# Patent

## Title
Detection and use of antiviral resistance mutations

## Abstract

The present invention relates generally to viral variants exhibiting reduced sensitivity to particular agents and/or reduced interactivity with immunological reagents. More particularly, the present invention is directed to hepatitis B virus (HBV) variants exhibiting complete or partial resistance to nucleoside or nucleotide analogs and/or reduced interactivity with antibodies to viral surface components including reduced sensitivity to these antibodies. Vaccines and diagnostic assays are also contemplated herein.

## Background
This application is U.S. National Phase of International Application PCT/AU2007/000785, filed Jun. 4, 2007 designating the U.S., and published in English as WO 2007/140522 on Dec. 13, 2007, which claims priority to Australian Patent Application No. 2006903065 filed Jun. 6, 2006.
FIELD
The present invention relates generally to viral variants exhibiting reduced sensitivity to particular agents and/or reduced interactivity with immunological reagents. More particularly, the present invention is directed to hepatitis B virus (HBV) variants exhibiting complete or partial resistance to nucleoside or nucleotide analogs and/or reduced interactivity with antibodies to viral surface components including reduced sensitivity to these antibodies. Vaccines and diagnostic assays are also contemplated herein.
BACKGROUND
Bibliographic details of the publications referred to in this specification are also collected at the end of the description.
The reference to any prior art in this specification is not, and should not be taken as, an acknowledgment or any form of suggestion that that prior art forms part of the common general knowledge in any country.
Hepatitis B virus (HBV) can cause debilitating disease conditions and can lead to acute liver failure. HBV is a DNA virus which replicates via an RNA intermediate and utilizes reverse transcription in its replication strategy (Summers and Mason, Cell 29:403-415, 1982). The HBV genome is of a complex nature having a partially double-stranded DNA structure with overlapping open reading frames encoding surface, core, polymerase and X genes. The complex nature of the HBV genome is represented in FIG. 1. The polymerase consists of four functional regions, the terminal protein (TP), spacer, reverse transcriptase (rt) and ribonuclease (RNAse).
The polymerase gene of HBV overlaps the envelope gene, mutations in the catalytic domain of the polymerase gene can also affect the nucleotide and the deduced amino acid sequence of the envelope protein and vice versa. In particular, the genetic sequence for the neutralization domain of HBV known as the ‘a’ determinant, which is found within the HBsAg and located between amino acids 99 and 169, actually overlaps the major catalytic regions of the viral polymerase protein and in particular domains A and B.
The presence of an HBV DNA polymerase has led to the proposition that nucleoside or nucleotide analogs could act as effective anti-viral agents. Examples of nucleoside or nucleotide analogs currently being tested are penciclovir and its oral form (FCV) [Vere Hodge, Antiviral Chem Chemother 4: 67-84, 1993; Boyd et al, Antiviral Chem Chemother. 32:358-363, 1987; Kruger et al, Hepatology 22:219 A, 1994; Main et al, J. Viral Hepatitis 3:211-215, 1996], Lamivudine [(−)-β-2′-deoxy-3′-thiacytidine]; (3TC or LMV) [Severini et al, Antimicrobial Agents Chemother. 39:430-435, 1995; Dienstag et al, New England J Med 333:1657-1661, 1995]. New nucleoside or nucleotide analogs which have already progressed to clinical trials include the pyrimidines Emtricitabine, ((−)-β-L-2′-3′-dideoxy-5-fluoro-3′-thiacydidine; FTC), the 5-fluoro derivative of 3TC, and Clevudine (1-(2-fluoro-5-methyl-β-L-arabino-furanosyl) uracil; L-FMAU), a thymidine analog. The beta-Lthymidine analogue (LdT has recently been given FDA approval other similar compounds include beta-L-2′-deoxycytidine (LdC) and beta-L-2′-deoxyadenosine (LdA) [Standring et al., Antivir Chem Chemother. 2001; 12 Suppl 1:119-29]. Like 3TC, these are pyrimidine derivatives with an unnatural “L”—configuration. Several purine derivatives have also progressed to clinical trials; they include Entecavir (BMS-200, 475; ETV), a carbocyclic deoxyguanosine analog, diaminopurine dioxolane (DAPD), an oral pro-drug for dioxolane guanine ((−)-β-D-2-aminopurine dioxolane; DXG) and Adefovir dipivoxil, an oral prodrug for the acyclic deoxyadenosine monophosphate nucleoside or nucleotide analog Adefovir (9-[phosphoryl-methoxyethyl]-adenine; PMEA). Other drugs in pre-clinical and clinical trials include FLG [Medivir], ACH-126,443 (L-d4C) [Archillion Pharmaceuticals], ICN 2001-3 (ICN) and Racivir (RCV) [Pharmassett].
Whilst these agents are highly effective in inhibiting HBV DNA synthesis, there is the potential for resistant mutants of HBV to emerge during long term antiviral chemotherapy. In patients on prolonged LMV therapy, key resistance mutations are selected in the rt domain within the polymerase at rtM204I/V+/−rtL180M as well as other mutations. The nomenclature used for the polymerase mutations is in accordance with that proposed by Stuyver et al, 2001, supra. LMV is a nucleoside or anucleotide analog that has been approved for use against chronic HBV infection. LMV is a particularly potent inhibitor of HBV replication and reduces HBV DNA titres in the sera of chronically infected patients after orthotopic liver transplantation (OLT) by inhibiting viral DNA synthesis. LMV monotherapy seems unlikely to be able to control HBV replication in the longer term. This is because emergence of LMV-resistant strains of HBV seems almost inevitable during monotherapy.
Adefovir dipivoxil (ADV: formerly, bis-pom PMEA) is an orally available prodrug of the acyclic deoxyadenosine monophosphate analog adefovir (formerly, PMEA) (FIG. 2). ADV is also a potent inhibitor of HBV replication and has been given FDA approval for use against chronic HBV infection. Adefovir dipivoxil differs from other agents in this class in that it is a nucleotide (vs. nucleoside) analog and as such bypasses the first phosphorylation reaction during drug activation. This step is often rate-limiting. Adefovir dipivoxil has demonstrated clinical activity against both wild-type and lamivudine-resistant strains of HBV and is currently in phase III clinical Testing (Gilson et al, J Viral Hepat 6:387-395, 1999; Perrillo et al, Hepatology 32:129-134, 2000; Peters et al, Transplantation 68:1912-1914, 1999; Benhamou et al, Lancet 358:718-723, 2001). During phase II studies a 30 mg daily dose of adefovir dipivoxil resulted in a mean 4 log10 decrease in viremia over 12 weeks (Heathcote et al, Hepatology 28:A620, 1998).
ADV is a substituted acyclic nucleoside phosphonate. This class of compounds also includes tenofovir disoproxil fumarate (also referred to as tenofovir DF, or tenofovir, or (TFV) or 9-R-(2-phosphonomethoxypropyl)adenine (PMPA) and is marketed as Viread by Gilead sciences).
TFV has antiviral activity against both HBV and HIV (Ying et al, J Viral Hepat. 7(2):161-165, 2000; Ying et al, J. Viral Hepat. 7(1):79-83, 2000, Suo et al, J Biol Chem. 273(42):27250-27258. 1998).
FTC has activity against HBV and HIV (Frick et al, Antimicrob Agents Chemother 37:2285-2292, 1993).
LdT, LdC and LdA have activity against HBV (Standring et al, in supra)
Nucleoside or nucleotide analog therapy may be administered as monotherapy or combination therapy where two or more nucleoside or nucleotide analogs may be administered. The nucleoside or nucleotide analogs may also be administered in combination with other antiviral agents such as interferon or hepatitis B immunoglobulin (HBIG).
There is a need to monitor for the emergence of nucleoside/nucleotide-analog- or antibody-resistant strains of HBV and to develop diagnostic protocols to detect these resistant viruses and/or to use them to screen for and/or develop or design agents having properties making them useful as anti-viral agents. Defective forms of these resistant strains or antigenic components therefrom are also proposed to be useful in the development of therapeutic vaccine compositions as are antibodies directed to viral surface components.
SUMMARY
Throughout this specification, unless the context requires otherwise, the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element or integer or group of elements or integers but not the exclusion of any other element or integer or group of elements or integers.
Nucleotide and amino acid sequences are referred to by a sequence identifier number (SEQ ID NO:). The SEQ ID NOs: correspond numerically to the sequence identifiers <400>1 (SEQ ID NO:1), <400>2 (SEQ ID NO:2), etc. A summary of the sequence identifiers is provided in Table 1. A sequence listing is provided after the claims.
Specific mutations in an amino acid sequence are represented herein as “Xaa1nXaa2” where Xaa1 is the original amino acid residue before mutation, n is the residue number and Xaa2 is the mutant amino acid. The abbreviation “Xaa” may be the three letter or single letter (i.e. “X”) code. An “rt” before “Xaa1nXaa2” means “reverse transcriptase”. An “s” means an envelope gene. The amino acid residues for HBV DNA polymerase are numbered with the residue methionine in the motif Tyr Met Asp Asp (YMDD) being residue number 204 (Stuyver et al, Hepatology 33:751-757, 2001). The amino acid residues for hepatitis B virus surface antigen are number according to Norder et al, (J. Gen. Virol. 74:341-1348, 1993). Both single and three letter abbreviations are used to define amino acid residues and these are summarized in Table 2.
The selection of HBV variants is identified in patients with chronic HBV infection treated with antiviral agents including nucleosides and nucleotide analogs including TFV and/or LMV, or LMV and/or ADV and/or ETV. Consequently, HBV rt variants are contemplated which are resistant to, or which exhibit reduced sensitivity to antiviral agents including nucleosides and nucleotide analogs including, ADV, LMV, TFV, ETV or FTC, or LdT; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. Corresponding mutations in the surface antigen also occur. The identification of these HBV variants is important for the development of assays to monitor ADV, LMV, FTC, TFV, LdT and/or ETV resistance and/or resistance to other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and to screen for agents which are useful as alternative therapeutic agents.
Reference herein to “anti-HBV agents” includes nucleoside and nucleotide analogs as well as immunological reagents (e.g. antibodies to HBV surface components) and chemical, proteinaceous and nucleic acid agents which inhibit or otherwise interfere with viral replication, maintenance, infection, assembly or release.
The detection of such HBV variants is particularly important in the management of therapeutic protocols including the selection of appropriate agents for treating HBV infection. The method of this aspect of the present invention is predicated in part on monitoring the development in a subject of an increased HBV load in the presence of a nucleoside or nucleotide analog or other anti-HBV agents or combinations thereof. The clinician is then able to modify an existing treatment protocol or select an appropriate treatment protocol accordingly.
Accordingly, one aspectis directed to an isolated Hepatitis B virus (HBV) variant wherein said variant comprises a nucleotide mutation in a gene encoding a DNA polymerase resulting in at least one amino acid addition, substitution and/or deletion to said DNA polymerase and wherein said variant exhibits decreased sensitivity to one or more nucleoside or nucleotide analogs selected from the list consisting of ADV, LMV, TFV, ETV, LdT or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. The variant HBV comprises a mutation in an overlapping open reading frame in its genome in a region defined by one or more of domains F and G and domain A through to E of HBV DNA polymerase.
Another aspect provides an isolated HBV variant comprising a nucleotide mutation in the S gene resulting in at least one amino acid addition, substitution and/or deletion to the surface antigen and which exhibits decreased sensitivity to one or more nucleoside or nucleotide analogs selected from the list consisting of ADV, LMV, TFV, ETV, or LdT or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof:
Useful mutants in the rt region include, in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation.
Particularly useful mutants are co-mutations at codons 180, 184 and 204 such as rtL180M and rtT184S and rtM204V, or co-mutations at codons 85, 180, 184, 202, 204 and 236 such as rtS85T, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V. Alternative useful mutations contemplated herein include rtP170H, rtT184A, rtY221H/Y, rtI233T/I, rtT240N/T, rtK241R, rtR242K/R, rtW243R/W, rtI253V, rtI254I/F, rtS256R/S rtW257G/W, rtY257H or mutations at codon 239.
Mutations in the putative tri-phosphate binding site at rtN236T region are proposed herein to be important in antiviral resistance against ADV and/or TFV and/or other nucleoside or nucleotide treatments. Important codons apart from codons 236 include codons 239 which is highly conserved and codons 240, 241, 242 and 243.
In a particular embodiment, an isolated Hepatitis B virus (HBV) variant is provided wherein said variant comprises a nucleotide mutation in a gene encoding a DNA polymerase resulting in at least one amino acid addition, substitution and/or deletion to said DNA polymerase wherein the mutation is selected from the group consisting of:

