Evaluation of the usefulness of various PCR method variations and nucleic acid hybridization for CMV infection in immunosuppressed patients

In diagnosis of CMV infection various laboratory methods are used. The methods based on detection of viral nucleic acids have been introduced routinely in many laboratories. The aim of this study was to compare nucleic acid hybridisation method and various variants of PCR methods with respect to their ability to detect CMV DNA. The studied material comprised 60 blood samples from 19 patients including 13 renal transplant recipients and 6 with acute leukaemia. The samples were subjected to hybridisation (Murex Hybrid Capture System CMV DNA) and PCR carried out in 3 variants: with one pair of primers (single PCR), nested PCR and Digene SHARP System with detection of PCR product using a genetic probe in ELISA system. The sensitivity of the variants ranged from 10(0) particles of viral DNA in nested PCR to 10(2) in single PCR. The producer claimed the sensitivity of the hybridisation test to be 3 x 10(5) and it seems to be sufficient for detection of CMV infection. The obtained results show that sensitivity of hybridisation was comparable to that of single PCR and the possibility of obtaining quantitative results makes it superior, on efficacy of antiviral therapy, especially in monitoring CMV infection in immunossuppressed patients and in following the efficacy of antiviral treatment.     

Identification of cytomegalovirus (CMV) infection by different laboratory methods in renal transplant recipients undergoing triple-drug immunosupressive treatment.

Early diagnosis of CMV infection is very important mainly in transplant recipients because CMV infection is a frequent complication after transplantation. In this work we compared different laboratory methods: ELISA (IgG, IgM), Western blot,shell vial, antigenemia assay (pp65), the immunofluorescent method with epithelial cells from urine (IF), DNA in leukocytes by PCR and DNA in leukocytes by hybridization (HCS) to estimate the most proper method for diagnosis of CMV in renal transplant recipients. This preliminary study showed that HCS, PCR and Western blot are sensitive methods for detecting CMV infection. Using HCS in quantitative variant we obtained a very good correlation between DNA load and clinical symptoms.     

检测巨细胞病毒(CMV)DNA及其即刻早期抗原、pp65和pp67在肾移植受者术后巨细胞病毒感染早期诊断中的价值

目的探讨检测巨细胞病毒(CMV)DNA及其即刻早期抗原(IE)、巨细胞病毒pp65和pp67抗体对肾移植受者术后巨细胞病毒感染早期诊断的临床应用价值。方法按肾移植术受者术后3个月外周血是否出现CMV抗原,将71例患者分为CMV感染组(56例)和CMV未感染组(15例),肾移植术受者手术前和术后第1个月每周检查1次,第2、3个月每2周检查1次外周血巨细胞病毒pp65和巨细胞病毒pp67、即刻早期抗原(immediate early antigen,IE),巨细胞病毒DNA和IgM、IgG,共8次;以监测与分析评价肾移植术受者手术前后各项指标变化。结果肾移植术前71例肾移植受者PP65、PP67、IE、CMV DNA均为阴性;肾移植术后CMV感染组的pp65、pp67、IE、CMV DNA阳性率分别为67.8%(38/56)、66.1%(37/56)、64.2%(36/56)和48.2%(27/56),CMV未感染组4项指标值分别为0%、0%、13.3%(2/15)、和0%,两组差异均有统计学意义(P均0.01)。肾移植术后CMV感染组(56例)和CMV未感染组(15例)CMV IgG均为阳性,而IgM阳性率在CMV感染组仅为3.5%(2/56),在CMV未感染组为0%,IgM表达率在CMV感染组和未感染组无统计学差异(P0.05)。观察期内感染组与未感染组相比,术后CMV pp65,pp67,CMV DNA和IE指标出现阳性的例数及阳性出现的具体时间均有显著性差别(P均0.01),而IgM和IgG则均无显著性差别(P均0.05)。结论肾移植术后患者外周血CMV DNA,IE,pp65和pp67抗原检测阳性与其术后巨细胞病毒感染相关。检测CMV DNA、IE、pp65和pp67抗原可能更早更准确反映器官移植术后CMV活动性感染。而CMV IgG和IgM不能作为肾移植后患者CMV感染的诊断指标。     

