Reverse Transcriptase-polymerase Research Articles

Molecular impact of the M184V mutation in human immunodeficiency virus type 1 reverse transcriptase.

The generation of drug-resistant variants of human immunodeficiency virus (HIV) type 1 (HIV-1) in vivo as well as in vitro is a consequence of the error proneness of the HIV-1 reverse transcriptase (RT) enzyme. During viral replication, RT copies the single-stranded RNA genome into double-stranded DNA. Due to the lack of 3′ exonuclease proofreading activity, the incorporation of missense nucleotides occurs at a relatively high frequency. The misincorporation rate of the RT enzyme ranges from 10−4 to 10−5, depending on the nature of the template and the source of the RT (4, 7, 31, 39, 54). During in vivo and in vitro selections, drug-resistant variants emerge; competition for replication then results in outgrowth of the fittest variant. The M184V mutation in HIV-1 RT is associated with high-level resistance to the antiviral drug 2′,3′-dideoxy-3′-thiacytidine (3TC) and has been extensively studied from the clinical, biological, and enzymatic perspectives. In fact, the first report of a change from a methionine to valine at residue 184 (M184V) in HIV was in regard to selection for resistance in tissue culture to didanosine (ddI) (23). Later, this mutation was shown to be responsible for both high-level resistance to 3TC (6, 17, 18, 22, 57, 63, 69) and low-level resistance to almost all the molecules that act as nucleoside analog RT inhibitors (NRTIs) (Table ​(Table1)1) (25, 53, 64). The appearance of the M184V substitution was found to be transiently preceded by another mutation, M184I, that also confers high-level resistance (about 1,000-fold) to 3TC (6) and occurs in patients treated with 3TC (58). Longitudinal sampling revealed a transient appearance of the M184I variant, which subsequently disappeared from the viral population due to the outgrowth of the M184V variant (3, 37). Eventual outgrowth of the M184V variant at the expense of M184I during therapy is consistent with superior RT polymerase function (3, 8, 11) and a higher viral replication rate of the M184V variant in primary cells (3). Inspection of the nucleotide sequences of both 3TC-resistant variants indicates that M184V (GTG) originates from wild-type (WT) Met (ATG) and not from the initial M184I variant (ATA) (34). Both variants are generated from the WT ATG sequence by transitional substitutions (G to A for 184I and A to G for 184V). The reason that M184I appears before M184V is that the G→A substitution is the type of mutation that most commonly occurs during HIV-1 replication (13, 24). TABLE 1. Resistance profile of the M184V mutation in RT

Incorporation of (α-P-Borano)-2′,3′-dideoxycytidine 5′-Triphosphate into DNA by Drug-Resistant MMLV Reverse Transcriptase and Taq DNA Polymerase

The Rp-stereoisomer of 5′-(α-P-borano)triphosphates of 2′-deoxycytidine (Rp-dCTPαB) and 2′,3′-dideoxycytidine (Rp-ddCTPαB) were synthesized. Their steady-state kinetics of incorporation by ddNTP-resistant enzymes, e.g., MMLV reverse transcriptase (RT) and Taq DNA polymerase, were investigated and compared with incorporation of dCTP and ddCTP. The α-boranophosphate substitution in ddCTP results in a 28-fold increase in efficiency of incorporation of the Rp-ddCTPαB isomer by MMLV RT, yet has minimal effect on the efficiency of incorporation by Taq DNA polymerase.

Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli

A better understanding of aptamer function in bacteria would help to establish simple model systems for screening RNA-protein interactions within an intracellular context. Escherichia coli DNA polymerase I mutants (Pol I(ts)) fail to grow at 37 degrees C unless an exogenous DNA polymerase such as HIV-1 reverse transcriptase (RT) is expressed within the cell. Here, we show that four RNA aptamers that inhibit HIV-1 RT in vitro block complementation by HIV-1 RT when expressed in vivo. No other essential functions are impaired by aptamer expression at either temperature. Intracellular aptamer RNA concentrations from induced cultures were measured to range from 76 to 180 nM, which is comparable with exogenously expressed HIV-1 RT levels in these cells. RT polymerase activity was reduced to background levels in cell-free extracts prepared from cultures expressing both HIV-1 RT and the 70.28 aptamer, compared with extracts from cultures expressing HIV-1 RT alone. Intracellularly expressed RNA aptamers can thus be used to generate conditional null mutants in bacteria by titrating an essential protein.

