US20060223057A1 - Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 - Google Patents
Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 Download PDFInfo
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- US20060223057A1 US20060223057A1 US11/372,586 US37258606A US2006223057A1 US 20060223057 A1 US20060223057 A1 US 20060223057A1 US 37258606 A US37258606 A US 37258606A US 2006223057 A1 US2006223057 A1 US 2006223057A1
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Definitions
- the present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immunodeficiency Virus (HIV).
- HIV Human Immunodeficiency Virus
- nucleic acid hybridization is based on the ability of two strands of nucleic acid containing complementary sequences to anneal to each other under the appropriate conditions, thus forming a double stranded structure.
- the complementary strand is labeled, the label can be detected and is indicative for the presence of the target sequence.
- these methods have become an important tool in viral diagnosis, in particular for the detection of human immunodeficiency virus (HIV).
- Nucleic acid amplification techniques are especially useful as an additional technique in cases where serological methods give doubtful results or in cases where there may be a considerable time period between infection and the development of antibodies to the virus. With HIV, seroconversion usually can occur some 36 months after exposure to the virus. Thus, whereas no antibodies will be detected with conventional immunoassays, proviral DNA or circulating viral RNA may already be detectable. Also in monitoring antiviral therapy, methods based on nucleic acid amplification have several advantages over serological methods. Especially quantitative amplification methods provide a powerful tool in assessing the changes in the amount of virus present before and during therapy.
- the choice of the oligonucleotides to be used as primers and probes in the amplification and detection of nucleic acid sequences is critical for the sensitivity and specificity of the assay.
- the sequence to be amplified is usually only present in a sample (for example a blood sample obtained from a patient suspected of having a viral infection) in minute amounts.
- the primers should be sufficiently complementary to the target sequence to allow efficient amplification of the viral nucleic acid present in the sample. If the primers do not anneal properly (due to mispairing of the bases on the nucleotides in both strands) to the target sequence, amplification is seriously hampered. This will affect the sensitivity of the assay and may result in false negative test results.
- the HIV virus shows a high heterogeneity. Genetic variability has been demonstrated amongst isolates from different continents but also between individuals and between different stages of the disease. Based on sequence analysis two groups within HIV-1 have been identified: group M (M for “major”), and group O (O for “outlier”). Within group M subtypes (A-H), each constituting a phylogenetic separate set of sequences, have been assigned and additional ones are being identified. This sequence variation is not uniformly distributed throughout the genome.
- the HIV-1 genome like all retroviral genomes, roughly consists of the following regions:
- the gag gene of the HIV-1 genome is the region encoding the core proteins of the virus (for example, p24).
- the env gene encodes a large precursor protein, gp160, which is processed into the envelop proteins gp120 and gp41.
- the pol gene encodes the polymerase of the virus (reverse transcriptase).
- the Long Terminal Repeat regions (LTRs) are the regions on the viral genome that participate in the integration of the virus with the host cell and in the regulation of transcription of the viral genes. Some regions are more prone to sequence variation than others. Especially in the env domain sequence variation can be as high as 30% between members of the different subtypes.
- primer selection should be based on knowledge of interstrain variability in candidate primer sequences and the consequences of mismatching at primer sites.
- McCutchan et al J. AIDS, 4, 1241-1250, 1991, used PCR to make a genetic comparison of different HIV-1 isolates.
- anchored PCR varying sense primers were used with a constant antisense primer. primers were chosen from relatively conserved regions in gag, env and LTR, the effect of primer mispairing on the amount of PCR product obtained was also investigated. Mispairing at the 3′ end of the primer decreased the amount of product sometimes more then 100-fold.
- the primers used for amplification were derived from the gag gene and the LTR region.
- the patients tested in this study were all from neighbouring areas, which makes it likely that they represent only a limited number of different viral strains.
- nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid.
- the oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained.
- the benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity. So far no primer pairs or hybridization probes have been developed that would allow the detection of such a broad range of HIV-1 variants.
- oligonucleotide sequences according to the present invention are especially useful in methods for the amplification of nucleic acid.
- PCR polymerase chain reaction
- the strands of the double stranded DNA are separated from each other by thermal denaturation and each strand serves as a template for primer annealing and subsequent elongation in a following cycle.
- the PCR method has been described in Saiki et al., Science 230, 135, 1985 and in European Patents no. EP 200362 and EP 201184.
- TAS transcription based amplification system
- TAS transcription based amplification system
- Transcription based amplification techniques usually comprise treating target nucleic acid with two oligonucleotides one of which comprises a promoter sequence, to generate a template including a functional promoter. Multiple copies of RNA are transcribed from said template and can serve as a basis for further amplification.
- NASBA NASBA
- T7 RNA polymerase T7 RNA polymerase
- Other transcription based amplification techniques are described in EP 408295.
- EP 408295 is primarily concerned with a two-enzyme transcription based amplification method.
- Transcription based amplification methods such as the NASBA method as described in EP 329822, are usually employed with a set of oligonucleotides, one of which is provided with a promoter sequence that is recognized by a DNA dependent RNA polymerase such as, for example, T7 polymerase.
- RNA amplification a transcription based amplification technique
- Amplification using PCR can also be based on an RNA template.
- RT-PCR reverse transcription step
- DNAse treatment prior to RT-PCR can be employed (Bitsch, A. et al., J. Infect. Dis 167, 740-743, 1993; Meyer, T. et al., Mol. Cell Probes. 8, 261-271., 1994), but sometimes fails to remove contaminating DNA sufficiently (Bitsch, A. et al., 1993).
- NASBA In contrast to RT-PCR, NASBA, which is based on RNA transcription by T7 RNA polymerase (Kievits et al., 1991; Compton, 1991), does not need differentiation between RNA- and DNA-derived amplification products since it uses RNA as its principal target. NASBA enables specific amplification of RNA targets even in a background of DNA.
- oligonucleotides according to the invention are not limited to any particular amplification technique or any particular modification thereof. It is evident that the oligonucleotides according to the invention find their use in many different nucleic acid amplification techniques and various methods for detecting the presence of (amplified) nucleic acid of HIV.
- the oligonucleotides of the present invention can likewise be used in quantitative amplification methods. An example if such quantitative method is described in EP 525882.
- oligonucleotide refers to a molecule comprised of two or more deoxyribonucleotides or ribonucleotides. Such oligonucleotides may be used as primers and probes.
- analogues of oligonucleotides can also be prepared.
- Such analogues may constitute alternative structures such as “PNA” (molecules with a peptide-like backbone instead of the phosphate sugar backbone of normal nucleic acid) or the like. It is evident that these alternative structures, representing the sequences of the present invention are likewise part of the present invention.
- primer refers to an oligonucleotide either naturally occurring (e.g. as a restriction fragment) or produced synthetically, which is capable of acting as a point of initiation of synthesis of a primer extension product which is complementary to a nucleic acid strand (template or target sequence) when placed under suitable conditions (e.g. buffer, salt, temperature and pH) in the presence of nucleotides and an agent for nucleic acid polymerization, such as DNA dependent or RNA dependent polymerase.
- a primer must be sufficiently long to prime the synthesis of extension products in the presence of an agent for polymerization.
- a typical primer contains at least about 10 nucleotides in length of a sequence substantially complementary or homologous to the target sequence, but somewhat longer primers are preferred. Usually primers contain about 15-26 nucleotides but longer primers may also be employed, especially when the primers contain additional sequences such as a promoter sequence for a particular polymerase.
- a set of primers will consist of at least two primers, one ‘upstream’ and one ‘downstream’ primer which together define the amplificate (the sequence that will be amplified using said primers);
- the oligonucleotides according to the invention may also be linked to a promoter sequence.
- promoter sequence defines a region of a nucleic acid sequence that is specifically recognized by an RNA polymerase that binds to a recognized sequence and initiates the process of transcription by which an RNA transcript is produced.
- any promoter sequence may be employed for which there is a known and available polymerase that is capable of recognizing the initiation sequence.
- Known and useful promoters are those that are recognized by certain bacteriophage RNA polymerases such as bacteriophage T3, T7 or SP6.
- Oligonucleotides linked to a promoter sequence are commonly referred to as “promoter primers”. Their function as a primer, e.g. the starting point for an elongation reaction, however, may be blocked, as already mentioned above, or absent in some embodiments of transcription based amplification reactions.
- An oligonucleotide according to the present invention is substantially complementary to a sequence of the LTR region of a nucleic acid sequence of a HIV genome, said oligonucleotide being 1050 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of: SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT SEQ ID 8: AGT GTG TGC CCG TCT GTT SEQ ID 12: GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT or the complementary sequence
- oligonucleotides consisting of the sequences of the present invention may contain minor deletions, additions and/or substitutions of nucleic acid bases, to the extent that such alterations do not negatively affect the yield or product obtained to a significant degree.
