Discordance between primer pairs in the polymerase chain reaction for detection of human immunodeficiency virus type 1: a role for taq polymerase inhibitors

Discrepant test findings in early infant diagnosis of HIV in a national reference laboratory in Kenya: challenges and opportunities for programs

BACKGROUND

In Kenya, the availability of a cheap diagnostic service for HIV-exposed infants has helped scale-up access to treatment, and provided a means by which programs that support Prevention of Mother to Child Transmission of HIV can be evaluated. As expected for any large testing program, discrepant and indeterminate results present a significant challenge.

METHODS

Dried Blood Spots were collected from health centers countrywide and couriered to four laboratories for tests. Results were dispatched either by email, telephone, GSM SMS printer or courier. Between 2006 and 2009, tests were conducted with the Manual Roche v. 1.5 Assay. In 2010 the labs switched fully to the Cobas® AmpliPrep/ Cobas® TaqMan® HIV-1 Qual automated Roche Test.

RESULTS

Between 2006 and 2010, the KEMRI CVR EID Lab conducted 64 591 HIV tests in on children <18 months of age. HIV tests (38 834) used the manual assay, while 17 133 tests used the automated assay. Overall, 10.7% (6915) of the samples tested positive, while 86.6% (55 967) tested negative. A total of 1.6% (1041) tested indeterminate and required a re-bleed of the infant. Two hundred positive tests by the manual assay were retrieved randomly and retested using the automated assay. Among them, 192 (96%) remained positive, 5 (2.5%) were negative while 3 (1.5%) failed. A total of 160 negative samples by the manual assay were retrieved and retested with the automated assay. Among them, 154 (96.24%) remained negative, 3 (1.88%) tested positive while 3 (1.88%) failed. A total of 215 samples that gave indeterminate results by the manual assay were retested using the automated system. Among them, 62 (28.8%) gave positive results, 144 (66.97%) negative and 6 (2.8%) samples still gave discrepant results. Three (1.4%) did not amplify successfully. A few infants who were apparently positive appeared to test HIV negative with age.

CONCLUSIONS

Indeterminate results are a significant challenge for HIV diagnostic services, as seen in the Kenyan EID Program. In our experience, they are more often negative than they are positive. False positive and false negative results can arise from clerical error, contamination and limitations of the technologies available. To forestall the consequences of such outcomes, the sensitivity and specificity of available assays must be further improved. All HIV positive samples should be retested for confirmation, and if confirmed, a new sample must be drawn and tested for DNA at the time the infant receives their initial results or starts antiretroviral therapy. Viral clearance is a phenomenon that requires further studies.

Performance of the Amplicor human immunodeficiency virus type 1 PCR and analysis of specimens with false-negative results

Over a 4-year period, the Roche Amplicor kit was used in a United Kingdom reference laboratory for the detection or confirmation of human immunodeficiency virus (HIV) type 1 infection, particularly in infants born to HIV-infected mothers. Of 408 specimens from adults and older children tested, the 122 seronegative specimens were all Amplicor negative. Of the 286 seropositive specimens, 268 were Amplicor positive. On the basis of these results, the Amplicor assay has a specificity of 100% and a sensitivity of 93.7%. In addition, for 247 specimens from infants and young children, serological results may not have been diagnostic because of placental transfer of maternal antibodies. Forty-eight were Amplicor positive, and of the 199 Amplicor-negative specimens, 19 were assumed to be false negative on the basis of clinical data, serological markers (including p24 antigen), and/or results for previous or follow-up specimens. This represents a sensitivity of 75% for the Amplicor test for specimens from patients under 2 years of age. Of these 37 false-negative specimens plus 2 specimens from other laboratories, 31 could be characterized by amplifying extracted material from them by an in-house nested gag PCR spanning the Amplicor target region. The amplicons were sequenced and found to represent subtypes A (35.5%), B (22.6%), C (22.6%), D (16.1%), and G (3.2%). False-negative results by the Amplicor assay may be ascribed to low-target copy number, the physical behavior of one primer (SK462), and sequence variation in the target region of the other primer (SK431).