Conformational Properties of Nucleotide-Based Template-Competitive HIV-1 Reverse Transcriptase Inhibitors: Analysis of Enzyme Binding Modes#

Nucleotides 2-(4-azidophenacyl)thio-1,N6-etheno-2′-deoxyadenosine 5′-triphosphate 1 and its tetrafluoro analog 2 inhibit HIV-1 reverse transcriptase (RT) competitively relative to template. These template-competitive RT inhibitors (TCRTIs) were analyzed for conformational properties by molecular modeling and NMR analysis. Both inhibitors prefer sugar conformations of C2′-endo/C3′-exo with a high-anti glycosidic bond rotation and +sc/ap phosphate conformation (γ). The major effect of the etheno group is to favor an extended, fully staggered anti conformation in the N1-C2-S-CH2 ψ 1 side chain rotation, and NMR analysis detects a long range sugar H4′ to side chain phenyl meta-H NOE, a result consistent with this compact structure as an important contributor to the solution structure. The binding model generated places the phenyl side chain in a lipophilic pocket in the template grip region of the RT polymerase domain with the Mg-triphosphate complexed to active site carboxylates. The structures of the TCRTIs are compared with that of the template-competitive DNA polymerase inhibitor 2-(4-azidophenacyl)thio-2′-deoxyadenosine 5′-triphosphate 3, and a theoretical model for selectivity is proposed.

Interleukin-1β does not contribute to genetic strain-based differences in iNOS expression and activity in chicken macrophages

The expression of IL-1β and inducible nitric oxide synthase (iNOS) from iNOS hypo (GB2, B 6B 6) and hyper (K-strain, B 15B 15) responder chickens was examined. Compared to GB2, macrophages from K-strain expressed higher iNOS mRNA as quantitated by reverse transcriptase polymerase (RT-PCR) chain reaction after stimulation with 1 μg/ml of Escherichia coli ( E. coli) lipopolysaccharide (LPS). On the contrary, IL-1β mRNA expression was comparable between K and GB2 macrophages at 3 h post-LPS stimulation but persisted up to 9 h only in GB2 macrophages. The LPS-inducible interleukin-1 (IL-1) surface receptor expression, measured by flow cytometry, was higher in GB2 than on K-strain macrophages. Blocking of IL-1 receptor by the anti-IL-1 receptor antibody reduced the LPS-mediated iNOS expression by 50% as quantified by competitive RT-PCR. Furthermore, iNOS activity (nitrite) was also reduced to 50%. However, this magnitude of inhibition was similar in both K and GB2 macrophages. While these observations suggest that IL-1β is involved in mediating LPS-induced iNOS expression and activity, the differential response of GB1 and K-strain macrophages in terms of LPS-induced iNOS expression and activity is unlikely to be modulated by IL-1β.

Acute and chronic hepatitis: Working Group Report of the First World Congress of Pediatric Gastroenterology, Hepatology, and Nutrition.

Acute and chronic hepatitis: Working Group Report of the First World Congress of Pediatric Gastroenterology, Hepatology, and Nutrition.

Lamivudine: in children and adolescents with chronic hepatitis B virus infection.

Lamivudine, the negative enantiomer of 2'-deoxy-3'-thiacytidine, is a dideoxynucleoside analog that prevents hepatitis B virus (HBV) DNA synthesis by competitively inhibiting the viral reverse transcriptase and DNA polymerase stages of HBV replication and by terminating proviral DNA chain extension. A dose-ranging study established that once daily oral lamivudine 3 mg/kg up to a maximum of 100 mg/day has the optimum efficacy and tolerability profile for achieving a maximal reduction in serum HBV DNA levels in children aged 2 to 12 years and adolescents aged 13 to 17 years with chronic HBV infection and active viral replication (chronic hepatitis B). Significantly more children and adolescents with chronic hepatitis B receiving lamivudine demonstrated a virologic response (undetectable serum hepatitis Be antigen and undetectable HBV DNA level) [23 vs 13%; p = 0.04] and/or biochemical response (55 vs 12%; p < 0.001) compared with placebo in a large, randomized, double-blind, 52-week phase III study. Despite the emergence of YMDD-variant HBV in 19% of lamivudine-treated children and adolescents, serum alanine aminotransferase and HBV DNA levels remained below baseline in these patients. Oral lamivudine is generally well tolerated by children and adolescents with chronic hepatitis B, with a similar tolerability profile to placebo at the recommended once daily dosage of 3 mg/kg up to a maximum of 100 mg/day.

Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase.

Two distinct mechanisms can be envisioned for resistance of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) to nucleoside analogs: one in which the mutations interfere with the ability of HIV-1 RT to incorporate the analog, and the other in which the mutations enhance the excision of the analog after it has been incorporated. It has been clear for some time that there are mutations that selectively interfere with the incorporation of nucleoside analogs; however, it has only recently been proposed that zidovudine (AZT) resistance can involve the excision of the nucleoside analog after it has been incorporated into viral DNA. Although this proposal resolves some important issues, it leaves some questions unanswered. In particular, how do the AZT resistance mutations enhance excision, and what mechanism(s) causes the excision reaction to be relatively specific for AZT? We have used both structural and biochemical data to develop a model. In this model, several of the mutations associated with AZT resistance act primarily to enhance the binding of ATP, which is the most likely pyrophosphate donor in the in vivo excision reaction. The AZT resistance mutations serve to increase the affinity of RT for ATP so that, at physiological ATP concentrations, excision is reasonably efficient. So far as we can determine, the specificity of the excision reaction for an AZT-terminated primer is not due to the mutations that confer resistance, but depends instead on the structure of the region around the HIV-1 RT polymerase active site and on its interactions with the azido group of AZT. Steric constraints involving the azido group cause the end of an AZT 5'-monophosphate-terminated primer to preferentially reside at the nucleotide binding site, which favors excision.

Evolution of AZT resistance in HIV-1: the 41-70 intermediate that is not observed in vivo has a replication defect.

The human immunodeficiency virus type 1 (HIV-1) is notorious for its ability to evolve drug-resistance in patients treated with potent antivirals. Resistance to inhibitors of the viral reverse transcriptase (RT) enzyme is frequently mediated by a single amino acid substitution within RT. Resistance against the nucleoside analogue AZT is remarkable in that multiple amino acid changes accumulate over time to yield virus variants with high-level drug resistance. We now report that in addition to drug-resistance properties, the relative replication capacity of the virus variants affects the evolution of AZT resistance. Some of the typical AZT-resistance mutations have a negative impact on virus replication, and the 41-70 double mutant was found to represent a particularly poor virus. Furthermore, introduction of additional AZT-resistance mutations (41-70-215) leads to nearly complete restoration of virus replication. These results may explain the absence of the 41-70 double mutant in clinical samples and indicate that the evolution of AZT resistance is also influenced by virus replication parameters. Prolonged passage of the replication-impaired 41-70 virus in the absence of AZT yielded several fast-replicating variants. These revertants have compensatory changes in the RT polymerase, some of which have been observed previously in AZT-treated patients. Because we could select for these changes without drug pressure, these changes are likely to improve the RT enzyme function and the HIV-1 replication capacity.

Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.

We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual 'unzipping' of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage.

Evidence of porcine endogenous retroviruses in porcine factor VIII and evaluation of transmission to recipients with hemophilia.

Since 1984, unheated porcine clotting factor VIII (Hyate:C) has been used to treat severe bleeding episodes in persons with hemophilia who have antibodies to human clotting factor. We document the presence of porcine endogenous retrovirus (PERV) in plasma samples of pigs and in clinical lots of Hyate:C. Both gag and pol PERV RNA sequences were detected by reverse-transcriptase (RT) polymerase chain reaction in 13 of 13 lots of Hyate:C tested. Among 10 of these lots, RT activity also was detected, which confirms the presence of retroviral particles. To assess the transmission of PERV to Hyate:C recipients, we tested serum specimens from 88 recipients of Hyate:C and 23 noninfused control subjects for anti-PERV antibodies by using a Western blot assay. None of the samples was positive. Our data document that PERV particles are a common contaminant of Hyate:C products and suggest that the risk of PERV transmission from these percutaneous exposures is very low.

