Search

EP-4147249-B1 - PATHOGEN TESTING

EP4147249B1EP 4147249 B1EP4147249 B1EP 4147249B1EP-4147249-B1

Inventors

  • SPURBECK, Rachel R.
  • JOHNSON, CHRISTOPHER
  • LILLY, Jacob
  • SCHUETTER, Jared M.
  • WILSON, Patrick H.

Dates

Publication Date
20260506
Application Date
20210506

Claims (9)

  1. A process for using waste water to determine infection of a region, the process comprising: receiving a sample of waste water, wherein the sample includes location information; performing diagnostics on the sample of waste water to determine viral load information associated with the sample; conveying the viral load information over a map associated with the region by: generating a first layer associated with the viral load information; generating a second layer associated with census information; and displaying the first layer and the second layer independently of each other on a layer associated with a map of the region; and identifying high areas of risk for a potential outbreak based on the viral load of the samples and the census information.
  2. The process of claim 1, wherein performing diagnostics on the sample of waste water to determine viral load information associated with the sample further comprises accounting for a dilution of the sample.
  3. The process of claim 1, wherein performing diagnostics on the sample of waste water to determine viral load information associated with the sample further comprises accounting for a time that has passed since stool in the sample has been excreted.
  4. The process of claim 1, wherein performing diagnostics on the sample of waste water to determine viral load information associated with the sample comprises: performing real-time Polymerase chain reaction; and performing targeted sequencing based on a genome of a virus associated with the viral load.
  5. The process of claim 1, wherein conveying the viral load information over a map associated with the region comprises: generating a layer of the viral load information; and displaying the layer of the viral load information on a layer associated with the map.
  6. The process of claim 1 further comprising: determining a risk based on the viral load information; and displaying the risk.
  7. The process of claim 1 further comprising: obtaining demographic information about confirmed cases associated with the viral load; identifying gaps in testing based on a reconciliation between the demographic information and the viral load information; and communicating the gaps in testing to a user.
  8. The process of claim 7, wherein identifying gaps in testing based on a reconciliation between the demographic information and the viral load information further comprises: determining a location-based model based on sampling information from that location, demographics, and infection rate; determining a predicted infection rate for the location by inverting the location-based model; and comparing the predicted infection rate to the demographic information about confirmed cases associated with the viral load.
  9. The process of claim 1, wherein performing diagnostics on the sample of waste water to determine viral load information associated with the sample further comprises using real-time polymerase chain reaction diagnostics performed on the sample as a gate keeper to pass the sample onto targeted sequencing diagnostics.

Description

TECHNICAL FIELD Various aspects of the present disclosure relate generally to diagnostics and in particular, to diagnostics that can be used for pathogen testing. The monitoring of particulate matter has received an increasing amount of attention in recent years because of the potential impact of particulates on human health. As an illustration, it may be desirable to detect the presence of particulates such as naturally occurring or artificially produced pathogens, allergens, bacteria, viruses, fungi biological or chemical agents, etc., on persons, or in an particular environments, including for example, in water supplies. PARKAS KATA ET AL: "Seasonal and spatial dynamics of enteric viruses in wastewater and in riverine and estuarine receiving waters", SCIENCE OF THE TOTAL ENVIRONMENT , vol. 634 1 September 2018 (2018-09-01), pages 1174-1183, XP055825973, AMSTERDAM, NL ISSN: 0048-9697, DOI: 10.1016/j.scitotenv.2018.04.038 relates to detection and determination of decay of enteric viruses in wastewater. Brouwer Andrew F. ET AL: "Epidemiology of the silent polio outbreak in Rahat, Israel, based on modeling of environmental surveillance data | PNAS", , 18 October 2018 (2018-10-18), pages 1-29, XP055825972, relates to a modeling framework for environmentally mediated infectious disease. Biobot Analytics: "Testing for COVID-19 beyond the clinic: using wastewater epidemiology to proactively detect outbreaks | by Biobot Analytics | Medium", , 13 March 2020 (2020-03-13), pages 1-6, XP055825963, relates to the detection of viral outbreaks by monitoring wastewater. Anonymous: "Covid19 sewage - Press Office - Newcastle University", , 23 April 2020 (2020-04-23), pages 1-3, XP055825959, relates to the estimation of virus concentrations based on the monitoring of sewage. Thomas Macaulay: "Startup will map the coronavirus spread by looking at poo", , 20 March 2020 (2020-03-20), pages 1-4, XP055825962, relates to the mapping of a pandemic by analyzing data from sewage samples. DISCLOSURE OF INVENTION According to aspects of the present disclosure, a point of care device, comprises a chamber configured to contain a swab, a buffer delivery system that introduces a buffer into the chamber, a source to lyse cells collected onto the swab placed in the chamber, and a probe delivery system that introduces a probe into the chamber. In some embodiments, the point of care device can directly output a test result, e.g., via output to a portable electronic device such as a smartphone or via other approach. According to further embodiments, a process for using waste water to determine infection of a region is disclosed. The process comprises receiving a sample of waste water. The sample is associated with location information of where the sample was taken. Diagnostics are then performed on the sample to determine viral load information associated with the sample. Further, a risk assessment is determined based on the viral load information and the location information. The viral load information and the risk assessment is displayed in conjunction with a map of the region. According to yet further embodiments, a process for generating a database to identify pathogens is provided. The process comprises generating a database that includes reference sequences of pathogens found in the human biome, non-pathogens found in the human microbiome, and subsets of genes known to be virulence factors, antibiotic resistance genes, genes encoding unique structural features, or host response factors. Identified regions within the sequences are used to identify a pathogen in broad characteristics, and an incomplete sequence associated with a pathogen not associated a complete reference sequence in the database is added to the database. Further, the incomplete sequence is based on the broad characteristics. BRIEF DESCRIPTION OF DRAWINGS FIG. 1 is a schematic illustration of an assay cartridge, process workflow, cartridge reading, and other capabilities of a digital droplet point of care device, according to various aspects of the present disclosure;FIG. 2 is an example of a swab device, according to various aspects of the present disclosure;FIG. 3 illustrates an example extraction and droplet making module for use with the assay cartridge of FIG. 1, according to various aspects of the present disclosure;FIG. 4 is an example illustration of a digital PCR output, according to various aspects of the present disclosure;FIG. 5 illustrates an example diagnostics and therapy pipeline;FIG. 6 is a diagram illustrating a database to identify pathogens, according to various aspects of the present disclosure;FIG. 7 is a diagram illustrating a process for comparing virus risk models, according to various aspects of the present disclosure;FIG. 8 is a flow chart illustrating a process for using wastewater to determine infection of a region, according to aspects of the present disclosure;FIG. 9 is an example dashboard for a bioanalysis tool via wastewater analysis, acc