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US5176995A Expired / Lapsed US ⏱️ 0.0 years remaining

Detection of viruses by amplification and hybridization

Assignee: Roche Molecular Systems Inc
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Filing: 1989-08-15
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Granted: 1993-01-05
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Expires: 2009-08-15
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Abstract

Abstract The presence or absence of a nucleic acid sequence associated with one or more related viruses in a sample containing one or more nucleic acids and suspected of containing such sequence can be detected by amplifying the sequence using primers to form extension products as templates and detecting the amplified product if it is present. This may be accomplished by adding a labeled hybridization probe to the amplified product either free in solution or after immobilization on a solid support. Preferably the virus constitutes AIDs viruses and hepadnaviruses.

Inventors

  • 👤 John J. Sninsky
  • 👤 Shirley Y. Kwok
  • 👤 David H. Mack
  • 👤 Henry A. Ehrlich
  • 👤 Kary B. Mullis

Bibliographic Details

Application Number —
Jurisdiction US
Data Source google_patents
Last Synchronized 2026-11-04 04:42
CPC Classifications
B; B01; B01L; B01L7/00; B01L7/52; C; C07; C07K; C07K14/00; C07K14/795; C07K14/805; C12; C12N; C12N15/00; C12N15/09; C12N15/10; C12Q; C12Q1/00; C12Q1/68; C12Q1/6813; C12Q1/6816; C12Q1/6823; C12Q1/6844; C12Q1/6853; C12Q1/686; C12Q1/6865; C12Q1/6876; C12Q1/6881; C12Q1/6883; C12Q1/70; C12Q1/701; C12Q1/702; C12Q1/703; C12Q1/706; B01J; B01J2219/00; B01J2219/00274; B01J2219/00277; B01J2219/00495; B01J2219/00583; B01J2219/0059; B01J2219/00718; B01J2219/0072; B01J2219/00722; C40; C40B; C40B40/00; C40B40/04; C40B40/06; C40B60/00; C40B60/14; Y; Y10; Y10S; Y10S435/00; Y10S435/81; Y10S436/00; Y10S436/811