Comparison of real-time and nested PCR assays for detection of herpes simplex virus DNA

We performed a real-time PCR assay to detect herpes simplex virus (HSV) DNA, and compared it prospectively with a nested PCR assay in 164 clinical samples (109 cerebrospinal fluid and 55 sera) from patients suspected of having neonatal HSV infection or HSV encephalitis. In 25 of 164 samples, HSV DNA was detected by the nested PCR assay. All samples positive for HSV DNA in the nested PCR assay were also positive in the real-time PCR assay, and all but two samples negative for HSV DNA in the nested assay were negative in the real-time assay. The real-time PCR assay thus had a sensitivity of 100% and a specificity of 99%, when compared with the nested assay. Sequential assays in a case of disseminated HSV showed that a decrease in HSV DNA paralleled clinical improvement. Quantification of HSV DNA by real-time PCR was useful for diagnosing and monitoring patients with HSV encephalitis and neonatal HSV infection.     

Comparison of real-time PCR and pp65 antigen assays for monitoring the development of Cytomegalovirus disease in recipients of solid organ and bone marrow transplants

Cytomegalovirus (CMV) infection is a frequent complication in transplant recipients. This retrospective study compared real-time PCR (rt-PCR) and a pp65 antigen assay as tools for monitoring CMV infection in solid organ (SOT) and bone marrow (SCT) transplant patients. The study tested 2662 samples by rt-PCR, and 1284 specimens with a pp65 antigen assay. 24.3% of the rt-PCR samples and 4.1% of the pp65 antigen samples were positive. 793 specimens, from 230 patients, were tested with both assays. In 6.7% of samples, both tests were positive; in 72.7% both were negative; in the remaining 20.6% of cases, the results were discordant. CMV disease was diagnosed in 50 patients. Results from the two methods were poorly correlated (r=0.460). The sensitivity of rt-PCR (94%) was higher than that of the pp65 antigen assay (27%). Both assays showed high specificity (92% and 99%, respectively). ROC curve analysis, performed separately for SOT and SCT patients, confirmed that rt-PCR outperformed the pp65 assay in the detection of CMV. These findings provide evidence that rt-PCR is a reliable diagnostic tool, and that it can be more effective than pp65 based assays in monitoring CMV infection progression and in guiding therapy in immunocompromised patients.     

Polymerase chain reaction for identification of herpes simplex virus (HSV-1), cytomegalovirus (CMV) and human herpes virus-type 6 (HHV-6) in oral swabs

Considering that sensitive and specific methods to detect HSV-1, CMV and HHV-6 on oral mucosa have a great impact on oral diagnosis practice and research, together with the evidence that PCR is a rapid and reliable method, the purpose of the present study was to develop primer sets to detect HSV-1, CMV and HHV-6 in oral swabs by nested polymerase chain reaction (nested PCR). We developed a practical method for sample collection without tissue trauma, and the swabs were stored until used for DNA extraction. After the nested PCR a DNA fragment of 241 bp corresponding to HSV-1 was amplified. DNA fragments of 224 and 369 bp were amplified corresponding to CMV and HHV-6, respectively. DNA sequencing analysis confirmed the expected sequences of each virus. In conclusion, it was demonstrated that these new primer sets are able to identify HSV-1, CMV and HHV-6 in oral swab using nested PCR.     

Quantitative detection of CMV DNA by PCR and hybridizaton methods in renal transplant recipients

The comparison of two quantitative tests: hybridization (Murex Hybrid Capture System) and PCR (COBAS AMPLICOR CMV Monitor) detected CMV DNA was made. Investigation of viral load in serum by PCR gave better correlation with clinical manifestation in renal transplant recipients.     