    (i) a mutation at codon 239, 240, 241, 242 and/or 243;
    (ii) a mutation resulting in an N236I/D/V substitution;
    (iii) a mutation resulting in an S246H/P/Y/S substitution;
    (iv) a mutation resulting in a P170H substitution;
    (v) a mutation resulting in an I253V substitution;
    (vi) co-mutations of two or more substitutions selected from the list consisting of rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V;
    (vii) co-mutations of two or more substitutions selected from the list consisting of rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S; and
    (viii) co-mutations of two or more substitutions selected from the list consisting of rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V;

wherein the HBV variant exhibits decreased sensitivity to a nucleoside or nucleotide analog.



Useful mutations in the S gene include, in one embodiment include sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation.
Particularly useful mutants are sI110V, sP120Q, sF134L/F, sL162I, sL173F, sL175F, sL176V and sP178P/L.
A method is further contemplated for determining the potential for an HBV to exhibit reduced sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof by isolating DNA or corresponding mRNA from the HBV and screening for a mutation in the nucleotide sequence encoding HBV DNA polymerase resulting in at least one amino acid substitution, deletion and/or addition in any one or more of domains F and G and domains A through to E or a region proximal thereto of the DNA polymerase and associated with resistance or decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
The presence of such a mutation is an indication of the likelihood of resistance to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
Also provided is a composition comprising a variant HBV resistant to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof or an HBV surface antigen from the variant HBV or a recombinant or derivative form thereof or its chemical equivalent and one or more pharmaceutically acceptable carriers and/or diluents.
Yet another aspect provides a use of the aforementioned composition or a variant HBV comprising a nucleotide mutation in a gene encoding a DNA polymerase resulting in at least one amino acid addition, substitution and/or deletion to the DNA polymerase and a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof in the manufacture of a medicament for the treatment and/or prophylaxis of hepatitis B virus infection.
Also contemplated is a method for determining whether an HBV strain exhibits reduced sensitivity to a nucleoside or nucleotide analog or other anti-HBV agents or by isolating DNA or corresponding mRNA from the HBV and screening for a mutation in the nucleotide sequence encoding the DNA polymerase wherein the presence of the following mutations in the rt region: in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent one or more other mutation is indicative of a variant which exhibits a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and Thy; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
Still a further methodology comprises screening for a mutation in the nucleotide sequence encoding the envelope genes (s) wherein the presence of the following mutations in the s gene: in one embodiment include sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment include sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or combinations thereof or an equivalent one or more other mutation is indicative of a variant which exhibits a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof.
In a particular embodiment, the variants are in an isolated form such that they have undergone at least one purification step away from naturally occurring body fluid. Alternatively, the variants may be maintained in isolated body fluid or may be in DNA form. The present invention also contemplates infectious molecular clones comprising the genome or parts thereof from a variant HBV. The detection of HBV or its components in cells, cell lysates, cultured supernatant fluid and bodily fluid may be by any convenient means including any nucleic acid-based detection means, for example, by nucleic acid hybridization techniques or via one or more polymerase chain reactions (PCRs). The term “bodily fluid” includes any fluid derived from the blood, lymph, tissue or organ systems including serum, whole blood, biopsy and biopsy fluid, organ explants and organ suspension such as liver suspensions.
Another aspect is directed to a variant HBV comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or a truncation compared to a surface antigen from a reference or wild type HBV and wherein an antibody generated to the reference or wild type surface antigen exhibits an altered immunological profile relative to the HBV variant. One altered profile includes a reduced capacity for neutralizing the HBV. More particularly, the surface antigen of the variant HBV exhibits an altered immunological profile compared to a pre-treatment HBV where the variant HBV is selected for by a nucleoside or nucleotide analog or other anti-HBV agents of the HBV DNA polymerase. The variant HBV of this aspect of the invention may also comprise a nucleotide sequence comprising a single or multiple nucleotide substitution, addition and/or deletion compared to a pre-treatment HBV.
Further contemplated is a method for detecting a variant HBV exhibiting an altered immunological profile said method comprising isolating an HBV from a subject exposed to a nucleoside or nucleotide analog or combination of analogs selected from the listed consisting of ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, and then contacting said HBV with a panel of one or more antibodies to a surface antigen and screening for any change in binding affinity or binding spectrum.
In a related aspect, a method is provided for detecting a variant HBV exhibiting an altered immunological profile said method comprising isolating a serum sample from a subject exposed to a nucleoside or nucleotide analog selected from the listed consisting of ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, and then contacting the serum with a panel of HBV surface antigens or antibody-binding fragments thereof and screening for any change in binding affinity or binding spectrum.
An isolated HBsAg is provided or a recombinant form thereof or derivative or chemical equivalent thereof corresponding to the variant HBV. Generally, the HBsAg or its recombinant or derivative form or its chemical equivalent comprises an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or a truncation compared to an HBsAg from a reference HBV and wherein an antibody directed to a reference HBV exhibits an altered immunological profile to an HBV carrying said variant HBsAg. In one embodiment, the altered immunological profile comprises a reduction in the ability to neutralize the variant HBV.
Another aspect contemplates a method for detecting an agent which exhibits inhibitory activity to an HBV by generating a genetic construct comprising a replication competent-effective amount of the genome from the HBV contained in a plasmid vector and then transfecting said cells with said construct, contacting the cells, before, during and/or after transfection, with the agent to be tested, culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agents; and the subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent. In a preferred embodiment, the plasmid vector in a baculovirus vector and the method comprises generating a genetic construct comprising a replication competent-effective amount of the genome from the HBV contained in or fused to an amount of a baculovirus genome effective to infect cells and then infecting said cells with said construct, contacting the cells, before, during and/or after infection, with the agent to be tested, culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agent and then subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent.
In connection with these methods, the plasmid vector may include genes encoding part or all of other viral vectors such as baculovirus vectors or adenovirus vectors (see Ren and Nassal, J. Virol. 75(3):1104-1116, 2001).
In an alternative embodiment, the method comprises generating a continuous cell line comprising an infectious copy of the genome of the HBV in a replication competent effective amount such that said infectious HBV genome is stably integrated into said continuous cell line such as but not limited to the 2.2.15 or AD cell line, contacting the cells with the agent to be tested, culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to the agent and then subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent.
In an alternative embodiment, a method is contemplated for detecting an agent which exhibits inhibitory activity to an HBV polymerase in an in vitro polymerase assay. The HBV polymerase activity can be examined using established assays (Gaillard et al, Antimicrob Agents Chemother. 46(4):1005-1013, 2002; Xiong et al, Hepatology, 28(6):1669-73, 1998). The HBV polymerase may be a wild-type or reference HBV polymerase or mutant HBV polymerase.
The identification of viral variants enables the production of vaccines comprising particular recombinant viral components such as polymerases or envelope genes PreS1, PreS2, S encoding for L, M, S proteins as well as therapeutic vaccines comprising defective HBV variants. Rational drug design may also be employed to identify or generate therapeutic molecules capable of interacting with a polymerase or envelope genes PreS1, PreS2, S encoding for L, M, S proteins or other component of the HBV. Such drugs may also have diagnostic potential. In addition, defective HBV variants may also be used as therapeutic compositions to generate an immune response against the same, similar or homologous viruses. Alternatively, antibodies generated to the HBV variants or surface components thereof may be used in passive immunization of subjects against infection by HBV variants or similar or homologous viruses. Furthermore, agents such as nucleoside or nucleotide analogs, RNAi or siRNA molecules (both DNA-derived or synthetic), antisense or sense oligonucleotides, chemical or proteinaceous molecules having an ability to down-regulate the activity of a component of HBV and inhibit replication, maintenance, infection, assembly or release are contemplated by the present invention.
A summary of the abbreviations used throughout the subject specification are provided in Table 3.
A summary of sequence identifiers used throughout the subject specification is provided in Table 1.







