Simultaneous detection of 6 human herpesviruses in cerebrospinal fluid and aqueous fluid by a single PCR using stair primers

Syndrome Evaluation System for Simultaneous Detection Pathogens Causing Acute Encephalitic Syndrome in India, Part-1: Development and Standardization of the Assay

A large number of organisms are known to cause acute encephalitic syndrome (AES). A number of diagnostic tests have to be performed in order to arrive at a probable pathogen causing AES thus making it a very time consuming, laborious and expensive. The problem is further compounded by the lack of availability of sufficient volume of Cerebrospinal fluid (CSF). Thus, there is an urgent need of a diagnostic tool for the simultaneous detection of all probable pathogens responsible for causing AES. Here we report the development of a novel diagnostic method, Syndrome Evaluation System (SES) for the simultaneous detection of 22 pathogens including RNA and DNA Viruses, bacteria, fungi, and parasite all endemic to India and Southeast Asia in a single sample using a novel multiplexing strategy. Syndrome Evaluation System (SES) involves isolation of nucleic acid, multiplex amplification of the DNA, and cDNA followed by identification of the amplified product by sequence specific hybridization on SES platform with the final read out being a visually recordable colored signal. The total time required to carry out this diagnostic procedure is 7 h. The SES was standardized using the commercially available vaccines, panels and cell culture grown quantified viruses/bacteria/fungi. The limit of detection (LOD) of SES ranged between 0.1 and 50 viral particles per ml of CSF and 100 to 200 bacterial cells or 5 parasites per ml of CSF, along with 100% specificity. Precision studies carried out as per the Clinical Laboratory Improvement Amendments (CLIA) guidelines, using two concentrations of each pathogen one the LOD and the other double the LOD, clearly demonstrated, that inter/intra assay variability was within the limits prescribed by the guidelines. SES is a rapid molecular diagnostic tool for simultaneous identification of 22 etiological agents of AES encountered both in sporadic and outbreak settings.

Molecular diagnosis of infectious diseases using cytological specimens

Pathologists have an important role in the diagnosis of infectious disease (ID). In many cases, a definitive diagnosis can be made using cytopathology alone. However, several ancillary techniques can be used on cytological material to reach a specific diagnosis by identifying the causative agent and consequently defining the management of the patient. This review aims to present the effectiveness of the application of molecular studies on cytological material to diagnose IDs and discuss the advantages and disadvantages of the various molecular techniques according to the type of cytological specimen and the infectious agents.

Biomarkers for neural injury and infection in small animals

Cross-sectional imaging techniques have facilitated diagnosis of central nervous system (CNS) diseases. However, there is still frequently a lack of definition of the cause of neurologic lesions, because tissue sampling from the pathologic site is often difficult and there are few clinical diagnostic tools to assist diagnosis. Biomarkers can assist in understanding the cause, diagnosis, severity, and prognosis for neural injury. Integration of conventional testing and new diagnostic techniques will overcome shortcomings in understanding infectious diseases of the CNS. Diagnostic tests may be limited by poor positive and negative predictive values, which must be recognized when interpreting test results.

Enterovirus-related activation of the cardiomyocyte mitochondrial apoptotic pathway in patients with acute myocarditis

AIMS

We examined the impact of enterovirus (EV) cardiac replication activity on the endomyocardial mitochondrial pathway in patients with acute myocarditis.

METHODS AND RESULTS

Levels of apoptotic cardiomyocytes were determined by TUNEL and ligation-mediated polymerase chain reaction (PCR) assays and EV replication activity was assessed by immunostaining of EV VP1 capsid protein in ventricular myocytes of patients with acute myocarditis (n = 25), and healthy heart controls (n = 15). Ratio of cytosolic/mitochondrial cytochrome c concentrations was determined by ELISA assay, levels of active caspase-9 were determined by western blot analysis and Bax/Bcl2 mRNA ratio was assessed by real-time reverse transcription-polymerase chain reaction (RT-PCR) in the same cardiac tissues. Patients with EV-associated acute myocarditis (n = 15) exhibited a significantly higher number of apoptotic cardiomyocytes than those with non-EV-associated acute myocarditis (n = 10) and controls (n = 15) (P < 0.001). Endomyocardial ratio of cytosolic/mitochondrial cytochrome c concentrations and levels of active caspase-9 protein were significantly increased in EV than in non-EV-related myocarditis patients (P < 0.001). Moreover, Bax/Bcl2 mRNA ratio was significantly increased in EV than in non-EV-related myocarditis patients (P < 0.001).