Epstein Barr viral load monitoring by quantitative PCR in renal transplant patients

Post-transplant lymphoproliferative disorders (PTLD), ranging from lymphoid hyperplasia to clonal malignancy, are a severe complication arising in solid organ transplant patients. Their reported incidence ranges from 1 to 20%, according to factors such as type of transplanted organ and the age of recipients. A strong correlation between Epstein Barr virus (EBV) infection, the grade and type of immunosuppression and the development of PTLD has been recognized. The detection and quantification of EBV-DNA load in peripheral blood have been utilized as prognostic markers for the development of PTLD, showing a correlation between high levels of EBV-DNA in the blood and the development of PTLD. In this study, we monitored EBV viral load monthly in 15 renal transplant recipients for six months. The number of EBV-DNA copies was measured in peripheral blood mononuclear cells (PBMC) and serum samples by a quantitative PCR protocol developed in our laboratory that employes a previous screening of samples containing a significant number of viral DNA copies (> or =1000 copies/10(5) PBMC or 100 microl serum) by semi-quantitative PCR followed by a precise quantification of the only significant samples by quantitative-competitive (QC)-PCR. Our 15 renal transplant patients neither developed PTLD nor had recurrent acute illnesses or acute graft rejections during the study. The results obtained in the monthly follow up of EB viral load in PBMC samples confirmed its fluctuation in asymptomatic patients reported in literature. In particular, 5/14 (35.7%) of EBV seropositive patients had an EBV-DNA load equal to 1000 EBV copies /10(5) PBMC (roughly corresponding to 10.000 copies/microg PBMC DNA), and 1/14 (7.1%) reached 5000 EBV copies /10(5) PBMC (roughly corresponding to 50.000 copies/microg PBMC DNA), at least once in our study. In the EBV seronegative patient, EBV-DNA in PBMC samples was always undetectable (less than 100 DNA copies/10(5) PBMC). EBV-DNA load in all serum samples was less than threshold value of our quantification protocol (<100 DNA copies/100 microl serum), supporting the literature data. With regard to immunosuppressive treatment, 66.7% of the six patients in whom EBV load reached values equal to or higher than 1000 DNA copies/10(5) PBMC, were on FK506 whereas only 33.3% of them were on CyA. In conclusion, further investigations are needed to better understand the role of EBV infection in the pathogenesis of PTLD in immunosuppressed patients. Given the high positive predictive value of EB viral load in peripheral blood for diagnosis of PTLD reported by several authors, and the described absence of correlation between the serological evidence of EBV reactivation and EB viral load, EBV viral load measurement in PBMC and serum samples using quantitative PCR techniques is a powerful diagnostic tool to monitor transplanted patients at risk to develop PTLD.     

Assessment of the status of cell-mediated immunity in cytomegalovirus-infected renal allograft recipients.

Renal allograft recipients are unusually susceptible to cytomegalovirus (CMV) infections. Since humoral immunity to CMV is uncompromised in these patients, it was felt desirable to assess the competence of cell mediated immunity (CMI). Several parameters were used. On skin testing with candida, SK-SD, mumps, and PPD-5 antigens, 80.0% of patients and 5.0% of controls were unreactive. T-lymphocyte ratios (SRBC rosette test) were 18.7% in transplant patients, vs. 40.3% in controls. These differences are statistically significant. Lymphocyte stimulation assay ([³H] thymidine uptake) was developed to study CMI to CMV. Lymphocytes from all the normal seropositive subjects (10) had increased [³H]thymidine uptake on exposure to CMV antigens. There was no antigen specific stimulation of lymphocytes from the seronegative controls (five). Six of nine (67.7%) CMV infected renal allograft recipients, studied six or more months post-transplantation, had no evidence of CMI to CMV by this assay.     

Detection and typing of BKV,JCV, and SV40 by multiplex nested polymerase chain reaction

A multiplex nested polymerase chain reaction (PCR) method was developed for detecting and differentiating simultaneously the DNA of polyomaviruses JC, BK, and SV40 in a single tube. In the first amplification step the same set of primers was used to amplify a conserved DNA region of the large T antigen gene of JCV, BKV, and SV40. The second round was carried out using a set of primers designed to obtain products of different size for each related virus. Subsequently, the sensitivity of the multiplex nested PCR was maximized by optimizing parameters such as primer, magnesium, and dNTP concentrations. The sensitivity of the method ranged between 1 and 10 copies of the polyomavirus genome. The assay was then used for detecting polyomavirus DNA in urine, serum, and biopsy specimens from renal transplant recipients. Based on the results obtained, the multiplex nested PCR developed in our study represents a useful tool for supporting the diagnosis of polyomavirus infection and could be used for epidemiological purposes and to better define the role of polyomaviruses in human pathology.     