Interaction of HIV-1 Reverse Transcriptase and T7 RNA Polymerase with Phosphonate Analogs of NTP and Inorganic Pyrophosphate

We have examined the interaction of human immunodeficiency virus reverse transcriptase (HIV RT) and T7 RNA polymerase (T7 RNAP) with modified nucleoside triphosphates and inorganic pyrophosphate (PPi) analogs containing nonhydrolyzable bisphosphonate groups. We have synthesized a number of derivatives of bisphosphonic acid having different aromatic and nonaromatic side substituents, as well as the NTP derivatives whose incorporation into the growing nucleotide chain during the polymerization reaction results in formation of bisphosphonates as leaving groups. The competitive character of inhibition of both enzymes has been revealed for all the compounds under study, and the inhibition constants have been estimated. One of PPianalogs containing a bulky aromatic substituent is characterized by similar inhibition constants for both T7 RNAP and RT. The universal character of this inhibitor can serve as evidence for a similar structure of the NPT-binding sites in the two polymerases. It has been shown that nonsubstituted methylenebisphosphate is a better leaving group than that containing additional methyl and hydroxyl groups. The NTP analogs are very weak inhibitors of T7 RNAP, whereas HIV RT is more sensitive to this type of compounds. On the basis of the X-ray crystallographic data on the T7 RNAP complex with a template and NTP, we have modeled the binding of some derivatives of bisphosphonic acid in the active center of the enzyme. The peculiarities observed in the model correlate well with the experimental data on inhibition.

Quantification of HIV-1 RNA Using a Homogeneous Single-Tube Assay

Quantification of HIV RNA has become an essential tool in the management of HIV infection and monitoring of gene expression. Although direct quantification of nucleic acids has been demonstrated, the principal method of quantifying nucleic acids still involves nucleic acid amplification and quantification of the specific amplification products. Most commonly, quantification of nucleic acids involves either real-time monitoring of the amplification products \[with fluorescently labeled probes (TaqMan; Molecular Beacons)] or postamplification quantification [e.g., electrochemiluminescence (Nuclisens™)\] (1)(2)(3). Real-time monitoring increases the dynamic range of quantification, but it also leads to more complex instrumentation, and the absence of an internal control in the reaction may lead to erroneous quantification because of sample interference. Quantitative nucleic acid sequence-based amplification (NASBA™) is carried out using internal controls added to the sample, but the presence of three internal controls and a postamplification electrochemiluminescence detection scheme makes this method susceptible to contamination of samples with previously amplified products. We have combined highly sensitive NASBA with a highly sensitive chemiluminescent detection technology, Luminescent Oxygen Channeling Immunoassay (LOCI™), for homogeneous quantification of nucleic acids. NASBA is an isothermal exponential nucleic acid amplification system, based on an activity of avian myeloblastosis virus reverse transcriptase, RNase H, and T7 RNA polymerase, which predominantly produces a single-stranded RNA product. The specificity of HIV-1 amplification and detection is ensured by the use of specific primers and is further enhanced by the use of specific probe sequences for detection. The product concentration can be as high as 8.0 μmol/L after a typical NASBA reaction. Because the amplification product is single-stranded, there is no need to denature at the end of amplification for the binding of specific probes for either detection or quantification. Addition of an internal control (Qa), which bears sequence resemblance and is coamplified with the same primers …

Clinical manifestations and management of antiretroviral nucleoside analog-related mitochondrial toxicity

ObjectivesThis article reviews the clinical manifestations of mitochondrial toxicity associated with the use of nucleoside analog reverse transcriptase inhibitors (NRTIs) and outlines strategies to manage these sequelae. BackgroundNRTIs are the key components of the antiretroviral combinations used in the management of patients infected with HIV. The available NRTIs differ in their convenience of administration, frequency of dosing, resistance profiles, and side-effect profiles. NRTIs act as competitive inhibitors of the RNA/DNA polymerase reverse transcriptase of HIV and cause chain termination in the growing viral DNA chain. Many of the important and treatment-limiting side effects of NRTIs may be related to the effect of these agents on human DNA polymerases, in particular, mitochondrial DNA polymerase gamma. Depletion of mitochondrial DNA during chronic NRTI therapy may lead to cellular respiratory dysfunction and generalized and tissueand drug-specific toxicities, including myopathy, peripheral neuropathy, and lactic acidosis. Recently, it has been proposed that the fat redistribution syndrome, or lipodystrophy, reported during chronic antiretroviral therapy is a manifestation of the differential impact of at least some NRTIs on peripheral and visceral adipocytes. Management of potential mitochondrial toxicity during NRTI therapy remains a challenge. A range of nutritional supplements, both as treatments and prophylaxes, have been proposed, and some have been investigated in vitro; no in vivo studies have yet been conducted. MethodsThe information in this review was compiled using MEDLINE® and AIDSLINE® searches of the literature, including conference abstracts. ConclusionsAt present, interruption of NRTI therapy or substitution of the probable causative agent with alternative NRTIs that appear to be better tolerated represents the mainstay of management for mitochondrial toxicity and its clinical manifestations.