- the alterations should not result in lowering the hybridization efficiency of the probe.
- sequences of the present invention are reflected as DNA sequences.
- RNA equivalents of these sequences are likewise part of the present invention.
- Preferred oligonucleotides according to the invention are oligonucleotides consisting essentially of a sequence selected from the group consisting of: SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT. SEQ ID 8: AGT GTG TGC CCG TCT GTT.
- SEQ ID 9 aat tct aat acg act cac tat agg gAG AGG GGC GCC ACT GCT AGA GA
- SEQ ID 10 aat tct aat acg act cac tat agg gAG AGG TTC GGG CGC CAC TGC TAG A
- SEQ ID 11 aat tct aat acg act cac tat agg gCGGGCGCCACTGCTA
- SEQ ID 12 GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT
- SEQ ID 9-11 actually comprise the sequence as reflected by SEQ ID 1-3.
- the sequences of SEQ ID 1-3 are operably linked to a promoter sequence (the T7 promoter sequence). This makes the sequences especially suitable for use as upstream primer in a transcription based amplification technique such as NASBA.
- a preferred embodiment of the present invention is a combination of two oligonucleotides according to the invention, for use as a set in nucleic acid amplification.
- Such a pair of oligonucleotides for use as a set in the amplification of a target sequence located within the LTR region of the genome of HIV-1, consists of a first oligonucleotide being 10-50 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of: SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA
- oligonucleotide being 10-50 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of: SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA. SEQ ID 12: GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT
- One of the oligonucleotides may serve as an “upstream oligonucleotide”, i.e., an upstream-primer, while the second oligonucleotide serves as a “downstream oligonucleotide”, i.e. downstream primer, in the amplification reaction.
- the location on the HIV-genome (or the sequence complementary thereto) to which both oligonucleotides comprised in such a pair according to the invention can anneal, will together define the sequence of the nucleic acid that is amplified.
- the amplified sequence is located between the “primer-binding sites” within the LTR region of the HIV-genome. It has been found that, by using a pair of oligonucleotides according to the invention in an amplification reaction, accurate and reliable amplification of nucleic acid derived from all presently know sub-types of HIV can be achieved.
- a most preferred pair of oligonucleotides according to the invention will consist of a first primer comprising the sequence of SEQ ID NO 1 and a second primer with the sequence of SEQ ID NO 5.
- the oligonucleotide with SEQ ID NO 9 is preferred, in combination with an oligonucleotide with the sequence of SEQ ID NO 5.
- oligonucleotides according to the invention are particularly suitable for use as a probe in the detection of nucleic acid amplified with a pair of oligonucleotides according to the invention.
- said oligonucleotides may be provided with a detectable label.
- Oligonucleotides according to the invention that are especially suitable as a probe consist essentially of the sequence SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT or SEQ ID 8: AGT GTG TGC CCG TCT GTT provided with a detectable label.
- a most preferred oligonucleotide in this respect is an oligonucleotide with a sequence as depicted in SEQ ID 6.
- labeling moieties are known in the art.
- Said moiety may, for example, either be a radioactive compound, a detectable enzyme (e.g. horse radish peroxidase (HRP)), a hapten like biotin, or any other moiety capable of generating a detectable signal such as a calorimetric, fluorescent, chemiluminescent or electrochemiluminescent signal.
- HRP horse radish peroxidase
- Hybrids between oligonucleotides according to the invention and (amplified) target nucleic acid may also be detected by other methods known to those skilled in the art.
- test kits for the amplification and detection of HIV nucleic acid.
- the use of said test-kits enables accurate and sensitive screening of samples suspected of containing HIV derived nucleic acid.
- Such test-kits may contain a pair of oligonucleotides according to the invention and optionally also an oligonucleotide according to the invention that can be used as a probe for the detection of the amplified material.
- the test-kit may contain suitable amplification reagents. These reagents are for example the suitable enzymes for carrying out the amplification reaction.
- a kit, adapted for use with NASBA for example may contain suitable amounts of reverse transcriptase, RNase H and T7 RNA polymerase.
- Said enzymes may be present in the kit in a buffered solution but can likewise be provided as a lyophilized composition, for example, a lyophilized spherical particle. Such lyophilized particles have been disclosed in PCT appl. no. EP95/01268.
- the kit may further be furnished with buffer compositions, suitable for carrying out an amplification reaction.
- Said buffers may be optimized for the particular amplification technique for which the kit is intended as well as for use with the particular oligonucleotides that are provided with the kit. In transcription based amplification techniques, such as NASBA, said buffers may contain, for example, DMSO, which enhances the amplification reaction (as is disclosed in PCT appl. no. US90/04733).
- kit may be provided with an internal control as a check on the amplification procedure and to prevent the occurrence of false negative test results due to failures in the amplification procedure.
- internal controls in transcription based amplification techniques is described in PCT appl. no. EP 93/02248.
- An optimal control sequence is selected in such a way that it will not compete with the target nucleic acid in the amplification reaction.
- Kits may also contain reagents for the isolation of nucleic acid from biological specimen prior to amplification. A suitable method for the isolation of nucleic acid is disclosed in EP389063.
- FIG. 1 is a diagrammatic representation of FIG. 1 :
- Lane 1 SEQ ID 9-SEQ ID 10, lane 2; SEQ ID 9-SEQ ID 5, lane 3: SEQ ID 10-SEQ ID 4, lane 4: SEQ ID 10-SEQ ID 5, lane 5: SEQ ID 3-SEQ ID 12.
- nucleic acids isolation was performed according to Boom et al., 1990, Journal of Clinical Microbiology 28, 495-503 and European patent no. EP0389063.
- a volume of 200 ⁇ l of pooled plasma's from healthy donors negative for HBsAg, anti-HIV and anti-HCV was added to 900 ⁇ l of lysis buffer (47 mM Tris-HCl pH 7.2, 20 mM EDTA, 1.2% Triton X-100, 4.7 M guanidine thiocyanate (GuSCN, Fluka, Buchs, Switzerland)).
- the silicon pellets were dried during ten minutes in a 56° C. heating block.
- the nucleic acids were eluted from the silicon by adding 50 ⁇ l elution buffer (1.0 mM Tris-HCl, pH 8.5) and incubation at 56° C. for 10 minutes. Subsequently, 5 ⁇ l of the eluate was taken of the pellet for further use in the amplification reaction. The remaining eluate was stored at ⁇ 70° C.
- Amplifications were carried out in a reaction volume of 20 ⁇ l which is composed of 10 ⁇ l primer mixture, 5 ⁇ l (isolated) nucleic acids and 5 ⁇ l enzyme mixture.
- the primer mixture was made by reconstitution of a lyophilized accusphere into 50 ⁇ l accusphere diluent, 51.6 ⁇ l water, 8.4 ⁇ l 2 M KCl and 5 ⁇ l of each primer (10 ⁇ M). The mixture was thoroughly vortexed before use. From this primer mixture 10 ⁇ l was added to 5 ⁇ l of the (isolated) HIV-1 RNA (standard). This mixture was incubated for 5 minutes at 65° C. and subsequently incubated at 41° C. for another 5 minutes.
- each amplification reaction contained the following reagents:
- amplified products were analyzed using an agarose gel (100 ml of 2% Pronarose and 0.5 ⁇ g/ml ethidium bromide) and 1 * TAE (40 mM Trisacetate, 1 mM EDTA pH 8.0) running buffer are used. Electrophoresis was carried out at 100 volts for approximately 30 minutes. The ethidium bromide-stained bands of the amplified products were visualized using UV irradiation.
- the blot was hybridized with biotin probe (3 ⁇ M) in hybridization mix (750 mM NaCl, 75 mM sodium citrate, 20 mM Na 2 HPO 4 /NaH 2 PO 4 (pH 6.7), 10* Denhardts) by incubating the blot for 4 hours at 50° C. After hybridization the blot was washed two times for 5 minutes at 50° C. with 450 mM NaCl, 45 mM sodium citrate pH 6.4 (2* SSPE) and 1% sodium dodecyl sulphate (SDS) solution and one time for 10 minutes with 20 mM Na 2 HPO 4 pH 7.4, 360 mM NaCl, 2 mM EDTA and 0.1% SDS at room temperature.