The future of HPV testing in clinical laboratories and applied virology research

BACKGROUND

Human papillomaviruses (HPV) are now considered etiologic agents of cancer of the uterine cervix. Adjunctive diagnostic procedures for the detection of HPV infection could increase the sensitivity of primary and secondary screening of cervical cancer. HPV testing could also improve the specificity of screening programs resulting in avoidance of overtreatment and saving of costs for confirmatory procedures.

OBJECTIVES

To review the rationale of HPV testing in genital diseases and the potential applications of HPV DNA detection methods for clinical and epidemiological purposes.

RESULTS

Progression of HPV infection is associated with the persistence of HPV infection, involvement of high-risk HPV types, high HPV viral load in specimens, integration of viral DNA and possibly the presence of cofactors. The design of HPV diagnostic tests will need to take into account these parameters of disease progression. HPV DNA detection techniques based on signal-amplification are standardized, commercially available and detect several high-risk HPV types. They increase the sensitivity of screening for high-grade and low-grade lesions. Although they may yield false-negative results in the presence of significant HPV-related disease, new test formats could resolve this weakness. Amplification techniques are ideal instruments for epidemiologic purposes since they minimize misclassification of HPV infection status and allow for the detection of low viral burden infections. They are currently not readily applicable to diagnostic laboratories.

CONCLUSIONS

Before recommending HPV testing, prospective trials of untreated LSIL with HPV testing as well as the determination of the efficacy and cost-effectiveness of novel HPV tests, need to be completed.

Nested PCR assays with novel primers yield greater sensitivity to Tanzanian HIV-1 samples than a commercial PCR detection kit

To investigate the efficacy of the SK431/SK145 primer pair and two nested primer assays in amplifying African HIV-1 samples, a total of 35 Tanzanian PBMC samples were examined. These were assayed by two HIV-1 specific nested in-house PCR assays and a commercial HIV-1 PCR kit (GeneAmp) using SK431/SK145 as the primer pair. One of the nested PCR assays has been evaluated previously (old assay), whereas the modified assay was constructed from the HIV-1 sequence alignment released in August 1993. The modified nested primer assay showed increased sensitivity in the gag and env regions compared to the old nested primer assay. However, both the old and the modified nested primer assays displayed higher sensitivity for the detection of Tanzanian HIV-1 proviruses than the GeneAmp assay. When two regions were used (gag and env) as targets for the amplification, the modified nested primer assay detected 97.1% (34/35) of the proteinase K lysed samples, compared to 68.6% (24/35) using the SK431/SK145 primer pair (P < 0.01**). The results indicate that the SK431/SK145 primer pair may be less suitable when HIV-1 samples from Africa are analysed. The results also show that continuous modification of primer sequences can improve and maintain high sensitivity for the detection of highly divergent HIV-1 strains.

Improved detection of JC virus DNA in cerebrospinal fluid for diagnosis of AIDS-related progressive multifocal leukoencephalopathy

Several methods to increase the sensitivity of JC virus (JCV) DNA detection in cerebrospinal fluid (CSF) for a noninvasive diagnosis of AIDS-related progressive multifocal leukoencephalopathy (PML) were investigated. When CSF collected at clinical presentation was tested, JCV DNA was detected in 8 of 19 patients with PML by standard PCR (sensitivity, 42%; 95% confidence interval [CI], 21 to 66%) and in 14 of 19 by nested PCR (sensitivity, 74% [95% CI, 49 to 90%]; P = 0.014 [McNemar's test]. For multiple serial CSF samples, standard PCR yielded JCV DNA for 11 of 19 PML patients (sensitivity, 58% [95% CI, 34 to 79%]) and nested PCR yielded JCV DNA for 17 of 19 patients (sensitivity, 90% [95% CI, 66 to 98%]; P = 0.014). The majority of the false-negative samples were found to contain PCR inhibitors. Standard PCR did not detect JCV DNA in CSF from any of the 83 AIDS patients with other diagnosis (100% specificity [95% CI, 95 to 100%]); JCV DNA was found in CSF from one control patient by nested PCR (99% specificity [95% CI, 93 to 100%]).

