US20030152917A1

US20030152917A1 - Method of managing the chemotherapy of patients who are HIV positive based on the phenotypic drug sensitivity of human HIV strains

Info

Publication number: US20030152917A1
Application number: US10/342,188
Authority: US
Inventors: Marie-Pierre de Bethune; Kurt Hertogs; Rudi Pauwels
Original assignee: Virco BVBA
Current assignee: Virco BVBA
Priority date: 1996-01-26
Filing date: 2003-01-15
Publication date: 2003-08-14
Also published as: ES2177922T3; SK100298A3; US6528251B2; CN1991365A; EP0877937B1; NO321329B1; BR9707204A; CN1209875A; KR100495690B1; KR19990082027A; DE69712731T2; TR199801443T2; AU717755B2; US20020042679A1; EP0877937A1; HUP9902618A2; DE69712731D1; NO983300L; US6221578B1; CZ292899B6

Abstract

The present invention is drawn to a method of managing HIV chemotherapy of patients who are HIV positive, by transfecting a cell line susceptible to infection by HIV with a sequence from the pol gene of HIV, which sequence encodes at least one desired target enzyme selected from integrase, protease or reverse transcriptase, obtained by isolating viral RNA from a sample of a biological material from a patient and reverse transcribing the desired region of the pol gene, and a HIV-DNA construct that lacks a sequence encoding the desired target enzyme, culturing the transfected cells so as to create a stock of chimeric viruses, assessing the phenotypic sensitivity of the chimeric viruses to at least one inhibitor of the target enzyme encoded by the pol gene of HIV, and assigning a value thereto, constructing a data set containing the value for chimeric virus sensitivity and the corresponding value for a chimeric wild-type strain of HIV, repeating the sensitivity assessment for at least two further inhibitors and thereby constructing at least three such data sets in total, representing the at least one data sets in two dimensional or three dimensional graphical form such that the difference between the chimeric and wild-type sensitivities in the case of each data set provides a visual measure of the resistance of the chimeric stock to treatment by the inhibitor in question, and selecting the optimum inhibitor(s) on the basis of the graphical representation of the resistances so measured.

Description

TECHNICAL FIELD

The present invention relates to a method of managing the chemotherapy of patients who are HIV positive, as well as a clinical management device for use by physicians treating such patients based on the phenotypic drug sensitivity of human HIV strains for inhibitors of one or more enzymes of the pol gene of HIV, as well as a method for simultaneously determining the phenotypic drug sensitivity of two or more of the enzymes of the pol gene of HIV to inhibitors thereof.

BACKGROUND ART

To date, several chemotherapeutic regimens have been developed for treating HIV infected patients. Certain of these regimens have been approved for clinical use, and others are the subject of on-going clinical trials. It can be assumed that the number of approved chemotherapeutic regimens will increase steadily in the near future. Increasingly, combination therapy or multiple drug treatment regimens are being used because of the development of drug-resistant HIV variants during therapy. Although these chemotherapeutic regimens have been shown to exert an effect on virological (viral load), immunological and clinical parameters of HIV disease, practical experience teaches that these effects are transient. In particular, one finds that the HIV strains infecting an individual patient after a while start to display reduced sensitivity to the drug or drug combination with which said patient is being treated. The loss of efficacy of the chemotherapy can vary from patient to patient, from drug to drug, or from drug combination to drug combination. It is well established that the loss of efficacy to a particular type of chemotherapy can be associated with a genotypic pattern of amino acid changes in the genome of the HIV strains infecting the patient. This probably renders these HIV strains less susceptible to the chemotherapy. As an HIV infected patient is exposed to several chemotherapeutic regimens over extended periods of time, more complex patterns of amino acid changes in the genome of infecting HIV strains occur which for the present defeat a rational approach to the further treatment of the infected patient. As implied in the previous explanation, one can routinely determine the genotypic changes occurring in HIV strains exposed to different chemotherapeutic regimens involving single or multiple anti-HIV drugs, but thus far it has proven very difficult to derive from these data information enabling a physician in charge of prescribing the chemotherapy whether or not it is sensible to initiate or continue a particular chemotherapeutic regimen. In other words, the genotypic information which is available on a limited scale, cannot routinely be translated into phenotypic information enabling the responsible physician to make the crucial decision as to which chemotherapy a patient should preferably follow. The problem also exists for drug-naive patients who become infected by drug-resistant HIV strains.

Viral load monitoring is becoming a routine aspect of HIV care. However, viral load number alone cannot be used as a basis for deciding which drugs to use alone or in combination.

Combination therapy is becoming increasingly the chemotherapeutic regimen of choice. When a person using a combination of drugs begins to experience drug failure, it is impossible to know with certainty which of the drugs in the combination is no longer active. One cannot simply replace all of the drugs, because of the limited number of drugs currently available. Furthermore, if one replaces an entire chemotherapeutic regimen, one may discard one or more drugs which are active for that particular patient. Furthermore, it is possible for viruses which display resistance to a particular inhibitor to also display varying degrees of cross-resistance to other inhibitors.

Ideally, therefore, every time a person has a viral load test and a viral load increase is detected, a drug sensitivity/resistance test should also be carried out. Until effective curative therapy is developed, management of HIV disease will require such testing.

Currently there does exist a phenotyping method which is based on virus isolation from plasma in the presence of donor peripheral blood mononuclear cells (PBMCs), and subsequent phenotyping in said cells (Japour, A. J., et al. (1993) Antimicrobial Agents and Chemotherapy; Vol. 37, No. 5, p1095-1101). This co-cultivation method, which is advocated by the AIDS Clinical Trial Group (ACTG)—particularly for phenotyping AZT (synonymous herein with zidovudine/Retrovir (Retrovir is a Trade Mark)) resistance, is time-consuming, costly and too complex to be used on a routine basis.

A phenotypic recombinant virus assay for assessment of drug susceptibility of HIV Type 1 isolates to reverse transcriptase (RT) inhibitors has been developed by Kellam, P. and Larder, B. A. (Antimicrobial Agents and Chemotherapy (1994) Vol. 38, No. 1, p23-30). This procedure allows the generation of viable virus by homologous recombination of a PCR-derived pool of RT coding sequences into an RT-deleted, noninfectious proviral clone, pHIVΔRTBstEII. Analysis of two patients during the course of zidovudine therapy showed that this approach produced viruses which accurately exhibited the same genotype and phenotype as that of the original infected PBL DNA. However, the procedure involves isolation of the patient virus by co-cultivation of patient plasma or patient PBMCs with donor PBMCs. Such prior cultivation of virus may distort the original virus composition. Furthermore, this method, although allowing one to determine the sensitivity of the isolates to various inhibitors, does not provide the physician with information as to whether to continue with the existing chemotherapeutic regimen or to alter the therapy.

Also when one enzyme only of the pol gene is being studied, the method does not readily lend itself to routine phenotypic assessment of combination therapy which conventionally involves the use of one protease and 2 RT inhibitors.

The nested PCR (polymerase chain reaction) procedure used in the recombinant virus assay can lead to a situation where the recombinant virus does not truly reflect the situation with the HIV strains infecting the patient under investigation. This problem resides in DNA sequence homology and the minimum amount of homology required for homologous recombination in mammalian cells (C. Rubnitz, J. and Subramini, S. (1984) Molecular and Cellular Biology Vol. 4, No. 11, p2253-2258). Accordingly, any phenotypic assay based on the recombinant virus approach should endeavour to ensure that as much as possible of the patient material is amplified and that there is maximum recombination.

Thus, the RNA extraction and nested PCR procedures employed should ensure that the viral genetic material is amplified such that the amplified material maximally reflects the viral genetic diversity in the patient being investigated.

In current clinical practice there is therefore a hard-felt need (a) to determine rapidly and on a routine basis the phenotypic drug sensitivity of HIV strains infecting a particular patient, (b) to process the thus obtained data into easily understood information, and (c) to initiate, continue or adjust on the basis of said information the chemotherapy prescribed for said particular patients.

DISCLOSURE OF THE INVENTION

According to a first aspect of the invention there is provided a method of managing HIV chemotherapy of patients who are HIV positive, which comprises transfecting a cell line susceptible to infection by HIV with a sequence from the pol gene of HIV, obtained by isolating viral RNA from a sample of a biological material from a patient and reverse transcribing the desired region of said pol gene, and a HIV-DNA construct from which said sequence has been deleted, culturing said transfected cells so as to create a stock of chimeric viruses providing an indication of the resistance profile of the circulating virus, assessing the phenotypic sensitivity of said chimeric viruses to an inhibitor of said enzyme encoded by the pol gene of HIV and assigning a value thereto constructing a data set comprising said value for chimeric virus sensitivity and the corresponding value for a chimeric wild-type strain HIV, repeating the sensitivity assessment for at least two further inhibitors and thereby constructing at least three such data sets in total, representing said data sets in two dimensional or three dimensional graphical form such that the difference between the chimeric and wild-type sensitivities in the case of each data set provides a visual measure the resistance of the chimeric stock to treatment by the inhibitor in question, and selecting the optimum inhibitor(s) on the basis of the graphical representation of the resistances so measured.

The method according to the invention yields phenotypic information on individual HIV infected patients on a large scale, economically and rapidly. The method is applicable to all currently available chemotherapeutic regimens and it is expected to be equally applicable to future chemotherapeutic regimens.

The method according to the invention provides the physician with phenotypic data on patient HIV strains which can be immediately used to determine whether a particular chemotherapeutic regimen should be initiated, continued or adjusted.

Preferably, the data sets are represented on a polygonal or quasi-circular graph comprising:

(a) a plurality of normalised axes extending radially from an origin, each axis corresponding to one data set or inhibitor or combination thereof;

(b) the axes being normalised such that the sensitivity values for wild-type HIV for the various inhibitors are equal on each axis, the data points for wild-type HIV being optionally represented and connected to form a regular polygon whose vertices lie on the axes and whose center is defined by the origin;

(c) on each axis a data point representing the sensitivity value of the chimeric HIV stock against the inhibitor corresponding to said axis is plotted, the chimeric data points being optionally connected to form a regular or irregular polygon the shape of which represents the resistance of the chimeric stock to a range of inhibitors.

A polygonal or quasi-circular graph provides the advantage that the patient's resistance to a number of drugs is characterised in terms of the degree of divergence between the polygon representing the patient's chimeric HIV stock and the polygon representing the wild-type strain.

The areas of the polygons will generally diverge more in some areas than in others, indicating in each case a greater or lesser degree of resistance to the inhibitor whose axis passes through the area in question.

Thus, the method according to the invention takes a chimeric HIV stock and provides a map of the resistance of this stock across a range of inhibitors. In this way the map or graph provides a technical characterisation of an aspect of the chimeric stock which is not obtained by conventional measurements.

In a preferred embodiment, the normalised axes are equiangular from one another.

Further, preferably, each axis has a logarithmic scale.

Further, preferably, eccentric data points in the chimeric polygon, if represented, identify inhibitors whose usefulness can be assumed to be of little or no benefit to the patient, while data points lying within, on or close outside the wild-type polygon identify inhibitors whose usefulness can be assumed to be of substantial benefit to the patient.

When worst case values are represented along with the chimeric and wild-type HIV, a usually irregular polygon encloses the chimeric and wild-type polygons. The meaning of the term “eccentric” as used above denotes a data point lying relatively close to the worst-case border and relatively far from the wild-type polygon. Similarly the term “close outside the wild-type polygon” refers to relative closeness to the wild-type polygon when compared to the distance from the worst-case border.