- biotin probe 3 ⁇ M
- hybridization mix 750 mM NaCl, 75 mM sodium citrate, 20 mM Na 2 HPO 4 /NaH 2 PO 4 (pH 6.7), 10* Denhardts
- the blot was incubated for 30 minutes with 2 ⁇ l streptavidin/horse radish peroxidase solution (500 U/ml from the enhanced chemiluminescence detection kit of Amersham Life Science) in 10 ml 50 mM Na 2 HPO 4 , 900 mM NaCl, 5 mM EDTA, pH 7.4 and 0.5% SDS. Following washes respectively two times for 5 minutes in 2*SSPE, 0.1% SDS and once for 10 minutes in 2*SSPE at room temperature the blot was dried between tissues, developed and exposed to a film according to the Amersham kit protocol.
- streptavidin/horse radish peroxidase solution 500 U/ml from the enhanced chemiluminescence detection kit of Amersham Life Science
- ECL Electrochemiluminescence
- the amplification products were diluted two times in detection diluent (1.0 mM Tris/HCl, pH 8.5 and 0.2 g/l 2-methylisothiazolone HCl). Subsequently, 5 ⁇ l of the diluted amplification product was incubated for 30 minutes at 41° C.
- detection diluent 1.0 mM Tris/HCl, pH 8.5 and 0.2 g/l 2-methylisothiazolone HCl
- assay buffer solution 100 mM tripropylamine, pH 7.5
- ECL detection instrument NASBA QR-system from Organon Teknika BV
- the following primer pairs were tested on 10 4 copies (as determined by spectrophotometry at 260 nm) of the HIV-1 RNA standard.
- the RNA was added directly into the amplification.
- the analysis of the amplified products was performed by gel electophoresis as described in example 1. The results are shown in the FIG. 1 .
- detected % detected 200 4:4 100% 4:4 100% 100 8:8 100% 8:8 100% 50 8:8 100% 8:8 100% 25 7:8 87.5% 7:8 87.5% 12 6:8 75% 4:8 50% 6 2:8 25% 4:7 57% 3 0:8 0% 2:7 28.5% 0 0:8 0% 0:7 0%
- Both primer pairs have approximately the same sensitivity for the HIV-1 RNA standard respectively a detection rate of 70% for the primer pair SEQ ID 9/SEQ ID 5 and a detection rate of 63% for the primer pair SEQ ID 3/SEQ ID 5.
- the primer pair SEQ ID 9/SEQ ID 5 and probe with the sequence of SEQ ID 7 was tested on dilution series of the HIV-1 RNA standard in presence of an internal control (ic-) RNA.
- the ic-RNA is an in vitro transcript which contains part of the LTR sequence of HIV-1 HXB-2 and 10 4 copies (as determined by spectrophotometry at 260 nm) are added prior to nucleic acids isolation.
- the isolation, amplification and ECL detection was performed as described in example 1.
- separate amplification and detection was performed using a primer pair located in the HIV-1 gag region (P1/P2) previously described by Van Gemen et al, 1993, Journal of Virological Methods 43, 177-188.
- the probes used to detect the amplification products generated by the gag based primer pair were: Biotin probe: 5′-TGTTAAAAGAGACCATCAATGAGGA ECL probe: 5′-GAATGGGATAGAGTGCATCCAGTG.
- Both the LTR primer pair of this example and the gag primer pair were able to detect a similar amount of HIV-1 RNA in an assay controlled by an in vitro produced RNA which was added prior to the nucleic acids isolation.
- HIV-1 positive samples from various geographical locations were analyzed for presence of HIV-1 RNA. All samples were isolated by the nucleic acids isolation method described in example 1. Amplification and detection were carried out as described in example 1 using primer pair SEQ ID 9/SEQ ID 5 and probe with the sequence of SEQ ID 7 or probe with the sequence of SEQ ID 8.
- primer probe combinations derived from the LTR region of HIV-1 described in this example were able to detect HIV-1 from all the samples tested.
- primer probe combination of the gag assay failed to detect HIV-1 genomic RNA from a great number of samples.
- HIV-1 RNA was detected from all 33 HIV-1 samples using LTR primer pair SEQ ID 9/SEQ ID 5 and probe with sequence of SEQ ID 7.
- the assay using the gag primers probes combination as described in example 3 failed to detect subtype A and subtype E each from one of the samples and all samples containing HIV-1 RNA from group O members.
- the samples missed by the LTR primer probe combination are not detected due to a low viral load below the detection level since by using a sample volume of one ml the Quantiplex HIV-1 RNA 2.0 (Chiron) assay quantitated HIV-1 RNA levels of 30 or below 30 HIV-1 RNA copies per 50 ⁇ l of these samples.
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Abstract
Description
- This application is a continuation application of, and claims priority to U.S. application Ser. No. 11/108,233 (pending), filed Apr. 18, 2005, which is a continuation of U.S. application Ser. No. 09/463,352, filed Jan. 21, 2000 and issued Apr. 19, 2005 as U.S. Pat. No. 6,881,537, which is a 35 U.S.C. § 371 National Phase Application of International Application Serial No. PCT/EP98/04945, filed Aug. 5, 1998 and published in English as PCT Publication No. WO 99/07898 on Feb. 18, 1999, which claims priority to European Patent Application No. EP 97202455.8, filed Aug. 8, 1997. Each of these applications is incorporated herein by reference in its entirety.
- The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immunodeficiency Virus (HIV).
- Whereas conventional virus diagnosis has been based predominantly on the detection of viral antigens or specific antibodies thereto, in recent years attention has shifted towards methods for the direct detection of the genome of viruses or nucleic acid sequences derived thereof, both RNA and DNA. These methods are usually based on nucleic acid hybridization. Nucleic acid hybridization is based on the ability of two strands of nucleic acid containing complementary sequences to anneal to each other under the appropriate conditions, thus forming a double stranded structure. When the complementary strand is labeled, the label can be detected and is indicative for the presence of the target sequence. Especially in combination with methods for the amplification of nucleic acid sequences these methods have become an important tool in viral diagnosis, in particular for the detection of human immunodeficiency virus (HIV).
- Nucleic acid amplification techniques are especially useful as an additional technique in cases where serological methods give doubtful results or in cases where there may be a considerable time period between infection and the development of antibodies to the virus. With HIV, seroconversion usually can occur some 36 months after exposure to the virus. Thus, whereas no antibodies will be detected with conventional immunoassays, proviral DNA or circulating viral RNA may already be detectable. Also in monitoring antiviral therapy, methods based on nucleic acid amplification have several advantages over serological methods. Especially quantitative amplification methods provide a powerful tool in assessing the changes in the amount of virus present before and during therapy.
- The choice of the oligonucleotides to be used as primers and probes in the amplification and detection of nucleic acid sequences is critical for the sensitivity and specificity of the assay. The sequence to be amplified is usually only present in a sample (for example a blood sample obtained from a patient suspected of having a viral infection) in minute amounts. The primers should be sufficiently complementary to the target sequence to allow efficient amplification of the viral nucleic acid present in the sample. If the primers do not anneal properly (due to mispairing of the bases on the nucleotides in both strands) to the target sequence, amplification is seriously hampered. This will affect the sensitivity of the assay and may result in false negative test results. Due to the heterogeneity of viral genomes false negative test results may be obtained if the primers and probes are capable of recognizing sequences present in only part of the variants of the virus. The HIV virus shows a high heterogeneity. Genetic variability has been demonstrated amongst isolates from different continents but also between individuals and between different stages of the disease. Based on sequence analysis two groups within HIV-1 have been identified: group M (M for “major”), and group O (O for “outlier”). Within group M subtypes (A-H), each constituting a phylogenetic separate set of sequences, have been assigned and additional ones are being identified. This sequence variation is not uniformly distributed throughout the genome. The HIV-1 genome, like all retroviral genomes, roughly consists of the following regions: The gag gene of the HIV-1 genome is the region encoding the core proteins of the virus (for example, p24). The env gene encodes a large precursor protein, gp160, which is processed into the envelop proteins gp120 and gp41. The pol gene encodes the polymerase of the virus (reverse transcriptase). The Long Terminal Repeat regions (LTRs) are the regions on the viral genome that participate in the integration of the virus with the host cell and in the regulation of transcription of the viral genes. Some regions are more prone to sequence variation than others. Especially in the env domain sequence variation can be as high as 30% between members of the different subtypes. Ideally, primer selection should be based on knowledge of interstrain variability in candidate primer sequences and the consequences of mismatching at primer sites. McCutchan et al, J. AIDS, 4, 1241-1250, 1991, used PCR to make a genetic comparison of different HIV-1 isolates. Using anchored PCR (varying sense primers were used with a constant antisense primer. primers were chosen from relatively conserved regions in gag, env and LTR), the effect of primer mispairing on the amount of PCR product obtained was also investigated. Mispairing at the 3′ end of the primer decreased the amount of product sometimes more then 100-fold.
