WO2002099130A3 - Virus detection using degenerate pcr primers - Google Patents

Virus detection using degenerate pcr primers Download PDF

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Publication number
WO2002099130A3
WO2002099130A3 PCT/GB2002/002642 GB0202642W WO02099130A3 WO 2002099130 A3 WO2002099130 A3 WO 2002099130A3 GB 0202642 W GB0202642 W GB 0202642W WO 02099130 A3 WO02099130 A3 WO 02099130A3
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WO
WIPO (PCT)
Prior art keywords
sequence
database
pcr primers
virus detection
family
Prior art date
Application number
PCT/GB2002/002642
Other languages
French (fr)
Other versions
WO2002099130A2 (en
Inventor
David John Griffiths
Paul Kellam
Robert Anthony Weiss
Original Assignee
Univ London
David John Griffiths
Paul Kellam
Robert Anthony Weiss
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Univ London, David John Griffiths, Paul Kellam, Robert Anthony Weiss filed Critical Univ London
Priority to AU2002345244A priority Critical patent/AU2002345244A1/en
Publication of WO2002099130A2 publication Critical patent/WO2002099130A2/en
Publication of WO2002099130A3 publication Critical patent/WO2002099130A3/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage

Abstract

A high throughput method for screening a biological sample for unknown viruses, which method comprises: (a) subjecting DNA from the sample to PCR amplication conditions using simultaneously multiple pairs of degenerate primers, wherein each primer binds a sequence that is conserved across members of a family of viruses and each pair of primers selectively directs amplication of sequence of said family; (b) sequencing PCR product obtained in step (a); and (c) comparing the sequence of the PCR product with the sequences in at least one database comprising viral sequences to determine whether the sequence is present in, or absent from, the database, wherein absence of the sequence from the database suggests that the sequence may be from an unknown virus.
PCT/GB2002/002642 2001-06-07 2002-06-07 Virus detection using degenerate pcr primers WO2002099130A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002345244A AU2002345244A1 (en) 2001-06-07 2002-06-07 Virus detection using degenerate pcr primers

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB0113907A GB0113907D0 (en) 2001-06-07 2001-06-07 Virus detection using degenerate PCR primers
GB0113907.0 2001-06-07

Publications (2)

Publication Number Publication Date
WO2002099130A2 WO2002099130A2 (en) 2002-12-12
WO2002099130A3 true WO2002099130A3 (en) 2003-09-04

Family

ID=9916127

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2002/002642 WO2002099130A2 (en) 2001-06-07 2002-06-07 Virus detection using degenerate pcr primers

Country Status (3)

Country Link
AU (1) AU2002345244A1 (en)
GB (1) GB0113907D0 (en)
WO (1) WO2002099130A2 (en)