The method as hereinabove defined is limited in the sense that the measurable resistance against an inhibitor is dependent on the particular range of concentrations of the inhibitor used. Also one must endeavour to reduce the effects of biological variability. Accordingly, it is desirable to obtain a value for maximum or worst-case measurable resistance where it is assumed that a given inhibitor has no effect. This concentration, e.g. 100 μM, is generally the maximum concentration that can practically be tested, but may also be derived from e.g. pharmacological, toxicological or pharmacokinetic studies. The comparison of the resistance level of the patient under investigation and the maximum measurable resistance determines what is the significant level of resistance for the patient under investigation. The maximum measurable resistance and the actual resistance can be suitably shown on a bar graph as hereinafter described.

In a still further preferred embodiment of the invention each of said three or more data sets further comprises a value for worst-case measurable resistance for the inhibitor in question, said worst case values being represented on said graphical representations such that the data point for the chimeric stock can be compared both to wild-type and to worst-case HIV, thereby providing an assessment of the relative value of the inhibitor in a particular case.

Experiments with in excess of 150 patient samples have revealed a close correlation between resistance development and therapy history as hereinafter further illustrated in the Examples. A close correlation has been found with the data generated in accordance with the invention relative to classical virus isolation and phenotyping techniques.

The method in accordance with the invention can thus be used for an individualised and more rational management of HIV chemotherapy. Thus, use of the method according to the invention in combination with the proper administration of anti-HIV drugs should ultimately lead to better treatment and survival of patients infected with the HIV virus.

The method according to the invention has particular application where an individual patient has been receiving many different drugs and his mutation pattern is not readily interpreted by attending physicians.

According to a further aspect of the invention there is provided a method of managing HIV chemotherapy of patients who are HIV positive, which comprises the steps of:

(a) periodically assessing the phenotypic sensitivity of a patient's HIV strains by a method hereinabove described;

(b) maintaining the chemotherapy with the selected inhibitor while the patient's HIV strains remain susceptible to the selected chemotherapy;

(c) selecting a different inhibitor if and when the susceptibility of the original inhibitor decreases.

According to a still further aspect of the invention there is provided a clinical management device for use in the management of chemotherapy of patients who are HIV positive, said device bearing a graphical representation of a plurality of data sets as hereinabove defined.

We have coined the term “Antivirogram” for the clinical management device according to the invention and this term will be used hereinafter in the specification. This device provides the physician with a clear representation of the relative changes and susceptibilities for different inhibitors which are or which may be used in the clinical management of individual HIV-infected patients.

Preferably, the phenotypic sensitivity of said chimeric viruses to inhibitors of at least two enzymes encoded by the pol gene of HIV is simultaneously assessed.

In a further aspect of the invention there is provided a method of determining the phenotypic drug sensitivity of individual HIV strains in a patient to inhibitors of at least two enzymes encoded by the pol gene o HIV, which comprises transfecting a cell line susceptible to infection by HIV with a sequence from the pol gene of HIV, obtained by isolating viral RNA from a sample of a biological material from a patient and reverse transcribing the desired region of said pol gene, and a HIV-DNA construct from which said sequence has been deleted, culturing said transfected cells so as to create a stock of chimeric viruses providing an indication of the resistance profile of the circulating virus and assessing the phenotypic sensitivity of said chimeric viruses to inhibitors of said enzymes encoded by the pol gene of HIV.

The desired sequence from the pol gene is isolated from a sample of a biological material obtained from the patient whose phenotypic drug sensitivity is being determined. A wide variety of biological materials can be used for the isolation of the desired sequence.

Thus, the biological material can be selected from plasma, serum or a cell-free body fluid selected from semen and vaginal fluid. Plasma is particularly preferred and is particularly advantageous relative to the use of PBMCs as used in the prior art described above.

Alternatively, the biological material can be whole blood to which an RNA stabiliser has been added.

In a still further embodiment, the biological material can be a solid tissue material selected from brain tissue or lymph nodal tissue, or other tissue obtained by biopsy.

As hereinafter demonstrated, when a biological material such as plasma is used in the isolation of the desired sequence, a minimal volume of plasma can be used, typically about 100-250 μl, more particularly of the order of 200 μl.

Further, preferably the two enzymes selected will be selected from HIV RT, protease and integrase.

Viral RNA is conveniently isolated in accordance with the invention by methods known per se, for example the method of Boom, R. et al. (Journal of Clinical Microbiology (1990) Vol. 28, No. 3, p.495-503).

In the case of plasma, serum and cell-free body fluids, one can also use the QIAamp viral RNA kit marketed by the Qiagen group of companies.

Preferably, the cell line susceptible to infection by HIV is a CD4 ⁺ T-cell line.

Further, preferably, the CD4 ⁺ T-cell line is the MT4 cell line or the HeLa CD4⁺ cell line.

Reverse transcription can be carried out with a commercial kit such as the GeneAmp Reverse Transcriptase Kit marketed by Perkin Elmer.

The desired region of the patient pol gene is preferably reverse transcribed using a specific downstream primer.

In the case where the sequence to be reverse transcribed is that coding for reverse transcriptase or reverse transcriptase and protease, the downstream primer is preferably OUT3: 5′-CAT TGC TCT CCA ATT ACT GTG ATA TTT CTC ATG-3′ (SEQ ID NO: 1).

In a particularly preferred embodiment a patient's HIV RT gene and HIV protease gene are reverse transcribed using the HIV-1 specific OUT 3 primer and a genetically engineered reverse transcriptase lacking RNase H activity, such that the total RNA to be transcribed is converted to cDNA without being degraded. Such a genetically engineered reverse transcriptase, the Expand (Expand is a Trade Mark) reverse transcriptase, can be obtained from Boehringer Mannheim GmbH.

Expand reverse transcriptase is a RNA directed DNA polymerase. The enzyme is a genetically engineered version of the Moloney Murine Leukaemia Virus reverse transcriptase (M-MuLV-RT). Point mutation within the RNase H sequence reduces the RNase H activity to below the detectable level. Using this genetically engineered reverse transcriptase enables one to obtain higher amounts of full length cDNA transcripts.

Following reverse transcription the transcribed DNA is amplified using the technique of PCR.

Preferably, the product of reverse transcription is amplified using a nested PCR technique.

Preferably, in the case where the region of interest is the RT region, a nested PCR technique is used using inner and outer primers as described by Kellam, P. and Larder, B. A. (1994 supra). When the region of interest is that spanning the RT and protease genes, the specific primers used are preferably a combination of OUT 3/IN 3 (downstream) and RVP 5 (upstream).

The primer RVP 5 (Maschera, B., et al. Journal of Virology, 69, 5431-5436) has the sequence 5′-GGGAAGATCTGGCC TTCCTACAAGGG-3′(SEQ ID NO: 2).

A schematic representation of the amplification is set forth in FIG. 3 and is described in greater detail in Example 2.

The amplification of the protease cDNA actually involves a hemi-nested PCR procedure as will be apparent from FIG. 3.

The nested PCR technique has the advantage over the known simple PCR techniques in that it enables one to obtain the most specific PCR product.

However, to obtain an even higher fidelity and yield during PCR, one can make use of a mixture of thermostable polymerases (Barnes, W. M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2216-2220). Such a polymerase mixture is available from Boehringer Mannheim GmbH, namely the Expand (Expand is a Trade Mark) high fidelity PCR system. Using this system we have obtained increased sensitivity, namely a sensitivity which is ten times or greater than that obtained with a conventional PCR procedure using Taq polymerase alone.

When the region of the pol gene is that embracing the RT and protease genes, preferably the HIV-DNA construct is one from which the RT and protease genes are deleted and is the plasmid pGEMT3-ΔPRT as deposited at the Belgian Coordinated Collections of Microorganisms-BCCM LMBP-Collection on Nov. 8, 1996 under the number LMBP3590.

However, several approaches can be adopted to generate a plasmid containing the HIV-1 provirus carrying a deletion for the protease as well as for the RT gene. One possibility is the introduction of the desired deletion by means of oligonucleotide-mediated mutagenesis. However, the procedure adopted hereinafter in Example 2 involves the generation of the desired construct by making use of specific restriction enzymes and subcloning procedures, as hereinafter described. Although the final results depend on the available restriction sites a major advantage of this procedure is that one can obtain conclusive results rapidly.

To ensure the most efficient outcome for the transfection, the PCR-product, being transfected, should ideally be purified by anion exchange spin columns in a manner known per se. A suitable kit is the QIAquick PCR Purification Kit marketed by the Qiagen group of companies.

Transfection can be achieved by electroporation or, alternatively, by the use of lipids, especially cathionic lipids, DEAE dextran, CaHPO ₄, etc.

In the case of lipid transfection one can avail of a PERFECT (PERFECT is a Trade Mark) transfection kit marketed by Invitrogen B. V. of Leek, the Netherlands.

Thus, for transfection an HIV-DNA construct from which the gene or genes of choice from the pol gene has/have been deleted is used in conjunction with the product obtained following amplification.

The construct can be the plasmid pHIVΔRT (obtainable from the Medical Research Council (MRC)) if it is the RT gene only that is deleted. When the RT and protease genes are both deleted a suitable HIV DNA construct is the plasmid pGEMT3-ΔPRT described herein and which is a high copy vector. Such plasmids are linearised prior to transfection according to methods known per se.

A particular advantage of using a construct coding for more than one pol gene enzyme, for example a ΔPRT construct, is that one is more likely to include more of the original patient material in the construct than if a single gene is used, so that the amplified material reflects to a greater extent the viral genetic diversity in the particular patient being investigated.

It will be appreciated that it is preferable that the specific primers selected for the nested PCR are located outside the body sequences of the target enzymes to be amplified and investigated. It will furthermore be appreciated that a combination of RT and protease is likely to provide better results for studying RT than RT alone, because forty more amino acids are patient borne relative to the situation with RT alone. For studying the protease, one should be aware that the first nine amino acids of the protease are still derived from the construct's (pGEMT3-ΔPRT) wild-type backbone.

When the transfection of the cells is achieved through electroporation, the parameters selected are optimized to achieve good cell growth and virus production. The electroporation can conveniently be conducted at approximately 250 μF and 300V. Preferably, the electroporation is conducted in the presence of about 10 μg of linearised plasmid e.g. pHIVΔRTBstEII and about 5 μg of amplified PCR product e.g. RT PCR product. Upon successful intracellular homologous recombination, new chimeric HIV is formed within 5 to 10 days. With known techniques typical cultivation times are 12-14 days before chimeric HIV is formed. Culture supernatant aliquots are stored at −70° C. or lower temperatures.

It is readily seen that one can use the above methods for isolating and amplifying other HIV genes, e.g. the integrase gene, or more than one other HIV gene, e.g. both the RT and the integrase gene, and transfecting a CD4 ⁺ T-cell with the respective integrase or RT/integrase PCR products in conjunction with an appropriate linearised HIV-DNA construct from which the relevant gene (or genes) is deleted.

The newly formed chimeric viruses are titrated and then analysed for their phenotypic sensitivity (i.e. susceptibility) to the different pol gene enzyme inhibitors, preferably in an automated cell-based assay.

Preferably, the phenotypic drug sensitivity of the chimeric viruses and of the wild HIV strain, which is suitably a recombinant wild HIV strain, to one or more RT, protease or integrase inhibitor(s) is expressed as an inhibitory concentration (IC value).

The susceptibilites of the chimeric viruses and of the wild type HIV strain to one or more RT inhibitors and/or one or more protease inhibitors and/or one or more integrase inhibitors can be expressed as for example 50% or 90% inhibitory concentrations (IC ₅₀or IC₉₀values).