- The detection of all presently known subtypes of HIV-1 is of extreme importance, especially with regard to patient management, security of blood and blood products and clinical and epidemiological studies. Current assays for the amplification and subsequent detection of HIV-1 derived nucleic acid sequences are usually based on amplification of sequences in the gag region of the viral genome. These assays have been developed for subtype B, which is the major subtype in European countries and the United States. However, the presence of other subtypes, which were geographically confined before, is increasing due to frequent travel between these countries and, for example, African countries. Sensitive assays are therefore needed that are capable of detecting as much variants of the HIV-1 virus as possible (preferably all).
- Research aimed at identifying suitable primer sets for the reliable amplification of HIV-1 derived nucleic acid sequences has been ongoing for the past years. Engelbrecht et al., J. Virol. Meth., 55, 391400, 1995, describe a study aimed at the development of a specific and sensitive PCR protocol using env, gag and LTR primer pairs to detect subtypes present in the Western Cape, South Africa. Twenty four strains of which it was known that they belonged to subtypes B, C and D were analyzed. It was found that the performance of the primer pairs was greatly dependent on the optimization of the reaction conditions for the different primer pairs. Only when less stringent conditions were used (for example, with the LTR primer pair an increased cycle time and lower annealing temperatures were required) these particular strains of HIV could be detected with sufficient sensitivity and reproducibility with all primer pairs.
- Zazzi et al., J. Med. Virol., 38, 172-174, 1992, developed a two-step PCR reaction (using nested primers) for the detection of HIV-1 DNA in clinical samples. The primers used for amplification were derived from the gag gene and the LTR region. The patients tested in this study were all from neighbouring areas, which makes it likely that they represent only a limited number of different viral strains.
- A quantitative PCR method using LTR derived nested primers was described by Vener et al. in BioTechniques, 21, 248255, 1996. This procedure was only tested on HIV-1.sub.MN infected peripheral blood mononuclear cells (PBMC). Thus nothing can be said about the suitability of the primers used for detecting different subtypes of the virus.
- With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity. So far no primer pairs or hybridization probes have been developed that would allow the detection of such a broad range of HIV-1 variants.
- The oligonucleotide sequences according to the present invention are especially useful in methods for the amplification of nucleic acid.
- Various techniques for amplifying nucleic acid are known in the art. One example of a technique for the amplification of a DNA target segment is the so-called “polymerase chain reaction” (PCR). With the PCR technique the copy number of a particular target segment is increased exponentially with a number of cycles. A pair of primers is used and in each cycle a DNA primer is annealed to the 3′ side of each of the two strands of the double stranded DNA-target sequence. The primers are extended with a DNA polymerase in the presence of the various mononucleotides to generate double stranded DNA again. The strands of the double stranded DNA are separated from each other by thermal denaturation and each strand serves as a template for primer annealing and subsequent elongation in a following cycle. The PCR method has been described in Saiki et al., Science 230, 135, 1985 and in European Patents no. EP 200362 and EP 201184.
- Another technique for the amplification of nucleic acid is the so-called transcription based amplification system (TAS). The TAS method is described in International Patent Appl. no. WO 88/10315. Transcription based amplification techniques usually comprise treating target nucleic acid with two oligonucleotides one of which comprises a promoter sequence, to generate a template including a functional promoter. Multiple copies of RNA are transcribed from said template and can serve as a basis for further amplification.
- An isothermal continuous transcription based amplification method is the so-called NASBA process (“NASBA”) as described in European Patent no. EP 329822. NASBA includes the use of T7 RNA polymerase to transcribe multiple copies of RNA from a template including a T7 promoter. Other transcription based amplification techniques are described in EP 408295. EP 408295 is primarily concerned with a two-enzyme transcription based amplification method. Transcription based amplification methods, such as the NASBA method as described in EP 329822, are usually employed with a set of oligonucleotides, one of which is provided with a promoter sequence that is recognized by a DNA dependent RNA polymerase such as, for example, T7 polymerase. Several modifications of transcription based techniques are known in the art. These modifications comprise, for example, the use of blocked oligonucleotides (that may be provided with a promoter sequence). These oligos are blocked so as to inhibit an extension reaction proceeding therefrom (U.S. Pat. No. 5,554,516). One or more “promoter-primers” (oligonucleotides provided with a promoter sequence) may be used in transcription based amplification techniques, optionally combined with the use of one or more oligonucleotides that are not provided with a promoter sequence. For RNA amplification, a transcription based amplification technique, is a preferred technology. Amplification using PCR can also be based on an RNA template. The actual PCR needs to be preceded by a reverse transcription step to copy the RNA into DNA (RT-PCR). However, if RT-PCR is used for the detection of viral transcripts differentiation of mRNA- and DNA-derived PCR products is necessary. DNAse treatment prior to RT-PCR can be employed (Bitsch, A. et al., J. Infect. Dis 167, 740-743, 1993; Meyer, T. et al., Mol. Cell Probes. 8, 261-271., 1994), but sometimes fails to remove contaminating DNA sufficiently (Bitsch, A. et al., 1993).
- In contrast to RT-PCR, NASBA, which is based on RNA transcription by T7 RNA polymerase (Kievits et al., 1991; Compton, 1991), does not need differentiation between RNA- and DNA-derived amplification products since it uses RNA as its principal target. NASBA enables specific amplification of RNA targets even in a background of DNA.
- The use of the oligonucleotides according to the invention is not limited to any particular amplification technique or any particular modification thereof. It is evident that the oligonucleotides according to the invention find their use in many different nucleic acid amplification techniques and various methods for detecting the presence of (amplified) nucleic acid of HIV. The oligonucleotides of the present invention can likewise be used in quantitative amplification methods. An example if such quantitative method is described in EP 525882.
- The term “oligonucleotide” as used herein refers to a molecule comprised of two or more deoxyribonucleotides or ribonucleotides. Such oligonucleotides may be used as primers and probes.
- Of course, based on the sequences of the oligonucleotides of the present invention, analogues of oligonucleotides can also be prepared. Such analogues may constitute alternative structures such as “PNA” (molecules with a peptide-like backbone instead of the phosphate sugar backbone of normal nucleic acid) or the like. It is evident that these alternative structures, representing the sequences of the present invention are likewise part of the present invention.
- The term “primer” as used herein refers to an oligonucleotide either naturally occurring (e.g. as a restriction fragment) or produced synthetically, which is capable of acting as a point of initiation of synthesis of a primer extension product which is complementary to a nucleic acid strand (template or target sequence) when placed under suitable conditions (e.g. buffer, salt, temperature and pH) in the presence of nucleotides and an agent for nucleic acid polymerization, such as DNA dependent or RNA dependent polymerase. A primer must be sufficiently long to prime the synthesis of extension products in the presence of an agent for polymerization. A typical primer contains at least about 10 nucleotides in length of a sequence substantially complementary or homologous to the target sequence, but somewhat longer primers are preferred. Usually primers contain about 15-26 nucleotides but longer primers may also be employed, especially when the primers contain additional sequences such as a promoter sequence for a particular polymerase.
- Normally a set of primers will consist of at least two primers, one ‘upstream’ and one ‘downstream’ primer which together define the amplificate (the sequence that will be amplified using said primers);
- Primarily for the use in transcription based amplification techniques, the oligonucleotides according to the invention may also be linked to a promoter sequence. The term “promoter sequence” defines a region of a nucleic acid sequence that is specifically recognized by an RNA polymerase that binds to a recognized sequence and initiates the process of transcription by which an RNA transcript is produced. In principle any promoter sequence may be employed for which there is a known and available polymerase that is capable of recognizing the initiation sequence. Known and useful promoters are those that are recognized by certain bacteriophage RNA polymerases such as bacteriophage T3, T7 or SP6. Oligonucleotides linked to a promoter sequence are commonly referred to as “promoter primers”. Their function as a primer, e.g. the starting point for an elongation reaction, however, may be blocked, as already mentioned above, or absent in some embodiments of transcription based amplification reactions.
- An oligonucleotide according to the present invention is substantially complementary to a sequence of the LTR region of a nucleic acid sequence of a HIV genome, said oligonucleotide being 1050 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of:
SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT SEQ ID 8: AGT GTG TGC CCG TCT GTT SEQ ID 12: GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT
or the complementary sequence thereof. - It is understood that oligonucleotides consisting of the sequences of the present invention may contain minor deletions, additions and/or substitutions of nucleic acid bases, to the extent that such alterations do not negatively affect the yield or product obtained to a significant degree. Where oligonucleotides according to the present invention are used as probes, the alterations should not result in lowering the hybridization efficiency of the probe. For example, in case of transcription based amplification techniques, wherein one or more of the primers may be provided with a promoter sequence, the introduction of a purine-rich (=G or A) hybridizing sequence, just after the promoter sequence may have positive effects on the transcription (when there are C's and T's abortive transcription may occur). If no such sequence is available in the target nucleic acid a purine-rich sequence can be inserted in the oligonucleotide just following the last three G residues of the promoter sequence.