Claims Analysis

Total Claims: 42
Claim 1
Independent Claim 242 words
A process for detecting or monitoring a virus nucleic acid which nucleic acid sequence is specific to nucleic acids in isolates of said virus or related isolates and which nucleic acid sequence is suspected of being contained in a sample, which process comprises: (a) treating the sample with two oligonucleotide primers, four different nucleoside triphosphates, and an agent for polymerization, under hybridizing conditions, which primers are sufficiently complementary to nucleic acid sequences of said virus or related virus isolates to hybridize therewith, such that for each strand of the viral nucleic acid sequence an extension product of each primer is synthesized which is substantially complementary to a strand of the virus nucleic acid sequence being detected or monitored, such that the extension product synthesized for each primer, when separated from its complement, can serve as a template for synthesis of the extension product of the other primer; (b) treating the sample under denaturing conditions to separate the primer extension products from their templates; (c) treating the product of step (b) with oligonucleotide primers such that a primer extension product is synthesized using each of the single strands produced in step (b) as a template, resulting in amplification of the sequence specific to the nucleic acids in the viruses; (d) repeating step (b) and (c) to synthesize detectable amounts of said viral nucleic acid sequence if present in said sample providing an amplified nucleic acid sequence; and (e) determining if amplification has occurred.
Claim 2
Dependent Claim 242 words
A process for detecting or monitoring a virus nucleic acid which nucleic acid sequence is specific to nucleic acids in isolates of said virus or related isolates and which nucleic acid sequence is suspected of being contained in a sample, which process comprises: (a) treating the sample with two oligonucleotide primers, four different nucleoside triphosphates, and an agent for polymerization, under hybridizing conditions, which primers are sufficiently complementary to nucleic acid sequences of said virus or related virus isolates to hybridize therewith, such that for each strand of the viral nucleic acid sequence an extension product of each primer is synthesized which is substantially complementary to a strand of the virus nucleic acid sequence being detected or monitored, such that the extension product synthesized for each primer, when separated from its complement, can serve as a template for synthesis of the extension product of the other primer; (b) treating the sample under denaturing conditions to separate the primer extension products from their templates; (c) treating the product of step (b) with oligonucleotide primers such that a primer extension product is synthesized using each of the single strands produced in step (b) as a template, resulting in amplification of the sequence specific to the nucleic acids in the viruses; (d) repeating step (b) and (c) to synthesize detectable amounts of said viral nucleic acid sequence if present in said sample providing an amplified nucleic acid sequence; and (e) determining if amplification has occurred.
Claim 3
Dependent Claim 27 words
The process of claim 1, wherein said sample is selected from the group consisting of blood, semen, mononuclear cells, semen supernatant, chorionic villi, and amniotic cell samples.
Claim 4
Dependent Claim 43 words
The process of claim 1, wherein said sample is from a human individual having at least one characteristic, with respect to viral infection, selected from the group of characteristics consisting of culture positive, culture negative, asymptomatic, symptomatic, antibody positive and antibody negative characteristics.
Claim 5
Dependent Claim 38 words
The process of claim 1, wherein said nucleic acid is selected from the group consisting of double-stranded and single-stranded nucleic acids, and wherein if it is double-stranded, the strands are separated by denaturing before or during step (a).
Claim 6
Dependent Claim 18 words
The process of claim 1, wherein at least one strand of said nucleic acid is DNA or RNA.
Claim 7
Dependent Claim 25 words
The process of claim 1, wherein said agent of polymerization is a DNA polymerase, said nucleic acid sequence is DNA, and said primers are oligodeoxyribonucleotides.
Claim 8
Dependent Claim 39 words
The process of claim 1, wherein said primers comprise a nucleic acid sequence which sequence is sufficiently complementary to the viral nucleic acid sequence to hybridize therewith and which complementary nucleic acid sequence is greater than six nucleotides long.
Claim 9
Dependent Claim 14 words
The process of claim 1, wherein said virus constitutes a hepadnavirus or a herpesvirus.
Claim 10
Dependent Claim 12 words
The process of claim 8, wherein said virus is hepatitis B virus.