Development and validation of multiplex real-time PCR assays for rapid detection of cytomegalovirus,Epstein-Barr virus,and polyomavirus BK in whole blood from transplant candidates

Transplant recipients are more susceptible to bacterial and viral infections. Cytomegalovirus (CMV), Epstein-Barr virus (EBV), and polyomavirus BK (BK) are risk factors for graft dysfunction. All three of them are latent viruses that can cause serious disease in immunocompromised patients. Mainly qualitative PCR tests are required for diagnosis and quantitative monitoring, which are used to follow the response to transplantation. We developed a multiplex real-time PCR (qPCR) method to detect these viruses during blood screenings of transplant recipients. We also validated analytical and clinical performance tests using the developed multiplex qPCR. The limit of detection (LOD) was 100, 125, and 183 copies/ml for CMV, EBV, and BK, respectively. These results had high linearity (R² = 0.997) and reproducibility (CV range, 0.95–2.38%, 0.52–3.32%, and 0.31–2.45%, respectively). Among 183 samples, we detected 8 samples that were positive for CMV, while only 6 were positive for EBV, and 3 were positive for BK. Therefore, the viral infection prevalence in transplant candidates was 4.40% for CMV, 3.29% for EBV, and 1.64% for BK. This multiplex qPCR method should be used widely for diagnosing and monitoring latent viral infections in transplant recipients.     

Comparison of quantitative methods of DNA CMV investigation in clinical samples obtained from symptomatic and asymptomatic patients undergo renal transplantation

Cytomegalovirus infection is one of the main problem in immunocompromised patiens. Quantitative assessment of CMV load (viral load), rate of increase of load and determination of DNA level above which the likelihood of disease is high (viral load thresholdfor disease) have significant prognostic and therapeutic importance at transplant recipients. The aim of this work was the comparison of 3 quantitative molecular techniques and assessment the threshold for disease for each of them. The study was undertaken with 37 samples of serum and the whole from 17 renal transplant recipients. Part of samples (n=16) comes from symptomatic patients, and were taken in period of clinical symptoms demonstration. The samples ware investigated by hybridization method (HC) performed accordingly to Hybrid the Capture procedure, (r-t PCR) Amplicor test (COBAS AMPLICOR CMV the Monitor test) nd real time PCR (r-t PCR). In 21 out of 37 samples DNA CMV was detected by all 3 methods, 2 samples gave concordant negative results. The CMV DNA level measured by all 3 methods was significantly higher (p < 0.05; t-Student test) in samples from symptomatic patients than from asymptomatic: 4.79 versus 3.58 for HC; 3.06 versus 1.36 for PCR-Amplicor and 4.23 versus 2.88 log DNA copies/ml for r-t PCR. The threshold for disease connected with high likelihood of disease (p < 0.05; Fisher test) was established at 4 log for r-t PCR method, 4,61 for hybridization and 3 log DNA CMV copies/ml for PCR Amplicor.     

Quantitative nested PCR for human cytomegalovirus DNA: analysis using NucleoScan 2001

A quantitative nested DNA PCR for human cytomegalovirus (CMV) was developed using PCR mimic DNA as an internal standard. A combination of ultra-thin gel and enhanced detection of ethidium bromide-stained PCR bands allowed us to achieve a 25-fold increase in sensitivity over the conventional gel electrophoreses, down to 0.1 ng of DNA per band.When the technique was applied to measuring CMV load in CMV positive leucocyte DNA preparations its sensitivity spanned the range from single to hundreds of CMV DNA copies in 0.1 microg of total white blood cell DNA.     