CONCLUSION

Our findings evidence an EV-related activation of the cardiomyocyte mitochondrial apoptotic pathway in patients with acute myocarditis. Moreover, our results indicate that this EV-induced pro-apoptotic mechanism could be partly related to an up-regulation of Bax expression, and suggest that inhibition of this cell death process may constitute the basis for novel therapies.

Usefulness of Herpes Consensus PCR methodology to routine diagnostic testing for herpesviruses infections in clinical specimens

The purposes of the study were to assess the usefulness of simultaneously amplifying herpes simplex virus 1 and 2, varicella-zoster virus, cytomegalovirus, Epstein-Barr virus and human herpesvirus 6 DNA in various clinical specimens and to analyze clinical events in patients presenting positive results. A total of 763 clinical samples obtained from 758 patients, including 115 cerebrospinal fluids, 102 aqueous fluids, 445 swabs from genital (152), oro-facial (138) and other (155) skin lesions, 96 eye swabs and 5 bronchoalveolar lavages, were tested by using the Consensus polymerase chain reaction methodology. The clinical files of the patients were consulted retrospectively. 171 of the 758 patients (22.5%) were positive for at least one of the six target viruses: herpes simplex virus 1 (n = 95), varicella-zoster virus (n = 40), herpes simplex virus 2 (n = 21), herpes simplex virus 1 plus herpes simplex virus 2 (n = 8), cytomegalovirus (n = 4), Epstein-Barr virus (n = 1), human herpesvirus 6 (n = 1), and herpes simplex virus 1 plus human herpesvirus 6 (n = 1). The Consensus methodology enabled the rapid and accurate detection of herpesviruses in various clinical specimens and provided a reliable tool in the diagnosis of herpetic infections.

The investigation of Chlamydophila pneumoniae in patients with multiple sclerosis

Totally 32 cerebrospinal fluid samples from Multiple sclerosis (MS) patients were collected. DNA was extracted by High Pure PCR Template Preparation Kit. Two genomic segments, outer membrane protein genes ompA and omp9, were targeted for the detection of C. pneumoniae DNA in the samples by PCR tests. To detect ompA, a nested-PCR assay was designed, whereas for omp9, a PCR-Enyzme immunoassay (PCR-EIA) depending on streptavidin-biotin capture and dig detection of the PCR products was performed. C. pneumoniae DNA was not detected by each assays in patient samples.

Acute bilateral uveitis associated with an active human herpesvirus-6 infection

Human herpesvirus 6 (HHV-6), which is usually responsible for exanthem subitum in children, can reactivate from its latent form after primary infection. It has been implicated in hepatitis, pneumonitis, retinitis and severe infections of the central nervous system in both immunosuppressed and immunocompetent patients. However, involvement of HHV-6 in these infections has not yet been clearly demonstrated. We report the case of a patient presenting a bilateral uveitis from whom HHV-6 was isolated in both aqueous fluid and cerebrospinal fluid (CSF). No other pathogenic agents were found. Diagnosis by polymerase chain reaction (PCR) followed by sequencing of part of the genome revealed the presence of HHV-6 in both aqueous fluid and CSF. Serum IgM and IgG HHV-6 antibodies were significantly elevated in two successive examinations by immunofluorescence. Patient recovery following antiviral therapy suggested that a protocol based on foscarnet followed by ganciclovir was effective. HHV-6 may be responsible for uveo-meningitis. Diagnosis by PCR analysis is essential to identify HHV-6 and to initiate a specific antiviral therapy as fast as possible.

Diagnosis of herpes simplex virus infections of the CNS

Advances in the diagnosis of herpes simplex virus infections of the CNS have occurred rapidly over the past 10 years. The development and application of PCR technology to the detection of herpes simplex virus DNA from cerebrospinal fluid has resulted in tremendous improvements in the management of patients with suspected herpes simplex virus CNS infections, not the least of which is decreasing the necessity for invasive brain biopsy to establish the diagnosis. The pace of discovery has continued in recent years with the development of more rapid DNA amplification techniques that do not require postamplification analysis using amplified products (real-time PCR). However, despite the power of these new diagnostic modalities, test results must always be considered in the context of the patient, and physician judgment should never be usurped by technological advances. This article will summarize the advances in the diagnosis of herpes simplex virus CNS disease within the context of how these advances can enhance the care of individual patients.