TABLE 1







Summary of sequence identifiers








SEQUENCE



ID NO:
DESCRIPTION











1
PCR primer OSI 5′


2
PCR primer TTA3 5′


3
PCR primer JM 5′


4
PCR primer TTA4 5′


5
PCR primer OS2 5′


6
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient A


7
Deduced amino acid sequence of catalytic 



region of polymerase resistant HBV Patient A


8
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient A


9
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient B


10
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient B


11
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient B


12
Nucleotide sequence of catalytic region of 



polymerase from resistant HBV Patient C


13
Deduced amino acid sequence of catalytic 



region of polymerase resistant HBV Patient C


14
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient C


15
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient D


16
Deduced amino acid sequence of catalytic region 



of polymerase resistant HBV Patient D


17
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient D


18
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient E


19
Deduced amino acid sequence of catalytic 



region of polymerase resistant HBV Patient E


20
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient E


21
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient F


22
Deduced amino acid sequence of catalytic 



region of polymerase resistant HBV Patient F


23
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient F


24
Nucleotide sequence of catalytic region 



of polymerase from resistant HBV Patient G


25
Deduced amino acid sequence of catalytic 



region of polymerase resistant HBV Patient G


26
Deduced amino acid sequence of envelope 



gene from resistant HBV from Patient G


27
Nucleotide sequence of catalytic region of



polymerase from resistant HBV Patient H


28
Deduced amino acid sequence of catalytic region



of polymerase resistant HBV Patient H


29
Deduced amino acid sequence of envelope



gene from resistant HBV from Patient H


30
Nucleotide sequence of catalytic region of



polymerase from resistant HBV Patient I


31
Deduced amino acid sequence of catalytic region



of polymerase resistant HBV Patient I


32
Deduced amino acid sequence of envelope



gene from resistant HBV from Patient I
















TABLE 2







Single and three letter amino acid abbreviations











Amino Acid
Three-letter Abbreviation
One-letter symbol






Alanine
Ala
A



Arginine
Arg
R



Asparagine
Asn
N



Aspartic acid
Asp
D



Cysteine
Cys
C



Glutamine
Gln
Q



Glutamic acid
Glu
E



Glycine
Gly
G



Histidine
His
H



Isoleucine
Ile
I



Leucine
Leu
L



Lysine
Lys
K



Methionine
Met
M



Phenylalanine
Phe
F



Proline
Pro
P



Serine
Ser
S



Threonine
The
T



Tryptophan
Trp
W



Tyrosine
Tyr
Y



Valine
Val
V



Any residue
Xaa
X
















TABLE 3







Abbreviations








ABBREVIATION
DESCRIPTION





3TC
(LMV); (−)-β-2′-deoxy-3′-thiacytidine


ADV
adefovir dipivoxil


DAPD
diaminopurine dioxalone


DXG
dioxolane guanine


ETV
entecavir


FAM
famciclovir


FCV
famciclovir


FTC
emtricitabine


HBIG
hepatitis B immunoglobulin


HBsAg
hepatitis B surface antigen


HBV
hepatitis B virus


LdT
beta-Lthymidine


LMV
lamividuine


PMEA
9-[phosphonyl-methoxyethyl]-adenine;



adefovir


PMPA
9-R-(2-phosphonomethoxypropyl)adenine


RNase
ribonuclease


rt (“rt” before “Xaa1nXaa2”
reverse transcriptase


means reverse transcriptase)



s (as used in a mutation,
envelope gene


e.g. sF134V)



TFV
tenofovir disoproxil fumarate


YMDD
Tyr Met Asp Asp-a motif in the



polymerase protein; where the Met



residue is designated residue number



204 of the reverse transcriptase












BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a diagrammatic representation showing the partially double stranded DNA HBV genome showing the overlapping open reading frames encoding surface (S), core (C), polymerase (P) and X gene.
FIG. 2 is a diagrammatic representation of the chemical structure of ADV.
FIG. 3 is a diagrammatic representation of the chemical structure of Tenofovir.
FIG. 4 is a representation showing comparison of the HBV nucleotide sequence (SEQ ID NO: 6) encoding the catalytic region of the polymerase gene in samples from Patient A.
FIG. 5 is a representation showing comparison of the deduced amino acid sequence SEQ ID NO: 7 of the catalytic region of the polymerase gene in samples from Patient A.
FIG. 6 is a representation showing comparison of the deduced amino acid sequence SEQ ID NO: 8 of the envelope gene in samples from Patient A.
FIG. 7 is a representation showing comparison of the HBV nucleotide sequence SEQ ID NO: 9 encoding the catalytic region of the polymerase gene in samples from Patient B
FIG. 8 is a representation showing comparison of the deduced amino acid sequence SEQ ID NO: 10 of the catalytic region of the polymerase gene in samples from Patient B
FIG. 9 is a representation showing comparison of the deduced amino acid sequence SEQ ID NO: 11 of the envelope gene in samples from Patient B.
FIG. 10 is a representation the HBV nucleotide sequence SEQ ID NO: 12 that also includes the encoding the catalytic region of the polymerase gene in samples from Patient C
FIG. 11 is a representation the deduced amino acid sequence SEQ ID NO: 13 of the polymerase gene in samples from Patient C.
FIG. 12 is a representation the deduced amino acid sequence SEQ ID NO: 14 of the envelope gene in samples from Patient C.
FIG. 13 is a representation the HBV nucleotide sequence SEQ ID NO: 15 encoding the catalytic region of the polymerase gene in samples from Patient D.
FIG. 14 is a representation the deduced amino acid sequence SEQ ID NO: 16 of the catalytic region of the polymerase gene in samples from Patient D.
FIG. 15 is a representation the deduced amino acid sequence SEQ ID NO: 17 of the envelope gene in samples from Patient D.
FIG. 16 is a representation the HBV nucleotide sequence SEQ ID NO: 18 encoding the catalytic region of the polymerase gene in samples from Patient E.
FIG. 17 is a representation the deduced amino acid sequence SEQ ID NO: 19 of the catalytic region of the polymerase gene in samples from Patient E.
FIG. 18 is a representation the deduced amino acid sequence SEQ ID NO: 20 of the envelope gene in samples from Patient E.
FIG. 19 is a representation the HBV nucleotide sequence SEQ ID NO: 21 encoding the catalytic region of the polymerase gene in samples from Patient F.
FIG. 20 is a representation the deduced amino acid sequence SEQ ID NO: 22 of the catalytic region of the polymerase gene in samples from Patient F.
FIG. 21 is a representation the deduced amino acid sequence SEQ ID NO: 23 of the envelope gene in samples from Patient F.
FIG. 22 is a representation the HBV nucleotide sequence SEQ ID NO: 24 encoding the catalytic region of the polymerase gene in samples from Patient G.
FIG. 23 is a representation the deduced amino acid sequence SEQ ID NO: 25 of the catalytic region of the polymerase gene in samples from Patient G.
FIG. 24 is a representation the deduced amino acid sequence SEQ ID NO: 26 of the envelope gene in samples from Patient G.
FIG. 25 is a representation the HBV nucleotide sequence SEQ ID NO: 27 encoding the catalytic region of the polymerase gene in samples from Patient H.
FIG. 26 is a representation the deduced amino acid sequence SEQ ID NO: 28 of the catalytic region of the polymerase gene in samples from Patient H.
FIG. 27 is a representation the deduced amino acid sequence SEQ ID NO: 29 of the envelope gene in samples from Patient H.
FIG. 28 is a representation the HBV nucleotide sequence SEQ ID NO: 30 encoding the catalytic region of the polymerase gene in samples from Patient I.
FIG. 29 is a representation the deduced amino acid sequence SEQ ID NO: 31 of the catalytic region of the polymerase gene in samples from Patient I.
FIG. 30 is a representation the deduced amino acid sequence SEQ ID NO: 32 of the envelope gene in samples from Patient I.



DETAILED DESCRIPTION
The present invention is predicated in part on the identification and isolation of nucleoside or nucleotide analog-resistant variants of HBV following treatment of patients with either ADV or LMV or ETV or more particularly ADV and LMV or TFV and LMV, or ETV and optionally one or more other nucleoside analogs or nucleotide analogs or other anti-HBV agents such as TFV, LdT, or FTC. In particular, ADV or ADV and LMV or ETV treated patients gave rise to variants of HBV exhibiting decreased or reduced sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. Reference herein to “decreased” or “reduced” in relation to sensitivity to ADV and/or LMV and/or FTC and/or TFV and/or ETV includes and encompasses a complete or substantial resistance to the nucleoside or nucleotide analog or other anti-HBV agents as well as partial resistance and includes a replication rate or replication efficiency which is more than a wild-type in the presence of a nucleoside or nucleotide analog or other anti-HBV agents. In one aspect, this is conveniently measured by an increase in viral load during treatment, or alternatively, there is no substantial decrease in HBV DNA viral load from pre-treatment HBV DNA levels during treatment (i.e., non-response to treatment).
Accordingly, one aspect contemplates an isolated Hepatitis B virus (HBV) variant wherein said variant comprises a nucleotide mutation in a gene encoding a DNA polymerase resulting in at least one amino acid addition, substitution and/or deletion to said DNA polymerase and wherein said variant exhibits decreased sensitivity to one or more nucleoside or nucleotide analogs selected from the list consisting of ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
Another aspect provides a method for determining the potential for an HBV to exhibit reduced sensitivity to a nucleoside or nucleotide analog selected from ADV, LMV, TFV, LdT, FTC and ETV or a combination thereof or optionally other nucleoside or nucleotide analogs, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding HBV DNA polymerase resulting in at least one amino acid substitution, deletion and/or addition in any one or more of domains F and A through E or a region proximal thereto of said DNA polymerase and associated with resistance or decreases sensitivity to one or more of ADV, LMV, TFV, FTC and/or wherein the presence of such a mutation is an indication of the likelihood of resistance to said one or more of ADV, LMV, TFV, LdT, FTC and/or ETV.
A further aspect provides an isolated Hepatitis B virus (HBV) variant is provided wherein said variant comprises a nucleotide mutation in a gene encoding a DNA polymerase resulting in at least one amino acid addition, substitution and/or deletion to said DNA polymerase wherein the mutation is selected from the group consisting of:

    (i) a mutation at codon 239, 240, 241, 242 and/or 243;
    (ii) a mutation resulting in an N236I/D/V substitution;
    (iii) a mutation resulting in an S246H/P/Y/S substitution;
    (iv) a mutation resulting in a P170H substitution;
    (v) a mutation resulting in an I253V substitution;
    (vi) co-mutations of two or more substitutions selected from the list consisting of rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V;
    (vii) co-mutations of two or more substitutions selected from the list consisting of rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S; and
    (viii) co-mutations of two or more substitutions selected from the list consisting of rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V;

wherein the HBV variant exhibits decreased sensitivity to a nucleoside or nucleotide analog.