- The sequences of the present invention are reflected as DNA sequences. The RNA equivalents of these sequences are likewise part of the present invention.
- Preferred oligonucleotides according to the invention are oligonucleotides consisting essentially of a sequence selected from the group consisting of:
SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT. SEQ ID 8: AGT GTG TGC CCG TCT GTT. SEQ ID 9: aat tct aat acg act cac tat agg gAG AGG GGC GCC ACT GCT AGA GA SEQ ID 10: aat tct aat acg act cac tat agg gAG AGG TTC GGG CGC CAC TGC TAG A SEQ ID 11: aat tct aat acg act cac tat agg gCGGGCGCCACTGCTA SEQ ID 12: GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT - SEQ ID 9-11 actually comprise the sequence as reflected by SEQ ID 1-3. In SEQ ID 9-11, the sequences of SEQ ID 1-3 are operably linked to a promoter sequence (the T7 promoter sequence). This makes the sequences especially suitable for use as upstream primer in a transcription based amplification technique such as NASBA.
- A preferred embodiment of the present invention is a combination of two oligonucleotides according to the invention, for use as a set in nucleic acid amplification.
- Such a pair of oligonucleotides, for use as a set in the amplification of a target sequence located within the LTR region of the genome of HIV-1, consists of a first oligonucleotide being 10-50 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of:
SEQ ID 1: G GGC GCC ACT GCT AGA GA SEQ ID 2: G TTC GGG CGC CAC TGC TAG A SEQ ID 3: CGGGCGCCACTGCTA - and a second oligonucleotide being 10-50 nucleotides in length and comprising, at least a fragment of 10 nucleotides, of a sequence selected from the group consisting of:
SEQ ID 4: CTG CTT AAA GCC TCA ATA AA SEQ ID 5: CTC AAT AAA GCT TGC CTT GA. SEQ ID 12: GAT GCA TGC TCA ATA AAG CTT GCC TTG AGT - One of the oligonucleotides may serve as an “upstream oligonucleotide”, i.e., an upstream-primer, while the second oligonucleotide serves as a “downstream oligonucleotide”, i.e. downstream primer, in the amplification reaction. The location on the HIV-genome (or the sequence complementary thereto) to which both oligonucleotides comprised in such a pair according to the invention can anneal, will together define the sequence of the nucleic acid that is amplified. The amplified sequence is located between the “primer-binding sites” within the LTR region of the HIV-genome. It has been found that, by using a pair of oligonucleotides according to the invention in an amplification reaction, accurate and reliable amplification of nucleic acid derived from all presently know sub-types of HIV can be achieved.
- A most preferred pair of oligonucleotides according to the invention will consist of a first primer comprising the sequence of
SEQ ID NO 1 and a second primer with the sequence ofSEQ ID NO 5. For use in a transcription based amplification method, the oligonucleotide with SEQ ID NO 9 is preferred, in combination with an oligonucleotide with the sequence ofSEQ ID NO 5. - Part of the oligonucleotides according to the invention are particularly suitable for use as a probe in the detection of nucleic acid amplified with a pair of oligonucleotides according to the invention. When used as a probe, said oligonucleotides may be provided with a detectable label. Oligonucleotides according to the invention that are especially suitable as a probe consist essentially of the sequence
SEQ ID 6: TCT GGT AAC TAG AGA TCC CTC SEQ ID 7: TAG TGT GTG CCC GTC TGT or SEQ ID 8: AGT GTG TGC CCG TCT GTT
provided with a detectable label. A most preferred oligonucleotide in this respect is an oligonucleotide with a sequence as depicted in SEQ ID 6. - Various labeling moieties are known in the art. Said moiety may, for example, either be a radioactive compound, a detectable enzyme (e.g. horse radish peroxidase (HRP)), a hapten like biotin, or any other moiety capable of generating a detectable signal such as a calorimetric, fluorescent, chemiluminescent or electrochemiluminescent signal.
- Hybrids between oligonucleotides according to the invention and (amplified) target nucleic acid may also be detected by other methods known to those skilled in the art.
- Evidently methods for amplification of nucleic acid, like the ones that have been mentioned above, using the oligonucleotides according to the present invention are also part of the invention.
- The present invention further provides test kits for the amplification and detection of HIV nucleic acid. The use of said test-kits enables accurate and sensitive screening of samples suspected of containing HIV derived nucleic acid. Such test-kits may contain a pair of oligonucleotides according to the invention and optionally also an oligonucleotide according to the invention that can be used as a probe for the detection of the amplified material. Furthermore the test-kit may contain suitable amplification reagents. These reagents are for example the suitable enzymes for carrying out the amplification reaction. A kit, adapted for use with NASBA, for example may contain suitable amounts of reverse transcriptase, RNase H and T7 RNA polymerase. Said enzymes may be present in the kit in a buffered solution but can likewise be provided as a lyophilized composition, for example, a lyophilized spherical particle. Such lyophilized particles have been disclosed in PCT appl. no. EP95/01268. The kit may further be furnished with buffer compositions, suitable for carrying out an amplification reaction. Said buffers may be optimized for the particular amplification technique for which the kit is intended as well as for use with the particular oligonucleotides that are provided with the kit. In transcription based amplification techniques, such as NASBA, said buffers may contain, for example, DMSO, which enhances the amplification reaction (as is disclosed in PCT appl. no. US90/04733).
- Furthermore the kit may be provided with an internal control as a check on the amplification procedure and to prevent the occurrence of false negative test results due to failures in the amplification procedure. The use of internal controls in transcription based amplification techniques is described in PCT appl. no. EP 93/02248. An optimal control sequence is selected in such a way that it will not compete with the target nucleic acid in the amplification reaction. Kits may also contain reagents for the isolation of nucleic acid from biological specimen prior to amplification. A suitable method for the isolation of nucleic acid is disclosed in EP389063.
-
FIG. 1 : - Amplification products after blotting and detection by enhanced chemiluminiscence obtained after amplification in presence (panel A) or absence (panel B) of HIV-1 RNA using the following primer pairs. Lane 1: SEQ ID 9-SEQ ID 10,
lane 2; SEQ ID 9-SEQ ID 5, lane 3: SEQ ID 10-SEQ ID 4, lane 4: SEQ ID 10-SEQ ID 5, lane 5: SEQ ID 3-SEQ ID 12. - The following procedures were applied to amplify and detect HIV-1 genomic RNA from samples as described in the following examples.
- Sample Preparation and Nucleic Acid Isolation.
- The isolation of the nucleic acids was performed according to Boom et al., 1990, Journal of Clinical Microbiology 28, 495-503 and European patent no. EP0389063. In short: A volume of 200 μl of pooled plasma's from healthy donors (negative for HBsAg, anti-HIV and anti-HCV) was added to 900 μl of lysis buffer (47 mM Tris-HCl pH 7.2, 20 mM EDTA, 1.2% Triton X-100, 4.7 M guanidine thiocyanate (GuSCN, Fluka, Buchs, Switzerland)). After vortexing and centrifugation (30 seconds, 13,000 rpm) a dilution series of HIV-1 RNA subtype B standard, characterized and described by Layne et al., 1992, Virology 189, 695-714 or HIV-1 positive specimens, was added. Upon addition of 50 μl activated silicon (0.4 g/ml suspension in 0.1 N HCl), the suspension was incubated for 10 minutes at room temperature with regular vortexing. After centrifugation (30-60 seconds, 13,000 rpm) the silicon pellet was washed twice with 1 ml of wash buffer (5.25 M GuSCN, 50 mM Tris-HCl pH 6.4), followed by two 70% ethanol washes and one acetone wash step. Subsequently, the silicon pellets were dried during ten minutes in a 56° C. heating block. The nucleic acids were eluted from the silicon by adding 50 μl elution buffer (1.0 mM Tris-HCl, pH 8.5) and incubation at 56° C. for 10 minutes. Subsequently, 5 μl of the eluate was taken of the pellet for further use in the amplification reaction. The remaining eluate was stored at −70° C.
- NASBA Amplification.
