Comparison of a point mutation assay with a line probe assay for the detection of the major mutations in the HIV-1 reverse transcriptase gene associated with reduced susceptibility to nucleoside analogues

Prevalence of Genotypic Resistance to Nucleoside Analogues and Protease Inhibitors in Antiretroviral-Naive HIV Patients in Campania, Italy

The aim of our study was to determine the prevalence of genotypic resistance to nucleoside analogues and protease inhibitors before and after 1997, the year of introduction of Highly Active Antiretroviral Therapy (HAART) in Campania (Italy). Forty-eight plasma HIV-RNA positive patients who had not been previously treated for HIV infection (naïve) were enrolled in two Divisions of Infectious Diseases. The main demographic characteristics were collected for each subject and the primary mutant genotypes were sought only in HIV-RNA positive patients with viral loads higher than 10,000 copies/ml. The diagnosis of HIV infection dated back to before 1996 for 21 out of 48 patients and to after 2000 for the other 27. INNO-Line Probe Assay (LiPA) HIV-RT and INNO-LiPA HIV protease (Innogenetics, Italy) were used to detect mutations conferring resistance to zidovudine, didanosine, zalcitabine, lamivudine, stavudine, saquinavir, indinavir, rotonavir, nelfinavir and amprenavir. No mutations associated with primary resistance to nucleoside analogues and protease inhibitors were detected in the 21 patients who had acquired HIV infection before 1996, whereas one or more mutations were seen in three of the 27 (11.1%) patients with HIV infection diagnosed after 2000. This study confirms that LiPA is a suitable tool for epidemiological surveys of HIV genotypic primary resistance. Drug-resistant HIV-1 genotypes, resistant both to nucleoside analogues and protease inhibitors, were detected only in subjects who had acquired HIV infection after 2000, most of whom had zidovudine-resistant mutants. These data suggest that the introduction of HAART has brought about the circulation of drug-resistant HIV genotypes.

Evaluation of the LiPA HIV-1 RT assay version 1: comparison of sequence and hybridization based genotyping systems

BACKGROUND

Specific mutations in the reverse transcriptase (RT) gene of HIV-1 are associated with reduced activity of nucleoside inhibitors used in the antiretroviral treatment of infected patients. The appearance of these mutations may result in therapy failure. Therefore, HIV-1 genotyping is an important tool for monitoring antiretroviral therapy. At present different assay systems are used to obtain information about the changes in the viral genome.

OBJECTIVE

The aim of this study was to evaluate the LiPA HIV-1 RT assay version 1 for monitoring drug resistance mutations in comparison to full-length sequencing.

STUDY DESIGN

Two hundred and forty-four samples were analyzed using the LiPA HIV-1 RT assay version 1 and were compared with full RT gene sequences obtained by in-house sequencing.

RESULTS

In 129/244 (52.9%) samples full concordance between both systems was found, in 86/244 (35.2%) samples at least one position was not detected by the LiPA assay, in 19/244 (7.8%) samples the results were contradictory, and in 10/244 (4.1%) contradictory as well as absent signals from the LiPA assay were found. Analyzing total codons, missing signals were observed at 137 codons, mainly found at positions 41 (40/137) and 215 (41/137). The 32 contradictions between LiPA and sequencing were equally distributed across all codons except for position 184 with only one case. The main reason for missing signals is the heterogeneity of the HIV genome, which could not be fully covered by the LiPA probes, e.g. unusual mutations or polymorphisms in the vicinity of the relevant positions. The same is the case for some contradictions, although most of them are not evident (19/32 positions).

CONCLUSIONS

We analyzed a patient population with partly multiple therapy failures. The LiPA HIV-1 RT assay version 1 gives a high degree of samples with at least one missing signal (39.4%) in our cohort and this is not acceptable for a diagnostic tool. However, the LiPA assay might work better in untreated patients and could, therefore, still be used for screening.

Genetic variation of hepatitis B surface antigen coding region among infants with chronic hepatitis B virus infection

Variants in the amino acid composition of the primary antibody-binding site of hepatitis B surface antigen (HBsAg) have been identified in a number of populations with chronic hepatitis B virus (HBV) infection. Direct sequencing of amplified or cloned PCR products, solid phase detection of sequence-specific PCR products (SP-PCR), and limiting dilution cloning PCR (LDC-PCR) were compared to determine their sensitivity in detecting differing concentrations of HBsAg variants. LDC-PCR had the greatest sensitivity and could detect HBsAg variants at a concentration of 0.1% of the total viral population. HBsAg variants were detected in 51% of infants with chronic HBV infection acquired after postexposure prophylaxis, and more than half of the variants were detected only by the most sensitive methods.