Unless otherwise indicated, the present disclosure is not limited to specific formulations of components, manufacturing methods, dosage regimens, or the like, as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
It must be noted that, as used in the subject specification, the singular forms “a”, “an” and “the” include plural aspects unless the context clearly dictates otherwise. Thus, for example, reference to “a nucleoside or nucleotide analog” includes a single analog, as well as two or more analogs; reference to “an HBV variant” includes reference to two or more HBV variants; reference to “the invention” includes reference to a single or multiple aspect of the invention; and so forth.
The terms “analog”, “compound”, “active agent”, “pharmacologically active agent”, “medicament”, “active” and “drug” are used interchangeably herein to refer to a chemical compound that induces a desired effect such as inhibit viral replication, infection, maintenance, assembly and/or the function of an enzyme such as HBV DNA polymerase. The terms also encompass pharmaceutically acceptable and pharmacologically active ingredients of those active agents specifically mentioned herein including but not limited to salts, esters, amides, prodrugs, active metabolites, analogs and the like. When the terms “analog”, “compound”, “active agent”, “pharmacologically active agent”, “medicament”, “active” and “drug” are used, then it is to be understood that this includes the active agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, prodrugs, metabolites, analogs, etc.
Therefore, compounds are contemplated which are useful in inhibiting HBV replication, infection, maintenance, assembly and/or the function of an enzyme such as HBV DNA polymerase. Reference to an “analog”, “compound”, “active agent”, “pharmacologically active agent”, “medicament”, “active” and “drug” such as ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. A “combination” also includes a two-part or more such as a multi-part anti-HBV therapeutic composition where the agents are provided separately and given or dispensed separately or admixed together prior to dispensation.
The terms “effective amount” and “therapeutically effective amount” of an agent as used herein mean a sufficient amount of the agent to provide the desired therapeutic or physiological effect of inhibiting HBV replication, infection, maintenance, assembly and/or the function of an enzyme such as HBV DNA polymerase. Furthermore, an “effective HBV-inhibiting amount” or “effective symptom-ameloriating amount” of an agent is a sufficient amount of the agent to directly or indirectly inhibit replication, infection, maintenance, assembly and/or the function of an enzyme such as HBV DNA polymerase. Undesirable effects, e.g. side effects, are sometimes manifested along with the desired therapeutic effect; hence, a practitioner balances the potential benefits against the potential risks in determining what is an appropriate “effective amount”. The exact amount required will vary from subject to subject, depending on the species, age and general condition of the subject, mode of administration and the like. Thus, it may not be possible to specify an exact “effective amount”. However, an appropriate “effective amount” in any individual case may be determined by one of ordinary skill in the art using only routine experimentation.
By “pharmaceutically acceptable” carrier, excipient or diluent is meant a pharmaceutical vehicle comprised of a material that is not biologically or otherwise undesirable, i.e. the material may be administered to a subject along with the selected active agent without causing any or a substantial adverse reaction. Carriers may include excipients and other additives such as diluents, detergents, coloring agents, wetting or emulsifying agents, pH buffering agents, preservatives, and the like.
Similarly, a “pharmacologically acceptable” salt, ester, emide, prodrug or derivative of a compound as provided herein is a salt, ester, amide, prodrug or derivative that this not biologically or otherwise undesirable.
The terms “treating” and “treatment” as used herein refer to reduction in severity and/or frequency of symptoms, elimination of symptoms and/or underlying cause, prevention of the occurrence, of symptoms and/or their underlying cause, and improvement or remediation of damage in relation to HBV infection. Thus, for example, “treating” a patient involves prevention of HBV infection as well as treatment of a clinically HBV symptomatic individual by inhibiting HBV replication, infection, maintenance, assembly and/or the function of an enzyme such as HBV DNA polymerase. Thus, for example, the present method of “treating” a patient with HBV infection or with a propensity for one to develop encompasses both prevention of HBV infection as well as treating HBV infection or symptoms thereof. In any event, the present invention contemplates the treatment or prophylaxis of HBV infection.
“Patient” as used herein refers to an animal, preferably a mammal and more preferably a primate including a lower primate and even more preferably, a human who can benefit from the formulations and methods of the present invention. A patient regardless of whether a human or non-human animal may be referred to as an individual, subject, animal, host or recipient. The compounds and methods of the present invention have applications in human medicine, veterinary medicine as well as in general, domestic or wild animal husbandry. For convenience, an “animal” includes an avian species such as a poultry bird (including ducks, chicken, turkeys and geese), an aviary bird or game bird. The condition in a non-human animal may not be a naturally occurring HBV infection but HBV-like infection may be induced.
As indicated above, the preferred animals are humans, non-human primates such as marmossets, baboons, orangatangs, lower primates such as tupia, livestock animals, laboratory test animals, companion animals or captive wild animals. A human is the most preferred target. However, non-human animal models may be used.
Examples of laboratory test animals include mice, rats, rabbits, guinea pigs and hamsters. Rabbits and rodent animals, such as rats and mice, provide a convenient test system or animal model as do primates and lower primates. Livestock animals include sheep, cows, pigs, goats, horses and donkeys. Non-mammalian animals such as avian species, zebrafish, amphibians (including cane toads) and Drosophila species such as Drosophila melanogaster are also contemplated. Instead of a live animal model, a test system may also comprise a tissue culture system.
An “anti-HBV agent” includes a nucleoside or nucleotide analog, protein, chemical compound, RNA or DNA or RNAi or siRNA oligonucleotide (either DNA-derived or synthetic).
In a particular embodiment, the decreased sensitivity is in respect of ETV. Alternatively, the decreased sensitivity is in respect of ADV or LMV. Alternatively, the decreased sensitivity is in respect of TFV. Alternatively, the decreased sensitivity is in respect of FTC. Alternatively, the decreased sensitivity is in respect of ETV and optionally ADV and LMV. Alternatively, the decreased sensitivity is in respect of ADV and TFV and optionally ETV. Alternatively, the decreased sensitivity is in respect of LMV and TFV and optionally ETV. Alternatively, the decreased sensitivity is in respect of ADV and FTC and optionally ETV. Alternatively, the decreased sensitivity is in respect to FTC and TFV and optionally ETV. Alternatively, the decreased sensitivity is in respect of FTC and LMV and optionally ETV. Alternatively, the decreased sensitivity is in respect of ADV and LMV and TFV and optionally ETV. Alternatively, the decreased sensitivity is in respect to ADV and TFV and FTC and optionally ETV. Alternatively, the decreased sensitivity is in respect to LMV and TFV and FTC and optionally ETV. Alternatively, the decrease sensitivity is in respect of ADV and LMV and FTC and optionally ETV. Alternatively, the decreased sensitivity is in respect of ADV and FTC and TFV and LMV and optionally ETV.
Reference herein to “anti-HBV agents” includes nucleoside and nucleotide analogs as well as immunological reagents (e.g. antibodies to HBV surface components) and chemical, proteinaceous and nucleic acid agents which inhibit or otherwise interfere with viral replication, maintenance, infection, assembly or release. Reference herein to “nucleic acid” includes reference to a sense or antisense molecule, RNA or DNA, oligonucleotides and RNAi and siRNA molecules and complexes containing same.
In addition to a mutation in the gene encoding DNA polymerase, due to the overlapping nature of the HBV genome (FIG. 1), a corresponding mutation may also occur in the gene encoding the S gene encoding the surface antigen (HBsAg) resulting in reduced interactivity of immunological reagents such as antibodies and immune cells to HBsAg. The reduction in the interactivity of immunological reagents to a viral surface component generally includes the absence of immunological memory to recognize or substantially recognize the viral surface component. The present invention extends, therefore, to an HBV variant exhibiting decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof or a reduced interactivity of an immunological reagent to HBsAg wherein the variant is selected for following ADV and/or LMV combination or sequential treatment. The term “sequential” in this respect means ADV followed by LMV and/or TFV and/or ETV, and/or FTC, LMV followed by ADV and/or TFV and/or FTC and/or ETV or ETV followed by one or more of ADV, FTC, LMV and/or TFV, or multiple sequential administrations of each of ETV, ADV, LMV and/or TFV and/or FTC.
A viral variant may, therefore, carry a mutation only in the DNA polymerase gene or both in the DNA polymerase gene and the S gene. The term “mutation” is to be read in its broadest context and includes multiple mutations.
A mutation in any domain of the HBV DNA polymerase and in particular regions F and G, and domains A through to E is contemplated herein provided the mutation leads to decreased sensitivity to ADV and/or LMV and/or TFV and/or ETV and/or FTC and/or LdT or combinations thereof.
In this specification, reference is particularly made to the conserved regions of the DNA polymerase as defined by domains A to E. Regions A to E are defined by the amino acid sequence set forth in Formula II in Australian Patent No. 734831.
Particularly, the mutation results in an altered amino acid sequence in any one or more of domains F and G, and domains A through to E or regions proximal thereto of the HBV DNA polymerase.
Another aspect provides an HBV variant comprising a mutation in an overlapping open reading frame in its genome wherein said mutation is in a region defined by one or more of domains F and G, and domains A through to E of HBV DNA polymerase and wherein said variant exhibits decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
A further aspect contemplates an HBV variant comprising a mutation in the nucleotide sequence encoding HBsAg resulting in an amino acid addition, substitution and/or deletion in said HBsAg wherein said variant exhibits decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
More particularly, a variant HBV is provided comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or a truncation compared to a surface antigen from a reference or wild-type HBV and wherein an antibody generated to the reference or wild-type surface antigen exhibits reduced capacity for neutralizing said HBV variant, said variant selected by exposure of a subject to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
The term “combination therapy” means that both combinations of ADV, LMV, FTC, LdT, TFV, and/or ETV are co-administered in the same composition or simultaneously in separate compositions. The term “sequential therapy” means that the two agents are administered within seconds, minutes, hours, days or weeks of each other and in either order. Sequential therapy also encompasses completing a therapeutic course with one or other of ADV, LMV, FTC, TFV, LdT or ETV and then completing a second or third or subsequent therapeutic courses with the other of ADV, LMV, FTC, TFV, LdT or ETV.
Accordingly, another aspect of contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
A further aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to LMV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to FTC therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to TFV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant BBV is selected for by exposure of a subject to LdT therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Even yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV and LMV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Even still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV and TFV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV and ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
A further aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to LMV and TFV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet a further aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to LMV and ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV and FTC therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to TFV and FTC therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to TFV and ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to FTC and LMV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Even another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to FTC and ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Even yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV, LMV and TFV and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Even still another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV, LMV and TFV and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
A further aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV, LMV and FTC and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to FTC, LMV and TFV and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV, FTC and TFV and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Still yet another aspect contemplates an HBV variant comprising a surface antigen having an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or truncation compared to the pretreatment HBV and wherein the surface antigen of the variant HBV exhibits an altered immunological profile compared to the pretreatment HBV where the said variant HBV is selected for by exposure of a subject to ADV, LMV, FTC and TFV and/or ETV therapy or therapy by one or more other nucleoside or nucleotide analogs or other anti-HBV agents.
Particularly, the variants are in isolated form such that they have undergone at least one purification step away from naturally occurring body fluid. Alternatively, the variants may be maintained in isolated body fluid or may be in DNA form. The present invention also contemplates infectious molecular clones comprising the genome or parts thereof from a variant HBV. Furthermore, the present invention provides isolated components from the variant HBVs such as but not limited to an isolated HBsAg. Accordingly, the present invention provides an isolated HBsAg or a recombinant form thereof or derivative or chemical equivalent thereof, said HBsAg being from a variant HBV selected by exposure of a subject to one or more of ADV, LMV, FTC, TFV and/or ETV or optionally one or more nucleoside or nucleotide analogs or other anti-HBV agents.
More particularly, an isolated variant HBsAg or a recombinant or derivative form thereof or a chemical equivalent thereof is provided wherein said HBsAg or its recombinant or derivative form or its chemical equivalent exhibits an altered immunological profile compared to an HBsAg from a reference HBV, said HBsAg being from a variant HBV selected by exposure of a subject to one or more of ADV, LMV, FTC, TFV and/or ETV or optionally one or more nucleoside or nucleotide analogs or other anti-HBV agents.
Even more particularly, an isolated variant HBsAg or a recombinant or derivative form thereof or a chemical equivalent thereof is provided wherein said HBsAg or its recombinant or derivative form or its chemical equivalent comprises an amino acid sequence with a single or multiple amino acid substitution, addition and/or deletion or a truncation compared to an HBsAg from a reference HBV and wherein a neutralizing antibody directed to a reference HBV exhibits no or reduced neutralising activity to an HBV carrying said variant HBsAg, said HBsAg being from a variant HBV selected by exposure of a subject to one or more of ADV, LMV, FTC, TFV and/or ETV or optionally one or more nucleoside or nucleotide analogs or other anti-HBV agents.
Particular mutations in the HBV DNA polymerase include variants selected from patients with HBV recurrence following ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. Nucleoside or nucleotide analogs or other anti-HBV agents may be indicated during, after or prior to a transplantation procedure (e.g. bone marrow transplantation (BMT) or OLT) or following treatment of patients diagnosed with hepatitis. Following selection of variants, viral loads are obtainable at levels similar to pre-treatment levels or increase while on therapy.
Useful mutants in the rt region include, in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation.
Particularly useful mutants are co-mutations at codons 180, 184 and 204 such as rtL180M and rtT184S and rtM204V, or co-mutations at codons 85, 180, 184, 202, 204 and 236 such as rtS85T, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/DN. Alternative useful mutations contemplated herein include rtP170H, rtT184A, rtY221H/Y, rtI233T/I, rtT240N/T, rtK241R, rtR242K/R, rtW243R/W, rtI253V, rtI254I/F, rtS256R/S rtW257G/W, rtY257H or mutations at codon 239. A “co-mutation” means that a variant will comprise mutations at all mentioned codons. The present invention is particularly directed to co-mutations at codons 180, 184 and 204 as well as co-mutations at codons 85, 180, 184, 202, 204 and 236 but does not extend to a double mutation at codons 180 and 204 alone.
Such HBV variants are proposed to exhibit a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof. It should be noted that the nomenclature system for amino acid positions is based on the methionine residues in the YMDD motif being designated codon rtM204. This numbering system is different to that in Australian Patent No. 734831 where the methionine residue in the YMDD motif within the polymerase gene is designated codon 550. In this regard, rtL180M and rtM204V correspond to L526M and M550V, respectively, in Australian Patent No. 734831. Corresponding mutations may also occur in envelope genes such as in one or more of PreS1, PreS2 and S.
Another potential mode of action of ADV and other acyclic nucleoside phosphonates is that of immune stimulation (Calio et al, Antiviral Res. 23:77-89, 1994). A number of mutations resulted in changes in the envelope gene detected in HBV variants which may be associated with immune escape. These changes include in one embodiment include sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation.
Particularly useful mutants are sI110V, sP120Q, sF134L/F, sL162I, sL173F, sL175F, sL176V and sP178P/L.
The identification of the variants herein permits the generation of a range of assays to detect such variants. The detection of such variants may be important in identifying resistant variants to determine the appropriate form of chemotherapy and/or to monitor vaccination protocols, or develop new or modified vaccine preparations.
Still another aspect contemplates a method for determining the potential for an HBV to exhibit reduced sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding HBV DNA polymerase resulting in at least one amino acid substitution, deletion and/or addition in any one or more of domains F and G, and A domains through to E or a region proximal thereto of said DNA polymerase and associated with resistance or decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents wherein the presence of such a mutation is an indication of the likelihood of resistance to said ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents.
Accordingly, another aspect provides a method for determining the potential for an HBV to exhibit reduced sensitivity to a nucleoside or nucleotide analog selected from ADV, LMV, TFV, LdT, FTC and ETV or optionally other nucleoside or nucleotide analogs, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding HBV DNA polymerase resulting in at least one amino acid substitution, deletion and/or addition in any one or more of domains F and A through E or a region proximal thereto of said DNA polymerase and associated with resistance or decreases sensitivity to one or more of ADV, LMV, TFV, LdT, FTC and/or ETV wherein the presence of such a mutation is an indication of the likelihood of resistance to said one or more of ADV, LMV, TFV, LdT, FTC and/or ETV.
Particularly, the assay detects one or more of the following mutations: in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation is indicative of a variant wherein said variant exhibits a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof.
Accordingly, another aspect produces a method for determining whether an HBV strain exhibits reduced sensitivity to a nucleoside or nucleotide analog or other anti-HBV agents, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding the DNA polymerase and/or a corresponding region of the S gene, wherein the presence of a mutation selected from, in one embodiment include sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation, in even still another embodiment one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM2041/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or combinations thereof or an equivalent one or more other mutation is indicative of a variant which exhibits a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
A further aspect produces a method for determining whether an HBV strain exhibits reduced sensitivity to a nucleoside or nucleotide analog or other anti-HBV agents, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding the DNA polymerase and/or a corresponding region of the S gene, wherein the presence of a mutation selected from, in one embodiment include s192T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL1621 and sI195M or a combination thereof or an equivalent mutation, in even still another embodiment, in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or combinations thereof or an equivalent one or more other mutation is indicative of a variant which exhibits a decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
The detection of HBV or its components in cells, cell lysates, cultured supernatant fluid and bodily fluid may be by any convenient means including any nucleic acid-based detection means, for example, by nucleic acid hybridization techniques or via one or more polymerase chain reactions (PCRs). The term “bodily fluid” includes any fluid derived from the blood, lymph, tissue or organ systems including serum, whole blood, biopsy and biopsy fluid, organ explants and organ suspension such as liver suspensions. The invention further encompasses the use of different assay formats of said nucleic acid-based detection means, including restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), single-strand chain polymorphism (SSCP), amplification and mismatch detection (AMD), interspersed repetitive sequence polymerase chain reaction (IRS-PCR), inverse polymerase chain reaction (iPCR) and reverse transcription polymerase chain reaction (RT-PCR), amongst others. Other forms of detection include Northern blots, Southern blots, PCR sequencing, antibody procedures such as ELISA, Western blot and immunohistochemistry. A particularly useful assay includes the reagents and components required for immobilized oligonucleotide- or oligopeptide-mediated detection systems.
One particularly useful nucleic acid detection system is the reverse hybridization technique. In this technique, DNA from an HBV sample is amplified using a biotin or other ligand-labeled primer to generate a labeled amplificon. Oligonucleotides immobilized to a solid support such as a nitrocellulose film are then used to capture amplified DNA by hybridization. Specific nucleic acid fragments are identified via biotin or the ligand. Generally, the labeled primer is specific for a particular nucleotide variation to be detected. Amplification occurs only if the variation to be detected is present. There are many forms of the reverse hybridization assay and all are encompassed by the present invention.
Another aspect contemplated herein provides a method for detecting a variant HBV exhibiting an altered immunological profile said method comprising isolating an HBV from a subject exposed to a nucleoside or nucleotide analog selected from the listed consisting of ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, and then contacting said HBV with a panel of one or more antibodies to a surface antigen and screening for any change in binding affinity or binding spectrum.
In a related embodiment, a method is contemplated for detecting a variant HBV exhibiting an altered immunological profile said method comprising isolating a serum sample from a subject exposed to a nucleoside or nucleotide analog selected from the listed consisting of ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, and then contacting the serum with a panel of HBV surface antigens or antibody-binding fragments thereof and screening for any change in binding affinity or binding spectrum.
Detecting HBV replication in cell culture is particularly useful.
This and other aspects are particularly amenable to microarray analysis such as to identify oligonucleotides including sense and antisense molecules, RNAi or siRNA molecules or DNA or RNA-binding molecules which down-regulate genomic sequences or transcripts of HBV. Microarray analysis may also be used to identify particular mutations in the HBV genome such as within the HBV DNA polymerase-coding region or the HBsAg-coding region.
Another aspect of contemplates a method for detecting an agent which exhibits inhibitory activity to an HBV by:

    
    
        generating a genetic construct comprising a replication competent-effective amount of the genome from the HBV contained in a plasmid vector and then transfecting said cells with said construct;
        contacting the cells, before, during and/or after transfection, with the agent to be tested;
        culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agents; and
        then subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent.
    
    


In a particular embodiment, the plasmid vector may include genes encoding part or all of other viral vectors such as baculovirus or adenovirus (Ren and Nassal, 2001, supra) and the method comprises:

    
    
        generating a genetic construct comprising a replication competent-effective amount of the genome from the HBV contained in or fused to an amount of a baculovirus genome or adenovirus genome effective to infect cells and then infecting said cells with said construct;
        contacting the cells, before, during and/or after infection, with the agent to be tested;
        culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agent; and
        then subjecting the Cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent.
    
    


In an alternative embodiment, the method comprises:

    
    
        generating a continuous cell line comprising an infectious copy of the genome of the HBV in a replication competent effective amount such that said infectious HBV genome is stably integrated into said continuous cell line such as but not limited to 2.2.15 or AD;
        contacting the cells with the agent to be tested;
        culturing the cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to the agent; and
        then subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of the agent.
    
    


The above-mentioned methods are particularly useful in identifying or developing agents against HBV variants such as those carrying mutations, in one embodiment includes rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation; in a further embodiment includes sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation.
Accordingly, another aspect contemplates a method for determining whether an HBV strain exhibits reduced sensitivity to a nucleoside or nucleotide analog or other potential anti-HBV agent, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence of the envelope genes or DNA polymerase gene selected from, in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation; in a further embodiment, in one embodiment include sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY2251I/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL1621 and sI195M or a combination thereof or an equivalent mutation and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof.
The detection of amino acid variants of DNA polymerase is conveniently accomplished by a range of amino acid detection techniques. Where an HBV variant comprises an amino acid change, then such an isolate is considered a putative HBV variant having an altered DNA polymerase activity.
Further contemplated herein are agents which inhibit ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof resistant HBV variants. Such agents are particularly useful if long term treatment by ADV, LMV, FTC, TFV, LdT and/or ETV and/or optionally other nucleoside or nucleotide analogs such as TFV is contemplated by the clinician. The agents may be DNA or RNA or proteinaceous or non-proteinaceous chemical molecules. Natural product screening such as from plants, coral and microorganisms is also contemplated as a useful potential source of masking agents as is the screening of combinatorial or chemical libraries. The agents may be in isolated form or in the form of a pharmaceutical composition or formulation and may be administered in place of or sequentially or simultaneously with a nucleoside or nucleotide analog. Furthermore, rationale drug design is contemplated including solving the crystal or NMR structure of, for example, HBV DNA polymerase and designing agents which can bind to the enzyme's active site. This approach may also be adapted to other HBV components.
Accordingly, another aspect contemplates a method for detecting an agent which exhibits inhibitory activity to an HBV which exhibits resistance or decreased sensitivity ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof, said method comprising:

    
    
        generating a genetic construct comprising a replication competent-effective amount of the genome from said HBV contained in a plasmid vector and then transfecting said cells with said construct;
        contacting said cells, before, during and/or after transfection, with the agent to be tested;
        culturing said cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agent; and
        subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of said agent.
    
