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Oligonucleotides for the amplification and detection of epstein barr virus (EBV) nucleic acid

a technology of oligonucleotides and epstein barr virus, which is applied in the field of oligonucleotides for the amplification and detection of epstein barr virus (ebv) nucleic acid, can solve the problems of lymphoproliferative disease, full-blown malignancy, and detection of epithelial replication of the virus

Inactive Publication Date: 2004-09-16
VERVOORT M B H J MARCEL BARTOLINA HENDRIKUS JOHANNES +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0047] 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.

Problems solved by technology

In the vast majority of cases EBV infection results in a lymphoproliferative disease that may be temporarily debilitating, but is always benign and self-limiting.
In certain immunosuppressive individuals, however, the result can be uncontrolled lymphoproliferative leading to full-blown malignancy.
In addition, in such patients uncontrolled epithelial replication of the virus is detectable in lesions of oral hairy leukoplakia.
Application of RT-PCR is seriously hampered by the need for spliced mRNA in order to allow viral gene expression in a viral DNA background therefore limiting its use to only a selected set of spliced viral genes.
In addition, the need for high temperatures in the PCR part of the RT-PCR reaction seriously limits its application to in situ diagnostic approaches.
Another drawback of RT-PCR is the requirement of splice sites within the transcript of interest to exclude amplification of genomic DNA and the fact that it is a step reaction.

Method used

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  • Oligonucleotides for the amplification and detection of epstein barr virus (EBV) nucleic acid
  • Oligonucleotides for the amplification and detection of epstein barr virus (EBV) nucleic acid
  • Oligonucleotides for the amplification and detection of epstein barr virus (EBV) nucleic acid

Examples

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example 1

[0063] Selection and Optimization of Specific Primer and Probe Sequences for the Detection of EBNA-1 mRNA.

[0064] From a large panel of in vitro cultured BL and LCL cell lines obtained from different parts of the world and from fresh tumor biopsy specimens from a variety of EBV positive tumor tissues, the specific nucleotide sequence of the BKRF1 reading frame was determined and aligned with the prototype B95-8 sequence. Surprisingly, it became apparent from these data that the field isolates of EBV were rather more conserved when aligned with each other than when compared to the B95-8 sequence, making the latter rather a mutant strain. In addition, certain mutations were observed that were more common among NPC- and LCL's derived sequences obtained from SE-Asia, whereas other mutations were more common among LCL and BL-derived isolates from central Africa, indicative of regional strain differences, in the different LCL's analysed, B95-8 transformed lines could be clearly discriminat...

example 2

[0071] Detection of Additional EBV RNA Targets Using Optimized Primer Sets.

[0072] Similarly, sequence comparison and primer optimization studies allowed the selection of specific sets of reagents for the detection of EBV-encoded mRNA for LMP-1, LMP-2, EBER-1 and other EBV gene targets. For some targets the results are shown in FIG. 2, panels A-D.

[0073] FIG. 2 panels A and B shows the results of NASBA reactions for LMP-1 and LMP-2 on dilution series of EBV-positive JY cells in 50,000 EBV-negative RAMOS cells as described for EBNA1.

[0074] The data indicate that LMP-1 specific primerset 1.1 (SEQ.ID.No.: 12) combined with 2.1 (SEQ.ID.No.: 14), giving a product of 248 bp, allows the detection of mRNA equivalent to 1-10 JY cells in a background of 50,000 EBV-negative RAMOS cells. The LMP-2 set 1.2 (SEQ.ID.No.: 18) combined with 2.1 (SEQ.ID.No.: 19), giving a product of 196 bp, allows the dear detection of 1 JY cell in the presence of 50,000 RAMOS cells, which is slightly better than the c...

example 3

[0077] Optimization of EBV-RNA Isolation and NASBA Reaction Conditions.

[0078] Optimization of RNA isolation method or NASBA reaction conditions, such as concentration of DMSO, KCl or Betaine (N,N,N-trimethylglycine) may improve the sensitivity of detection of EBV-specific RMA without affecting its specificity.

[0079] FIG. 3A shows the comparison of two RNA isolation methods for the isolation of the small molecular weight EBER1 RNA's, which are present at high abundance in EBV-transformed cells like JY, but which are not isolated with high efficiency by the silica method of Boom et al. Standardized quantities of in vitro generated 170 bp runoff transcripts were used as input for RNA isolation using the RNAzol (Cinna Biotex) and Boom isolation methods. Isolated RNA was used as input for NASBA with primers 1.1 (SEQ.ID.No.: 6) and 2.2 (SEQ.ID.No.: 7) giving a product of 140 bp. The results show that the RNAzol method results in a 10-100 fold more efficient extraction level of this small ...

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Abstract

The present invention is concerned with oligonucleotides that can be used as in the amplification and detection of Epstein Barr Virus (EBV) nucleic acid, in particular RNA-specific sequences. Furthermore a method for the diagnosis of EBV associated malignant and non-malignant diseases is provided. The oligonucleotides according to the present invention are specifically suited for the detection of EBV gene expression in circulating peripheral blood cells, in human (tumor) tissue samples and thin sections thereof using "in solution" amplification or "in situ" amplification techniques and in other biological samples potentially containing EBV-infected cells.

Description

[0001] The present invention is concerned with oligonucleotides that can be used in the amplification and detection of Epstein Barr Virus (EBV) mRNA. Furthermore a method for the diagnosis of EBV associated malignant and non-malignant diseases is provided.[0002] The oligonucleotides according to the present invention are specifically suited for the detection of EBV gene expression in circulating peripheral blood cells, in human (tumor) tissue samples and thin sections thereof using "in solution" amplification or "in situ" amplification techniques and in other biological samples potentially containing EBV-infected cells.GENERAL BACKGROUND[0003] Epstein-Barr Virus (EBV) is an ubiquitous human herpes virus that was first discovered in association with the African (endemic or e) form of Burkitt's lymphoma (BL). Subsequently the virus was also found associated with nasopharyngeal carcinoma (NPC) and was shown to be the causative agent of infectious mononucleosis (IM). Infection usually o...

Claims

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Application Information

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IPC IPC(8): C12N15/09C12Q1/68C12Q1/70
CPCC12Q1/705C12Q1/68
Inventor VERVOORT M.B.H.J., MARCEL BARTOLINA HENDRIKUS JOHANNESBRULE VAN DEN A.J.C., ADRIANUS JOHANNES CHRISTIAANMIDDELDORP J.M., JAAP MICHIEL
Owner VERVOORT M B H J MARCEL BARTOLINA HENDRIKUS JOHANNES
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