Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

The invention describes a method to identify and stage human herpesvirus-mediated neurodegenerations by measuring secreted herpesvirus protein and RNA levels in a blood sample and comparing that level to an individual's baseline or reference level. Combining herpesvirus secretome levels with other neurodegeneration biomarkers, such as coagulation factors and cell adhesion molecules, can aid in diagnosis and staging of neuropathology. Sensitive and economical ELISA diagnostic kits can detect and quantify the herpesvirus secretome and neurodegeneration biomarkers to diagnose herpesvirus-mediated neurodegeneration, stage disease, and predict disease progression. Finally, this method will elucidate herpesvirus-mediated neurodegenerations and aid in developing therapeutics.

A method for testing target nucleic acid includes the steps from (1) through (5) below: (1) mixing a specimen containing target nucleic acid with positive control nucleic acid to obtain a specimen mixture of the specimen and the positive control nucleic acid; (2) mixing the specimen mixture with a PCR buffer solution containing a surfactant to obtain a buffer solution mixture; (3) adding a portion of the buffer mixture to a solid composition for PCR control containing DNA polymerase, positive control nucleic acid, and PCR reaction control nucleic acid; (4) adding a portion of the buffer mixture to a solid composition for PCR reaction containing DNA polymerase and one or more kinds of PCR primer pair; and (5) detecting a PCR product generated as a result of the steps (3) and (4).

The present invention relates to a method for determining presence of a pre-determined nucleic acid sequence in a sample, the method comprising the steps of adding one or more enzyme(s) providing activities of RNA- and/or DNA-dependent DNA polymerase activity and strand-displacement activity to the sample to be analysed for the presence of the pre-determined nucleic acid sequence; adding at least five DNA primers to the sample to be analysed for the presence of the pre-determined nucleic acid sequence, wherein at least one DNA primer comprises a sequence hybridisable to the nucleic acid sequence and at least one DNA primer comprises a sequence hybridisable to the DNA sequence reverse-complementary to the nucleic acid sequence; incubating the sample resulting at a fixed temperature; determining whether an elongated DNA sequence is present in the sample, wherein presence of the elongated DNA sequence in the sample is indicative of the presence of the pre-determined nucleic acid sequence in the sample, wherein the sample is obtained from a human subject and wherein no F3 primer is used.

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.

Disclosed are oligonucleotides, oligonucleotide compositions, kits, methods, formulations, and reaction mixtures that provide for sensitive and specific detection of a target nucleic acid sequence, or amplicon generated from a target nucleic acid sequence, of Varicella-Zoster Virus (VZV1 (if present) in a sample. The oligonucleotides, compositions, kits, methods, formulations, and reaction mixtures can be used to detect the presence of VZV in a sample. The oligonucleotides, compositions, kits, methods, formulations, and reaction mixtures can also be used to amplify specific target nucleic acid regions of VZV.

A method for detection and/or quantification of a human cytomegalovirus (hCMV) virion mRNA in a sample obtained from a patient to identify and/or quantify hCMV infection includes: i) optionally removing from the sample any cellular component that might be present, obtaining a cell-free sample; ii) extracting RNA from a cell-free sample obtained from the patient or obtained in step i); iii) forming a reaction mixture by contacting said RNA extracted in step ii); iv) subjecting the reaction mixture to a reverse transcription process under conditions suitable to generate a cDNA corresponding to the hCMV virion mRNA; v) subjecting the cDNA to an amplification process under conditions adapted to generate an amplification product constituted by DNA; and vi) detecting a presence and/or quantifying the quantity of the amplification product constituted by DNA, as an indication of the presence and/or of the quantity of hCMV virion mRNA in the sample.

Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

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).