    


Still another aspect provides a method for detecting an agent which exhibits inhibitory activity to an HBV which exhibits resistance or decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof, method comprising:

    
    
        generating a genetic construct comprising a replication competent-effective amount of the genome from said HBV contained in or fused to an amount of a baculovirus genome effective to infect cells and then infecting said cells with said construct;
        contacting said cells, before, during and/or after infection, with the agent to be tested;
        culturing said cells for a time and under conditions sufficient for the HBV to replicate, express genetic sequences and/or assemble and/or release virus or virus-like particles if resistant to said agent; and
        subjecting the cells, cell lysates or culture supernatant fluid to viral- or viral-component-detection means to determine whether or not the virus has replicated, expressed genetic material and/or assembled and/or been released in the presence of said agent.
    
    


Particularly, the HBV genome is stably integrated into the cells' genome.
Useful cells include 2.2.15 cells (Price et al, Proc. Natl. Acad. Sci. USA 86(21):8541-8544, 1989 or AD cells (also known as HepAD32 cells or HepAD79 cells [Ying et al, 2000, supra].
Whilst the baculovirus vector is a particularly useful in the practice of the instant method a range of other vectors may also be used such as but not limited to adenoviral vectors.
Cell lines (e.g. 2.2.15 or AD cells) carrying genetic constructs comprising all or a portion of an HBV genome or a gene or part of a gene therefrom are also contemplated herein.
Also provided is the use of the subject HBV variants to screen for anti-viral agents. These anti-viral agents inhibit the virus. The term “inhibit” includes antagonizing or otherwise preventing infection, replication, assembly and/or release or any intermediate step. Particular anti-viral agents include nucleoside or nucleotide analogs or anti-HBV agents, as well as non-nucleoside molecules.
In addition, rational drug design is also contemplated to identify or generate chemical molecules which either mimic a nucleoside or which interact with a particular nucleotide sequence or a particular nucleotide. Combinatorial chemistry and two hybrid screening are some of a number of techniques which can be employed to identify potential therapeutic or diagnostic agents.
In one example, the crystal structure or the NMR structure of polymerase or the surface antigen is used to rationally design small chemical molecules likely to interact with key regions of the molecule required for function and/or antigenicity. Such agents may be useful as inhibitors of polymerase activity and/or may alter an epitope on the surface antigen.
Several models of the HBV polymerase have been prepared due to the similarity with reverse transcriptase from HIV (Das et al, J. Virol. 75(10:4771-4779, 2001; Bartholomeusz et al, Intervirology 40(5-6):337-342 1997; Allen et al, Hepatology 27(6):1670-1677, 1998). The models of the HBV polymerase can be used for the rational drug design of new agents effective against HBV encoding the resistant mutations as well as wild type virus. The rational drug that is designed may be based on a modification of an existing antiviral agent such as the agent used in the selection of the HBV encoding the mutations associated with resistance. Viruses or clones expressing HBV genomic material encoding the mutations may also be used to screen for new antiviral agents.
In an alternative embodiment, a method is contemplated for detecting an agent which exhibits inhibitory activity to an HBV polymerase in an in vitro polymerase assay. The HBV polymerase activity can be examined using established assays (Gaillard et al, 2002, supra; Xiong et al, 1998, supra).
As indicated above, microarray technology is also a useful means of identifying agents which are capable of interacting with defined HBV internal or external components. For example, arrays of HBV DNA polymerase or peptide fragments thereof carrying different amino acid variants may be used to screen for agents which are capable of binding or otherwise interacting with these molecules. This is a convenient way of determining the differential binding patterns of agents between HBV variants. Arrays of antibodies may also be used to screen for altered HBsAg molecules. Microarrays are also useful in proteomic analysis to identify molecules such as antibodies, interferons or cytokines which have an ability to interact with an HBV component. Microarrays of DNA and RNA molecules may also be employed to identify sense and antisense molecules for genetic regions on the HBV genome or transcripts thereof.
The above methods are particularly useful in identifying an inhibitor of an HBV resistant to or exhibiting reduced sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof. The present invention extends, therefore, to compositions of the inhibitors. The inhibitors may also be in the form of antibodies or genetic molecules such as ribozymes, antisense molecules and/or sense molecules for co-suppression or the induction of RNAi or may be other nucleoside or nucleotide analogs or other anti-HBV agents or derivatives of known analogs. Reference to RNAi includes reference to short, interfering RNAs (siRNA) and all RNAi-type molecules may be DNA-derived or synthetic.
The term “composition” includes a “pharmaceutical composition” or a formulation.
The inhibitor is referred to below as an “active ingredient” or “active compound” and may be selected from the list of inhibitors given above.
The composition may include an antigenic component of the HBV, a defective HBV variant or an agent identified through natural product screening or rational drug design (including combinatorial chemistry).
Pharmaceutically acceptable carriers and/or diluents include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, use thereof in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
The pharmaceutical composition may also comprise genetic molecules such as a vector capable of transfecting target cells where the vector carries a nucleic acid molecule capable of encoding an aspartyl protease inhibitor. The vector may, for example, be a viral vector.
Pharmaceutical forms suitable for injectable use include sterile aqueous solutions (where water soluble) and sterile powders for the extemporaneous preparation of sterile injectable solutions. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dilution medium comprising, for example, water, ethanol, polyol (for example, glycerol, propylene glycol and liquid polyethylene glycol, and the like), suitable mixtures thereof and vegetable oils. The proper fluidity can be maintained, for example, by the use of superfactants. The preventions of the action of microorganisms can be brought about by various anti-bacterial and anti-fungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminium monostearate and gelatin.
Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with the active ingredient and optionally other active ingredients as required, followed by filtered sterilization or other appropriate means of sterilization. In the case of sterile powders for the preparation of sterile injectable solutions, suitable methods of preparation include vacuum drying and the freeze-drying technique which yield a powder of active ingredient plus any additionally desired ingredient.
When the active ingredient is suitably protected, it may be orally administered, for example, with an inert diluent or with an assimilable edible carrier, or it may be enclosed in hard or soft shell gelatin capsule, or it may be compressed into tablets. For oral therapeutic administration, the active ingredient may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers and the like. Such compositions and preparations should contain at least 1% by weight of active compound. The percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 5 to about 80% of the weight of the unit. The amount of active compound in such therapeutically useful compositions is such that a suitable dosage will be obtained. Preferred compositions or preparations according to the present invention are prepared so that an oral dosage unit form contains between about 0.1 μg and 200 mg of active compound. Alternative dosage amounts include from about 1 μg to about 1000 mg and from about 10 μg to about 500 mg. These dosages may be per individual or per kg body weight. Administration may be per hour, day, week, month or year.
The tablets, troches, pills, capsules and the like may also contain the components as listed hereafter. A binder such as gum, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, lactose or saccharin may be added or a flavouring agent such as peppermint, oil of wintergreen or cherry flavouring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills or capsules may be coated with shellac, sugar or both. A syrup or elixir may contain the active compound, sucrose as a sweetening agent, methyl and propylparabens as preservatives, a dye and a flavouring. Of course, any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed. In addition, the active compound(s) may be incorporated into sustained-release preparations and formulations.
As stated above, the present invention further extends to an isolated HBsAg from the HBV variants herein described. More particularly, the present invention provides an HBsAg or a recombinant form thereof or derivative or chemical equivalent thereof. The isolated surface component and, more particularly, isolated surface antigen or its recombinant, derivative or chemical equivalents are useful in the development of biological compositions such as vaccine formulations.
Yet another aspect provides a composition comprising a variant HBV resistant to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or an HBV surface antigen from said variant HBV or a recombinant or derivative form thereof or its chemical equivalent and one or more pharmaceutically acceptable carriers and/or diluents. Such a composition may be regarded as a therapeutic composition and is useful in generating an immune response including a humoral response. Generally, the HBV variants are “defective” and in themselves are unable to cause a sustained infection in a subject.
As indicated above, antibodies may be generated to the mutant HBV agents and used for passive or direct vaccination against infection by these viruses. The antibodies may be generated in humans or non-human animals. In the case of the latter, the non-human antibodies may need to be deimmunized or more specifically humanized prior to use. Deimmunized may include, for example, grafting complimentarity determining regions (CDRs) from the variable region of a murine or non-human animal anti-HBV antibody onto a human consensus fragment antibody binding (Fab) polypeptide. Alternatively, amino acids defining epitopes in the variable region of the antibody may be mutated so that the epitopes are no longer recognized by the human MHC II complex.
Insofar as ribozyme, antisense or co-suppression (RNAi) or siRNA or complexes thereof repression is concerned, this is conveniently aimed at post-transcription gene silencing. DNA or RNA may be administered or a complex comprising RNAi or a chemical analog thereof specific for HBV mRNA may be employed.
All such molecules may be incorporated into pharmaceutical compositions.
In another embodiment, provided is a biological composition comprising a variant HBV or an HBsAg or L, M or S proteins from said variant HBV or a recombinant or derivative form thereof or its chemical equivalent.
Generally, if an HBV is used, it is first attenuated. The biological composition generally further comprises one or more pharmaceutically acceptable carriers and/or diluents.
The biological composition may comprise HBsAg or like molecule from one HBV variant or the composition may be a cocktail of HbsAgs or L, M or S proteins or like molecules from a range of ADV- and/or LMV- and/or, FTC-LdT-, and/or TFV-resistant HBV variants. Similar inclusions apply where the composition comprises an HBV.
Further provided is the use of defective HBV variants in the manufacture of therapeutic vaccines to vaccinate individuals against infection by HBV strains having a particular nucleotide sequence or encoding a particular polymerase or surface antigen or L, M or S proteins.
Examples of suitable vaccine candidates are defective forms of HBV variants comprising a mutation selected from, in one embodiment includes, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation; in a further embodiment, sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation.
In one embodiment, for example, an HBV variant may be identified having a particular mutation in its polymerase conferring resistance or decreased sensitivity to a nucleoside or nucleotide analog. This variant may then be mutated to render it defective, i.e. attenuated or unable to cause infection. Such a defective, nucleoside or nucleotide analog-resistant virus may then be used as a therapeutic vaccine against virulent viruses having the same mutation in its polymerase.
The subject invention extends to kits for assays for variant HBV resistant to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof. Such kits may, for example, contain the reagents from PCR or other nucleic acid hybridization technology or reagents for immunologically based detection techniques. A particularly useful assay includes the reagents and components required for immobilized oligonucleotide- or oligopeptide-mediated detection systems.
Still another aspect of contemplates a method for determining the potential for an HBV to exhibit reduced sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combination thereof, said method comprising isolating DNA or corresponding mRNA from said HBV and screening for a mutation in the nucleotide sequence encoding HBV DNA polymerase resulting in at least one amino acid substitution, deletion and/or addition in any one or more of domains F and G, and domains A through to E or a region proximal thereto of said DNA polymerase and associated with resistance or decreased sensitivity to ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof, wherein the presence of such a mutation is an indication of the likelihood of resistance to said ADV, LMV, TFV, LdT, ETV or FTC; ADV and LMV; ADV and TFV; LMV and TFV; FTC and ADV; FTC and TFV; FTC and LMV; ETV and ADV; ETV and LMV; ETV and FTC; ETV and TFV; ADV and LMV and TFV; or ADV and FTC and TFV; TFV and FTC and LMV; ADV and LMV and ETV, ADV and ETV and TFV; ETV and LMV and TFV; ADV and LMV and FTC; ADV and FTC and LMV and TFV; ETV and FTC and LMV and TFV; ADV and ETV and LMV and TFV; ADV and FTC and ETV and TFV; ADV and FTC and LMV and ETV; or ADV and FTC and LMV and TFV and ETV and/or optionally other nucleoside or nucleotide analogs or other anti-HBV agents or combinations thereof.
An assessment of a potential viral variant is important for selection of an appropriate therapeutic protocol. Such an assessment is suitably facilitated with the assistance of a computer programmed with software, which inter alia adds input codes for at least two features associated with the viral variants to provide a value corresponding to the resistance or sensitivity of a viral variant to a particular chemical compound or immunological agent. The value can be selected from (a) the ability to exhibit resistance for reduced sensitivity to a particular compound or immunological agent; (b) an altered DNA polymerase from wild-type HBV; (c) an altered surface antigen from wild-type HBV; or (d) morbidity or recovery potential of a patient. Thus, in accordance with the present invention, the values for such features are stored in a machine-readable storage medium, which is capable of processing the data to provide a value for a particular viral variant or a biological specimen comprising same.
Thus, in another aspect, a computer program product is contemplated for assessing the likely usefulness of a viral variant or biological sample comprising same for determining an appropriate therapeutic protocol in a subject (FIG. 15), said product comprising:

    
    
        (1) code that receives as input code for at least two features associated with said viral agents or biological sample comprising same, wherein said features are selected from:
        
            (a) the ability to exhibit resistance for reduced sensitivity to a particular compound or immunological agent;
            (b) an altered DNA polymerase from wild-type HBV;
            (c) an altered surface antigen from wild-type HBV; or
            (d) morbidity or recovery potential of a patient;
        
        
        (2) code that adds said input code to provide a sum corresponding to a value for said viral variants or biological samples; and
        (3) a computer readable medium that stores the codes.
    
    


In a related aspect, a computer is provided for assessing the likely usefulness of a viral variant or biological sample comprising same in a subject, wherein said computer comprises:

    
    
        (1) a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said machine-readable data comprise input codes for at least two features associated with said viral variant or biological sample; wherein said features are selected from:—
        
            (a) the ability to exhibit resistance for reduced sensitivity to a particular compound or immunological agent;
            (b) an altered DNA polymerase from wild-type HBV;
            (c) an altered surface antigen from wild-type HBV; or
            (d) morbidity or recovery potential of a patient;
        
        
        (2) a working memory for storing instructions for processing said machine-readable data;
        (3) a central-processing unit coupled to said working memory and to said machine-readable data storage medium, for processing said machine readable data to provide a sum of said input code corresponding to a value for said compound(s); and
        (4) an output hardware coupled to said central processing unit, for receiving said value.
    
    


Any general or special purpose computer system is contemplated by the present invention and includes a processor in electrical communication with both a memory and at least one input/output device, such as a terminal. FIG. 15 shows a generally suitable computer system. Such a system may include, but is not limited, to personal computers, workstations or mainframes. The processor may be a general purpose processor or microprocessor or a specialized processor executing programs located in RAM memory. The programs may be placed in RAM from a storage device, such as a disk or pre-programmed ROM memory. The RAM memory in one embodiment is used both for data storage and program execution. The computer system also embraces systems where the processor and memory reside in different physical entities but which are in electrical communication by means of a network.
In an alternative embodiment, the program screens for a mutation selected from, in one embodiment, rtS256R/S and rtW257G/W, in another embodiment includes rtH9D, rtL180M, rtM204V, rtT184S and rtN238T, or yet another embodiment includes rtQ215S, rtR242K/R, and rtW243R/W, or yet another embodiment includes rtN118S, rtR120R, rtT184A and rtY257H, or still another embodiment includes rtH216H/P, rtL229M/L, rtI233T/I, rtT240N/T, rtK241R and rtH248N or yet another embodiment includes rtL180M, rtA181V, rtM207V, rtH216H/P, rtE218D/E, rtH238D, rtR242K/R, rtW243G/W and rtI254I/F, or still another embodiment includes rtY221H/Y, rtV214A, rtA181A/V and rtN236T, or still another embodiment includes rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V and rtN236I/D/V, or yet another embodiment includes rtF61L, rtS78T, rtV84MN, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S, or finally in another embodiment includes rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V, or a combination thereof or an equivalent mutation; in a further embodiment sI92T/I, sL175F and sI195M, in another embodiment include sS207R, or yet another embodiment include sI110V and sP120Q, or yet another embodiment include sF80S, sI208I/L, sS210K, sF220L/F and sY225H/Y, or yet another embodiment includes sF134L/F and sL173F, or yet another embodiment includes sC76Y and sL173F, or yet another embodiment includes sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M, or yet another embodiment includes sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S and sY225H/Y, and finally in another embodiment includes sL20F, sI42L, sV144D, sL162I and sI195M or a combination thereof or an equivalent mutation.
The present invention is further described by the following non-limiting Examples.
EXAMPLE 1
Overlapping Genome of HBV
The overlapping genome of HBV is represented in FIG. 1. The gene encoding DNA polymerase (P), overlaps the viral envelope genes, Pre-S1 and Pre-S2, and partially overlaps the X and core (C) genes. The HBV envelope comprises small, middle and large proteins HBV surface antigens. The large protein component is referred to as the HBV surface antigen (HBsAg) and is encoded by the S gene sequence. The Pre-S1 and Pre-S2 gene sequences encode the other envelope components.
EXAMPLE 2
Patients on TFV and LMV and Analysis of HBV DNA
Patient A: During TFV and LMV treatment, unique HBV mutations were detected by sequencing (Table 4). This patent has had selected unique mutations at rtS256R/S and rtW257G/W (Table 4, FIGS. 4, 5, and 6) during virological breakthrough on treatment. These changes do not alter the HBsAg in the overlapping reading frame as they are after the termination codon in the HBsAg reading frame.
Patient B: During TFV and LMV treatment, unique HBV mutations were detected by sequencing (Table 5 and FIGS. 7, 8, and 9). The unique changes in the rt region of the HBV DNA polymerase include rtL180M+rtM204V previously demonstrated to be associated with LMV resistance inconjunction with a mutation at codon 184 (rtT184S) and rtH9D and rtN238T. The change at codon 184 in the rt has been previously noted with ETV+/−LMV resistance (Tenney et al, Antimicrob Agents Chemother 48(9):3498-507, 2004) but has not been reported with TFV+LMV resistance and virological breakthrough during treatment.
The changes in the HBsAg while on TFV and LMV treatment include sI92T/I, sL175F and sI195M. The last two changes correspond to changes in the polymerase at rtT184S and rtM204V, respectively.
Patient C: The HBV mutations during LMV and TFV treatment are listed in Table 6 and FIGS. 10, 11, 12. The unique changes in the rt region of the HBV DNA polymerase include rtR242K/R, W243R/W and rtQ215S. The changes in the HBsAg while on LMV and TFV treatment include sS207R.
Patient D: The HBV mutations during LMV and TFV treatment are listed in Table 7 and FIGS. 13, 14, 15. The unique changes in the rt region of the HBV DNA polymerase include rtT184A and rtY257H other changes include rtN118S and rtR102E.
The changes in the HBsAg while on LMV and TFV treatment include sI110V and sP120Q.
EXAMPLE 3
Patients on Antiviral Therapy and Analysis of HBV DNA
Treatment of patients with chronic hepatitis B virus with nucleos(t)ide analogs can result in the selection of HBV variants encoding mutations that may be associated with reduced sensitivity to the antiviral agent.
Resistance to ADV has been associated with a mutations in the putative tri-phosphate binding site at rtN236T (Angus et al, Gastroenterolog. 125(2):292-297, 2003). Therefore other mutations in this region selected by ADV or other antiviral treatments may be important in antiviral resistance against ADV and/or other nucleos(t)ide treatments. Important codons include 239 which is highly conserved, 240, 241, 242 and 243.
In addition to the mutation at rtN236T, other mutations may increase resistance and/or replication. Once such mutation is at codon 221
Patient E: The HBV mutations during LMV treatment are listed in Table 8 and FIGS. 16, 17, and 18. The unique changes in the rt region of the HBV DNA polymerase include rtT240N/T and rtK241R. Other important unique changes include rtH216H/P, rtL229M/L, rtI233T.
The changes in the HBsAg while on LMV treatment include sF80S, sI208UL, sS210K, sF220L/F and sY225H/Y.
Patient F: The HBV mutations during LMV treatment are listed in Table 9 and FIGS. 19, 20, and 21. The unique changes in the rt region of the HBV DNA polymerase include, rtR242R/K and rtW243G/W. Other important unique changes include rtL180M, rtA181T, rtH216H/P and rtE218D/E, refer to Table 9 for all other changes.
The important changes in the HBsAg in or near the “a” determinant while on LMV treatment include sF134L/F and sL173F (refer to Table 9 for all other changes).
Patient G: The HBV mutations during LMV treatment are listed in Table 10 and FIGS. 22, 23 and 24. The unique changes in the rt region of the HBV DNA polymerase include rtY221H/Y. Other important unique changes include rtV214A, rtA181A/V and rtN236T. (Refer to Table 9 for all other changes).
The important changes in the HBsAg in or near the “a” determinant while on LMV treatment include sL173F (refer to Table 9 for all other changes).
Patient H.
Patient H has been previously treated with a number of nucleoside/nucleotide analogs and was resistant individually to LMV, then ETV, then ADV. The patient was subsequently treated with combination LMV and ADV and ETV and is now resistant to all these agents. The HBV mutations during treatment are listed in FIGS. 25, 26 and 27.
This patient has selected unique combinations of mutations rtL42L/V, rtS78T, rtS85T, rtT128N, rtL180M, rtT184G, rtS202I, rtM204V, and rtN236I/D/V.
This includes the known LMV resistant mutations at rtL180M and rtM204V also the known ETV resistant mutations at rtL180M, rtT184G, rtS202I, and rtM204V. This patient has selected unique mutations at codon 236 at rtN236I/D/V that have not previously been reported with ADV resistance. Together all these mutations may be important for the combined ADV, LMV and ETV resistance mutations.
Changes in the HBsAg include sD33D/E, sC69 Stop, sC76 Stop, sR79H, sP120T, sL176V, sV194F and sI195M.
Patient I
Patient I was previously treated with LMV, then ADV. This patient is now being treated with TFV and LMV and has selected mutations which may be associated with reduced sensitivity to these agents. The HBV mutations during TDF and LMV treatment are listed in FIGS. 28, 29 and 30.
This includes the mutations at rtF61L, rtS78T, rtV84M/V, rtV142E, rtQ149Q/R, rtM204I/M, rtI233T/I and rtS246H/P/Y/S. In particular the mutation at rtI233T/I was not detected previously in HBV isolated from this patient pre-TFV treatment.
Changes in the HBsAg include sC69Stop, sM75I/M, sY134N, sK141K/E, sP178P/L, sW196stop/W, s210R/S, and sY225H/Y.
Patient J
Patient J was previously treated with LMV and selected HBV with mutations associated with LMV resistance this includes the polymerase mutations at rtI29L, rtY50S, rtP170H, rtL180M, rtM204V and rtI253V and the envelope mutations at sL20F, sI42L, sV144D, sL162I and sI195M.
This patient was subsequently treated with ADV and did not respond and then ETV and also did not respond. This suggests that this patient may have selected mutations during LMV treatment that may have affected the subsequent antiviral non-response or primary resistance to ADV and then ETV.
In particular the mutations at rtI253V and rtP170H may be important for the primary resistance to ADV and ETV.
EXAMPLE 4
Detection of Viral Markers
Hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), anti-HBe and hepatitis B core antigen (HBcAg) specific IgG and IgM were measured using commercially available immunoassays (Abbott Laboratories, North Chicago, Ill., USA). Hepatitis B viral DNA levels were measured using a capture hybridization assay according to the manufacturer's directions (Digene Hybrid Capture II, Digene Diagnostics Inc., Beltsville, Md.). The manufacturers stated cut-off for detecting HBV viremia in clinical specimens was 0.7×106 copies/ml or 2.5 pg/ml, [Hendricks et al, Am J Clin Pathol 104:537-46, 1995]. HBV DNA levels can also be quantitated using other commercial kits such as Cobas amplification HBV monitor kit (Roche).
EXAMPLE 5
Sequencing of HBV DNA
HBV DNA was extracted from 100 μl of serum as described previously by Aye et al, J. Hepatol. 26:1148-1153, 1997. Oligonucleotides were synthesized by Geneworks, Adelaide, Australia. Amplification of the HBV polymerase gene has been described by Aye et al, 1997, supra.
The specific amplified products were purified using PCR purification columns from MO BIO Laboratories Inc (La Jolla, Calif.) and directly sequenced using Big Dye terminator Cycle sequencing Ready Reaction Kit (Perkin Elmer, Cetus Norwalk, Conn.). The PCR primers were used as sequencing primers, OS1 5′-GCC TCA TTT TGT GGG TCA CCA TA-3′ (nt 1408-1430) [SEQ ID NO:1], TTA3 5′-AAA TTC GCA GTC CCC AAA-3′ (nt2128-2145) [SEQ ID NO:2], JM 5′-TTG GGG TGG AGC CCT CAG GCT-3′ (nt1676-1696) [SEQ ID NO:3], TTA4 5′-GAA AAT TGG TAA CAG CGG-3′ (nt 2615-2632) [SEQ ID NO:4], OS2 5′ TCT CTG ACA TAC TTT CCA AT 3′ (nt 2798-2817) [SEQ ID NO:5], to sequence the internal regions of the PCR products.
EXAMPLE 6
Adefovir Dipivoxil
ADV
ADV (formerly Bis-pom PMEA)) is a potent inhibitor of HBV replication. The structure of ADV is shown in FIG. 2 and its synthesis is described by Benzaria et al, J Med Chem. 39:4958-4965, 1996.
EXAMPLE 7
Tenofovir
TFV
TFV (formerly Bis-pom PMPA) is a potent inhibitor of HBV replication. The structure of tenofovir is shown in FIG. 3 and its synthesis is described by Srinivas and Fridland, Antimicrob Agents Chemother. 42(6):1484-1487, 1998.
Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations of any two or more of said steps or features.