Main adult herpes virus infections of the CNS

Herpes viruses are widely involved in human infectious diseases, and some are life threatening, such as CNS infections. These manifestations vary according to the type of virus involved and the immune status of the patient. This article will review the clinical manifestations (encephalitis, myelitis, meningitis and postinfectious encephalomyelitis), the diagnostic strategies and the presently used drugs (acyclovir, valacyclovir, ganciclovir, valgancyclovir, foscarnet and cidofovir). The review will also discuss drugs that are currently in the pipeline and that could be used in the future.

DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses

Viral infections of the central nervous system (CNS) are caused by a variety of viruses, namely, herpesviruses, enteroviruses, and flaviviruses. The similar clinical signs provoked by these viruses make the diagnosis difficult. We report on the simultaneous detection of these major CNS pathogens using amplification by PCR and detection of amplified products using DNA microarray technology. Consensus primers were used for the amplification of all members of each genus. Sequences specific for the identification of each virus species were selected from the sequence alignments of each target gene and were synthesized on a high-density microarray. The amplified products were pooled, labeled, and cleaved, followed by hybridization on a single array. This method was successfully used to identify herpesviruses, namely, herpes simplex virus type 1 (HSV-1), HSV-2, and cytomegalovirus; all serotypes of human enteroviruses; and five flaviviruses (West Nile virus, dengue viruses, and Langat virus). This approach, which used highly conserved consensus primers for amplification and specific sequences for identification, would be extremely useful for the detection of variants and would probably help solve some unexplained cases of encephalitis. The analytical sensitivity of the method was shown to be 500 genome equivalents ml(-1) for HSV-1, 0.3 50% tissue culture infectious doses (TCID50s) ml(-1) for the enterovirus coxsackievirus A9, and 200 TCID50s ml(-1) for West Nile virus. The clinical sensitivity of this method must now be evaluated.

Association between enterovirus endomyocardial infection and late severe cardiac events in some adult patients receiving heart transplants

Enteroviruses and other cardiotropic viruses have been associated with the development of late severe adverse cardiac events in infants receiving heart transplants. However, the source and the chronology of cardiac allograft infection by an enterovirus in patients receiving heart transplants remain unknown. Using RT-PCR and immunohistochemistry assays, endomyocardial tissue samples of 30 adult patients were tested to detect the presence of specific enterovirus 5' non-coding (5'NC) sequences and of VP1 capsid protein, and this at the time of cardiac transplantation and at the 12-month biopsy for graft rejection control. Moreover, the endomyocardial detection of genomic sequences of enteroviruses, Epstein-Barr virus, herpes simplex virus, cytomegalovirus (CMV), varicella-zoster virus, adenoviruses, and parvovirus B19 was carried out by RT-PCR and polymerase chain reaction (PCR) assays at the time of late severe cardiac events. Enterovirus RNA and VP1 antigen were both detected in 4 (13%) of 30 patients at the time of the 12-month biopsy for graft rejection control, whereas no enterovirus component was detected in the explanted and implanted heart tissues taken from these 4 patients at the time of transplantation. At the time when severe cardiac events were developed, within 3 months after the positive enterovirus cardiac detection, these four patients demonstrated the presence of endomyocardial enterovirus RNA sequences whereas they were tested negative for the endomyocardial detection of genomic sequences from DNA viruses (except for CMV in two cases), and for a significant level of pp65 CMV antigenemia. Taken together, these findings indicate that enteroviruses could be acquired as a new endomyocardial infection within 12 months after transplantation in adults receiving heart transplants, and suggest that this infection might be an etiological cause for unexplained late severe adverse cardiac events in the heart-transplantated adults.