The effect of template RNA structure on elongation by HIV-1 reverse transcriptase

Reverse transcription of the RNA genome of retroviruses has to proceed through some highly structured regions of the template. The RNA genome of the human immunodeficiency virus type 1 (HIV-1) contains two hairpin structures within the repeat (R) region at the 5′ end of the viral RNA (Fig. 1 ). These structures, the TAR and polyA hairpins, fulfil important functions in the viral life cycle. We analyzed the in vitro elongation properties of the HIV-1 reverse transcriptase (RT) enzyme on the wild-type RNA template and mutants thereof with either a stabilized or a destabilized polyA hairpin. Stable RNA structure was found to interfere with efficient elongation of the RT enzyme, as judged by the appearance of pause cDNA products. A direct relation was measured between the stability of template RNA structure and the extent of RT pausing. However, the position of structure-induced pause sites is rather diverse, with significant stops at a position approximately 6 nt ahead of the basepaired stem of the TAR and polyA hairpins. This suggests that the RT enzyme is stalled when its most forward domain contacts the RNA duplex. Addition of the viral nucleocapsid protein (NC) to the in vitro assay was found to overcome such structure-induced RT stops. These results indicate that the RT polymerase has problems penetrating regions of the template with stable RNA structure. This effect was more pronounced at high Mg2+ concentrations, which is known to stabilize RNA secondary structure. Such a structure-induced defect was not apparent in reverse transcription assays performed in virus-infected cells, which is either caused by the NC protein or other components of the virion particle. Thus, retroviruses can use relatively stable RNA structures to control different steps in the viral life cycle without interfering with the process of reverse transcription.

Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus.

Of the numerous endogenous retroviral elements that are present in the human genome, the abundant HERV-K family is distinct because several members are transcriptionally active and coding for biologically active proteins. A detailed phylogeny of the HERV-K family based on the partial sequence of the reverse transcriptase (RT) gene revealed a high incidence of an intact RT open reading frame within the HML-2 subgroup of HERV-K elements. In this study, we report the cloning of six full-length HML-2 RT genes, of which five contain an uninterrupted open reading frame. The RT enzymes were expressed as glutathione S-transferase fusion proteins in Escherichia coli, and several HERV-K RT enzymes demonstrated polymerase as well as RNase H activity. Several biochemical properties of the RT polymerase were analyzed, including the template requirements and optimal reaction conditions (temperature, type of divalent cation). Inspection of the nucleotide sequence of the HERV-K RT genes demonstrated a mosaic structure, suggesting that a high level of genetic recombination has occurred in this virus family, which is a hallmark of replication by means of reverse transcription. The selective pressure to maintain the RT coding potential is illustrated by the sequence of a particular HERV-K isolate that contains three 1-nucleotide deletions within a small RT segment, thus maintaining the open reading frame. These combined results may suggest that these endogenous RT enzymes still have a biological function. It is possible that the RT activity was involved in the spread of this major class of retroelements by retrotransposition, and in fact it cannot be excluded that this retrovirus group is still mobile. The endogenous RT activity may also have been involved in the shaping of the human genome, e.g., by formation of pseudogenes.