Multicenter evaluation of prototype real‐time PCR assays for Epstein‐Barr virus and cytomegalovirus DNA in whole blood samples from transplant recipients

Quantitative PCR is becoming widespread for diagnosing and monitoring post‐transplantation diseases associated with EBV and CMV. These assays need to be standardized to manage patients in different facilities. Five independent laboratories in Japan compared home‐brew assays and a prototype assay system to establish a standard quantitative procedure for measuring EBV and CMV. Reference standards and a total of 816 (642 EBV and 174 CMV) whole blood samples from post‐transplantation recipients were used for this multicenter evaluation. The prototype reference standard for EBV was compared to a panel of samples, with a theoretical expected value made using EBV‐positive cells containing two virus genome copies per cell. The mean ratio of the reference standard at each site to the standard of the prototype assay was ≤4.15 for EBV among three different sites and ≤3.0 for CMV between two laboratories. The mean of the theoretical expected number of the EBV genome: prototype reference was close to 1.0. The correlation coefficients between the viral copy numbers determined using the prototype assay and those using each home‐brew assay were high (EBV, 0.73–0.83, median = 0.78; CMV, 0.54–0.60, median = 0.57). The dynamics of the EBV and CMV loads in transplant recipients were similar between the assay types. There was an inter‐laboratory difference among the quantification results, indicating that a unified protocol and kit are favorable for standardizing the quantification of EBV and CMV. Such standardization will help to standardize the diagnosis and monitoring of diseases associated with EBV and CMV.     

Evaluation of Herpes Simplex Detection in Corneal Scrapings by Three Molecular Methods

Herpes simplex virus (HSV)-1 keratitis (HSK) is a sight-threatening ocular infection with worldwide occurrence. A prompt laboratory diagnosis is often very useful. The purpose of this study was to evaluate molecular methods as rapid diagnostic tools compared with cell culture of HSK. Corneal scrapings from patients with clinically suspected HSK were tested by direct immunofluorescence assay (IFA) for HSV-1 antigen and by polymerase chain reaction (PCR) for HSV-1 DNA, and an attempt for viral isolation was performed on Vero cell line culture. Positive samples by cell culture were 20.8%, whereas PCR was positive in 29.2%, and IFA was positive in 33.3%. IFA had better sensitivity (80%) and negative predictive value (81.8%) than PCR (70% and 76.9%, respectively); however, PCR had better specificity (71.4%) and positive predictive value (63.6%). This indicates that a combination of cell culture, IFA and PCR constitutes the best set of tools for diagnosis of clinically suspected cases of HSK. Documented infection can be further assessed by cell-culture technique or PCR depending laboratory availability.     

Detection of methicillin-resistant <Emphasis Type="BoldItalic">Staphylococcus aureus</Emphasis> (MRSA) from nasal samples by multiplex real-time PCR based on dual priming AT-rich primers

In this study, we reported on the design of a multiplex real-time PCR assay based on SYBR Green I, incorporating dual priming adenine-thymine (AT)-rich primers for direct detection of MRSA from nasal samples. The multiplex real-time polymerase chain reaction (RT-PCR) assay reported in this study is based on SYBR Green I with incorporation of six dual priming AT-rich primers designed from the SCCmec/orf junction. A string (4–6 bp) of low-melting bases, such as adenine and thymine, was incorporated into the primers, which virtually divided a single primer in two functional regions, thus decreasing non-specific PCR products. The analytical sensitivity and specificity of the RT-PCR assay was determined with genomic DNA of reference strains (MRSA, MSSA, and MRCoNS). RT-PCR assay was performed for analysis of 72 nasal swab specimens, and the results were confirmed by use of a culture method. Furthermore, the results of RT-PCR were compared with LightCycler MRSA advance test. The multiplex RT-PCR assay reproducibly detected a minimum of 1 pg genomic DNA (31.5 copy of genome) of MRSA reference strains and clinical isolates, with a specific melting peak at 83.5 ± 1.5°C, and neither fluorescence nor a melting peak was detected in non-target isolates. The concordance rate between RT-PCR assay and culture method was 87.5% with Cohen's kappa value (κ) 0.75, which showed good agreement between the two assays. The sensitivity, specificity, positive predictive value, and negative predictive value of the assay were 93.5%, 82.9%, 80.5%, and 94.4%, respectively. In a comparative study for the detection of 72 nasal samples, the sensitivity, specificity, positive predictive value, and negative predictive value of the multiplex RT-PCR assay with respect to LightCycler MRSA advance test was 84.2%, 88.2%, 89%, and, 83.3%, respectively. The results of RT-PCR assay demonstrated high specificity (88.2%) and positive predictive value (89%) for the direct detection of MRSA from nasal samples.     