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US7666588B2 (en) 2001-03-02 2010-02-23 Ibis Biosciences, Inc. Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy
US7226739B2 (en) 2001-03-02 2007-06-05 Isis Pharmaceuticals, Inc Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations
US20030027135A1 (en) 2001-03-02 2003-02-06 Ecker David J. Method for rapid detection and identification of bioagents
US20040121309A1 (en) 2002-12-06 2004-06-24 Ecker David J. Methods for rapid detection and identification of bioagents in blood, bodily fluids, and bodily tissues
US8073627B2 (en) 2001-06-26 2011-12-06 Ibis Biosciences, Inc. System for indentification of pathogens
US7217510B2 (en) 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
CA2508726A1 (en) 2002-12-06 2004-07-22 Isis Pharmaceuticals, Inc. Methods for rapid identification of pathogens in humans and animals
US8057993B2 (en) 2003-04-26 2011-11-15 Ibis Biosciences, Inc. Methods for identification of coronaviruses
US7964343B2 (en) 2003-05-13 2011-06-21 Ibis Biosciences, Inc. Method for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US8158354B2 (en) 2003-05-13 2012-04-17 Ibis Biosciences, Inc. Methods for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US8546082B2 (en) 2003-09-11 2013-10-01 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US8097416B2 (en) 2003-09-11 2012-01-17 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US7956175B2 (en) 2003-09-11 2011-06-07 Ibis Biosciences, Inc. Compositions for use in identification of bacteria
US7666592B2 (en) 2004-02-18 2010-02-23 Ibis Biosciences, Inc. Methods for concurrent identification and quantification of an unknown bioagent
WO2005117270A2 (en) 2004-05-24 2005-12-08 Isis Pharmaceuticals, Inc. Mass spectrometry with selective ion filtration by digital thresholding
US20050266411A1 (en) 2004-05-25 2005-12-01 Hofstadler Steven A Methods for rapid forensic analysis of mitochondrial DNA
US7811753B2 (en) 2004-07-14 2010-10-12 Ibis Biosciences, Inc. Methods for repairing degraded DNA
WO2006135400A2 (en) 2004-08-24 2006-12-21 Isis Pharmaceuticals, Inc. Methods for rapid identification of recombinant organisms
US8084207B2 (en) 2005-03-03 2011-12-27 Ibis Bioscience, Inc. Compositions for use in identification of papillomavirus
WO2006094238A2 (en) * 2005-03-03 2006-09-08 Isis Pharmaceuticals, Inc. Compositions for use in identification of adventitious viruses
CA2616281C (en) 2005-07-21 2014-04-22 Isis Pharmaceuticals, Inc. Methods for rapid identification and quantitation of mitochondrial dna variants
WO2007100397A2 (en) * 2005-11-28 2007-09-07 Isis Pharmaceuticals, Inc. Compositions for use in identification of adventitious contaminant viruses
AU2007353877B2 (en) 2006-09-14 2012-07-19 Ibis Biosciences, Inc. Targeted whole genome amplification method for identification of pathogens
WO2008104002A2 (en) 2007-02-23 2008-08-28 Ibis Biosciences, Inc. Methods for rapid forensic dna analysis
US9598724B2 (en) 2007-06-01 2017-03-21 Ibis Biosciences, Inc. Methods and compositions for multiple displacement amplification of nucleic acids
US9434997B2 (en) 2007-08-24 2016-09-06 Lawrence Livermore National Security, Llc Methods, compounds and systems for detecting a microorganism in a sample
US8534447B2 (en) 2008-09-16 2013-09-17 Ibis Biosciences, Inc. Microplate handling systems and related computer program products and methods
US8148163B2 (en) 2008-09-16 2012-04-03 Ibis Biosciences, Inc. Sample processing units, systems, and related methods
WO2010033599A2 (en) 2008-09-16 2010-03-25 Ibis Biosciences, Inc. Mixing cartridges, mixing stations, and related kits, systems, and methods
EP2396803A4 (en) 2009-02-12 2016-10-26 Ibis Biosciences Inc Ionization probe assemblies
EP2454000A4 (en) 2009-07-17 2016-08-10 Ibis Biosciences Inc Systems for bioagent identification
US8950604B2 (en) 2009-07-17 2015-02-10 Ibis Biosciences, Inc. Lift and mount apparatus
EP2957641B1 (en) 2009-10-15 2017-05-17 Ibis Biosciences, Inc. Multiple displacement amplification
JP2017535270A (en) * 2014-11-21 2017-11-30 ナントミクス，エルエルシー System and method for identification and differentiation of viral infections

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Patent Citations (4)

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US5478724A (en) * 1991-08-16 1995-12-26 The Rockefeller University Lentivirus-specific nucleotide probes and methods of use
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WO2002099129A2 (en) * 2001-06-07 2002-12-12 University College London Designing degenerate pcr primers

Non-Patent Citations (3)

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Title
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Also Published As

Publication number Publication date
AU2002345244A1 (en) 2002-12-16
WO2002099130A2 (en) 2002-12-12
GB0113907D0 (en) 2001-08-01

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