an antibody repertoire in a sample comprising multiple antibodies. The method can be used to characterize a phenotype in a sample, such as providing a diagnosis, prognosis or theranosis of a medical condition.

The present invention generally provides for a novel NEC-targeted strategy for the development of antiherpesviral drugs as well as for a novel antiviral strategy targeting the viral-cellular nuclear egress complex (NEC) for a small molecule-based therapy or prophylaxis to control infections with human cytomegalovirus or other pathogenic viruses of the group of the Herpesviridae. Methods for screening agents/compounds/small molecules modulating/inhibiting the nuclear egress complex of Herpesviridae are provided as well. Specifically novel drug targets of the viral nuclear egress complex of viruses of the Herpesviridae are provided.

Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including 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).

Early Nasopharyngeal Carcinoma (NPC) detection methods, devices, and kits are provided utilizing novel Epstein-Barr Virus (EBV) EBNA1 antigens to detect serum anti-EBNA1 IgA antibodies with superior correlation to NPC development within four years.

Disclosed herein are methods of selecting an allogeneic T cell line for therapeutic administration to a patient having or suspected of having a pathogen or cancer. Also disclosed are methods of selecting a donor from whom to derive an allogeneic T cell line for therapeutic administration to a patient having or suspected of having a pathogen or cancer.

The present disclosure relates to methods, systems and compositions for determining and improving overall survival probabilities in EBV-positive cancer subjects and the role of tumor infiltrating lymphocytes in cancer immunotherapy.

Provided herein are methods, compositions, kits, and systems for detecting Epstein Barr virus infection (EBV) in gastric cancer (GC) patients. In particular, provided herein are methods, composition, kits, and systems for diagnosing and treating EBV-positive gastric cancer (EBV.sup.+ GC) in a biological sample of an individual based on the presence and level of antibodies against particular Epstein Barr virus proteins. EBV.sup.+ GC is a distinct subtype of gastric cancer and is associated with unique molecular profiles. Also provided herein are methods for providing more personalized therapy for each of these distinct cancer subtypes and methods for determining an Epstein Barr virus-positive gastric cancer antibody signature, and kits comprising components and protocols for performing the methods of this disclosure.