Claim 11
Dependent Claim 44 words
The process of claim 8, wherein said virus is a hepadnavirus and said primers comprise a nucleic acid sequence sufficiently complementary to a nucleotide sequence contained with a region selected from the pol and the env regions of the hepadnavirus genome to hybridize therewith.
Claim 12
Dependent Claim 19 words
The process of claim 1, wherein said amplified sequence comprises a nucleic acid sequence greater than six nucleotides long.
Claim 13
Dependent Claim 46 words
The process of claim 1, wherein step (e) comprises the steps of: (1) adding to the product of step (d) a probe capable of hybridizing with the amplified nucleic acid sequence; and (2) determining whether the probe has hybridized to an amplified sequence in the sample.
Claim 14
Dependent Claim 29 words
The process of claim 1, wherein said primers are present at an initial concentration such that the ratio of primer:viral nucleic acid sequence is at least 10 8 :1.
Claim 15
Dependent Claim 21 words
The process of claim 2, wherein in step (a) said sample is treated without first culturing the virus in the sample.
Claim 16
Dependent Claim 29 words
The process of claim 4 wherein said nucleic acid is single-stranded RNA and said single-stranded RNA is reverse transcribed to a single stranded DNA template prior to step (a).
Claim 17
Dependent Claim 23 words
The process of claim 9, wherein at least one primer is selected from the group consisting of MD03, MD06, MD13, and MD14 primers.
Claim 18
Dependent Claim 33 words
The process of claim 12, wherein said hybridized probe is detected by means of a labelled oligonucleotide, wherein the label is selected from the group consisting of biotin, enzyme, fluorescent, and radioactive labels.
Claim 19
Dependent Claim 31 words
The process of claim 12, wherein step (1) comprises the steps of: (1) spotting the product of step (d) on a membrane; and (2) adding the probe to the spotted membrane.
Claim 20
Dependent Claim 31 words
The process of claim 12, wherein step (1) comprises the steps of: (1) spotting the probe on a membrane; and (2) adding the product of step (d) to the spotted membrane.
Claim 21
Dependent Claim 52 words
The process of claim 12, wherein step (2) comprises the steps of: (1) digesting the hybridized mixture from step (1) with a restriction enzyme recognizing a site within the probe; and (2) detecting whether the restriction digest contains a restriction fragment correlated with the presence of the virus sequence to be detected.
Claim 22
Dependent Claim 10 words
The process of claim 12, wherein said virus is latent.
Claim 23
Dependent Claim 46 words
The process of claim 20, wherein a positive control containing one or more nucleic acids with a sequence of the virus to be detected and/or a negative control which does not contain any nucleic acid(s) containing a sequence from the virus to be detected is utilized.
Claim 24
Dependent Claim 139 words
A kit for detecting or monitoring a viral nucleic acid sequence, which nucleic acid sequence is suspected of being contained in a sample, which nucleic acid sequence is specific to the nucleic acids in isolates of said virus or related isolates, said kit comprising: (a) two oligonucleotide primers at least one of the primers greater than six nucleotides and being selected to be sufficiently complementary to the viral nucleic acid sequence to hybridize therewith, such that an extension product synthesized from each primer is substantially complementary to a strand of the nucleic acid sequence being detected, such that the extension product synthesized from each primer, when separated from its complement, can serve as a template for the synthesis of the extension product of the other primer, and (b) a probe capable of hybridizing with the amplified nucleic acid sequence.
Claim 25
Dependent Claim 139 words
A kit for detecting or monitoring a viral nucleic acid sequence, which nucleic acid sequence is suspected of being contained in a sample, which nucleic acid sequence is specific to the nucleic acids in isolates of said virus or related isolates, said kit comprising: (a) two oligonucleotide primers at least one of the primers greater than six nucleotides and being selected to be sufficiently complementary to the viral nucleic acid sequence to hybridize therewith, such that an extension product synthesized from each primer is substantially complementary to a strand of the nucleic acid sequence being detected, such that the extension product synthesized from each primer, when separated from its complement, can serve as a template for the synthesis of the extension product of the other primer, and (b) a probe capable of hybridizing with the amplified nucleic acid sequence.
Claim 26
Dependent Claim 74 words