Does reduced DNA repair capacity play a role in HIV infection and progression in the lymphocytes of opiate addicts?

Opiate use in vivo and in vitro reduces the ability of human peripheral lymphocytes to repair DNA damage caused by both the physical and chemical mutagens that produce single-strand adducts. This decrease in repair leads to increased genetic damage to the individual cell as measured by cytogenetic damage, including sister chromatid exchanges and formation of micronuclei. The expected consequences of this increase in damage can also be established by increases in host cell mutation rate and rate of apoptosis. The effect of this increase in genetic damage can be expected to have significant consequences for HIV-1 or simian immunodeficiency virus infecting those lymphocytes. For example, DNA damaging agents have long been known to induce lentiviral growth and propagation, and this has been found to be true for HIV-1 following ultraviolet light treatment of lymphocytes. However, to date, no one has fully explored the consequences of increased host mutation rate on HIV growth and maintenance. Recent reports have demonstrated the role of viral mutation in such key physiologic processes as resistance to highly active antiretroviral therapy (HAART). Beyond the effects of random mutations in the viral genome, specific mutations in the HIV-1 transcriptase and protease lead to increased accumulation of mutant viruses and the gradual failure of HAART. It therefore remains to be tested whether changes in host cell mutation rate will also predict changes in susceptibility to drug therapy. This also leads to questions about whether the higher rate of viral mutation in HIV-infected drug addicts might be the basis for higher rates of neuroAIDS in this population. It would be attractive to speculate that the increase in the heterogeneity of the virus in addicts produces mutants with a greater capacity to attack neuronal tissue and a high affinity to replicate there.

Genotypic testing for human immunodeficiency virus type 1 drug resistance

There are 16 approved human immunodeficiency virus type 1 (HIV-1) drugs belonging to three mechanistic classes: protease inhibitors, nucleoside and nucleotide reverse transcriptase (RT) inhibitors, and nonnucleoside RT inhibitors. HIV-1 resistance to these drugs is caused by mutations in the protease and RT enzymes, the molecular targets of these drugs. Drug resistance mutations arise most often in treated individuals, resulting from selective drug pressure in the presence of incompletely suppressed virus replication. HIV-1 isolates with drug resistance mutations, however, may also be transmitted to newly infected individuals. Three expert panels have recommended that HIV-1 protease and RT susceptibility testing should be used to help select HIV drug therapy. Although genotypic testing is more complex than typical antimicrobial susceptibility tests, there is a rich literature supporting the prognostic value of HIV-1 protease and RT mutations. This review describes the genetic mechanisms of HIV-1 drug resistance and summarizes published data linking individual RT and protease mutations to in vitro and in vivo resistance to the currently available HIV drugs.

QUATTRO Steering Committee, Kaye S, Dunn DT, Babiker AG, Darbyshire JH, Hooker MH, Nesarantnam S, Newberry A, Weber J, Breckenridge A, Babiker A, Back D, Blatchford N, Darbyshire JH, Gazzard B, Gartland M, Hooker M, Jeffries D, Johnson M, Plummer K, Wills B, Kitchen V, Loveday C, Tedder R, Weber J, Weller IVD, Withnall R. Observations of HIV-1 Genotypic Drug Resistance in a Trial of Four Reverse Transcriptase Inhibitors (Quattro Trial)

The Quattro Trial compared the use of four HIV-1 reverse transcriptase (RT) inhibitors (zidovudine, lamivudine, loviride and zalcitabine), given either as four-drug combination therapy or monotherapy, with 8-week cycles of each drug, with zidovudine/lamivudine dual therapy. Observations of resistance associated and other mutations in the RT gene were made to determine whether therapy failure could be explained by acquisition of these mutations and whether novel mutation patterns developed. As in the intent-to-treat analysis, the use of cyclical monotherapy gave a smaller reduction in plasma virus load at 64 weeks (0.4 log10 copies/ml below baseline) than the quadruple or dual therapy arms (1.3 and 0.8 log10 copies/ml below baseline). Cyclical therapy appeared to generate less genotypic resistance to zidovudine, loviride or zalcitabine than the other arms. Resistance to lamivudine (mutation M184V) developed rapidly in all three arms. Resistance to zidovudine was acquired by a larger proportion of subjects on dual therapy than on quadruple therapy. Resistance to loviride or zalcitabine was rarely observed. During lamivudine monotherapy the M184V mutation was rapidly acquired and viral load rebounded. Zalcitabine monotherapy initially selected M184V mutants, but these were lost as therapy continued. Novel mutations that may have been associated with combination or cyclical quadruple therapy were observed infrequently. There was no clear correlation between changes in response to therapy and the development of previously described resistance mutations or with novel mutations in the RT gene.