- Amplifications were carried out in a reaction volume of 20 μl which is composed of 10 μl primer mixture, 5 μl (isolated) nucleic acids and 5 μl enzyme mixture. The primer mixture was made by reconstitution of a lyophilized accusphere into 50 μl accusphere diluent, 51.6 μl water, 8.4 μl 2 M KCl and 5 μl of each primer (10 μM). The mixture was thoroughly vortexed before use. From this primer mixture 10 μl was added to 5 μl of the (isolated) HIV-1 RNA (standard). This mixture was incubated for 5 minutes at 65° C. and subsequently incubated at 41° C. for another 5 minutes. After these
incubations 5 μl enzyme mixture was added and incubated for 5 minutes at 41° C. The tubes were transferred to the detection area and incubated for 90 minutes at 41° C. After the amplification reaction the tubes were stored at −20° C. until further use. Each amplification reaction contained the following reagents: - 40 mM Tris-HCl, pH 8.5
- 12 mM MgCl2
- 70 mM KCl
- 15% v/v dimethyl sulfoxide
- 5 mM dithiotreitol
- 1 mM of each deoxynucleoside triphosphate
- 2 mM of the nucleosides rATP, rCTP, rUTP
- 1.5 mM rGTP
- 0.5 mM ITP
- 0.105 μg/μl BSA
- 0.08 units RNaseH
- 32 units T7 RNA polymerase
- 6.4 units avian myeloblastosis virus reverse transcriptase (Seikagaku, USA)
- 0.2 μM of each primer
- 375 mM sorbitol
- 45.6 mM sucrose
- 28.5 mM mannitol
- 0.13 mM dextran T40
Detection of the Amplified Products.
A. Gel Electrophoresis. - The presence of amplified products was analyzed using an agarose gel (100 ml of 2% Pronarose and 0.5 μg/ml ethidium bromide) and 1 * TAE (40 mM Trisacetate, 1 mM EDTA pH 8.0) running buffer are used. Electrophoresis was carried out at 100 volts for approximately 30 minutes. The ethidium bromide-stained bands of the amplified products were visualized using UV irradiation. The blot was hybridized with biotin probe (3 μM) in hybridization mix (750 mM NaCl, 75 mM sodium citrate, 20 mM Na2HPO4/NaH2PO4 (pH 6.7), 10* Denhardts) by incubating the blot for 4 hours at 50° C. After hybridization the blot was washed two times for 5 minutes at 50° C. with 450 mM NaCl, 45 mM sodium citrate pH 6.4 (2* SSPE) and 1% sodium dodecyl sulphate (SDS) solution and one time for 10 minutes with 20 mM Na2HPO4 pH 7.4, 360 mM NaCl, 2 mM EDTA and 0.1% SDS at room temperature. Subsequently, the blot was incubated for 30 minutes with 2 μl streptavidin/horse radish peroxidase solution (500 U/ml from the enhanced chemiluminescence detection kit of Amersham Life Science) in 10 ml 50 mM Na2HPO4, 900 mM NaCl, 5 mM EDTA, pH 7.4 and 0.5% SDS. Following washes respectively two times for 5 minutes in 2*SSPE, 0.1% SDS and once for 10 minutes in 2*SSPE at room temperature the blot was dried between tissues, developed and exposed to a film according to the Amersham kit protocol.
- B. Electrochemiluminescence (ECL) Probe Hybridization.
- The amplification products were diluted two times in detection diluent (1.0 mM Tris/HCl, pH 8.5 and 0.2 g/l 2-methylisothiazolone HCl). Subsequently, 5 μl of the diluted amplification product was incubated for 30 minutes at 41° C. with 0.084 μM of the HIV-1 specific biotin probe bound to 5 μg streptavidin-coated magnetic beads (mean size 2.8 μm.+−.0.2 μm, Dynal, Great Neck, N.Y., USA) and 2*1011 molecules of an ECL (Tris[2,2-bipyridine]ruthenium[II] complex)-labeled probe, in a total volume of 25 μl 750 mM NaCl, 75 mM sodium citrate, pH 6.4 (5*SSC). As negative controls, detection diluent was also incubated with the bead-probe and ECL-probe mixtures. During incubation, tubes were agitated every 10 minutes to keep the beads in suspension. Subsequently, 300 μl of assay buffer solution (100 mM tripropylamine, pH 7.5) was added and the tubes were placed in an ECL detection instrument (NASBA QR-system from Organon Teknika BV) for reading the emitted ECL signals.
- The following primer pairs were tested on 104 copies (as determined by spectrophotometry at 260 nm) of the HIV-1 RNA standard. The RNA was added directly into the amplification. The analysis of the amplified products was performed by gel electophoresis as described in example 1. The results are shown in the
FIG. 1 . - All primer pairs and probes of the present invention were able to amplify and detect HIV-1 RNA from subtype B to a similar extent. Analytical sensitivity is shown for two primer pairs (SEQ ID 9/
SEQ ID 5 and SEQ ID 11/SEQ ID 5) using a dilution series of the HIV-1 RNA standard which has an initial concentration of 5.5*109 copies/ml. The detection was done with probes having the sequences as depicted in SEQ ID 7 and SEQ ID 6. The amplification and detection was carried out as described in example 1. Table 1 shows the results obtained with both primer pairs. \TABLE 1 HIV-1 RNA SEQ ID 3- SEQ ID 5SEQ ID 9- SEQ ID 5copies No. detected % detected No. detected % detected 200 4:4 100% 4:4 100% 100 8:8 100% 8:8 100% 50 8:8 100% 8:8 100% 25 7:8 87.5% 7:8 87.5% 12 6:8 75% 4:8 50% 6 2:8 25% 4:7 57% 3 0:8 0% 2:7 28.5% 0 0:8 0% 0:7 0% - Both primer pairs have approximately the same sensitivity for the HIV-1 RNA standard respectively a detection rate of 70% for the primer pair SEQ ID 9/
SEQ ID 5 and a detection rate of 63% for the primerpair SEQ ID 3/SEQ ID 5. - In this example the primer pair SEQ ID 9/
SEQ ID 5 and probe with the sequence of SEQ ID 7 was tested on dilution series of the HIV-1 RNA standard in presence of an internal control (ic-) RNA. The ic-RNA is an in vitro transcript which contains part of the LTR sequence of HIV-1 HXB-2 and 104 copies (as determined by spectrophotometry at 260 nm) are added prior to nucleic acids isolation. The isolation, amplification and ECL detection was performed as described in example 1. As a comparison, separate amplification and detection was performed using a primer pair located in the HIV-1 gag region (P1/P2) previously described by Van Gemen et al, 1993, Journal of Virological Methods 43, 177-188. The probes used to detect the amplification products generated by the gag based primer pair were:Biotin probe: 5′-TGTTAAAAGAGACCATCAATGAGGA ECL probe: 5′-GAATGGGATAGAGTGCATCCAGTG. - Results are shown in Table 2.
TABLE 2 HIV-1 RNA LTR SEQ ID 9- SEQ ID 5GAG P1/P2 copies/200 μl No. detected % detected No. detected % detected 320 9:10 90% nt* nt* 160 5:10 50% 8:10 80% 80 5:10 50% 5:10 50% 40 3:8 38% 4:10 40% 20 3:10 32% 1:10 10% 10 1:10 10% 2:10 20% 0 0:5 0% 1:5 20% - Both the LTR primer pair of this example and the gag primer pair were able to detect a similar amount of HIV-1 RNA in an assay controlled by an in vitro produced RNA which was added prior to the nucleic acids isolation.
- In this example, 40 HIV-1 positive samples from various geographical locations were analyzed for presence of HIV-1 RNA. All samples were isolated by the nucleic acids isolation method described in example 1. Amplification and detection were carried out as described in example 1 using primer pair SEQ ID 9/
SEQ ID 5 and probe with the sequence of SEQ ID 7 or probe with the sequence of SEQ ID 8. - For comparison, separate amplification and detection was carried out using the gag primer pair and probes as described in example 3. Presence of amplified products was detected by ECL probe hybridization according to the method of example 1. Result are shown in Table 3.
TABLE 3 Primer pair ECL Probe No. Detected % Detected DEQ ID 9/ SEQ ID 5SEQ ID 7 40/40 100% (LTR) SEQ ID 9/ SEQ ID 5SEQ 8 10/10 100% (LTR) P1/P2 )gag) 29/40 72.5% - Both primer probe combinations derived from the LTR region of HIV-1 described in this example were able to detect HIV-1 from all the samples tested. In contrast, the primer probe combination of the gag assay failed to detect HIV-1 genomic RNA from a great number of samples.
- In this example, 33 samples harbouring HIV-1 RNA of known envelope-based subtypes were tested. The samples originate from subtyped viruses propagated in cell cultures. Samples of cell culture supernatants from both variants of group M subtypes A through H and variants of group O were spiked to HIV-1 negative human plasma and treated according to the method from example 1. Amplification and detection was performed essentially as example 4. Results are shown table 4 as the number of samples of each type from which HIV-1 RNA was detected out of the total number of each type tested.