TABLE 4







Patient A HBV Polymerase and envelope mutations


detected duringTFV/LMV therapy










Viral Load
ALT




(IU/ml)
(IU/ml)
G′type
Polymerase #














114
A
wildtype



25
PCR-ve




24
PCR-ve



1.79E+07

A
S256R/S





W257G/w
















TABLE 5







Patient B HBV Polymerase and envelope mutations


detected duringTFV/LMV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#
















C
H9D
I92T/I





L180M
L175F





T184S
I195M





M204V



1.99E+07

C
H9D
I92T/I





L180M
L175F





T184S
I195M





M204V






N238T



1.06E+06

C
H9D
I92T/I





L180M
L175F





T184S
I195M





M204V






N238N/T



1.42E+05

C
H9D
I92T/I





L180M
L175F





T184S
I195I/M





M204/V



1.00E+08

C
H9D
I92T/I





L180M
L175F





T184S
I195M





M204V






N238T
















TABLE 6







Patient C HBV Polymerase and envelope mutations


detected duringTFV/LMV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#





1.70E+09
71
D
V191I/V
W182*/W





Q215P/S
S207R



55
D
V191I/V
W182*/W





Q215P/S
S207R


2.82E+05

D
Q215S
S207R





R242K/R






W243R/W
















TABLE 7







Patient D HBV Polymerase and envelope mutations


detected during TFV and LMV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#














D
N118S
I110V




R120R
P120Q




T184A





Y257H
















TABLE 8







Patient E HBV Polymerase and envelope


mutations detected during LMV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#














D
F122V/F
F80S




S135Y
I208I/L




H216H/P
S210K




L229M/L
F220L/F




I233T/I
Y225H/Y




T240N/T





K241R
















TABLE 9







Patient F HBV Polymerase and envelope


mutations detected during LMV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#














B
N124D
F134L/F




S135A
L173F




S143T/S
I208I/L




L180M
S210T/S




A181V





H216H/P





E218D/E





H238D





R242K/R





W243G/W





I254I/f
















TABLE 10







Patient G HBV Polymerase and envelope


mutations detected during ADV therapy











Viral Load
ALT





(IU/ml)
(IU/ml)
G′type
Polymerase #
HBsAG#





1.98E+06
467
B
L115M
W196S





M204I






V214A






M250I



1.42E+05


PCR-ve



1.61E+04


PCR-ve



2.00E+03


PCR-ve





B
N53D
C76Y





L115M
L173L/F





A181A/V






V214A






Y221H/Y






N236T









BIBLIOGRAPHY


    Allen et al, Hepatology 27(6):1670-1677, 1998
    Angus et al, Gastroenterology. 125(2):292-297, 2003
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REFERENCE TO SEQUENCE LISTING
A Sequence Listing submitted as an ASCII text file via EFS-Web is hereby incorporated by reference in accordance with 35 U.S.C. §1.52(e). The name of the ASCII text file for the Sequence Listing is 13143266—1.TXT, the date of creation of the ASCII text file is Apr. 19, 2012, and the size of the ASCII text file is 65.3 KB.

## Claims

1. A method for determining the potential for a Hepatitis B Virus (HBV) variant to exhibit reduced sensitivity to anti-viral agents adefovir (ADV), lamivudine (LMV) and entecavir (ETV), said method comprising:
isolating DNA or corresponding mRNA from said HBV;
amplifying one or more labeled amplicons from said DNA or mRNA by using one or more biotin- or other ligand-labeled primers,
wherein said one or more labeled primers hybridize to the DNA or mRNA which code for the isoleucine (I), aspartic acid (D), or valine (V) at a position corresponding to position 236 of SEQ ID NO: 28, valine (V) at a position corresponding to position 204 of SEQ ID NO: 28, methionine (M) at a position corresponding to position 180 of SEQ ID NO: 28, glycine (G) at a position corresponding to position 184 of SEQ ID NO: 28, and isoleucine (I) at a position corresponding to position 202 of SEQ ID NO: 28;
capturing said labeled amplicons by hybridizing to an oligonucleotide immobilized to a solid support;
detecting one or more a specific nucleic acid fragments by identifying the biotin- or other ligand-labeled amplicon; and
identifying the presence of a combination of amino acids in a reverse transcriptase (rt) portion of an HBV DNA polymerase comprising an isoleucine (I), aspartic acid (D), or valine (V) at a position corresponding to position 236 of SEQ ID NO: 28, a valine (V) at a position corresponding to position 204 of SEQ ID NO: 28, a methionine (M) at a position corresponding to position 180 of SEQ ID NO: 28, a glycine (G) at a position corresponding to position 184 of SEQ ID NO: 28, and an isoleucine (I) at a position corresponding to position 202 of SEQ ID NO: 28;
wherein the presence of the combination of amino acids is indicative of reduced sensitivity to said anti-viral agents.

2. The method of claim 1, further comprising identifying the presence of a threonine (T) at a position corresponding to position 85 of SEQ ID NO: 28, wherein said one or more primers hybridize to the DNA or mRNA which codes for a threonine (T) at a position corresponding to position 85 of SEQ ID NO: 28.

3. The method of claim 1, further comprising identifying the presence of a leucine (L) or a valine (V) at a position corresponding to position 42 of SEQ ID NO: 28, a threonine (T) at a position corresponding to position 78 of SEQ ID NO: 28, and an asparagine (N) at a position corresponding to position 128 of SEQ ID NO: 28 wherein said one or more primers hybridize to the DNA or mRNA which codes for a leucine (L) at position 42 of SEQ ID NO: 28, a valine (V) at a position corresponding to position 42 of SEQ ID NO: 28, a threonine (T) at a position corresponding to position 78 of SEQ ID NO: 28, or an asparagine (N) at a position corresponding to position 128 of SEQ ID NO: 28.

4. The method of claim 1, wherein the HBV variant also exhibits reduced sensitivity to tenofovir (TFV).

5. The method of claim 1, wherein in two or more amplicons are amplified.

6. The method of claim 2, wherein in two or more amplicons are amplified.

7. The method of claim 3, wherein in two or more amplicons are amplified.