Evaluation and comparison of the Amplicor HIV-1 PCR kit with an ‘in-house’ nested PCR

BACKGROUND

The polymerase chain reaction (PCR), a powerful gene amplification technique, is moving rapidly from the research laboratory into routine clinical use.

OBJECTIVES

To evaluate the specificity and sensitivity of a commercially available PCR kit, the Amplicor HIV-1 PCR kit (AMP) and to compare it with an in-house nested PCR, which amplified part of the POL gene (POL(n)).

STUDY DESIGN

A total of 517 samples were tested by AMP, including 159 fresh whole blood specimens from HIV-1 antibody positive Europeans and 358 archival samples (338 seropositive and 20 seronegative individuals) originating from 35 different countries in Africa and Europe. We compared the performance of AMP on the archival samples with POL(n).

RESULTS

The overall sensitivity and specificity as compared to HIV-1 serology were 93% and 100%, and 96% and 100%, for AMP and the in-house PCR, respectively. Repeat testing on co-cultured lymphocytes increased the sensitivity of AMP to 95%.

CONCLUSIONS

AMP is a rapid, and easy to use commercially available PCR kit, since only one amplification of the test sample is required. Moreover, the use of radioactivity is omitted, and reading of the test can be done with a spectrophotometer. The use of at least one additional primer pair may increase confidence in distinguishing a positive and negative sample by both PCR techniques.

Coamplification of HIV type 1 and beta-globin gene DNA sequences in a nonisotopic polymerase chain reaction assay to control for amplification efficiency

The polymerase chain reaction (PCR) fails to detect HIV-1 sequences in 5% of infected individuals. To screen for false-negative PCR tests, we developed a nonisotopic PCR assay in which sequences from the beta-globin gene and from the HIV-1 vpu-env region were coamplified with biotinylated and fluorescein-labeled primers, respectively. Coamplified products were reacted with specific internal digoxigenin-labeled RNA probes. Hybrids were detected in a microtiter plate coated with streptavidin or anti-fluorescein antibody, with enzyme-labeled anti-digoxigenin antibody. After the optimization of the coamplification conditions, the assay could detect 5 proviral DNA copies in a lysate from 100,000 peripheral blood mononuclear cells. Fifty-seven samples from 55 HIV-1-seropositive patients and 25 samples from 25 seronegative individuals were evaluated. Fifty-two samples from HIV-infected individuals were positive for HIV-1 vpu-env sequences. Three of the 5 PBMC lysates falsely negative for HIV-1 sequences had reactivities for beta-globin (3-23 fu) below that of 100,000 cells (304 fu). Nonisotopic coamplification allowed for the evaluation of the quality of specimens for PCR concurrently with the detection of the presence of viral template sequences.

Molecular detection of hepatitis C virus: impact of detection methodology on clinical and laboratory correlations

The clinical manifestations of hepatitis C virus (HCV) infection are generally indistinguishable from other causes of viral hepatitis. HCV infections are usually anicteric, asymptomatic, and rarely cause acute fulminant liver failure. Serological testing for HCV in conjunction with epidemiological studies have verified that HCV was the major cause of parenterally transmitted non-A, non-B hepatitis (NANBH). With the widespread introduction of serological screening of blood products for HCV antibody, the risk of transfusion-associated HCV infection has been dramatically reduced (to < 3 cases per 10,000 units transfused). Despite the virtual elimination of transfusion-associated infections, the diagnosis of HCV remains important because > 50% of infections are sporadic in origin, 50 to 70% of infected individuals develop chronic hepatitis, and these individuals are at risk of developing cirrhosis (> 20%) as well as hepatocellular carcinoma. Although currently available anti-HCV immunoassays function well as blood-donor screening assays, they are poor at detecting acute infection because of the prolonged lag time between infection and detection of seroconversion (approximately 10 to 26 weeks for second-generation immunoassays). In contrast, polymerase chain reaction (PCR)-based detection of HCV RNA in serum can detect infection in as little as 1 to 2 weeks after exposure. This review focuses on the impact of modern serologic and nucleic acid-based HCV detection methodology on the clinical understanding of HCV infection, its associated illnesses, and its transmissability. Quantitative and reproducible nucleic acid-based detection assays will be required to provide additional insights into the clinical spectrum of HCV infections as well as to assess the efficacy of antiviral agents.