Preferably, RT inhibitors are selected from nucleoside RT inhibitors such as AZT, ddI (didanosine/Videx (Videx is a Trade Mark), ddC (zalcitabine), 3TC (lamivudine), d4T (stavudine), non-nucleoside RT inhibitors such as delavirdine (U 9051125 (BMAP)/Rescriptor (Rescriptor is a Trade Mark)), loviride (alpha-APA), nevirapine (B1-RG-587/Viramune (Viramune is a Trade Mark) and tivirapine (8-Cl-TIBO(R86183)), protease inhibitors such as saquinavir, indinavir and ritonavir and integrase inhibitors such as caffeic acid phenylethyl ester (CAPE).

Suitable RT and/or protease inhibitors and/or integrase inhibitors are selected from nucleoside RT inhibitors such as AZT, ddI, ddC, 3TC, d4T, 1592U89 and the like, non-nucleoside RT inhibitors such as loviride, nevirapine, delaviridine, ateviridine, and tivirapine (8-Cl TIBO) and the like, protease inhibitors such as saquinavir, indinavir and ritonavir and the like, and integrase inhibitors such as caffeic acid phenylethyl ester (CAPE) and HIV integrase inhibitors of the type described in WO 95/08540 and GB 2,271,566.

The method according to the invention comprises the step of comparing the phenotypic drug sensitivity of patient HIV strains with one or more RT inhibitors and/or one or more protease inhibitors, and/or one or more integrase inhibitors to that of a wild type HIV strain. For an easy-to-understand representation of the relative changes in susceptibility to the different drug compounds (or combinations) tested, an Antivirogram graph, is constructed.

The graph should be interpreted as follows: eccentric data points in the antivirogram identify chemotherapeutic regimens unlikely to benefit the HIV infected patient any further, whereas data points within or on the reference polygon, or only slightly beyond the reference polygon, identify chemotherapeutic regimens likely to benefit the HIV infected patient.

The methods according to the invention in combination with the administration of the correct anti-HIV drugs should ultimately lead to better treatment, improved quality of life and improved survival of HIV infected patients; i.e. ineffective treatment (due to the presence of or emergence of resistant HIV strains) can be prevented or halted, and effective chemotherapy can be initiated in good time.

The present invention also concerns a clinical management device for use by physicians treating HIV infected patients comprising an Antivirogram obtainable by the methods hereinbefore described.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic representation of the construction of the plasmid pGEMT3-ΔPRT; [0082]
FIG. 2 is a further and complementary schematic representation of the construction of the plasmid pGEMT3-ΔPRT; [0083]
FIG. 3 is a schematic representation of that part of the HIV-HXB2D sequence containing protease and RT genes; [0084]
FIGS. [0085] 4A-H is a complete sequence for that part of the HIV-HXB2D sequence containing protease and RT genes;
FIG. 5 is an Antivirogram for a patient harbouring 3TC resistant HIV strains as described in Example 5; [0086]
FIG. 6 is an Antivirogram for a drug-naive patient harbouring wild type like HIV strains as described in Example 6; [0087]
FIG. 7A is a bar graph showing relative change in drug susceptibility for the patient of Example 7; [0088]
FIG. 7B is an Antivirogram for the patient the subject of Example 7; [0089]
FIG. 8A is a bar graph showing relative change in drug susceptibility for the patient of Example 8; [0090]
FIG. 8B is an Antivirogram for the patient the subject of Example 8; [0091]
FIG. 9A is a bar graph showing relative change in drug susceptibility for the patient of Example 9; [0092]
FIG. 9B is an Antivirogram for the patient the subject of Example 9; [0093]
FIG. 10A is a bar graph showing relative change in drug susceptibility for the patient of Example 10; [0094]
FIG. 10B is an Antivirogram for the patient the subject of Example 10; [0095]
FIG. 11A is a bar graph showing relative change in drug susceptibility for the patient of Example 11; [0096]
FIG. 11B is an Antivirogram for the patient the subject of Example 11; [0097]
FIG. 12A is a bar graph showing relative change in drug susceptibility for the patient of Example 12; and [0098]
FIG. 12B is an Antivirogram for the patient the subject of Example 12.[0099]
The invention will be further illustrated by the following Examples. [0100]

MODES FOR CARRYING OUT THE INVENTION

EXAMPLE 1

Protocol [0101]
1. Extraction and Amplification of Viral RNA. [0102]
RNA was isolated from 100 μl of plasma according to the method described by Boom, R. et al. (1990, supra), and was reverse transcribed with the GeneAmp reverse transcriptase kit (Perkin Elmer) as described by the manufacturer and using an HIV-1 specific downstream primer (OUT3: 5′-CAT TGC TCT CCA ATT ACT GTG ATA TTT CTC ATC-3′; SEQ ID NO: 1). PCR on reverse transcribed RNA was performed with inner and outer primers as described by Kellam, P. and Larder, B. A. (1994, supra). After chloroform extraction and centrifugation on [0103] Centricon 100 columns or centrifugation on anion-exchange spin columns (Quiagen), the isolated PCR product was ready for use in the transfection reactions.
2. Production and Isolation of Plasmid. [0104]
Production of pHIVΔRT (MCR) plasmid was performed in [0105] E. coli. Plasmid DNA was isolated from overnight cultures making use of Qiagen columns as described by the manufacturer. Yield of the isolated plasmid was determined spectrophotometrically by A260/280 measurement (optical density measurement at λ=260 and 280 nm). About 250 μg of ultrapure plasmid DNA was obtained from 500 ml of bacterial culture. The identity of the isolated plasmid was confirmed by restriction analysis. Subsequently, the isolated plasmid DNA was linearised with BstEII and purified again by a classical phenol/chloroform extraction.
3. Transfection of Cells. [0106]
[0107]
MT4 cells were subcultured at a density of 250,000 cells/ml before transfection (exponential growth phase). Cells were pelleted and resuspended in phosphate buffered saline (PBS) at a concentration of 3.1 10E6 cells/ml. A 0.8 ml portion (2.5 10E6 cells/ml) was used for each transfection. Transfection was performed with the Bio-Rad Gene pulser making use of 0.4 cm electrode cuvettes. Cells were electroporated in the presence of 10 μg of linearised pHIVΔRT plasmid and approximately 5 μg of RT PCR product at 250 μF and 300 V, followed by a 30-min incubation at room temperature. Subsequently, 10 ml of fresh culture medium was added to the cell suspension and incubation was performed at 37° C. in a humidified atmosphere of 5% CO[0108] ₂.
4. Culture and Follow-Up of Transfected Cells. [0109]
During 7 to 10 days following the transfection, cells were monitored for the appearance of cytopathogenic effect (CPE). In the absence thereof, cells were subcultured in different flasks. Subsequently, culture supernatants of transfected cells were used to create a stock of recombinant virus and stored in 1.5 ml aliquots at −70° C. [0110]
5. Analysis of Recombinant Virus from Patient Viral RNA. [0111]
After titration of the new viruses, the stocks were used for antiviral experiments in the presence of serial dilutions of different HIV inhibitors. Titres of the harvested supernatants were determined by limited serial dilution titration of virus in MT4 cells. [0112]
Viruses with a useful titre were used in antiviral experiments. For this purpose, 96-well microtitre plates were filled with 100 μl of complete culture medium. Subsequently, stock solutions of compounds were added in 25 μl volumes to series of duplicate wells. HIV- and mock-infected cell samples were included for each drug (or drug combination). Exponentially growing MT4 cells were then transferred to the microtitre plates at a density of 150,000 cells/ml. The cell cultures were then incubated at 37° C. in a humidified atmosphere of 5% CO[0113] ₂. Five days after infection, the viability of the mock- and HIV-infected cells was examined spectrophotometrically by the MTT method (Pauwels, R. et al.-J. Virol. Meth. (1988), 20: 309-321) as described in Section 6 below.
6. MTT Assay. [0114]
To each well of the microtiter plates, 20 μl of a solution of MTT (7.5 mg/ml in PBS) was added. The plates were further incubated at 37° C. for 1 h. Then, 150 μl of medium was removed without disturbing the MT4 cell clusters containing the formazan crystals. Solubilization of the formazan crystals was achieved by adding 100 [0115] μl 5% Triton X-100 in acidified isopropanol (5 ml concentrated HCl per litre solvent). Complete dissolution of the formazan crystals was obtained after the plates had been placed on a plate shaker for 10 min. Finally the absorbances were read at two wavelengths (540 and 690 nm). From these optical density (OD) data, 50% inhibitory (IC₅₀) and 50% cytotoxic (CC₅₀) concentrations were derived.

EXAMPLE 2

Construction of a pHIVΔRTBstEII-Variant with Deletion of the HIV-1 Protease and Reverse Transcriptase Gene. [0116]
The protocol described in Example 1 was repeated, except that the sequence of the HIV pol gene of interest was that coding for RT and protease and the construct prepared was pGEMT3-ΔPRT as described below. Other modifications relative to the procedure set out in Example 1 are set out below. [0117]
For amplification of viral RNA, reverse transcription from RNA to DNA was again carried out with the OUT3 primer. However, for the nested PCR procedure the primers used are as shown in FIG. 3. Thus, it will be observed that the nested PCR procedure uses as outer primers RVP5 and OUT3 and as inner primers RVP5 and IN3. Thus, this nested procedure is, in effect a hemi-nested PCR procedure. [0118]
Production and Isolation of pGEMT3-ΔPRT. [0119]
The final pGEMT3-ΔPRT construct is a derivative of pGEM9-Zf(−) (Promega). [0120]
In short, the pGEMT3-ΔPRT construct is built up by introducing the desired insert HIV-HXB2 (a protease and reverse transcriptase-deleted proviral HIV-1 clone, including flanking human sequences) into the XbaI restriction site of the vector pGEM9-Zf(−). The proviral genome has been deleted from the AhdI site within the protease gene (surrounding amino acid 9) to the BstEII site of the pHIVΔRTBstEII construct (MRC Repository reference: ADB231). At the junction of the ΔProRT deletion SmaI and BstEII sites are located which can be used for linearisation of the proviral construct prior to transfection. The construction of pGEMT3-ΔPRT is schematically represented in FIGS. 1 and 2. The yield of pGEMT3-ΔPRT was about 1 mg out of 500 ml bacterial culture. [0121]
As indicated above, the plasmid pGEMT3-ΔPRT was deposited at the Belgian Coordinated Collections of Microorganisms-BCCM LMBP-Collection on Nov. 8, 1996 under the number LMBP3590. [0122]
It was not expected that the introduction of the proviral genome into another vector (pGEM9-Zf(−) instead of pIB120) would cause major problems. pIB120, a derivative of pEMBL8(−) (according to information provided by Kodak Scientific Imaging Systems), and pGEM9-ZF(−) are similar vectors. Nevertheless the proviral vector pIB 120HIV may be unstable in recA+[0123] E. coli host cells (Maschera, B., et al. J. Virol. (1995) 69, 5431-5436. Therefore the stability of the pGEMT3-ΔPRT construct should be verified after every new preparation of plasmid.
HIV-HXB2 Sequence: [0124]
The region of interest within the HIV-HXB2D sequence ([0125] nucleotide 1800 to 4400) is represented in FIG. 3 (schematically) and FIG. 4 (complete sequence). The location of several genes, restriction sites, primers and deletions (ΔPro, ΔRT, ΔProRT) are also indicated.
The sequence of HIV-1 (isolate HXB2, reference genome, 9718bp) was obtained from the National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health via the ENTREZ Document Retrieval System. [0126]
Genbank name: HIVHXB2CG [0127]
Genbank Accesion No: Ø3455 [0128]
NCBI Seq.ID No: 327742 [0129]
Regions of Recombination: [0130]
In combination with RT-PCR fragments generated by RVP5 and OUT3/IN3 primers, the pGEMT3-ΔPRT vector can be used to transfect MT4 cells as described in Example 1, [0131] Section 3. The region for recombination at the 5′-end of ΔProRT contains 188 nucleotides. The region for recombination at the 3′-end of ΔProRT is similar to the one described earlier (Kellam, P. and Larder, B. A. (1994) supra) and contains 130 nucleotides.
The length of these regions for recombination is not unimportant. Previous data (Bandyopadhyay, P. K. et al. Proc. Natl. Acad. Sci. U.S.A., (1984) 81, 3476-3480; Rubnitz, J. and Subramani, S. (1984) supra) demonstrate that a 10-fold reduction in recombination frequency may occur when sequence homology is reduced from 214 to 163 base pairs. Furthermore, sufficient recombination events should occur within the electroporated cells to ensure that the generated viral phenotype is a reliable reflection of the quasi-species present in the treated HIV-positive patient. Optimisation of recombinant events can first be achieved by adjusting the ratio of linearised proviral vector to RT-PCR fragment that is used for electroporation of the target cells. The standard method therefore,with typical results of outcome, has previously been described by Kellam, P. and Larder, B. A. (1994 supra ). As a consequence, it was decided to increase the initial input of about 2 μg of PCR product (with 10 μg of vector) to about 5 μg or more. The result thereof was reflected in a faster appearance of visible virus growth (cytopathogenic effect) in the culture of transfected cells. [0132]
Another option for optimisation of recombination events would be the design of primers resulting in longer recombination sequences. [0133]
Nevertheless, the real input in the transfection reaction always depends on the yield after PCR. Some samples have a high yield and as a result there will be a higher input of amplified material in the transfection reaction (with better results on efficiency of recombination). However, despite a lower recombination efficiency, samples having a low yield can also be transfected and will result in viable virus with a reliable reflection of the virus population. [0134]

