Hdv nucleic acid molecules, fragments and applications thereof

A nucleic acid molecule, comprising at least one fragment of a variant HDV selected from the group consisting of the genome of an HDV, which in molecular terms exhibits, over its entire genome, a genetic divergence or distance ≧20% (less than 80% similarity) with respect to the sequences of an HDV genotype I, of an HDV genotype II or of an HDV genotype III,

• the genome of an HDV, which in molecular terms exhibits a genetic divergence or distance≧25% (less then 75% similarity), over a region referred to as R0, delimited by positions 889 to 1289 of the HDV genome, with respect to the corresponding R0 sequences of an HDV genotype I, of an HDV genotype II or of an HDV genotype III,
• the complete genomes of the HDV isolates or variants referred to as dFr45, dFr47, dFr73, dFr910, dFr48 and dFr644, which exhibit, respectively, the sequences SEQ ID NOS:
• 1, 6, 11, 16, 21 and 26, and
• the genome of an HDV which exhibits a genetic divergence or distance≦15% with at least one of the sequences SEQ ID NOS:
• 1, 6, 11, 16, 21 and 26,
• wherein the at least one fragment is selected from the group consisting of:
• a) the R0 fragments of the following isolated variant HDVs:
• dFr45, dFr47, dFr48, dFr69, dFr73, dFr644, dFr910, dFr1843, dFr1953, dFr2020 and dFr2066 which exhibit, respectively, the following sequences:
• SEQ ID NO:
• 48 to SEQ ID NO:
• 58,
• b) the R1 fragment which extends from position 307 to position 1289 of the HDV genome,
• c) the R2 fragment which extends from position 889 to position 328 of the HDV genome,
• d) the R3 fragment which extends from position 1486 to position 452 of the HDV genome,
• e) the R′1 fragment which extends from position 305 to position 1161 of the HDV genome,
• f) the R′2 fragment which extends from position 984 to position 331 of the HDV genome,
• g) the R644 fragment which extends from position 889 to position 446 of the HDV genome,
• h) the G910 fragment which extends from position 1206 to position 929 of the HDV genome,
• i) the p910 fragment which extends from position 553 to position 1550 of the HDV genome,
• j) the cDNAs encoding the sHD protein, of sequences SEQ ID NOS:
• 4, 9, 14, 19, 24 and 29,
• k) the cDNAs encoding the LHD protein, of sequences SEQ ID NOS:
• 2, 7, 12, 17, 22 and 27, and
• l) the primers of sequence SEQ ID NO:
• 33 to SEQ ID NO:
• 47.

A method for detection and for genotyping of HDV from a biological sample, which method comprises:

• (a) extracting the nucleic acid belonging to the genome of the HDV virus,
• (b) amplifying the region R0 delimited by position 889 to position 1289 of the HDV genome,
• (c) a first treatment of the amplified nucleic acid molecules with the SmaI and XhoI restriction enzymes, so as to produce a first set of restriction fragments,
• (d) a second treatment of nucleic acid molecules with the SacII restriction enzyme, so as to produce a second set of restriction fragments,
• (e) the combined analysis of the two sets of restriction fragments produced by RFLP (Restriction Fragment Length Polymorphism), so as to detect the presence and/or to determine the type of HDV present in said biological sample.