Polymerase chain reaction kinetics when using a positive internal control target to quantitatively detect cytomegalovirus target sequences

High-performance liquid chromatography (HPLC) was used to detect and quantify cytomegalovirus (CMV) specific polymerase chain reaction (PCR) products generated during PCR co-amplification. PCR of CMV AD 169 or a plasmid which contains the CMV AD 169 native target sequence using the CMV primer set of Hsia et al. (J. Clin. Microbiol. 27, 1802-1809) generates a 152 bp PCR product. A CMV control sequence plasmid which shared the primer sequence of native CMV AD 169 but when amplified produces a larger 362 bp product was constructed. Under co-amplification conditions there was a linear relationship (over 3 logs) between the molar ratio of input CMV native and control target sequence and the molar ratio of the output PCR products as detected by HPLC despite differences between the two PCR target and product sizes. Co-amplifying known amounts of CMV control sequence plasmid as an internal standard allowed accurate quantitation of the amount of CMV native target sequence in a sample when the two PCR targets were present in approximately equimolar amounts +/- 1.5 log (coefficient of variation (CV) < 12%). By modifying the amount of CMV control target sequence plasmid used for co-amplification, accurate detection of the amount of CMV native sequence in samples could be extended to 5 logs, standard error (S.E.) < or = 16%. Precise quantitation of PCR targets using co-amplification PCR requires multiple sample dilutions to ensure that the CMV native target sequence was in a close equimolar relationship with the CMV control sequence at the time of PCR amplification.

Recombinant retroviral vector delivered intramuscularly localizes to the site of injection in mice

A murine retroviral vector encoding the human immunodeficiency virus type 1 (HIV-1) env and rev genes can be used to induce cytotoxic T lymphocyte responses. Immune responses can be induced by an ex vivo treatment, in which autologous cells are transduced in vitro and re-introduced to the donor, or by direct administration of retroviral vector via intramuscular injection. In this study we have used polymerase chain reaction (PCR) analysis to examine the distribution of recombinant murine retrovirus directly administered to mice. Mice were injected intramuscularly with HIV-IT(V), an amphotropic murine leukemia virus (MLV)-based retroviral vector carrying the HIV-1 env/rev genes and a neomycin resistance marker gene. Detection of the HIV-1 env gene in DNA isolated from injection sites demonstrated in vivo transduction. No evidence of transduction was observed in the testes, spleen, kidney, or thymus. Retroviral DNA was detected in the liver of one animal in the study. These data suggest that retroviral vector administered intramuscularly to mice localizes primarily to the site of injection and that measurable transduction in the testes does not occur.

High-performance liquid chromatography to assess the effect of serum storage conditions on the detection of hepatitis C virus by the polymerase chain reaction

The effect of various serum storage conditions on the detection of hepatitis C virus (HCV) by the polymerase chain reaction (PCR) was assessed. 50 microliters aliquots of serum from four HCV PCR positive patients were subjected, in triplicate, to: (a) storage at -20 degrees C for 1, 5, 10 days; (b) storage at room temperature (RT) for 1, 2, 7 days; (c) 1, 3, 5, and 10 successive freeze-thaw cycles; (d) incubation at 37 degrees C, and 56 degrees C for 1, 3, 24 h; and (e) storage in guanidium-thiocyanate extraction buffer at RT, and 4 degrees C for 1, 5, 10 days. PCR products were detected by agarose gel electrophoresis (AGE) and quantitatively by high-performance liquid chromatography (HPLC). Only storage in extraction buffer at RT for 5-10 days and incubation at 56 degrees C for 24 h appeared to result in a loss of > or = 50% of detectable HCV PCR product. Up to 10 successive freeze-thaw cycles, storage at -20 degrees C for up to 10 days or at RT for up to 7 days, storage in extraction buffer at RT for 1 day or at 4 degrees C for up to 10 days, and incubation at 37 degrees C for up to 24 h resulted in minimal PCR signal loss. HPLC was a reproducible method of detecting and quantitating HCV PCR products, and was more sensitive than AGE.