EXAMPLE 3

Alternative Primers for RT-PCR of the ProRT Sequence: [0135]

New primers (A-D) have been designed relative to those used in Example 2 and should result in longer recombination sequences at both 5′ and 3′ end of the ProRT region. Two primers were designed at both the 5′ and 3′ end of the respective region to allow nested PCR. As indicated in FIGS. 3 and 4 the direct repeat present at the 5′ end of the ProRT region was taken into account when designing the respective primers. The new primers are as follows:


	A PRTO-5:
	5′-GCCCCTAGGA-AAAAGGGCTG-TTGG	(SEQ ID NO: 3)

	B PRTI-5:
	5′-TGAAAGATTG-TACTGAGAGA-CAGG	(SEQ ID NO: 4)

	C PRTI-3:
	5′-GATATTTCTC-ATGTTCATCT-TGGG	(SEQ ID NO: 5)

	D PRTO-3:
	5′-AGGTGGCAGG-TTAAAATCAC-TAGC	(SEQ ID NO: 6)

EXAMPLE 4

Construction of an Alternative ΔProRT Vector: [0137]
As mentioned above, construction of an alternative ProRT deleted vector can be achieved by oligonucleotide-mediated mutagenesis. However, it is also possible to enlarge the ProRT deletion from the current 3′-end to the next KpnI site in the RT gene (40 base pairs further downstream). Ligation of a Klenow-treated KpnI site to a Klenow-treated BstEII site will restore the initial BstEII recognition sequence. [0138]
As such, this alternative vector behaves similarly to the pGMT3-ΔPRT vector described in Example 2, but has a slightly larger RT deletion. [0139]

EXAMPLE 5

An HIV infected patient who received AZT from December 1989 until an undocumented later date, and switched to a combined chemotherapy of AZT+3TC (1: 1) from February 1994 until October 1995 donated plasma whose susceptibility to a number of RT inhibitors was determined according to the above described protocol of Example 1. Recombinant wild type HIV strain recIIIB was used in said protocol as a reference HIV virus. Table 1 shows the IC ₅₀values (μM) measured and the ratio of said values. The Antivirogram is shown in FIG. 5.

	TABLE 1


	Anti-HIV-1 activity
	IC₅₀(μM)

				recIIIB	ratio
Drug	Exp. 1	Exp. 2	Mean (1)	ref (2)	(1)/(2)

loviride	0.1	0.12	0.11	0.05	2
tivirapine	0.019	0.018	0.019	0.01	1.5
AZT	0.001	0.002	0.002	0.004	0.4
3TC	31.6	100	65.8	0.56	118
d4T	0.07	0.49	0.06	0.12	0.5
ddI	2.0	0.8	1.4	2.83	0.5
ddC	0.2	0.2	0.2	0.38	0.5
AZT + 3TC	0.001	0.001	0.001	0.002	0.5
(1:1)

From these data, one can determine that monotherapy with 3TC is unlikely to benefit this particular patient. Combined therapy of AZT+3TC (the current therapy), however, is still likely to exert a positive effect. [0141]

EXAMPLE6

A drug-naive HIV infected patient donated plasma whose susceptibility to a number of RT inhibitors was determined according to the above described protocol of Example 1. Recombinant wild type HIV strain recIIIB was used in said protocol as a reference HIV virus. Table 2 shows the IC ₅₀values (μM) measured and the ratio of said values. An Antivirogram was prepared and shown in FIG. 6.

	TABLE 2


	Anti-HIV-1 activity
	IC₅₀(μM)

				recIIIB	ratio
Drug	Exp. 1	Exp. 2	Mean (1)	ref (2)	(1)/(2)

3TC	1.81	2.02	1.91	3.08	1
ddI	3.07	4.47	3.77	8.58	0.4
ddC	1.45	1.47	1.46	2.21	1
AZT	0.04	0.05	0.05	0.06	1
d4T	1.31	0.97	1.14	1.74	1
AZT + 3TC	0.05	0.04	0.05	0.02	3
(1:1)
DDC + D4T	0.62	0.44	0.53	0.77	1
(1:1)
3TC + d4T	0.42	0.44	0.43	1.11	0.4
(1:1)

From these data one can determine that the patient is infected with HIV strains closely resembling the wild type HIV. None of the drug regimens is to be excluded, so chemotherapy can be initiated with a drug such as AZT having a positive track record. [0143]

EXAMPLE 7

A drug-naive HIV-infected patient donated plasma whose susceptibility to a number of RT inhibitors was determined according to the protocol set out in Example 1. Recombinant wild type HIV strain recIIIB was used as a reference HIV virus. Table 3 shows the IC ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptibility is shown in FIG. 7A. An Antivirogram was also prepared and is shown in FIG. 7B.

	TABLE 3


	Anti-HIV-1 activity
	IC₅₀(μM)

Drug	Exp. 1	Exp. 2	Mean (1)	recIIIB ref (2)	ratio (1)/(2)

AZT	0.052	0.050	0.051	0.023	2
3TC	2.173	ND	2.173	1.381	2
ddI	0.475	0.429	0.452	0.648	0.7
ddC	1.042	1.389	1.216	1.616	0.8
d4T	1.142	1.657	1.399	1.368	1
loviride	0.035	0.025	0.030	0.024	1
tivirapine	0.042	0.049	0.046	0.021	2

From these data one can determine that the patient is infected with a HIV strain closely resembling the wild type HIV. None of the drug regimens is to be excluded, so chemotherapy can be initiated with a drug such as AZT, 3TC or others having a positive track record. [0145]

EXAMPLE 8

An HIV-infected patient with a therapy history including AZT, 3TC and loviride donated plasma whose susceptibility to a number of RT inhibitors was determined according to the protocol set out in Example 1. Recombinant wild type HIV strain recIIIB was used as a reference HIV virus. Table 4 shows the IC ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptability is shown in FIG. 8A. An Antivirogram was also prepared and is shown in FIG. 8B.

	TABLE 4


	Anti-HIV-1 activity
	IC₅₀(μM)

				redIIIB	ratio
Drug	Exp. 1	Exp. 2	Mean (1)	ref(2)	(1)/(2)

AZT	18.264	22.251	20.257	0.084	241
3TC	>100.000	>100.000	>100.000	6.304	>16
ddI	26.861	15.435	21.148	1.586	13
ddC	9.290	8.506	8.898	1.931	5
d4T	7.500	7.097	7.298	5.465	1
loviride	>100.000	>100.000	>100.000	0.037	>2717
tivirapine	1.626	1.604	1.615	0.021	78

From this data one can determine that the patient is infected with a HIV strain displaying a decreased susceptibility towards most of the nucleoside and non-nucleoside antiretroviral drugs examined. Therapy can still be initiated with D4T or DDC. The possibility of including protease-inhibitors into the therapy can be considered. [0147]

EXAMPLE 9

An HIV-infected patient with a therapy history including multiple nucleoside analogue RT-inhibitors donated plasma whose susceptibility to a number of RT inhibitors was determined according to the protocol set out in Example 1. Recombinant wild type HIV strain recIIIB was used as a reference HIV virus. Table 5 shows the IC ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptibility is shown in FIG. 9A. An Antivirogram was also prepared and is shown in FIG. 9B.

	TABLE 5


	Anti-HIV-1 activity
	IC₅₀(μM)

				redIIIB	ratio
Drug	Exp. 1	Exp. 2	Mean (1)	ref(2)	(1)/(2)

AZT	>100.000	ND	>100.000	0.291	>344
3TC	>100.000	>100.000	>100.000	16.670	>6
ddI	>100.000	>100.000	>100.000	4.757	>21
ddC	60.079	73.049	66.564	3.444	19
d4T	>100.000	>100.000	>100.000	12.030	>8
loviride	0.064	0.058	0.061	0.065	0.9
tivirapine	0.052	0.043	0.048	0.042	1

From this data one can determine that the patient is infected with a HIV strain displaying a decreased susceptibility towards all nucleoside analogue antiretroviral drugs. Non-nucleoside antiretroviral drugs should not be excluded from therapy. Here also, the possibility of including protease inhibitors into the therapy can be considered. [0149]

EXAMPLE 10

A drug-naive HIV-infected patient donated plasma whose susceptibility to a number of RT inhibitors and protease inhibitors was determined according to the protocol set out in Example 1. Recombinant wild type HIV strain recIIIB was used as a reference HIV virus. Table 6 shows the IC[0150] ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptibility is shown in FIG. 10A. An Antivirogram was also prepared and is shown in FIG. 10B.

TABLE 6

Anti-HIV-1 activity

IC₅₀(μM)

recIIIB ratio

Drug Exp. 1 Exp. 2 Mean (1) ref (2) (1)/(2)

AZT 0.019 0.019 0.019 0.041 0.5

3TC 1.525 1.718 1.622 4.608 0.4

saquinavir 0.003 0.003 0.003 0.006 0.4

ritonavir 0.022 0.017 0.019 0.033 0.6

indinavir 0.013 0.013 0.013 0.016 0.8
From these data one can determine that the patient is infected with HIV strains closely resembling the wild type HIV. None of the drug regimens is to be excluded, so that chemotherapy can be initiated with a drug such as AZT, 3TC or others having a positive track record. [0151]

EXAMPLE 11

An HIV infected patient with a therapy history including RT and protease inhibitors donated plasma whose susceptibility to a number of RT inhibitors and protease inhibitors was determined according to the protocol set out in Example 1. Recombinant wild type HIV strain recIIIB was used as a reference HIV virus. Table 7 shows the IC[0152] ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptibility is shown in FIG. 11A. An Antivirogram was also prepared and is shown in FIG. 11B.

