Method for the amplification and detection of hbv dna using a transcription based amplification

Abstract

The present invention provides a method for the transcription based amplification of a target HBV nucleic acid sequence starting from HBV DNA optionally present in a sample, comprising the steps of,—incubating the sample, suspected to contain HBV, in an amplification buffer with one or more restriction enzymes capable of cleaving the HBV DNA at a selected restriction site, said restriction enzyme creating a defined 3′ end of the said HBV DNA strand(s), a promotor-primer, said promotor-primer having a 5′ region comprising the sequence of a promotor recognized by a DNA-dependent RNA polymerase and a 3′ region complementary to the define 3′ end of the DNA strand, a second or reverse primer, having the opposite polarity of the promotor-primer and comprising the 5′ end of the said target sequence, and in case of HBV ssDNA as the target sequence, a restriction primer,—maintaining the thus created reaction mixture under the appropriate conditions for a sufficient amount of time for a digestion by the restriction enzyme to take place,—subjecting the sample thus obtained to a heat treatment at a temperature and time sufficient to inactivate the restriction enzyme and/or to render at least partially a double strand single stranded,—adding the following reagents to the sample: an enzyme having RNA dependent DNA polymerase activity, an enzyme having DNA dependent DNA polymerase activity, an enzyme having Rnase H activity, an enzyme having RNA polymerase activity, and—maintaining the thus created reaction mixture under the appropriate conditions to a sufficient amount of time for the amplification to take place.

1 . A method for the transcription based amplification of a target HBV nucleic acid sequence starting from HBV DNA optionally present in a sample, said method comprising: 
 -a) incubating the sample, suspected to contain HBV, in an amplification buffer with    i) one or more restriction enzymes capable of cleaving the HBV DNA at a selected restriction site, said restriction enzyme creating a defined 3′ end of the said HBV DNA strand(s),    ii) a promoter-primer, said promoter-primer having a 5′ region comprising the sequence of a promoter recognized by a DNA-dependent RNA polymerase and a 3′ region complementary to the defined 3′ end of the DNA strand,    iii) a second or reverse primer, having the opposite polarity of the promoter-primer and comprising the 5′ end of the said target sequence, and    iv) in case of HBV ssDNA as the target sequence, a restriction primer;    -b) maintaining the thus created reaction mixture under the appropriate conditions for a sufficient amount of time for a digestion by the restriction enzyme to take place;    -c) subjecting the sample thus obtained to a heat treatment at a temperature and time sufficient to inactivate the restriction enzyme and/or to render at least partially a double strand single stranded;    -d) adding the following reagents to the sample: 
 i) an enzyme having RNA dependent DNA polymerase activity  
 ii) an enzyme having DNA dependent DNA polymerase activity  
 iii) an enzyme having Rnase H activity  
 iv) an enzyme having RNA polymerase activity; and  
   e) maintaining the thus created reaction mixture under the appropriate conditions for a sufficient amount of time for the amplification to take place.    
     
     
         2 . The method according to  claim 1 , wherein the DNA is double stranded HBV DNA.  
     
     
         3 . The method according to  claim 1 , wherein the DNA is single stranded and the promoter primer and the restriction primer are combined in using a combined promoter and restriction primer comprising a sequence complementary to the region including the restriction site of the target ssDNA and the sequence of a promoter recognized by a DNA-dependent RNA polymerase.  
     
     
         4 . The method according to  claim 1  in which nucleoside triphosphates are added to the initial incubation mixture prior to the heat treatment.  
     
     
         5 . The method according to  claim 1  in which a reverse transcriptase is used combining the activities of the enzyme having RNA dependent DNA polymerase activity and the enzyme having DNA dependent DNA activity.  
     
     
         6 . The method according to  claim 1 , in which a reverse transcriptase is used having inherent RNase H activity replacing 3 enzymes, namely the enzyme having RNA dependent DNA polymerase activity, the enzyme having DNA dependent DNA activity as well as the enzyme having Rnase H activity.  
     
     
         7 . The method according to  claim 1 , in which the incubation temperature is from about 35° C. to about 45° C.  
     
     
         8 . The method according to  claim 1  in which to the heating step is carried out at a temperature between about 92° C. and about 98° C.  
     
     
         9 . The method according to  claim 1 , wherein a restriction enzyme is used that cuts the HBV DNA at a site that is conserved among the different genotypes of HBV.  
     
     
         10 . The method according to  claim 1 , wherein the restriction site is located in the part of the HBV genome that encodes the surface antigen.  
     
     
         11 . The method according to  claim 10 , wherein the restriction site is an XbaI site located at nucleotides 247-252 according to the EcoRI site, the BssSI site located at nucleotides 253-258 according to the EcoRI site or an AvrII site located at nucleotides 178-183 according to the EcoRI site, and the restriction enzyme used is the XbaI, BssSI or AvrII restriction enzyme.  
     
     
         12 . The method according to  claim 1 , wherein the restriction primer is an oligonucleotide containing from about 10 to about 35 nucleotides which hybridize with the HBV target and comprise at least 10 nucleotides flanking the XbaI site located at nucleotides 247-252 according to the EcoRI site, the BssSI site located at nucleotides 253-258 according to the EcoRI site or the AvrII site located at nucleotides 178-183 according to the EcoRI site.  
     
     
         13 . The method according to  claim 12 , wherein the restriction primer has the oligonucleotide sequence of SEQ ID No. 8 or SEQ ID No 9.  
     
