Systems and processes for distinguishing pathogenic and non-pathogenic sequences from specimens
Inventors
AMINI, Sasan • Khaksar, Ramin • Taylor, Michael • Krishnan, Prasanna Thwar • Tran, David • Zhang, Shaokang • Shokralla, Shadi • Rhoden, Kyle • Lee, Susan Jisoon • Barney, Bryan Thomas • Mortazavi, Sima • Allred, Adam Forrest • Gehrmann, Henrik
Assignees
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Publication Number
US-12305231-B2
Publication Date
2025-05-20
Expiration Date
Abstract
Provided herein are fully-automated next-generation sequencing platforms and processes for detection of a target specimen (e.g., SARS-CoV-2) and for distinguishing infectious from non-infectious signals from the specimen. An analysis can provide simultaneous diagnosis and genomic surveillance of a multitude of distinct specimens in a sample information. The analysis can comprise distinguishing between infectious versus infectious specimens and provide a recommendation as to how infectious the sample can be. The information on can be used to better inform the status of a subject or a location with regards to infectivity from the specimen.
Core Innovation
The invention relates to a process for tracking an infectious disease in a population by geotagging. The process receives a sample comprising a plurality of nucleic acids and adds a geotag by providing geographic position information of the sample to a server so that the server creates a location based geotag based on the geographic position information. The server receives sequencing digital data and associates the geographic position information with the sequencing digital data to enable tracking of infectious disease.
The invention further prepares the sample for analysis by synthesizing a nucleic acid library from one or more nucleic acids from a target microorganism in the plurality of nucleic acids. The process performs a nucleic acid amplification reaction to generate amplicons from the nucleic acid library and then sequences the amplicons. Infectiousness is determined by sequencing amplicons of a length greater than 500 base pairs from two or more different regions of a genome of the target microorganism, while non-infectiousness is determined when such amplicons from two or more different regions are not detected.
The invention creates sequencing digital data having one or more nucleic acid digital sequences based on the infectiousness determination and transmits the sequences to the server. The server associates the geographic position information of the sample with the sequencing digital data transmitted to the server, and tracking of the infectious disease is performed by associating the one or more nucleic acid sequences derived from the microorganism with the geographic position information of the sample.
Claims Coverage
The document provides one independent claim directed to geotag-based tracking of infectious disease using long-amplicon multiplex sequencing-based infectious versus non-infectious determination. The coverage includes the independent claim’s full pipeline and additional dependent-claim refinements that specify sample sources, sequencing through a transmembrane pore, amplicon-length-related measurements, example amplicon length constraints, UI/reporting-related narrowing, delivery of reports for contact tracing, and illustrative target pathogen selections.
Geotagging-based infectious disease tracking with server association
Receiving a sample comprising a plurality of nucleic acids, adding a geotag by providing geographic position information of the sample to a server, transmitting sequencing digital data to the server, associating the geographic position information with the sequencing digital data, and tracking the infectious disease by associating nucleic acid sequences derived from the microorganism with the geographic position information of the sample.
Long-amplicon multiplex genomic detection to determine infectious versus non-infectious
Preparing a nucleic acid library from one or more nucleic acids of a target microorganism, performing a nucleic acid amplification reaction to generate amplicons, sequencing the amplicons, determining the target microorganism to be infectious when amplicons of a length greater than 500 base pairs from two or more different regions of a genome are detected, and determining the sample to be non-infectious when such amplicons from two or more different regions are not detected.
Overall, the independent claim combines geotagging and server-based association of sequencing digital data with geographic position and infectious versus non-infectious determination based on sequencing multiplex-amplified genomic regions using a length greater than 500 base pairs criterion from two or more different genome regions.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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