TABLE 4 HIV-1 Types Primer pair A B C D E F G H O Total SEQ ID 9/ SEQ ID 55:5 2:2 2:2 5:5 7:7 1:1 1:1 1:1 9:9 33:33 (LTR) 4:5 2:2 2:2 5:5 6:7 1:1 1:1 1:1 0:9 22:33 - HIV-1 RNA was detected from all 33 HIV-1 samples using LTR primer pair SEQ ID 9/
SEQ ID 5 and probe with sequence of SEQ ID 7. In contrast, the assay using the gag primers probes combination as described in example 3 failed to detect subtype A and subtype E each from one of the samples and all samples containing HIV-1 RNA from group O members. - In this example, 7 samples obtained from seropositive patients originating from Africa, South America and Asia were assayed for the presence of HIV-1 genomic RNA. Despite the fact that blood samples from these patients are both anti-p24 antibody (Abbott Laboratories, Abbott Park, Ill.) and western blot (Genelabs) positive, all specimens were scored negative by the NASBA HIV-1 RNA QL assay (Organon Teknika BV) which uses the gag primer pair and probe combination from example 3 and only a single sample (R9612222) was detected and quantitated (29.500 RNA copies/ml) by the Quantiplex HIV-1 RNA 2.0 (Chiron) assay using a sample volume of 50 .mu.l. In contrast, using an equal sample volume the primer pair SEQ ID 9/
SEQ ID 5 and the probe with sequence of SEQ ID 7 detected four out of seven samples (Table 5).TABLE 5 SEQ ID 9/ SEQ ID 5Sample code Country (LTR) R9610155 Thailand positive R9612222 Ghana positive R9700062 Brazil negative R9612218 Zaire negative R9611710 Liberia positive R9610718 Antilles positive R9607884 Rwanda negative - The samples missed by the LTR primer probe combination are not detected due to a low viral load below the detection level since by using a sample volume of one ml the Quantiplex HIV-1 RNA 2.0 (Chiron) assay quantitated HIV-1 RNA levels of 30 or below 30 HIV-1 RNA copies per 50 μl of these samples.
Claims (14)
Priority Applications (1)
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US09/463,352 US6881537B1 (en) | 1997-08-08 | 1998-08-05 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
PCT/EP1998/004945 WO1999007898A1 (en) | 1997-08-08 | 1998-08-05 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
US11/108,233 US8697352B2 (en) | 1997-08-08 | 2005-04-18 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/372,586 US20060223057A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
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US11/108,233 Expired - Fee Related US8697352B2 (en) | 1997-08-08 | 2005-04-18 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/372,586 Abandoned US20060223057A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/372,577 Abandoned US20060223056A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/372,585 Abandoned US20060228699A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US14/226,965 Expired - Fee Related US9074262B2 (en) | 1997-08-08 | 2014-03-27 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US14/733,320 Abandoned US20150292043A1 (en) | 1997-08-08 | 2015-06-08 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
US15/378,516 Abandoned US20170137900A1 (en) | 1997-08-08 | 2016-12-14 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
US15/378,510 Abandoned US20170145524A1 (en) | 1997-08-08 | 2016-12-14 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
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US09/463,352 Expired - Lifetime US6881537B1 (en) | 1997-08-08 | 1998-08-05 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/108,233 Expired - Fee Related US8697352B2 (en) | 1997-08-08 | 2005-04-18 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
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US11/372,577 Abandoned US20060223056A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US11/372,585 Abandoned US20060228699A1 (en) | 1997-08-08 | 2006-03-10 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US14/226,965 Expired - Fee Related US9074262B2 (en) | 1997-08-08 | 2014-03-27 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
US14/733,320 Abandoned US20150292043A1 (en) | 1997-08-08 | 2015-06-08 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
US15/378,516 Abandoned US20170137900A1 (en) | 1997-08-08 | 2016-12-14 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
US15/378,510 Abandoned US20170145524A1 (en) | 1997-08-08 | 2016-12-14 | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of hiv-1 |
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US (9) | US6881537B1 (en) |
EP (3) | EP2336367B1 (en) |
JP (1) | JP3689333B2 (en) |
KR (1) | KR100615407B1 (en) |
AT (1) | ATE282720T1 (en) |
AU (1) | AU736503B2 (en) |
CA (1) | CA2299275C (en) |
DE (2) | DE1002138T1 (en) |
ES (3) | ES2438578T3 (en) |
GR (1) | GR20010300012T1 (en) |
ID (1) | ID25877A (en) |
WO (1) | WO1999007898A1 (en) |
ZA (1) | ZA987091B (en) |
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Families Citing this family (28)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
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DE19836559A1 (en) * | 1998-08-12 | 2000-03-23 | Antigen Gmbh | Blood collection vessel |
DE19850186A1 (en) * | 1998-10-30 | 2000-05-25 | Roche Diagnostics Gmbh | New primers and probes for the detection of HIV |
EP1422298B1 (en) | 1999-07-09 | 2010-01-27 | Gen-Probe Incorporated | Detection of hiv-1 by nucleic acid amplification |
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Citations (13)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5221610A (en) * | 1988-05-26 | 1993-06-22 | Institut Pasteur | Diagnostic method and composition for early detection of HIV infection |
US5306631A (en) * | 1987-08-21 | 1994-04-26 | University Of Colorado Foundation, Inc. | Compositions and method for inhibition of HIV production |
US5403707A (en) * | 1993-05-14 | 1995-04-04 | Eastman Kodak Company | Diagnostic compositions, elements, methods and test kits for amplification and detection of retroviral DNA using primers having matched melting temperatures |
US5413906A (en) * | 1990-08-31 | 1995-05-09 | Boehringer Mannheim Gmbh | Method of determining polymerase activity |
US5472840A (en) * | 1988-09-30 | 1995-12-05 | Amoco Corporation | Nucleic acid structures with catalytic and autocatalytic replicating features and methods of use |
US5474796A (en) * | 1991-09-04 | 1995-12-12 | Protogene Laboratories, Inc. | Method and apparatus for conducting an array of chemical reactions on a support surface |
US5576176A (en) * | 1994-03-03 | 1996-11-19 | The Regents Of The University Of California | Marker and an assay for detection and monitoring of human immunodeficiency virus latency and activation |
US5629413A (en) * | 1993-07-19 | 1997-05-13 | Gen-Probe Incorporated | Oligonucleotides with activity against human immunodeficiency virus |
US5712385A (en) * | 1989-07-11 | 1998-01-27 | Gen-Probe Incorporated | Detection of human immunodeficiency virus type 1 |
US5770428A (en) * | 1993-02-17 | 1998-06-23 | Wisconsin Alumni Research Foundation | Chimeric retrovial expression vectors and particles containing a simple retroviral long terminal repeat, BLV or HIV coding regions and cis-acting regulatory sequences, and an RNA translational enhancer with internal ribsome entry site |
US6001558A (en) * | 1997-06-25 | 1999-12-14 | Ortho Clinical Diagnostics, Inc. | Amplification and detection of HIV-1 and/or HIV 2 |
US6025124A (en) * | 1994-03-03 | 2000-02-15 | The Regents Of The University Of California | Marker, method and an assay for detection and monitoring of latency and activation of human immunodeficiency virus |
US6881537B1 (en) * | 1997-08-08 | 2005-04-19 | Biomerieux, B.V. | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
Family Cites Families (22)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5333675C1 (en) * | 1986-02-25 | 2001-05-01 | Perkin Elmer Corp | Apparatus and method for performing automated amplification of nucleic acid sequences and assays using heating and cooling steps |
