IN VIVO HCV RESISTANCE TO ANTI-VIRAL INHIBITORS
HCV mutations emerged in chimpanzees treated with a N5B polymerase inhibitor (Compound A) or a NS3 protease inhibitor (Compound B). Short term treatment with Compound A was followed by the initial emergence of an HCV with a S282T polymerase mutation following treatment. Short term treatment with Compound B selected for HCV with a R155K or D168T protease mutation.
1 . A method of determining the existence of a hepatitis C virus (HCV) genotype resistant to a HCV protease inhibitor or HCV polymerase inhibitor comprising the steps of:
a) removing HCV nucleic acid or polypeptide from a patient; and
b) determining whether HCV present in said patient comprises at least one amino acid substitution in:
i) position 282 of NS5B;
ii) position 155 of NS3; and
iii) position 168 of NS3,
wherein one or more amino acid substitutions indicates resistance.
2 . The method of claim 1 , wherein the at least one amino acid substitution is selected from the group consisting of:
a) a threonine at position 282 of NS5B;
b) a lysine, methionine, serine, threonine or glutamine at position 155 of NS3; and
c) an alanine, glutamic acid, glycine, histidine, valine, tyrosine, asparagine or threonine at position 168 of NS3.
3 . The method of claim 2 , wherein the at least one amino acid substitution is selected from the group consisting of:
a) a lysine at position 155 of NS3; and
b) a threonine at position 168 of NS3.
4 . The method of any of claims 1 - 3 , wherein said NS3 is from an HCV genotype 1.
5 . The method of claim 4 , wherein said HCV genotype is 1a.
6 . The method of any of claims 1 - 3 , wherein said NS5B is from an HCV genotype 3a or an HCV genotype 1a.
7 . The method of any of claims 1 - 6 , wherein said method further comprises quantifying the level of said HCV that has at least one amino acid substitution.
8 . The method of any of claims 1 - 7 , wherein nucleic acid is isolated from said patient and the presence of a lysine at position 155 of NS3 is determined using a primer of SEQ ID NO: 2 or 5.
9 . The method of claim 8 , wherein said method further comprises the use of a reverse primer of SEQ ID NO: 3 and a probe comprising SEQ ID NO: 6.
10 . The method of any of claims 1 - 7 , wherein nucleic acid is isolated from said patient and the presence of a threonine at position 168 of NS3 is determined using a primer of SEQ ID NO: 8.
11 . The method of claim 10 , wherein said method further comprises the use of a reverse primer of SEQ ID NO: 9.
12 . The method of any of claims 1 - 7 , wherein nucleic acid is isolated from said patient and the presence of a threonine at position 282 of NS5B is determined using a primer of SEQ ID NO: 11.
13 . The method of claim 12 , wherein said method further comprises the use of a forward primer of SEQ ID NO: 12 and a probe comprising SEQ ID NO: 13.
14 . A nucleic acid 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, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16 and SEQ ID NO:17.