     
         14 . The method according to  claim 1 , wherein the promoter or forward primer is an oligonucleotide containing from about 10 to about 35 nucleotides which hybridize with the HBV target and comprising at least 10 nucleotides, counted from the cleavage site, of the nucleotide sequence of SEQ ID No 10 in combination with the restriction enzyme XbaI, or of SEQ ID No 11 in combination with BssSI or of SEQ ID No 12 in combination with AvrII, linked to a promoter sequence.  
     
     
         15 . The method according to  claim 14 , wherein the promoter oligonucleotide has the nucleotide sequence of SEQ ID No 1, SEQ ID No 2, or SEQ ID No. 3.  
     
     
         16 . The method according to  claim 1 , wherein the amplified HBV nucleic acid is additionally detected using a hybridization probe comprising an oligonucleotide sequence containing from about 10 to about 35 nucleotides which hybridize with the amplified HBV target and comprise at least 10 nucleotides of SEQ ID No. 13 or SEQ ID No 14.  
     
     
         17 . The method according to  claim 16 , wherein the probe has the oligonucleotide sequence of SEQ ID No 6 or SEQ ID No 7.  
     
     
         18 . The method according to  claim 1  wherein the second or reverse primer is an oligonucleotide containing from about 10 to about 35 nucleotides and comprising at least 10 nucleotides of the nucleotide sequence of SEQ ID No. 4 or SEQ ID No. 5.  
     
     
         19 . An oligonucleotide with an nucleotide sequence selected from the group consisting of SEQ ID No 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, and SEQ ID No. 14.  
     
     
         20 . A set of oligonucleotide primers suitable for use in the amplification of HBV nucleic acid according to the method of  claim 1  comprising a promoter primer, wherein the promoter primer is an oligonucleotide containing from about 10 to about 35 nucleotides which hybridize with the HBV target and comprising at least 10 nucleotides, counted from the cleavage site, of the nucleotide sequence of SEQ ID No. 10 in combination with the restriction enzyme XbaI, or of SEQ ID No. 11 in combination with BssSI or of SEQ ID No. 12 in combination with AvrII, linked to a promoter sequence and a reverse primer, wherein the reverse primer is an oligonucleotide containing from about 10 to about 35 nucleotides and comprising at least 10 nucleotides of the nucleotide sequence of SEQ ID No. 4 or SEQ ID No. 5.  
     
     
         21 . A test kit suitable for carrying out the transcription based amplification and detection of HBV DNA according to  claim 1  comprising a restriction enzyme capable of cleaving the HBV DNA at a selected restriction site, said restriction enzyme creating a defined 3′ end of the said HBV DNA strand(s), a forward primer that corresponds with the cleavage site of the restriction enzyme chosen, said forward primer having a 5′ region comprising the sequence of a promoter recognized by a DNA-dependent RNA polymerase and a 3′ region complementary to the defined 3′ end of the DNA strand, and is provided with a promoter sequence, other reagents for carrying out a transcription based amplification reaction, and means for detecting the amplified HBV DNA.  
     
     
         22 . The method according to  claim 1 , in which the incubation temperature is from about 37° C. to about 41° C.  
     
     
         23 . The method according to  claim 1 , in which the heating step is carried out at a temperature of about 95° C.  
     
     
         24 . The method according to  claim 1 , wherein the restriction primer is an oligonucleotide containing from about 15 to about 30 nucleotides which hybridize with the HBV target and comprise at least 15 nucleotides flanking the XbaI site located at nucleotides 247-252 according to the EcoRI site, the BssSI site located at nucleotides 253-258 according to the EcoRI site or the AvrII site located at nucleotides 178-183 according to the EcoRI site.  
     
     
         25 . The method according to  claim 1 , wherein the promoter or forward primer is an oligonucleotide containing from about 15 to about 30 nucleotides which hybridize with the HBV target and comprising at least 15 nucleotides, counted from the cleavage site, of the nucleotide sequence of SEQ ID No. 10 in combination with the restriction enzyme XbaI, or of SEQ ID No. 11 in combination with BssSI or of SEQ ID No. 12 in combination with AvrII, linked to a promoter sequence.  
     
     
         26 . The method according to  claim 1 , wherein the amplified HBV nucleic acid is additionally detected using a hybridization probe comprising an oligonucleotide sequence containing from about 15 to about 30 nucleotides which hybridize with the amplified HBV target and comprise at least 15 nucleotides of SEQ ID No. 13 or SEQ ID No. 14.  
     
     
         27 . The method according to  claim 1 , wherein the second or reverse primer is an oligonucleotide containing from about 15 to about 30 nucleotides and comprising at least 15 nucleotides of the nucleotide sequence of SEQ ID No. 4 or SEQ ID No. 5.  
     
     
         28 . A set of oligonucleotide primers comprising a promoter primer, wherein the promoter primer is an oligonucleotide containing from about 15 to about 30 nucleotides which hybridize with the HBV target and comprising at least 15 nucleotides, counted from the cleavage site, of the nucleotide sequence of SEQ ID No. 10 in combination with the restriction enzyme XbaI, or of SEQ ID No. 11 in combination with BssSI or of SEQ ID No. 12 in combination with AvrII, linked to a promoter sequence and a reverse primer, wherein the reverse primer is an oligonucleotide containing from about 15 to about 30 nucleotides and comprising at least 15 nucleotides of the nucleotide sequence of SEQ ID No. 4 or SEQ ID No. 5.