Provided herein are compositions and devices for diagnosing and treating a viral infection in a subject and/or detecting a viral nucleic acid in a sample. In one example, a sample is treated in a first chamber and the sample is flowed into a second chamber, where any pathogenic nucleic acid is detected by oligonucleotides that are specific to the pathogen under test. Further, the oligonucleotides comprise a cleavage site for a restriction enzyme in the second chamber, which cleaves oligonucleotide-pathogenic nucleic acid hybrid resulting in the exposure of an enzyme that was being held by the oligonucleotide to its substrate, which generates a colorimetric and/or another visual readout.

The invention relates to methods and kits for determining a SARS-CoV-2 strain in a sample. The invention also provides methods and kits for detecting a single nucleotide polymorphism (SNP) in a target nucleic acid, wherein the target nucleic acid is a SARS-CoV-2 nucleic acid. The invention further provides methods and kits for detecting one or more antibody biomarkers in a sample.

A sensor for detecting a target pathogen (e.g., a virus or a bacterium) in a specimen is disclosed, which includes at least two sensing units one of which is configured to detect at least one protein (such as a structural protein) associated with the target pathogen and another one is configured to detect at least one genetic component (e.g., an RNA or a DNA segment) associated with that pathogen (e.g., an RNA segment that is unique to that pathogen).

Described are devices, systems, kits, methods, and techniques for analyzing test fluids to determine presence, absence, or concentration of analytes in the test fluids and useful for performing diagnostic testing, such as to quickly identify whether or not an individual may have a particular disease or condition, such as infection by SARS-CoV-2 or a SARS-CoV-2 variant or vaccine-induced immunity or natural immunity to infection by SARS-CoV-2 or a SARS-CoV-2 variant. The devices, systems, kits, methods, and techniques described herein can be used to detect analytes in body fluids using a functionalized electrochemical test strip and potentiostatic measurements, allowing for prompt identification of whether or not an individual has a particular disease or condition, such as in a period of 5 minutes or less.

Methods for identifying viral protein constituents and quantifying the relative abundance of such viral protein constituents in a sample of viral particles are disclosed. In embodiments, the methods include first-dimension chromatography to separate intact viral capsid components of the sample, online denaturation of the viral capsid components to produce intact viral proteins, second-dimension chromatography to separate the viral proteins, and mass spectrometry to determine the masses of the viral proteins and identify the viral protein constituents of the sample.

Certain aspects of the present disclosure generally relate to systems and methods for determining viruses such as coronaviruses. For instance, some aspects are directed to systems and methods for determining viruses using a partitioning system. Within the partitioning system, free RNA or other nucleic acids may preferentially partition into one phase, while intact viruses may be present in the other phase or in both phases. Accordingly, in some cases, free RNA or other nucleic acids may be preferentially removed, e.g., as compared to intact RNA or other nucleic acids present within a virus. In some cases, the phase containing intact viruses can be determined to determine the infectiousness, e.g., of a sample arising from a subject. This may be useful, for example, for distinguishing subjects who are capable of spreading an infection from those who are not infectious.

Assays, arrays, and methods for distinguishing a bacterial infection from a viral infection are disclosed. The antibiotic crisis is in part driven by over prescription of antibiotics. There is a tendency, particular in pediatrics, to give an antibiotic even for viral infections. Thus, embodiments herein are directed to the problem of distinguishing a bacterial infection from a viral infection to reduce unnecessary antibiotic usage.

The present invention encompasses a diagnostic test and method to authenticate the veracity of a vaccine. The diagnostic test and method are especially useful in a specific and sensitive immunochromatographic assay, performable within about 15 minutes for the authentication, validation, and veracity of a vaccine, such as a COVID-19 vaccine, in a vial prior to administration to a human.

Anti-SARS-CoV-2 fusion peptides are provided. The anti-SARS-CoV-2 fusion peptides include peptide sequences corresponding to the sequence of the SARS-CoV-2 fusion complex heptad repeat domain HR2 and having at least one artificial mutation. The anti-SARS-CoV-2 fusion peptides may be 39-mers, such as peptides #121 (SEQ ID NO: 2) and #125 (SEQ ID NO: 5). These peptides may competitively bind to SARS-CoV-2 and prevent either membrane mediated SARS-CoV-2 fusion, endocytosis-mediated viral entry, or both. The anti-SARS-CoV-2 fusion peptides may be administered to a subject in need thereof to inhibit or prevent SARS-CoV-2 cellular entry.

Described herein are diagnostic and control fusion protein reagents and methods for use thereof in simple rapid and inexpensive hemagglutinin assays for the detection of subject antibodies directed to the SARS-CoV-2 virus.