TABLE 7

Anti-HIV-1 activity

IC₅₀(μM)

redIIIB ratio

Drug Exp. 1 Exp. 2 Mean (1) ref(2) (1)/(2)

AZT ND 0.015 0.015 0.047 0.3

3TC >100.000 93.962 96.981 5.178 19

saquinavir 0.014 0.015 0.014 0.012 1

ritonavir 1.198 1.739 1.468 0.062 24

indinavir 0.229 0.416 0.323 0.027 12
From these data one can determine that the patient is infected with a HIV strain displaying a decreased susceptibilty towards the RT-inhibitor 3TC and protease inhibitors indinavir and ritonavir. Accordingly, chemotherapy can be adjusted with drugs such as AZT or saquinavir having a positive track record. [0153]

EXAMPLE 12

An HIV infected patient with a therapy history including RT and protease inhibitors donated plasma whose susceptibility to a number of RT inhibitors and protease inhibitors was determined according to the protocol set out in Example 1. Table 8 shows the IC[0154] ₅₀values (μM) measured and the ratio of said values. A bar graph showing relative change in drug susceptibility is shown in FIG. 12A. An Antivirogram was also prepared and is shown in FIG. 12B.

TABLE 8

Anti-HIV-1 activity

IC₅₀(μM)

redIIIB ratio

Drug Exp. 1 Exp. 2 Mean (1) ref(2) (1)/(2)

AZT 3.833 3.355 3.594 0.041 88

3TC >100.000 >100.000 >100.000 4.608 22

saquinavir 0.350 0.352 0.351 0.006 56

ritonavir 1.610 1.530 1.570 0.033 47

indinavir 0.124 ND 0.124 0.016 8
From these data one can determine that the patient is infected with a HIV strain displaying a decreased susceptibility towards RT-inhibitors 3TC and AZT and protease inhibitors indinavir, ritonavir and saquinavir. [0155]

EXAMPLE 13

Comparison of Phenotyping Relative to Genotyping Plasma samples were obtained from HIV-infected individuals who had been receiving non-nucleoside RT inhibitor (NNRTI) long-term monotherapy. HIV-RNA was extracted, reverse-transcribed and amplified as described in Example 1. Starting from outer PCR material of positive samples, the first 785 nucleotides of the RT gene were amplified and this material was further used for genotyping. [0156]

Briefly, the 785 nucleotide fragment was subjected to cycle-sequencing reactions using the ThermoSequenase (ThermoSequenase is a Trade Mark) fluorescent labelled primer cycle sequencing kit with 7-deaza-dGTP from Amersham (cat# RPN2438). Four sequencing primers, chosen to allow for sequence determination in both directions from nucleotide 27 to nucleotide 681 of the RT gene, were used for each sample. The reactions were analysed on an ALF (ALF is a Trade Mark) automatic sequencer (Pharmacia). The generated sequences were exported to a Power Macintosh and further analysed with the GeneWorks 2.5 software (Oxford Molecular Group Inc.). Resulting amino acid sequences were compared with the corresponding sequence of the laboratory HIV-1 clone HXB2D and resistance-associated mutations identified in patient material. The results are shown in Table 9 where the one-letter amino acid code is used.

	TABLE 9


	RESISTANCE ASSOCIATED MUTATIONS	FOLD RESISTANCE TO

	M	D	K	A	K	K	V	E	Y	M	G	T	K			NNRTI	NNRTI
P	41	67	70	98	101	103	108	138	181	184	190	215	219	AZT	3TC		1	2

1						N								1	1	56	437
2						S								1	0.4	102	53
3						N								0.4	1	36	87
4														0.3	0.1	1	0.4
5														1	0.4	4	3
6						N								1	0.3	103	245
7						S								1	0.04	112	57
8						N								1	1	30	81
9									C					2	1	>1432	12
10						N								0.4	0.1	53	172
11	L	N	R			N				V		F	Q	94	>8	321	669
12	L											Y		28	2	1	3
13					E	K/N		A			G/A		Not	1	1	>1466	455
													Det
14						N								1	1	93	349
15						N								2	1	>2424	449
16						N				V					1	>8	21	115
17						N								1	1	29	102
18						S								1	1	95	181
19						N								1	1	78	260
20				G										0.4	1	22	25
21						N								1	0.4	47	68
22							I							1	0.4	3	3
23						N								0.2	0.2	9	9
24					Q									1	1	7	59