Association of cytomegalovirus with infantile hepatitis

Infantile hepatitis is occasionally seen in apparently healthy children. In most cases, the etiology of the infection is uncertain. However, cytomegalovirus (CMV), Epstein-Barr virus (EBV), human herpesvirus-6 (HHV-6), human herpesvirus-7 (HHV-7), human parvovirus B19, and TT virus (TTV) are considered to be associated with hepatitis in children. The objective of this study was to investigate the correlations between these viruses and infantile hepatitis. Twenty-six children from 1 to 24 months old (median age, 7 months) who had liver dysfunction of unknown etiology were enrolled in this study. Plasma samples were examined by a real-time PCR assay for CMV, EBV, HHV-6, HHV-7, parvovirus B19, and TTV DNA. The DNA of CMV was detected in the plasma of four patients (15.4%) and was detected significantly more often in the patient group than in the control group. The CMV-infected patients were 1 to 3 months old, which was significantly younger than the remaining patients. The serological findings did not always correlate with the results of the real-time PCR assay. The DNA of TTV was detected in four patients (15.4%), while human parvovirus B19 DNA was detected in three (11.5%). However, the detection frequencies of these viral DNAs were not significantly different from those in the control groups, and some of these patients had co-infections. These results indicate that CMV might be one of the major pathogens responsible for infantile hepatitis; however, serological tests have limited utility for the diagnosis of CMV infection in young children.     

Serum antibodies to individual cytomegalovirus structural polypeptides in renal transplant recipients during viral infection

In a longitudinal study we examined by immunoblotting (IB) the development and the evolution of the humoral immune response against individual cytomegalovirus (CMV) structural polypeptides in a total of 80 serum samples from 13 renal transplant recipients showing serological evidence of CMV infection and five renal transplant recipients with an anti-CMV antibody level unchanged over the observation period. The results showed that the IB reactivity at the time of transplantation may be a good index of the host's humoral immune status against CMV; by using this procedure it is possible to identify a seroconversion by the detection of antibodies reacting with some intermediate molecular weight proteins in sera examined at high dilution. Furthermore, IB is a very sensitive procedure also for IgM detection as it anticipates the positivity of the enzyme immune assay for IgM.     

Detection of lethal yellowing phytoplasma in coconut plantlets obtained through in vitro germination of zygotic embryos from the seeds of infected palms

Lethal yellowing (LY) is a disease caused by 16SrIV phytoplasmas that has devastated coconut plantations in the Americas. An alternative means of phytoplasma spread is through seeds. Therefore, we used a novel approach based on plumules from the embryos of LY‐diseased coconut palms. We cultured the plumules in vitro to determine the presence of phytoplasma DNA in the plantlets. In the first assay, 185 embryos were obtained. The results showed positive detection in 20 samples (11%) with the nested PCR and in 59 samples (32%) with the TaqMan real‐time PCR. A second assay was designed to trace plumules to their respective embryos and haustorial tissues to determine whether they had derived from an embryo with positive LY detection; a total of 124 embryos were obtained. The results showed no positive detection with the nested PCR and positive detection in 42 of the haustorial tissue samples (32%) with the TaqMan real‐time PCR. The 124 plumules isolated from the embryos were cultivated under in vitro conditions and divided into two groups. Group A was followed for shoot formation and Group B was followed to the plantlet stage. After 3 months of cultivation, 33 cultures (50%) within Group A became necrotic; the rest were analysed to evaluate LY phytoplasma DNA with the TaqMan real‐time PCR assay and 14 (42%) tested positive. After 18 months of cultivation, 20 cultures (34%) within Group B became necrotic. The rest were analysed for the detection of the LY phytoplasma DNA, and 15 and 11 (39% and 29%) of the samples tested positive with the TaqMan real‐time PCR and nested PCR assays, respectively. Blast analysis of the sequenced products revealed that the sequences showed 99% homology with LY‐phytoplasma subgroup 16SrIV‐A. The results presented here demonstrate, for the first time, the occurrence of the transmission of LY phytoplasmas from coconut embryos to plantlets.