Probe sets capable of detecting pathogen nucleic acids in a sample are described. The probe set can be provided on a solid support, such as a microarray. Methods of detecting pathogen nucleic acids in a sample using the probe set are also provided. In some examples, the probes and methods are capable of detecting one or more RNA viruses, one or more DNA viruses, one or more bacterial nucleic acids, and/or one or more protozoan nucleic acids in a sample.

Methods of concentrating RNA from wastewater and quantifying the RNA by digital amplification are provided.

Disclosed herein are methods of detecting viral nucleic acids in a sample that include contacting the sample with one or more sets of loop-mediated isothermal amplification (LAMP) primers specific for a viral nucleic acid of interest (such as hepatitis B virus, hepatitis C virus, hepatitis E virus, human immunodeficiency virus, West Nile virus, or Dengue virus nucleic acids) under conditions sufficient to produce an amplification product and detecting the amplification product(s). In some examples, the amplification product is detected by gel electrophoresis, while in other examples, the amplification product is detected by detecting signal from a label included in one or more of the LAMP primers. Primers and kits for use for detection of viral nucleic acids by LAMP are also disclosed herein.

FRET-based analytes detection and related methods and systems are described where a pair of FRET labeled primers and/or oligonucleotides are used that are specific for target sequences located at a distance up to four time the Förster distance of the FRET chromophores presented on the FRET labeled primers and/or oligonucleotides one with respect to the other in one or more polynucleotide analyte; in particular the pair of FRET labeled primers and/or oligonucleotides is combined with a sample and subjected to one or more polynucleotide amplification reactions before measuring FRET signals from at least one FRET chromophore.

Methods and uses for molecular tags are disclosed. Molecular tags may be attached to nucleic acid molecules. The attachment of the nucleic acid molecules prior to PCR amplification and sequencing improves the accuracy of genetic analysis and detection of genetic variations and diversity. Molecular tags may also be used for detection of drug-resistant variants. Methods for using molecular tags for determining and correcting PCR errors and/or sequencing error are also disclosed.

The present disclosure relates to methods using CRISPR-Cas13a enzyme, complexed with HIV or HCV crRNAs to specifically and sensitively detect and quantify the presence of HIV or HCV RNA in a sample. These methods can be used to diagnose HIV or HCV infection, quantify the concentration of HIV or HCV RNA present in a sample, identify the presence of different HIV or HCV splice variants, subtypes, or mutations, and to monitor reactivation of HIV or HCV transcription.

Embodiments disclosed herein provide a pan-tissue cell atlas of healthy and diseased subjects obtained by single cell sequencing. The present invention discloses novel markers for cell types. Moreover, genes associated with disease, including HIV infection and tuberculosis are identified. The invention provides for diagnostic assays based on gene markers and cell composition, as well as therapeutic targets for controlling immune regulations and cell-cell communication of the cell types disclosed herein. In addition, novel cell types and methods of quantitating, detecting and isolating the cell types are disclosed.

Methods, systems, and kits described herein are for detecting and sequencing nucleic acids (e.g., RNA) in a wide range of samples such as samples with low concentrations of nucleic acid, samples with degraded nucleic acid, samples that would not otherwise be amenable to conventional sequencing or RNA detection methods, poor quality samples, high quality samples in which rare mutations are sought, formalin-fixed paraffin-embedded samples, blood samples, etc. The methods of the present invention may use paired, large panels of primers to amplify many short fragments that overlap between but not within each panel. Each panel's amplicon set may fill the gaps between those of the opposing panel, thereby providing complete gene or genomic coverage. A preliminary, multiplex amplification step amplifies target nucleic acid for all downstream reactions such as Sanger sequencing, cloning, and NGS.

The invention provides a method for determining whether a human immunodeficiency virus is resistant to a viral entry inhibitor. The methods are particularly useful for determining resistance to inhibitors that act by a non-competitive mechanism. In certain aspects, the methods comprise determining whether an HIV population is resistant to an HIV entry inhibitor, comprising determining a log-sigmoid inhibition curve comprising data points for entry of the HIV population in the presence of varying concentrations of the HIV entry inhibitor, wherein if the entry of the HIV population cannot be completely inhibited by the HIV entry inhibitor, the HIV population is resistant to the HIV entry inhibitor.

A non-transitory computer-readable storage medium storing executable instructions to cause a system to detect a genetic variation in a polynucleotide analyte in a sample. A fluorophore is attached to a first primer, a quencher is attached to a second primer, and the first primer and the second primer are specific for the polynucleotide analyte. The primers are configured to amplify the polynucleotide analyte having the genetic variation and a corresponding polynucleotide analyte lacking the generic variation. There is a detectable difference between a measured change in signal generated by the fluorophore and quencher, when using the first and second primers to amplify the polynucleotide analyte with the genetic variation, and a change in signal generated by the fluorophore and quencher, when using the first and second primers to amplify the corresponding polynucleotide analyte lacking the genetic variation.