The top row of Table 9 shows the aminoacids (AA) found in the wild type sequence and their position. Amino acids changes at these positions are shown for each patient in the following rows. Only the positions at which changes were observed in patient material are shown. The right part of Table 9 presents the fold resistance to different RT inhibitors as determined by the method according to the invention for each of the patients' samples. [0158] NNRTI 1 is the non-nucleoside RT inhibitor that was administered to the patients. NNRTI 2 is another non-nucleoside RT inhibitor for which cross-resistance with the first one was observed to some extent.
The genotyping results regarding nucleoside analog RT inhbitors resistance are as follows: [0159]
M41L, D67N, K70R, T215F/Y and K219Q/E are AZT resistance-associated mutations (Larder, B. and Kemp, S. (1989) Science 246, 1155-1158; Kellam, P. et al. (1992) PNAS 89, 1934-1938). Their presence, individually or in different combinations, in the genome of HIV isolated from patient material correlates with the phenotypic resistance as determined by the Antivirogram generated (patients 11 and 12). [0160]
The same applies to resistance to 3TC associated with the M184V mutation (Tisdale, M. et al. (1993) PNAS 90, 5653-5656) which is observed only in the patients which show phenotypic resistance to the drug (patients 11 and 16). [0161]
The genotyping results regarding NNRTIs resistance are as follows: [0162]
Three patients (3, 4 and 12) have no NNRTI resistance-associated mutation and are phenotypically sensitive to the drug. [0163]
Most of the patients who show phenotypic resistance to the NNRTIs have a NNRTI resistance-associated mutation at position 103 (K103N/S). [0164]
One patient (9) has the Y181C NNRTI resistance-associated mutation and shows a high phenotypic resistance (>1432 fold) to [0165] NNRTI 1.
[0166] Patient 13 has several NNRTI resistance-associated mutations (K101E, K103N partially and G190A partially). This patient also shows a high phenotypic resistance (>1466 fold) to NNRTI 1. The E138A mutation observed in this sample is not associated so far with resistance. However, another mutation at this same position, i.e. E138K, has been demonstrated to play an important role in resistance to the TSAO compounds (Balzarini, J. et al. (1993) PNAS 90, 6952-9656). The role of the E138A mutation still needs to be assessed.
Patient 20 has the A98G NNRTI resistance-associated mutation and shows phenotypic resistance to the tested NNRTIs. [0167]
[0168] Patient 22 has the V108I NNRTI resistance-associated mutation but does not show any phenotypic resistance to the tested NNRTIs.
[0169] Patient 24 shows no NNRTI resistance-associated mutation (the K101Q mutation is found in several HIV-1 wild type genomes) but is phenotypically resistant to the tested NNRTIs.
1 15 1 33 DNA Human immunodeficiency virus type 1 1 cattgctctc caattactgt gatatttctc atg 33 2 26 DNA Human immunodeficiency virus type 1 2 gggaagatct ggccttccta caaggg 26 3 24 DNA Human immunodeficiency virus type 1 3 gcccctagga aaaagggctg ttgg 24 4 24 DNA Human immunodeficiency virus type 1 4 tgaaagattg tactgagaga cagg 24 5 24 DNA Human immunodeficiency virus type 1 5 gatatttctc atgttcatct tggg 24 6 24 DNA Human immunodeficiency virus type 1 6 aggtggcagg ttaaaatcac tagc 24 7 2601 DNA HIV-HXB2 CDS (1)..(492) gag Polyprotein 7 gga cca gcg gct aca cta gaa gaa atg atg aca gca tgt cag gga gta 48 Gly Pro Ala Ala Thr Leu Glu Glu Met Met Thr Ala Cys Gln Gly Val 1 5 10 15 gga gga ccc ggc cat aag gca aga gtt ttg gct gaa gca atg agc caa 96 Gly Gly Pro Gly His Lys Ala Arg Val Leu Ala Glu Ala Met Ser Gln 20 25 30 gta aca aat tca gct acc ata atg atg cag aga ggc aat ttt agg aac 144 Val Thr Asn Ser Ala Thr Ile Met Met Gln Arg Gly Asn Phe Arg Asn 35 40 45 caa aga aag att gtt aag tgt ttc aat tgt ggc aaa gaa ggg cac aca 192 Gln Arg Lys Ile Val Lys Cys Phe Asn Cys Gly Lys Glu Gly His Thr 50 55 60 gcc aga aat tgc agg gcc cct agg aaa aag ggc tgt tgg aaa tgt gga 240 Ala Arg Asn Cys Arg Ala Pro Arg Lys Lys Gly Cys Trp Lys Cys Gly 65 70 75 80 aag gaa gga cac caa atg aaa gat tgt act gag aga cag gct aat ttt 288 Lys Glu Gly His Gln Met Lys Asp Cys Thr Glu Arg Gln Ala Asn Phe 85 90 95 tta ggg aag atc tgg cct tcc tac aag gga agg cca ggg aat ttt ctt 336 Leu Gly Lys Ile Trp Pro Ser Tyr Lys Gly Arg Pro Gly Asn Phe Leu 100 105 110 cag agc aga cca gag cca aca gcc cca cca gaa gag agc ttc agg tct 384 Gln Ser Arg Pro Glu Pro Thr Ala Pro Pro Glu Glu Ser Phe Arg Ser 115 120 125 ggg gta gag aca aca act ccc cct cag aag cag gag ccg ata gac aag 432 Gly Val Glu Thr Thr Thr Pro Pro Gln Lys Gln Glu Pro Ile Asp Lys 130 135 140 gaa ctg tat cct tta act tcc ctc agg tca ctc ttt ggc aac gac ccc 480 Glu Leu Tyr Pro Leu Thr Ser Leu Arg Ser Leu Phe Gly Asn Asp Pro 145 150 155 160 tcg tca caa taa agataggggg gcaactaaag gaagctctat tagatacagg 532 Ser Ser Gln agcagatgat acagtattag aagaaatgag tttgccagga agatggaaac caaaaatgat 592 agggggaatt ggaggtttta tcaaagtaag acagtatgat cagatactca tagaaatctg 652 tggacataaa gctataggta cagtattagt aggacctaca cctgtcaaca taattggaag 712 aaatctgttg actcagattg gttgcacttt aaattttccc attagcccta ttgagactgt 772 accagtaaaa ttaaagccag gaatggatgg cccaaaagtt aaacaatggc cattgacaga 832 agaaaaaata aaagcattag tagaaatttg tacagagatg gaaaaggaag cgaaaatttc 892 aaaaattggg cctgaaaatc catacaatac tccagtattt gccataaaga aaaaagacag 952 tactaaatgg agaaaattag tagatttcag agaacttaat aagagaactc aagacttctg 1012 ggaagttcaa ttaggaatac cacatcccgc aggcttaaaa aagaaaaaat cagtaacagt 1072 actggatgtg ggtgatgcat atttttcagt tcccttagat gaagacttca ggaagtatac 1132 tgcatttacc atacctagta taaacaatga gacaccaggg attagatatc agtacaatgt 1192 gcttccacag ggatggaaag gatcaccagc aatattccaa agtagcatga caaaaatctt 1252 agagcctttt agaaaacaaa atccagacat agttatctat caatacatgg atgatttgta 1312 tgtaggatct gacttagaaa tagggcagca tagaacaaaa atagaggagc tgagacaaca 1372 tctgttgagg tggggactta ccacaccaga caaaaaacat cagaaagaac ctccattcct 1432 ttggatgggt tatgaactcc atcctgataa atggacagta cagcctatag tgctgccaga 1492 aaaagacagc tggactgtca atgacataca gaagttagtg gggaaattga attgggcaag 1552 tcagatttac ccagggatta aagtaaggca attatgtaaa ctccttagag gaaccaaagc 1612 actaacagaa gtaataccac taacagaaga agcagagcta gaactggcag aaaacagaga 1672 gattctaaaa gaaccagtac atggagtgta ttatgaccca tcaaaagact taatagcaga 1732 aatacagaag caggggcaag gccaatggac atatcaaatt tatcaagagc catttaaaaa 1792 tctgaaaaca ggaaaatatg caagaatgag gggtgcccac actaatgatg taaaacaatt 1852 aacagaggca gtgcaaaaaa taaccacaga aagcatagta atatggggaa agactcctaa 1912 atttaaactg cccatacaaa aggaaacatg ggaaacatgg tggacagagt attggcaagc 1972 cacctggatt cctgagtggg agtttgttaa tacccctccc ttagtgaaat tatggtacca 2032 gttagagaaa gaacccatag taggagcaga aaccttctat gtagatgggg cagctaacag 2092 ggagactaaa ttaggaaaag caggatatgt tactaataga ggaagacaaa aagttgtcac 2152 cctaactgac acaacaaatc agaagactga gttacaagca atttatctag ctttgcagga 2212 ttcgggatta gaagtaaaca tagtaacaga ctcacaatat gcattaggaa tcattcaagc 2272 acaaccagat caaagtgaat cagagttagt caatcaaata atagagcagt taataaaaaa 2332 ggaaaaggtc tatctggcat gggtaccagc acacaaagga attggaggaa atgaacaagt 2392 agataaatta gtcagtgctg gaatcaggaa agtactattt ttagatggaa tagataaggc 2452 ccaagatgaa catgagaaat atcacagtaa ttggagagca atggctagtg attttaacct 2512 gccacctgta gtagcaaaag aaatagtagc cagctgtgat aaatgtcagc taaaaggaga 2572 agccatgcat ggacaagtag actgtagtc 2601 8 163 PRT HIV-HXB2 8 Gly Pro Ala Ala Thr Leu Glu Glu Met Met Thr Ala Cys Gln Gly Val 1 5 10 15 Gly Gly Pro Gly His Lys Ala Arg Val Leu Ala Glu Ala Met Ser Gln 20 25 30 Val Thr Asn Ser Ala Thr Ile Met Met Gln Arg Gly Asn Phe Arg Asn 35 40 45 Gln Arg Lys Ile Val Lys Cys Phe Asn Cys Gly Lys Glu Gly His Thr 50 55 60 Ala Arg Asn Cys Arg Ala Pro Arg Lys Lys Gly Cys Trp Lys Cys Gly 65 70 75 80 Lys Glu Gly His Gln Met Lys Asp Cys Thr Glu Arg Gln Ala Asn Phe 85 90 95 Leu Gly Lys Ile Trp Pro Ser Tyr Lys Gly Arg Pro Gly Asn Phe Leu 100 105 110 Gln Ser Arg Pro Glu Pro Thr Ala Pro Pro Glu Glu Ser Phe Arg Ser 115 120 125 Gly Val Glu Thr Thr Thr Pro Pro Gln Lys Gln Glu Pro Ile Asp Lys 130 135 140 Glu Leu Tyr Pro Leu Thr Ser Leu Arg Ser Leu Phe Gly Asn Asp Pro 145 150 155 160 Ser Ser Gln 9 2601 DNA HIV-HXB2 CDS (334)..(489) gag P6 (52 AA) 9 ggaccagcgg ctacactaga agaaatgatg acagcatgtc agggagtagg aggacccggc 60 cataaggcaa gagttttggc tgaagcaatg agccaagtaa caaattcagc taccataatg 120 atgcagagag gcaattttag gaaccaaaga aagattgtta agtgtttcaa ttgtggcaaa 180 gaagggcaca cagccagaaa ttgcagggcc cctaggaaaa agggctgttg gaaatgtgga 240 aaggaaggac accaaatgaa agattgtact gagagacagg ctaatttttt agggaagatc 300 tggccttcct acaagggaag gccagggaat ttt ctt cag agc aga cca gag cca 354 Leu Gln Ser Arg Pro Glu Pro 1 5 aca gcc cca cca gaa gag agc ttc agg tct ggg gta gag aca aca act 402 Thr Ala Pro Pro Glu Glu Ser Phe Arg Ser Gly Val Glu Thr Thr Thr 10 15 20 ccc cct cag aag cag gag ccg ata gac aag gaa ctg tat cct tta act 450 Pro Pro Gln Lys Gln Glu Pro Ile Asp Lys Glu Leu Tyr Pro Leu Thr 25 30 35 tcc ctc agg tca ctc ttt ggc aac gac ccc tcg tca caa taaagatagg 499 Ser Leu Arg Ser Leu Phe Gly Asn Asp Pro Ser Ser Gln 40 45 50 ggggcaacta aaggaagctc tattagatac aggagcagat gatacagtat tagaagaaat 559 gagtttgcca ggaagatgga aaccaaaaat gataggggga attggaggtt ttatcaaagt 619 aagacagtat gatcagatac tcatagaaat ctgtggacat aaagctatag gtacagtatt 679 agtaggacct acacctgtca acataattgg aagaaatctg ttgactcaga ttggttgcac 739 tttaaatttt cccattagcc ctattgagac tgtaccagta aaattaaagc caggaatgga 799 tggcccaaaa gttaaacaat ggccattgac agaagaaaaa ataaaagcat tagtagaaat 859 ttgtacagag atggaaaagg aagcgaaaat ttcaaaaatt gggcctgaaa atccatacaa 919 tactccagta tttgccataa agaaaaaaga cagtactaaa tggagaaaat tagtagattt 979 cagagaactt aataagagaa ctcaagactt ctgggaagtt caattaggaa taccacatcc 1039 cgcaggctta aaaaagaaaa aatcagtaac agtactggat gtgggtgatg catatttttc 1099 agttccctta gatgaagact tcaggaagta tactgcattt accataccta gtataaacaa 1159 tgagacacca gggattagat atcagtacaa tgtgcttcca cagggatgga aaggatcacc 1219 agcaatattc caaagtagca tgacaaaaat cttagagcct tttagaaaac aaaatccaga 1279 catagttatc tatcaataca tggatgattt gtatgtagga tctgacttag aaatagggca 1339 gcatagaaca aaaatagagg agctgagaca acatctgttg aggtggggac ttaccacacc 1399 agacaaaaaa catcagaaag aacctccatt cctttggatg ggttatgaac tccatcctga 1459 taaatggaca gtacagccta tagtgctgcc agaaaaagac agctggactg tcaatgacat 1519 acagaagtta gtggggaaat tgaattgggc aagtcagatt tacccaggga ttaaagtaag 1579 gcaattatgt aaactcctta gaggaaccaa agcactaaca gaagtaatac cactaacaga 1639 agaagcagag ctagaactgg cagaaaacag agagattcta aaagaaccag tacatggagt 1699 gtattatgac ccatcaaaag acttaatagc agaaatacag aagcaggggc aaggccaatg 1759 gacatatcaa atttatcaag agccatttaa aaatctgaaa acaggaaaat atgcaagaat 1819 gaggggtgcc cacactaatg atgtaaaaca attaacagag gcagtgcaaa aaataaccac 1879 agaaagcata gtaatatggg gaaagactcc taaatttaaa ctgcccatac aaaaggaaac 1939 atgggaaaca tggtggacag agtattggca agccacctgg attcctgagt gggagtttgt 1999 taatacccct cccttagtga aattatggta ccagttagag aaagaaccca tagtaggagc 2059 agaaaccttc tatgtagatg gggcagctaa cagggagact aaattaggaa aagcaggata 2119 tgttactaat agaggaagac aaaaagttgt caccctaact gacacaacaa atcagaagac 2179 tgagttacaa gcaatttatc tagctttgca ggattcggga ttagaagtaa acatagtaac 2239 agactcacaa tatgcattag gaatcattca agcacaacca gatcaaagtg aatcagagtt 2299 agtcaatcaa ataatagagc agttaataaa aaaggaaaag gtctatctgg catgggtacc 2359 agcacacaaa ggaattggag gaaatgaaca agtagataaa ttagtcagtg ctggaatcag 2419 gaaagtacta tttttagatg gaatagataa ggcccaagat gaacatgaga aatatcacag 2479 taattggaga gcaatggcta gtgattttaa cctgccacct gtagtagcaa aagaaatagt 2539 agccagctgt gataaatgtc agctaaaagg agaagccatg catggacaag tagactgtag 2599 tc 2601 10 52 PRT HIV-HXB2 10 Leu Gln Ser Arg Pro Glu Pro Thr Ala Pro Pro Glu Glu Ser Phe Arg 1 5 10 15 Ser Gly Val Glu Thr Thr Thr Pro Pro Gln Lys Gln Glu Pro Ile Asp 20 25 30 Lys Glu Leu Tyr Pro Leu Thr Ser Leu Arg Ser Leu Phe Gly Asn Asp 35 40 45 Pro Ser Ser Gln 50 11 2601 DNA HIV-HXB2 CDS (453)..