Improved methods for the detection and quantitation of a target nucleic acid in a sample using a non-extending helper oligonucleotide are described. The methods include contacting nucleic acids in a sample with amplification reagents including one or more primers, one or more non-extending helper oligonucleotides, and one or more probes. The non-extending helper oligonucleotide facilitates and increases the target nucleic acid accessibility of one or more of the primers, result in greater accumulation of amplicon production, thereby increasing the efficiency and sensitivity of the amplification assay, including amplification assays for Hepatitis C Virus (HCV), for example, HCV Genotype 5. Kits, articles of manufacture, and reaction mixtures are also provided.

The disclosure provides control compositions used in nucleic acid amplification. Various modifications to the disclosed compositions and methods of using the same, devices, and kits are described.

A virus infection model which overcomes the drawbacks of conventional hepatitis virus infection models is provided.

A method for constructing a virus infection model capable of recapitulating a viral life cycle, comprising infecting a cell condensate formed by culturing a tissue or organ cell in vitro with a virus. A virus infection model capable of recapitulating a viral life cycle, comprising a virus-infected cell condensate, wherein the cell condensate is formed by culturing a tissue or organ cell in vitro. A method of screening for substances with antiviral activity, comprising using the virus infection model.

A method for diagnosing hepatitis virus infection or a hepatitis disease condition in a subject based on hepatitis virus-associated biomarkers present on exosomes in a bodily fluid sample from the subject is disclosed. Also disclosed are a method for monitoring the course of a hepatitis virus infection or a hepatitis disease condition in a subject and a method for monitoring effectiveness of treatment to a subject with an anti-hepatitis virus agent based on hepatitis virus-associated biomarkers present on exosomes in bodily fluid samples from the subject, as well as a kit for diagnosing hepatitis virus infection and/or a hepatitis disease condition in a subject based on hepatitis virus-associated biomarkers on exosomes in bodily fluid samples from the subject.

The present disclosure provides rapid and non-invasive methods for determining whether a patient will benefit from treatment with therapeutic agents that inhibit Hepatitis C virus (HCV). These methods are based on detecting HCV RNA and/or anti-HCV antibodies in small-volume dried biological fluid samples that are collected using a microsampling device. Kits for use in practicing the methods are also provided.

The present disclosure relates to oligonucleotide sequences for amplification primers and their use in performing nucleic acid amplifications of HCV, in particular regions that encode the NS3 polypeptide. In some embodiments the primers are used in nested PCR methods for the detection or sequencing of HCV NS3. The oligonucleotide sequences are also provided assembled as kits that can be used to amplify and detect or sequence HCV NS3.

A method for detecting a mutation in an amino acid at position 93 of a hepatitis C virus NS5A protein, the method including: synthesizing cDNA using, as a template, hepatitis C virus RNA in a sample; and performing a real-time PCR with a cycling probe method using, as a template, the cDNA; wherein a primer set used in the real-time PCR is a certain primer set; and wherein probes used in the real-time PCR include certain probes.

Methods for the rapid detection of the presence or absence of Hepatitis C Virus (HCV) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers and probes targeting HCV and kits are provided that are designed for the detection of HCV.

The present invention allows for the detection of pathogens in a urine specimen, such as bacteria and viruses, including HCV, STDs, and HIV in a urine analyte in patients. The invention accomplishes the detection with methods that employ amplification of DNA from cells in the urine specimen, for example, by using a PCR-based assay. The method can detect one or more high-risk forms of HCV, STDs, and HIV 1 and 2. The method is useful for all genders, including cisgender, transgender and nonbinary patients and can achieve high analytical sensitivity.

Systems, methods, and devices for detecting infections in a clinical sample are provided. Small-volume clinical samples obtained at a point-of-service (POS) location and may be tested at the POS location for multiple markers for multiple diseases, including upper and lower respiratory diseases. Samples may be tested for cytokines, or for inflammation indicators. Dilution of samples, or levels of detection, may be determined by the condition or past history of a subject. Test results may be obtained within a short amount of time after sample placement in a testing device, or within a short amount of time after being obtained from the subject. A prescription for treatment of a detected disorder may be provided, and may be filled, at the POS location. A bill may be automatically generated for the testing, or for the prescription, may be automatically sent to an insurance provider, and payment may be automatically obtained.