Improvements in the RT-PCR detection of enteric viruses in environmental samples

Current methods for the detection of nucleic acid from enteric viruses in environmental samples usually involve extensive concentration and purification of target viruses followed by RT-PCR amplification using two enzymes, reverse transcriptase and Taq polymerase. We have developed a modified method that improves RT-PCR assays by: (i) the use of an RT-PCR internal standard control RNA to identify potential false negative results caused by inhibition of RT-PCR enzymes; (ii) the use of rTth (Perkin-Elmer, Foster City, CA), a heat-stable enzyme that functions as both a reverse transcriptase and DNA polymerase in a single-tube, single-buffer, elevated-temperature reaction; and (iii) the use of thermolabile uracil N-glycosylase (HK-UNG) (Epicentre Technologies, Madison, WI) to prevent PCR product carryover contamination. The new method was compared to the traditional two-enzyme, RT-PCR method for detection of Norwalk virus (NV) and hepatitis A virus (HAV) in buffer, stool, clam and oyster samples. The new method was at least as sensitive in NV and HAV detection compared to the traditional two-enzyme method. The internal standard control successfully detected inhibitors to RT-PCR amplification. NV and HAV PCR products generated with dUTP replacing dTTP during amplification were seeded into subsequent samples to test the prevention of PCR product carryover contamination by HK-UNG. The new method successfully eliminated PCR product carryover contamination in contrast to the traditional two-enzyme method. These improvements to viral nucleic acid detection have the potential to improve sensitivity, specificity and confidence in RT-PCR results.

3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.

HIV reverse transcriptase (RT) is one of the main targets for the action of anti-AIDS drugs. Many of these drugs [e.g., 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI)] are analogues of the nucleoside substrates used by the HIV RT. One of the main problems in anti-HIV therapy is the selection of a mutant virus with reduced drug sensitivity. Drug resistance in HIV is generated for nucleoside analogue inhibitors by mutations in HIV RT. However, most of these mutations are situated some distance from the polymerase active site, giving rise to questions concerning the mechanism of resistance. To understand the possible structural bases for this, the crystal structures of AZT- and ddI-resistant RTs have been determined. For the ddI-resistant RT with a mutation at residue 74, no significant conformational changes were observed for the p66 subunit. In contrast, for the AZT-resistant RT (RTMC) bearing four mutations, two of these (at 215 and 219) give rise to a conformational change that propagates to the active site aspartate residues. Thus, these drug resistance mutations produce an effect at the RT polymerase site mediated simply by the protein. It is likely that such long-range effects could represent a common mechanism for generating drug resistance in other systems.

Single-step reverse transcription-polymerase chain reaction for the detection of hepatitis C virus RNA.

We developed a novel single-step reverse transcription-polymerase chain reaction (RT-PCR), which is equal in sensitivity and specificity to RT-nested PCR, based on both reverse transcriptase and Taq DNA polymerase working efficiently under single buffer reaction conditions. Using in vitro synthesized hepatitis C virus (HCV) RNA, it was demonstrated that 10-100 copies of HCV RNA could be detected with a set of primers that amplify a 144 base-pair sequence unique to the 5'-noncoding region of HCV RNA. Furthermore, this method was successfully performed on serum and liver biopsy specimens obtained from patients with chronic hepatitis C. In addition, HCV RNA from in vitro HCV-infected MT-2C cells, which supported HCV replication, was also detected by this method. The method is anticipated to improve the detection of small amounts of RNA, such as that of HCV, promoting both labor savings and the prevention of carry-over contamination.

Improvements in the RT-PCR detection of enteric viruses in environmental samples

Current methods for the detection of nucleic acid from enteric viruses in environmental samples usually involve extensive concentration and purification of target viruses followed by RT-PCR amplification using two enzymes, reverse transcriptase and Taq polymerase. We have developed a modified method that improves RT-PCR assays by: (i) the use of an RT-PCR internal standard control RNA to identify potential false negative results caused by inhibition of RT-PCR enzymes; (ii) the use of rTth (Perkin-Elmer, Foster City, CA), a heat-stable enzyme that functions as both a reverse transcriptase and DNA polymerase in a single-tube, single-buffer, elevated-temperature reaction; and (iii) the use of thermolabile uracil N-glycosylase (HK-UNG) (Epicentre Technologies, Madison, WI) to prevent PCR product carryover contamination. The new method was compared to the traditional two-enzyme, RT-PCR method for detection of Norwalk virus (NV) and hepatitis A virus (HAV) in buffer, stool, clam and oyster samples. The new method was at least as sensitive in NV and HAV detection compared to the traditional two-enzyme method. The internal standard control successfully detected inhibitors to RT-PCR amplification. NV and HAV PCR products generated with dUTP replacing dTTP during amplification were seeded into subsequent samples to test the prevention of PCR product carryover contamination by HK-UNG. The new method successfully eliminated PCR product carryover contamination in contrast to the traditional two-enzyme method. These improvements to viral nucleic acid detection have the potential to improve sensitivity, specificity and confidence in RT-PCR results.