(749) Protease 11 ggaccagcgg ctacactaga agaaatgatg acagcatgtc agggagtagg aggacccggc 60 cataaggcaa gagttttggc tgaagcaatg agccaagtaa caaattcagc taccataatg 120 atgcagagag gcaattttag gaaccaaaga aagattgtta agtgtttcaa ttgtggcaaa 180 gaagggcaca cagccagaaa ttgcagggcc cctaggaaaa agggctgttg gaaatgtgga 240 aaggaaggac accaaatgaa agattgtact gagagacagg ctaatttttt agggaagatc 300 tggccttcct acaagggaag gccagggaat tttcttcaga gcagaccaga gccaacagcc 360 ccaccagaag agagcttcag gtctggggta gagacaacaa ctccccctca gaagcaggag 420 ccgatagaca aggaactgta tcctttaact tc cct cag gtc act ctt tgg caa 473 Pro Gln Val Thr Leu Trp Gln 1 5 cga ccc ctc gtc aca ata aag ata ggg ggg caa cta aag gaa gct cta 521 Arg Pro Leu Val Thr Ile Lys Ile Gly Gly Gln Leu Lys Glu Ala Leu 10 15 20 tta gat aca gga gca gat gat aca gta tta gaa gaa atg agt ttg cca 569 Leu Asp Thr Gly Ala Asp Asp Thr Val Leu Glu Glu Met Ser Leu Pro 25 30 35 gga aga tgg aaa cca aaa atg ata ggg gga att gga ggt ttt atc aaa 617 Gly Arg Trp Lys Pro Lys Met Ile Gly Gly Ile Gly Gly Phe Ile Lys 40 45 50 55 gta aga cag tat gat cag ata ctc ata gaa atc tgt gga cat aaa gct 665 Val Arg Gln Tyr Asp Gln Ile Leu Ile Glu Ile Cys Gly His Lys Ala 60 65 70 ata ggt aca gta tta gta gga cct aca cct gtc aac ata att gga aga 713 Ile Gly Thr Val Leu Val Gly Pro Thr Pro Val Asn Ile Ile Gly Arg 75 80 85 aat ctg ttg act cag att ggt tgc act tta aat ttt cccattagcc 759 Asn Leu Leu Thr Gln Ile Gly Cys Thr Leu Asn Phe 90 95 ctattgagac tgtaccagta aaattaaagc caggaatgga tggcccaaaa gttaaacaat 819 ggccattgac agaagaaaaa ataaaagcat tagtagaaat ttgtacagag atggaaaagg 879 aagcgaaaat ttcaaaaatt gggcctgaaa atccatacaa tactccagta tttgccataa 939 agaaaaaaga cagtactaaa tggagaaaat tagtagattt cagagaactt aataagagaa 999 ctcaagactt ctgggaagtt caattaggaa taccacatcc cgcaggctta aaaaagaaaa 1059 aatcagtaac agtactggat gtgggtgatg catatttttc agttccctta gatgaagact 1119 tcaggaagta tactgcattt accataccta gtataaacaa tgagacacca gggattagat 1179 atcagtacaa tgtgcttcca cagggatgga aaggatcacc agcaatattc caaagtagca 1239 tgacaaaaat cttagagcct tttagaaaac aaaatccaga catagttatc tatcaataca 1299 tggatgattt gtatgtagga tctgacttag aaatagggca gcatagaaca aaaatagagg 1359 agctgagaca acatctgttg aggtggggac ttaccacacc agacaaaaaa catcagaaag 1419 aacctccatt cctttggatg ggttatgaac tccatcctga taaatggaca gtacagccta 1479 tagtgctgcc agaaaaagac agctggactg tcaatgacat acagaagtta gtggggaaat 1539 tgaattgggc aagtcagatt tacccaggga ttaaagtaag gcaattatgt aaactcctta 1599 gaggaaccaa agcactaaca gaagtaatac cactaacaga agaagcagag ctagaactgg 1659 cagaaaacag agagattcta aaagaaccag tacatggagt gtattatgac ccatcaaaag 1719 acttaatagc agaaatacag aagcaggggc aaggccaatg gacatatcaa atttatcaag 1779 agccatttaa aaatctgaaa acaggaaaat atgcaagaat gaggggtgcc cacactaatg 1839 atgtaaaaca attaacagag gcagtgcaaa aaataaccac agaaagcata gtaatatggg 1899 gaaagactcc taaatttaaa ctgcccatac aaaaggaaac atgggaaaca tggtggacag 1959 agtattggca agccacctgg attcctgagt gggagtttgt taatacccct cccttagtga 2019 aattatggta ccagttagag aaagaaccca tagtaggagc agaaaccttc tatgtagatg 2079 gggcagctaa cagggagact aaattaggaa aagcaggata tgttactaat agaggaagac 2139 aaaaagttgt caccctaact gacacaacaa atcagaagac tgagttacaa gcaatttatc 2199 tagctttgca ggattcggga ttagaagtaa acatagtaac agactcacaa tatgcattag 2259 gaatcattca agcacaacca gatcaaagtg aatcagagtt agtcaatcaa ataatagagc 2319 agttaataaa aaaggaaaag gtctatctgg catgggtacc agcacacaaa ggaattggag 2379 gaaatgaaca agtagataaa ttagtcagtg ctggaatcag gaaagtacta tttttagatg 2439 gaatagataa ggcccaagat gaacatgaga aatatcacag taattggaga gcaatggcta 2499 gtgattttaa cctgccacct gtagtagcaa aagaaatagt agccagctgt gataaatgtc 2559 agctaaaagg agaagccatg catggacaag tagactgtag tc 2601 12 99 PRT HIV-HXB2 12 Pro Gln Val Thr Leu Trp Gln Arg Pro Leu Val Thr Ile Lys Ile Gly 1 5 10 15 Gly Gln Leu Lys Glu Ala Leu Leu Asp Thr Gly Ala Asp Asp Thr Val 20 25 30 Leu Glu Glu Met Ser Leu Pro Gly Arg Trp Lys Pro Lys Met Ile Gly 35 40 45 Gly Ile Gly Gly Phe Ile Lys Val Arg Gln Tyr Asp Gln Ile Leu Ile 50 55 60 Glu Ile Cys Gly His Lys Ala Ile Gly Thr Val Leu Val Gly Pro Thr 65 70 75 80 Pro Val Asn Ile Ile Gly Arg Asn Leu Leu Thr Gln Ile Gly Cys Thr 85 90 95 Leu Asn Phe 13 2601 DNA HIV-HXB2 CDS (750)..(2435) Reverse Transcriptase 13 ggaccagcgg ctacactaga agaaatgatg acagcatgtc agggagtagg aggacccggc 60 cataaggcaa gagttttggc tgaagcaatg agccaagtaa caaattcagc taccataatg 120 atgcagagag gcaattttag gaaccaaaga aagattgtta agtgtttcaa ttgtggcaaa 180 gaagggcaca cagccagaaa ttgcagggcc cctaggaaaa agggctgttg gaaatgtgga 240 aaggaaggac accaaatgaa agattgtact gagagacagg ctaatttttt agggaagatc 300 tggccttcct acaagggaag gccagggaat tttcttcaga gcagaccaga gccaacagcc 360 ccaccagaag agagcttcag gtctggggta gagacaacaa ctccccctca gaagcaggag 420 ccgatagaca aggaactgta tcctttaact tccctcaggt cactctttgg caacgacccc 480 tcgtcacaat aaagataggg gggcaactaa aggaagctct attagataca ggagcagatg 540 atacagtatt agaagaaatg agtttgccag gaagatggaa accaaaaatg atagggggaa 600 ttggaggttt tatcaaagta agacagtatg atcagatact catagaaatc tgtggacata 660 aagctatagg tacagtatta gtaggaccta cacctgtcaa cataattgga agaaatctgt 720 tgactcagat tggttgcact ttaaatttt ccc att agc cct att gag act gta 773 Pro Ile Ser Pro Ile Glu Thr Val 1 5 cca gta aaa tta aag cca gga atg gat ggc cca aaa gtt aaa caa tgg 821 Pro Val Lys Leu Lys Pro Gly Met Asp Gly Pro Lys Val Lys Gln Trp 10 15 20 cca ttg aca gaa gaa aaa ata aaa gca tta gta gaa att tgt aca gag 869 Pro Leu Thr Glu Glu Lys Ile Lys Ala Leu Val Glu Ile Cys Thr Glu 25 30 35 40 atg gaa aag gaa gcg aaa att tca aaa att ggg cct gaa aat cca tac 917 Met Glu Lys Glu Ala Lys Ile Ser Lys Ile Gly Pro Glu Asn Pro Tyr 45 50 55 aat act cca gta ttt gcc ata aag aaa aaa gac agt act aaa tgg aga 965 Asn Thr Pro Val Phe Ala Ile Lys Lys Lys Asp Ser Thr Lys Trp Arg 60 65 70 aaa tta gta gat ttc aga gaa ctt aat aag aga act caa gac ttc tgg 1013 Lys Leu Val Asp Phe Arg Glu Leu Asn Lys Arg Thr Gln Asp Phe Trp 75 80 85 gaa gtt caa tta gga ata cca cat ccc gca ggc tta aaa aag aaa aaa 1061 Glu Val Gln Leu Gly Ile Pro His Pro Ala Gly Leu Lys Lys Lys Lys 90 95 100 tca gta aca gta ctg gat gtg ggt gat gca tat ttt tca gtt ccc tta 1109 Ser Val Thr Val Leu Asp Val Gly Asp Ala Tyr Phe Ser Val Pro Leu 105 110 115 120 gat gaa gac ttc agg aag tat act gca ttt acc ata cct agt ata aac 1157 Asp Glu Asp Phe Arg Lys Tyr Thr Ala Phe Thr Ile Pro Ser Ile Asn 125 130 135 aat gag aca cca ggg att aga tat cag tac aat gtg ctt cca cag gga 1205 Asn Glu Thr Pro Gly Ile Arg Tyr Gln Tyr Asn Val Leu Pro Gln Gly 140 145 150 tgg aaa gga tca cca gca ata ttc caa agt agc atg aca aaa atc tta 1253 Trp Lys Gly Ser Pro Ala Ile Phe Gln Ser Ser Met Thr Lys Ile Leu 155 160 165 gag cct ttt aga aaa caa aat cca gac ata gtt atc tat caa tac atg 1301 Glu Pro Phe Arg Lys Gln Asn Pro Asp Ile Val Ile Tyr Gln Tyr Met 170 175 180 gat gat ttg tat gta gga tct gac tta gaa ata ggg cag cat aga aca 1349 Asp Asp Leu Tyr Val Gly Ser Asp Leu Glu Ile Gly Gln His Arg Thr 185 190 195 200 aaa ata gag gag ctg aga caa cat ctg ttg agg tgg gga ctt acc aca 1397 Lys Ile Glu Glu Leu Arg Gln His Leu Leu Arg Trp Gly Leu Thr Thr 205 210 215 cca gac aaa aaa cat cag aaa gaa cct cca ttc ctt tgg atg ggt tat 1445 Pro Asp Lys Lys His Gln Lys Glu Pro Pro Phe Leu Trp Met Gly Tyr 220 225 230 gaa ctc cat cct gat aaa tgg aca gta cag cct ata gtg ctg cca gaa 1493 Glu Leu His Pro Asp Lys Trp Thr Val Gln Pro Ile Val Leu Pro Glu 235 240 245 aaa gac agc tgg act gtc aat gac ata cag aag tta gtg ggg aaa ttg 1541 Lys Asp Ser Trp Thr Val Asn Asp Ile Gln Lys Leu Val Gly Lys Leu 250 255 260 aat tgg gca agt cag att tac cca ggg att aaa gta agg caa tta tgt 1589 Asn Trp Ala Ser Gln Ile Tyr Pro Gly Ile Lys Val Arg Gln Leu Cys 265 270 275 280 aaa ctc ctt aga gga acc aaa gca cta aca gaa gta ata cca cta aca 1637 Lys Leu Leu Arg Gly Thr Lys Ala Leu Thr Glu Val Ile Pro Leu Thr 285 290 295 gaa gaa gca gag cta gaa ctg gca gaa aac aga gag att cta aaa gaa 1685 Glu Glu Ala Glu Leu Glu Leu Ala Glu Asn Arg Glu Ile Leu Lys Glu 300 305 310 cca gta cat gga gtg tat tat gac cca tca aaa gac tta ata gca gaa 1733 Pro Val His Gly Val Tyr Tyr Asp Pro Ser Lys Asp Leu Ile Ala Glu 315 320 325 ata cag aag cag ggg caa ggc caa tgg aca tat caa att tat caa gag 1781 Ile Gln Lys Gln Gly Gln Gly Gln Trp Thr Tyr Gln Ile Tyr Gln Glu 330 335 340 cca ttt aaa aat ctg aaa aca gga aaa tat gca aga atg agg ggt gcc 1829 Pro Phe Lys Asn Leu Lys Thr Gly Lys Tyr Ala Arg Met Arg Gly Ala 345 350 355 360 cac act aat gat gta aaa caa tta aca gag gca gtg caa aaa ata acc 1877 His Thr Asn Asp Val Lys Gln Leu Thr Glu Ala Val Gln Lys Ile Thr 365 370 375 aca gaa agc ata gta ata tgg gga aag act cct aaa ttt aaa ctg ccc 1925 Thr Glu Ser Ile Val Ile Trp Gly Lys Thr Pro Lys Phe Lys Leu Pro 380 385 390 ata caa aag gaa aca tgg gaa aca tgg tgg aca gag tat tgg caa gcc 1973 Ile Gln Lys Glu Thr Trp Glu Thr Trp Trp Thr Glu Tyr Trp Gln Ala 395 400 405 acc tgg att cct gag tgg gag ttt gtt aat acc cct ccc tta gtg aaa 2021 Thr Trp Ile Pro Glu Trp Glu Phe Val Asn Thr Pro Pro Leu Val Lys 410 415 420 tta tgg tac cag tta gag aaa gaa ccc ata gta gga gca gaa acc ttc 2069 Leu Trp Tyr Gln Leu Glu Lys Glu Pro Ile Val Gly Ala Glu Thr Phe 425 430 435 440 tat gta gat ggg gca gct aac agg gag act aaa tta gga aaa gca gga 2117 Tyr Val Asp Gly Ala Ala Asn Arg Glu Thr Lys Leu Gly Lys Ala Gly 445 450 455 tat gtt act aat aga gga aga caa aaa gtt gtc acc cta act gac aca 2165 Tyr Val Thr Asn Arg Gly Arg Gln Lys Val Val Thr Leu Thr Asp Thr 460 465 470 aca aat cag aag act gag tta caa gca att tat cta gct ttg cag gat 2213 Thr Asn Gln Lys Thr Glu Leu Gln Ala Ile Tyr Leu Ala Leu Gln Asp 475 480 485 tcg gga tta gaa gta aac ata gta aca gac tca caa tat gca tta gga 2261 Ser Gly Leu Glu Val Asn Ile Val Thr Asp Ser Gln Tyr Ala Leu Gly 490 495 500 atc att caa gca caa cca gat caa agt gaa tca gag tta gtc aat caa 2309 Ile Ile Gln Ala Gln Pro Asp Gln Ser Glu Ser Glu Leu Val Asn Gln 505 510 515 520 ata ata gag cag tta ata aaa aag gaa aag gtc tat ctg gca tgg gta 2357 Ile Ile Glu Gln Leu Ile Lys Lys Glu Lys Val Tyr Leu Ala Trp Val 525 530 535 cca gca cac aaa gga att gga gga aat gaa caa gta gat aaa tta gtc 2405 Pro Ala His Lys Gly Ile Gly Gly Asn Glu Gln Val Asp Lys Leu Val 540 545 550 agt gct gga atc agg aaa gta cta ttt tta gatggaatag ataaggccca 2455 Ser Ala Gly Ile Arg Lys Val Leu Phe Leu 555 560 agatgaacat gagaaatatc acagtaattg gagagcaatg gctagtgatt ttaacctgcc 2515 acctgtagta gcaaaagaaa tagtagccag ctgtgataaa tgtcagctaa aaggagaagc 2575 catgcatgga caagtagact gtagtc 2601 14 562 PRT HIV-HXB2 14 Pro Ile Ser Pro Ile Glu Thr Val Pro Val Lys Leu Lys Pro Gly Met 1 5 10 15 Asp Gly Pro Lys Val Lys Gln Trp Pro Leu Thr Glu Glu Lys Ile Lys 20 25 30 Ala Leu Val Glu Ile Cys Thr Glu Met Glu Lys Glu Ala Lys Ile Ser 35 40 45 Lys Ile Gly Pro Glu Asn Pro Tyr Asn Thr Pro Val Phe Ala Ile Lys 50 55 60 Lys Lys Asp Ser Thr Lys Trp Arg Lys Leu Val Asp Phe Arg Glu Leu 65 70 75 80 Asn Lys Arg Thr Gln Asp Phe Trp Glu Val Gln Leu Gly Ile Pro His 85 90 95 Pro Ala Gly Leu Lys Lys Lys Lys Ser Val Thr Val Leu Asp Val Gly 100 105 110 Asp Ala Tyr Phe Ser Val Pro Leu Asp Glu Asp Phe Arg Lys Tyr Thr 115 120 125 Ala Phe Thr Ile Pro Ser Ile Asn Asn Glu Thr Pro Gly Ile Arg Tyr 130 135 140 Gln Tyr Asn Val Leu Pro Gln Gly Trp Lys Gly Ser Pro Ala Ile Phe 145 150 155 160 Gln Ser Ser Met Thr Lys Ile Leu Glu Pro Phe Arg Lys Gln Asn Pro 165 170 175 Asp Ile Val Ile Tyr Gln Tyr Met Asp Asp Leu Tyr Val Gly Ser Asp 180 185 190 Leu Glu Ile Gly Gln His Arg Thr Lys Ile Glu Glu Leu Arg Gln His 195 200 205 Leu Leu Arg Trp Gly Leu Thr Thr Pro Asp Lys Lys His Gln Lys Glu 210 215 220 Pro Pro Phe Leu Trp Met Gly Tyr Glu Leu His Pro Asp Lys Trp Thr 225 230 235 240 Val Gln Pro Ile Val Leu Pro Glu Lys Asp Ser Trp Thr Val Asn Asp 245 250 255 Ile Gln Lys Leu Val Gly Lys Leu Asn Trp Ala Ser Gln Ile Tyr Pro 260 265 270 Gly Ile Lys Val Arg Gln Leu Cys Lys Leu Leu Arg Gly Thr Lys Ala 275 280 285 Leu Thr Glu Val Ile Pro Leu Thr Glu Glu Ala Glu Leu Glu Leu Ala 290 295 300 Glu Asn Arg Glu Ile Leu Lys Glu Pro Val His Gly Val Tyr Tyr Asp 305 310 315 320 Pro Ser Lys Asp Leu Ile Ala Glu Ile Gln Lys Gln Gly Gln Gly Gln 325 330 335 Trp Thr Tyr Gln Ile Tyr Gln Glu Pro Phe Lys Asn Leu Lys Thr Gly 340 345 350 Lys Tyr Ala Arg Met Arg Gly Ala His Thr Asn Asp Val Lys Gln Leu 355 360 365 Thr Glu Ala Val Gln Lys Ile Thr Thr Glu Ser Ile Val Ile Trp Gly 370 375 380 Lys Thr Pro Lys Phe Lys Leu Pro Ile Gln Lys Glu Thr Trp Glu Thr 385 390 395 400 Trp Trp Thr Glu Tyr Trp Gln Ala Thr Trp Ile Pro Glu Trp Glu Phe 405 410 415 Val Asn Thr Pro Pro Leu Val Lys Leu Trp Tyr Gln Leu Glu Lys Glu 420 425 430 Pro Ile Val Gly Ala Glu Thr Phe Tyr Val Asp Gly Ala Ala Asn Arg 435 440 445 Glu Thr Lys Leu Gly Lys Ala Gly Tyr Val Thr Asn Arg Gly Arg Gln 450 455 460 Lys Val Val Thr Leu Thr Asp Thr Thr Asn Gln Lys Thr Glu Leu Gln 465 470 475 480 Ala Ile Tyr Leu Ala Leu Gln Asp Ser Gly Leu Glu Val Asn Ile Val 485 490 495 Thr Asp Ser Gln Tyr Ala Leu Gly Ile Ile Gln Ala Gln Pro Asp Gln 500 505 510 Ser Glu Ser Glu Leu Val Asn Gln Ile Ile Glu Gln Leu Ile Lys Lys 515 520 525 Glu Lys Val Tyr Leu Ala Trp Val Pro Ala His Lys Gly Ile Gly Gly 530 535 540 Asn Glu Gln Val Asp Lys Leu Val Ser Ala Gly Ile Arg Lys Val Leu 545 550 555 560 Phe Leu 15 13 DNA Partial sequence of plasmid pGEMT3... 15 gacccgggtg acc 13