Detection of HIV-1 infections by PCR: evaluation in a seropositive subject population

To study the polymerase chain reaction (PCR) performance in detecting human immunodeficiency virus (HIV) infections, we tested 53 HIV-1 seropositive patients and 29 HIV-1 seronegative subjects for four different HIV-1 DNA regions. Fifty-one seropositive patients were found positive by PCR with at least one primer pair, but two were repeatedly negative for all primers. Weekly blood samples from 12 seropositive subjects all detected positive for at least one primer pair, but for three patients an irregular primer detection pattern was found. One additional HIV-1 seropositive sample, found negative for HIV DNA, was also negative for the beta-globin PCR control. The 29 seronegative specimens were HIV-1 DNA negative, as was a HIV-2 seropositive patient. This study demonstrates that PCR is almost as good as serological tests for detecting HIV infections, with a specificity of 100% and a sensitivity of 96% and that resampling the patients may improve detection performance.

Demonstration by the polymerase chain reaction of mixed Plasmodium falciparum and P. vivax infections undetected by conventional microscopy

Mixed malaria infections (Plasmodium falciparum and P. vivax) are suspected to occur at a greater frequency than is detected by conventional light microscopy. To determine this frequency we carried out a prospective 'blinded' comparison of diagnosis by conventional light microscopy and enzymatic amplification of the circumsporozoite gene extracted from dried spotted blood samples. Patients were previously healthy, active duty Thai soldiers assigned to a malaria risk area presenting with malaria. Microscopy (oil immersion objective at 1000 x magnification) involved examination of Giemsa-stained thick and thin blood films by an experienced microscopist. Whole blood samples (25 microliters) dried on filter paper were used for species-specific parasite deoxyribonucleic acid (DNA) amplification by the polymerase chain reaction (PCR) and hybridization with radiolabelled P. falciparum and P. vivax probes. Of 137 consecutive cases of malaria studied, 9% (3/32) of microscopically diagnosed P. falciparum infections and 5% (5/104) of microscopically diagnosed P. vivax infections were found to be mixed by the PCR/DNA probe systems, while 1 case was diagnosed as mixed by both microscopy and PCR. The possibility that malaria patients may have undetected mixed infections should be kept in mind because of the specific therapy required both for P. falciparum and for radical cure of P. vivax.

Circumsporozoite genotyping of global isolates of Plasmodium vivax from dried blood specimens

The prevalence and global distribution of two circumsporozoite (CS) genotypes of Plasmodium vivax (VK210 and VK247) were determined by genetic analysis of isolates from 234 malaria-infected patients. Whole blood specimens were collected on filter paper from patients infected with malaria in Thailand, Mexico, Papua New Guinea, Peru, Afghanistan (Pakistan), India, and western Africa and from 50 asymptomatic smear-negative controls. Following extraction of DNA from the filter paper samples, the CS gene was amplified by the polymerase chain reaction and genotyped by using oligoprobes specific for the VK210 and VK247 repeat epitopes. The sensitivity of genotyping from a single blood dot was 95.2%. The VK247 CS genotype was identified in the blood of patients from all seven study areas and was the predominant form present in samples from Thailand (83%) and Papua New Guinea (90%). In contrast, VK247 DNA was present in only 9% of isolates from Mexico. Individuals infected with both genotypes simultaneously were identified in all study areas except Mexico and were particularly common in Thailand (58%) and Papua New Guinea (60%). These findings indicate that the VK247 genotype of P. vivax is widely distributed but that its prevalence varies geographically. In addition, we conclude that use of samples of whole blood on filter paper is a practical and sensitive method for determining the genotypes of large numbers of malaria isolates collected in field settings.