A kit according to claim 23 further comprising at least one component selected from the group consisting of a positive control containing one or more nucleic acids with a sequence of the virus to be detected, a negative control which does not contain any nucleic acid(s) containing a sequence from among the viruses to be detected or monitored, and a restriction enzyme capable of cleaving a nucleic acid containing said virus nucleic acid(s) sequence.
Claim 27
Dependent Claim 18 words
The kit of claim 23, further comprising an agent for polymerization, and each of four different nucleoside triphosphates.
Claim 28
Dependent Claim 38 words
The kit of claim 25, wherein said agent for polymerization is an enzyme selected from the group consisting of E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase, reverse transcriptase, or a thermostable DNA polymerase.
Claim 29
Dependent Claim 28 words
The kit of claim 25, wherein said nucleic acid sequence is a DNA sequence, said primers are oligodeoxyribonucleotides, and said nucleoside triphosphates are dATP, dCTP, dGTP and TTP.
Claim 30
Dependent Claim 50 words
A kit according to claim 23, wherein said primers comprise a nucleic acid sequence which sequence is sufficiently complementary to the viral nucleic acid sequence to hybridize therewith and act as a point of initiation of synthesis in an amplification reaction, wherein said primers are greater than six nucleotides long.
Claim 31
Dependent Claim 20 words
A kit according to claim 28, wherein said virus is selected from the group consisting of hepadnaviruses and herpes viruses.
Claim 32
Dependent Claim 13 words
A kit according to claim 29, wherein said hepadnavirus is hepatitis B virus.
Claim 33
Dependent Claim 36 words
A kit according to claim 29, wherein said virus is a hepadnavirus, and said primers are sufficiently complementary to a region of the hepadnavirus genome selected from the group consisting of the env and pol regions.
Claim 34
Dependent Claim 17 words
A kit according to claim 28, wherein the primers are between 15 and 25 nucleotides in length.
Claim 35
Dependent Claim 32 words
A kit according to claim 23, wherein said probe comprises a nucleic acid sequence capable of hybridizing to a viral nucleic acid sequence amplified in a polymerase chain reaction by said primers.
Claim 36
Dependent Claim 33 words
A kit according to claim 33, wherein said probe is capable of hybridizing with a nucleic acid sequence obtained with a region selected from the env and pol regions of a hepadnavirus genome.
Claim 37
Dependent Claim 26 words
A kit according to claim 33, wherein said probe is capable of hybridizing to a nucleic acid sequence within the genome of a hepatitis B virus.
Claim 38
Dependent Claim 24 words
A kit according to claim 23, wherein said probe comprises a label selected from the group consisting of biotin, enzyme, fluorescent and radioactive labels.
Claim 39
Dependent Claim 50 words
A kit for detecting or monitoring a hepadnavirus nucleic acid sequence, which nucleic acid sequence is specific to the nucleic acids in hepadnaviruses, said kit comprising: (a) two oligonucleotide primers, wherein the primers are: 5'-CTCAAGCTTCATCATCCATATA-3' and 5'-CTTGGATCCTATGGGAGTGG-3'; and (b) a probe comprising the sequence; 5'-GGCCTCAGTCCGTTTCTCTTGGCTCAGTTTACTAGTGCCATTTGTTC-3' or a sequence complementary thereto.
Claim 40
Dependent Claim 50 words
A kit for detecting or monitoring a hepadnavirus nucleic acid sequence, which nucleic acid sequence is specific to the nucleic acids in hepadnaviruses, said kit comprising: (a) two oligonucleotide primers, wherein the primers are: 5'-CTCAAGCTTCATCATCCATATA-3' and 5'-CTTGGATCCTATGGGAGTGG-3'; and (b) a probe comprising the sequence; 5'-GGCCTCAGTCCGTTTCTCTTGGCTCAGTTTACTAGTGCCATTTGTTC-3' or a sequence complementary thereto.
Claim 41
Dependent Claim 50 words
A kit for detecting or monitoring a hepadnavirus nucleic acid sequence, which nucleic acid sequence is specific to the nucleic acids of hepadnaviruses, said kit comprising: (a) two oligonucleotide primers, wherein the primers are 5'-GCGGGATCCCATCTTCTTATTGGTTCTTCTGG-3' and 5'-GCGAAGCTTGTTAGGGTTTAAATGTATACCC-3'; and (b) a probe comprising the sequence: 5'-GGCCTCAGTCCGTTTCTCTTGGCTCAGTTTACTAGTGCCATTTGTTC-3' or a sequence complementary thereto.
Claim 42
Dependent Claim 50 words
A kit for detecting or monitoring a hepadnavirus nucleic acid sequence, which nucleic acid sequence is specific to the nucleic acids of hepadnaviruses, said kit comprising: (a) two oligonucleotide primers, wherein the primers are 5'-GCGGGATCCCATCTTCTTATTGGTTCTTCTGG-3' and 5'-GCGAAGCTTGTTAGGGTTTAAATGTATACCC-3'; and (b) a probe comprising the sequence: 5'-GGCCTCAGTCCGTTTCTCTTGGCTCAGTTTACTAGTGCCATTTGTTC-3' or a sequence complementary thereto.

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Annuity Stage Window Opens Payment Deadline Surcharge Period Until Estimated Fee Status
3.5 Years (Year 4) 1996-01-05 1996-07-06 1997-01-05 $2000.00 Window Closed / Lapsed
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