Claims

1. A method of managing HIV chemotherapy of patients who are HIV positive, which comprises

transfecting a cell line susceptible to infection by HIV with a sequence from the pol gene of HIV, which sequence encodes at least one desired target enzyme selected from integrase, protease or reverse transcriptase, obtained by isolating viral RNA from a sample of a biological material from a patient and reverse transcribing the desired region of said pol gene, and a HIV-DNA construct that lacks a sequence encoding said desired target enzyme,

culturing said transfected cells so as to create a stock of chimeric viruses,

assessing the phenotypic sensitivity of said chimeric viruses to at least one inhibitor of said target enzyme encoded by the pol gene of HIV, and

assigning a value thereto, constructing a data set comprising said value for chimeric virus sensitivity and the corresponding value for a chimeric wild-type strain of HIV,

repeating the sensitivity assessment for at least two further inhibitors and thereby constructing at least three such data sets in total,

representing said at least one data sets in two dimensional or three dimensional graphical form such that the difference between the chimeric and wild-type sensitivities in the case of each data set provides a visual measure of the resistance of the chimeric stock to treatment by the inhibitor in question, and

selecting the optimum inhibitor(s) on the basis of the graphical representation of the resistances so measured.

2. A method of managing HIV chemotherapy according to claim 1, wherein the data sets are represented on a polygonal or quasi-circular graph comprising:

3. A method according to claim 2, wherein each axis has a logarithmic scale.

4. A method according to claim 3, wherein eccentric data points in the chimeric polygon, if represented, identify inhibitors whose usefulness can be assumed to be of little or no benefit to the patient, while data points lying within, on or close outside the wild-type polygon identify inhibitors whose usefulness can be assumed to be of substantial benefit to the patient.

5. A method according to claim 1, wherein each of said three or more data sets further comprises a value for worst-case measurable resistance for the inhibitor in question, said worst case values being represented on said graphical representations such that the data point for the chimeric stock can be compared both to wild-type and to worst-case HIV, thereby providing an assessment of the relative value of the inhibitor in a particular case.

6. A method of managing HIV chemotherapy of patients who are HIV positive, which comprises the steps of:

(a) periodically assessing the phenotypic sensitivity of a patient's HIV strains according to claim 1;

7. A method according to claim 1, wherein the phenotypic sensitivity of said chimeric viruses to inhibitors of at least two enzymes encoded by the pol gene of HIV is simultaneously assessed.

8. A method according to claim 1, wherein said sequence from the pol gene is isolated from a sample of a biological material obtained from the patient whose phenotypic drug sensitivity is being determined.

9. A method according to claim 1, wherein said biological material is selected from plasma, serum or a cell-free body fluid selected from semen and vaginal fluid.

10. A method according to claim 1, wherein the biological material is whole blood to which an RNA stabiliser has been added.

11. A method according to claim 1, wherein the biological material is tissue material selected from brain tissue or lymph nodal tissue.

12. A method according to claim 1, wherein the cell line susceptible to infection by HIV is a CD4⁺ T-cell line.

13. A method according to claim 12, wherein the CD4⁺ T-cell line is the MT4 cell line or the HeLa CD4⁺ cell line.

14. A method according to claim 1, wherein the product of reverse transcription is amplified using a nested PCR technique.

15. A method according to claim 14, wherein at least one outer primer is selected from the group consisting of SEQ ID: 1 and 2.

16. A method according to claim 14, wherein at least one primer selected from the group consisting of SEQ ID: 3, 4, 5 and 6.

17. A method according to claim 1, wherein the transfection is achieved by electroporation.

18. A method according to claim 1, wherein the transfection is achieved by the use of cationic lipids.

19. A method according to claim 1, wherein the phenotypic drug sensitivity of the chimeric viruses to different RT, protease and integrase inhibitors is assessed in an automated cellular-based assay.

20. A method according to claim 1, wherein the phenotypic drug sensitivity of the chimeric viruses and of the wild HIV strain to one or more RT, protease or integrase inhibitor(s) is expressed as an inhibitory concentration (IC value).

21. A method according to claim 1, wherein RT inhibitors are selected from nucleoside RT inhibitors such as AZT, ddI, ddC, 3TC, d4T, 1592U89, non-nucleoside RT inhibitors such as loviride, nevirapine, delavirdine, ateviridine and tivirapine, protease inhibitors such as saquinavir, indinavir and ritonavir and integrase inhibitors such as caffeic acid phenylethyl ester (CAPE), or those described in GB 2,271,566 or WO 95/08540.

22. A method according to claim 1, wherein the patient is drug naïve.

23. A method according to claim 1, wherein the patient has an HIV drug therapy history.

24. A method according to claim 1, wherein the patient derived pol gene has at least one mutation vis a vis the sequence of the laboratory HIV-1 clone HXB2D.

25. A method according to claim 1, further selecting the optimum inhibitor by identifying resistance-associated mutations.