DK171161B1 (en) | 1985-03-28 | 1996-07-08 | Hoffmann La Roche | A method for detecting the presence or absence of at least one specific nucleic acid sequence in a sample or for distinguishing two different nucleic acid sequences in this sample |
US4683202A (en) | 1985-03-28 | 1987-07-28 | Cetus Corporation | Process for amplifying nucleic acid sequences |
US4772547A (en) * | 1986-02-03 | 1988-09-20 | Hoffmann-La Roche Inc. | HTLV-III envelope peptides |
IL86724A (en) | 1987-06-19 | 1995-01-24 | Siska Diagnostics Inc | Method and kits for the amplification and detection of nucleic acid sequences |
US4963532A (en) * | 1987-11-25 | 1990-10-16 | Hem Research, Inc. | dsRNA-based prevention of viral escape |
ATE208813T1 (en) * | 1988-02-16 | 2001-11-15 | Greatbatch Gen Aid Ltd | MODIFIED CELLS WITH RESISTANCE TO RETROVIRAL INFECTIONS |
CA1340807C (en) | 1988-02-24 | 1999-11-02 | Lawrence T. Malek | Nucleic acid amplification process |
US5622820A (en) * | 1988-03-10 | 1997-04-22 | City Of Hope | Method for amplification and detection of RNA and DNA sequences |
NL8900725A (en) | 1989-03-23 | 1990-10-16 | Az Univ Amsterdam | METHOD AND COMBINATION OF AGENTS FOR INSULATING NUCLEIC ACID. |
IE64040B1 (en) * | 1989-06-15 | 1995-06-28 | Akzo Nv | Method for determining nucleic acid |
DE69034177T2 (en) | 1989-07-11 | 2005-10-27 | Gen-Probe Inc., San Diego | Process for the amplification of nucleic acid sequences |
US5122457A (en) * | 1989-10-19 | 1992-06-16 | Schering Corporation | Expression systems utilizing bacteriophage t7 promoters, gene sequences, and t7 rna polymerase |
JPH05504475A (en) | 1989-11-30 | 1993-07-15 | ファルマシア バイオテック インコーポレイテッド | Method for detecting specific nucleic acid sequences in cell samples |
ATE184321T1 (en) * | 1990-01-10 | 1999-09-15 | Chiron Diagnostics Corp | DNA-DEPENDENT RNA POLYMERASE TRANSCRIPTS AS REPORTER MOLECULES FOR SIGNAL AMPLIFICATION IN NUCLEIC ACID HYBRIDIZATION STUDIES |
DK173091D0 (en) | 1991-10-11 | 1991-10-11 | Schleroseforeningen The Danish | BIOLOGICAL MATERIALS |
AU681082B2 (en) | 1992-05-06 | 1997-08-21 | Gen-Probe Incorporated | Nucleic acid sequence amplification method, composition and kit |
KR100325554B1 (en) | 1993-03-26 | 2002-11-02 | 젠-프로브 인코포레이티드 | Detection of Human Immunodeficiency Virus Type 1 |
US5622827A (en) * | 1995-02-07 | 1997-04-22 | Gen-Probe Incorporated | Amplification primers and nucleic acid probes targeted to coccidioides immitis nucleic acid |
US5599662A (en) | 1995-02-17 | 1997-02-04 | Hoffmann-La Roche Inc. | Oliconucleotide primers and probes for the detection of HIV-1 |
US5798542A (en) * | 1996-10-08 | 1998-08-25 | Eastman Kodak Company | Image sensor having ITO electrodes with overlapping color filters for increased sensitivity |
US9004733B2 (en) | 2012-04-05 | 2015-04-14 | Corning Cable Systems Llc | Optical fiber installation tool having a passive illumination feature |
-
1998
- 1998-08-05 EP EP20100183902 patent/EP2336367B1/en not_active Revoked
- 1998-08-05 JP JP2000506380A patent/JP3689333B2/en not_active Expired - Lifetime
- 1998-08-05 ES ES10183902T patent/ES2438578T3/en not_active Expired - Lifetime
- 1998-08-05 WO PCT/EP1998/004945 patent/WO1999007898A1/en active IP Right Grant
- 1998-08-05 EP EP20040077617 patent/EP1568787B1/en not_active Revoked
- 1998-08-05 CA CA002299275A patent/CA2299275C/en not_active Expired - Lifetime
- 1998-08-05 EP EP98943872A patent/EP1002138B1/en not_active Revoked
- 1998-08-05 ES ES98943872T patent/ES2153807T3/en not_active Expired - Lifetime
- 1998-08-05 DE DE1002138T patent/DE1002138T1/en active Pending
- 1998-08-05 KR KR1020007001327A patent/KR100615407B1/en not_active IP Right Cessation
- 1998-08-05 AT AT98943872T patent/ATE282720T1/en active
- 1998-08-05 US US09/463,352 patent/US6881537B1/en not_active Expired - Lifetime
- 1998-08-05 AU AU91611/98A patent/AU736503B2/en not_active Expired
- 1998-08-05 ID ID20000240D patent/ID25877A/en unknown
- 1998-08-05 DE DE1998604464 patent/DE69804464T2/en not_active Revoked
- 1998-08-05 ES ES04077617.1T patent/ES2479065T3/en not_active Expired - Lifetime
- 1998-08-06 ZA ZA987091A patent/ZA987091B/en unknown
-
2001
- 2001-04-30 GR GR20010300012T patent/GR20010300012T1/en unknown
-
2005
- 2005-04-18 US US11/108,233 patent/US8697352B2/en not_active Expired - Fee Related
-
2006
- 2006-03-10 US US11/372,586 patent/US20060223057A1/en not_active Abandoned
- 2006-03-10 US US11/372,577 patent/US20060223056A1/en not_active Abandoned
- 2006-03-10 US US11/372,585 patent/US20060228699A1/en not_active Abandoned
-
2014
- 2014-03-27 US US14/226,965 patent/US9074262B2/en not_active Expired - Fee Related
-
2015
- 2015-06-08 US US14/733,320 patent/US20150292043A1/en not_active Abandoned
-
2016
- 2016-12-14 US US15/378,516 patent/US20170137900A1/en not_active Abandoned
- 2016-12-14 US US15/378,510 patent/US20170145524A1/en not_active Abandoned
Patent Citations (13)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5306631A (en) * | 1987-08-21 | 1994-04-26 | University Of Colorado Foundation, Inc. | Compositions and method for inhibition of HIV production |
US5221610A (en) * | 1988-05-26 | 1993-06-22 | Institut Pasteur | Diagnostic method and composition for early detection of HIV infection |
US5472840A (en) * | 1988-09-30 | 1995-12-05 | Amoco Corporation | Nucleic acid structures with catalytic and autocatalytic replicating features and methods of use |
US5712385A (en) * | 1989-07-11 | 1998-01-27 | Gen-Probe Incorporated | Detection of human immunodeficiency virus type 1 |
US5413906A (en) * | 1990-08-31 | 1995-05-09 | Boehringer Mannheim Gmbh | Method of determining polymerase activity |
US5474796A (en) * | 1991-09-04 | 1995-12-12 | Protogene Laboratories, Inc. | Method and apparatus for conducting an array of chemical reactions on a support surface |
US5770428A (en) * | 1993-02-17 | 1998-06-23 | Wisconsin Alumni Research Foundation | Chimeric retrovial expression vectors and particles containing a simple retroviral long terminal repeat, BLV or HIV coding regions and cis-acting regulatory sequences, and an RNA translational enhancer with internal ribsome entry site |
US5403707A (en) * | 1993-05-14 | 1995-04-04 | Eastman Kodak Company | Diagnostic compositions, elements, methods and test kits for amplification and detection of retroviral DNA using primers having matched melting temperatures |
US5629413A (en) * | 1993-07-19 | 1997-05-13 | Gen-Probe Incorporated | Oligonucleotides with activity against human immunodeficiency virus |
US5576176A (en) * | 1994-03-03 | 1996-11-19 | The Regents Of The University Of California | Marker and an assay for detection and monitoring of human immunodeficiency virus latency and activation |
US6025124A (en) * | 1994-03-03 | 2000-02-15 | The Regents Of The University Of California | Marker, method and an assay for detection and monitoring of latency and activation of human immunodeficiency virus |
US6001558A (en) * | 1997-06-25 | 1999-12-14 | Ortho Clinical Diagnostics, Inc. | Amplification and detection of HIV-1 and/or HIV 2 |
US6881537B1 (en) * | 1997-08-08 | 2005-04-19 | Biomerieux, B.V. | Nucleic acid sequences that can be used as primers and probes in the amplification and detection of all subtypes of HIV-1 |
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US11447821B2 (en) | 2007-01-23 | 2022-09-20 | Cambridge Enterprise Limited | Nucleic acid amplification and testing |
US10301379B2 (en) | 2014-06-26 | 2019-05-28 | Janssen Vaccines & Prevention B.V. | Antibodies and antigen-binding fragments that specifically bind to microtubule-associated protein tau |
US10400034B2 (en) | 2014-06-26 | 2019-09-03 | Janssen Vaccines & Prevention, B.V. | Antibodies and antigen-binding fragments that specifically bind to microtubule-associated protein tau |
US10562963B2 (en) | 2014-06-26 | 2020-02-18 | Janssen Vaccines & Prevention, B.V. | Antibodies and antigen-binding fragments that specifically bind to microtubule-associated protein tau |
US11472869B2 (en) | 2014-06-26 | 2022-10-18 | Janssen Vaccines & Prevention B.V. | Antibodies and antigen-binding fragments that specifically bind to microtubule-associated protein tau |
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