Molecular methods for diagnosis of viral encephalitis

Hundreds of viruses cause central nervous system (CNS) disease, including meningoencephalitis and postinfectious encephalomyelitis, in humans. The cerebrospinal fluid (CSF) is abnormal in >90% of cases; however, routine CSF studies only rarely lead to identification of a specific etiologic agent. Diagnosis of viral infections of the CNS has been revolutionized by the advent of new molecular diagnostic technologies to amplify viral nucleic acid from CSF, including PCR, nucleic acid sequence-based amplification, and branched-DNA assay. PCR is ideally suited for identifying fastidious organisms that may be difficult or impossible to culture and has been widely applied for detection of both DNA and RNA viruses in CSF. The technique can be performed rapidly and inexpensively and has become an integral component of diagnostic medical practice in the United States and other developed countries. In addition to its use for identification of etiologic agents of CNS disease in the clinical setting, PCR has also been used to quantitate viral load and monitor duration and adequacy of antiviral drug therapy. PCR has also been applied in the research setting to help discriminate active versus postinfectious immune-mediate disease, identify determinants of drug resistance, and investigate the etiology of neurologic disease of uncertain cause. This review discusses general principles of PCR and reverse transcription-PCR, including qualitative, quantitative, and multiplex techniques, with comment on issues of sensitivity, specificity, and positive and negative predictive values. The application of molecular diagnostic methods for diagnosis of specific infectious entities is reviewed in detail, including viruses for which PCR is of proven efficacy and is widely available, viruses for which PCR is less widely available or for which PCR has unproven sensitivity and specificity, and nonviral entities which can mimic viral CNS disease.

Molecular analysis of cerebrospinal fluid in viral diseases of the central nervous system

The use of nucleic acid (NA) amplification techniques has transformed the diagnosis of viral infections of the central nervous system (CNS). Because of their enhanced sensitivity, these methods enable detection of even low amounts of viral genomes in cerebrospinal fluid. Following more than 10 years of experience, the polymerase chain reaction or other NA-based amplification techniques are nowadays performed in most diagnostic laboratories and have become the test of choice for the diagnosis of several viral CNS infections, such as herpes encephalitis, enterovirus meningitis and other viral infections occurring in human immunodeficiency virus-infected persons. Furthermore, they have been useful to establish a viral etiology in neurological syndromes of dubious origin and to recognise unusual or poorly characterised CNS diseases. Quantitative methods have provided a valuable additional tool for clinical management of these diseases, whereas post-amplification techniques have enabled precise genome characterisation. Current efforts are aiming at further improvement of the diagnostic efficiency of molecular techniques, their speed and standardisation, and to reduce the costs. The most relevant NA amplification strategies and clinical applications of to date will be the object of this review.

Detection of herpesvirus genomes by polymerase chain reaction in cerebrospinal fluid and clinical findings

BACKGROUND

The viruses of the Herpesviridae family, in particular herpes simplex virus types 1 (HSV-1) and 2 (HSV-2), cytomegalovirus (CMV), Epstein-Barr virus (EBV), varicella zoster virus (VZV), and human herpesvirus 6 (HHV-6), are responsible for numerous infections of the central nervous system (CNS). These infections manifest as diverse clinical signs, many of which are not specific. The diagnosis of these infections is necessary to make it possible to adapt treatment appropriately, as treatment is specific for the particular virus concerned.

OBJECTIVES

To apply a polymerase chain reaction (PCR) technique for the diagnosis in a single reaction of the six herpesviruses most frequently detected in the cerebrospinal fluid (CSF) and to analyse clinical events in patients presenting positive results in PCR for herpesviruses.

STUDY DESIGN

We studied 141 patients, from whom 180 CSF samples were collected. The clinical files of the patients were consulted retrospectively, and a list of clinical signs was recorded. After testing by targeted PCR, at the clinician's demand, we tested these samples by herpes consensus PCR, which detects six herpesviruses (HSV-1, HSV-2, CMV, EBV, VZV, HHV-6), in a single PCR.

RESULTS

Targeted PCR tests identified 25 CSF samples (13.9%), corresponding to 18 patients (12%), as positive. The herpes consensus PCR test detected 49 samples (27.2%) as positive, resulting in the identification of 54 individual viruses (four samples displayed co-infection) from 39 patients (27%). 130 CSF samples, from 101 patients, tested negative by both techniques. 23 HIV-positive patients (30.6%), three HIV-negative immunocompromised patients (27%), and 14 immunocompetent patients (25%) were CSF PCR-positive. In HIV-positive patients, CMV was the virus most frequently identified (13%), followed by EBV (10.6%), VZV (5.3%) and finally HSV-1 and HSV-2 (both 1.3%). We did not detect HHV-6 in any of these samples. We detected only HSV-2, EBV and VZV in the 11 HIV-negative immunocompromised patients. CSF samples of immunocompetent patients contained mostly VZV (9%) and HSV-1 (7.3%).

CONCLUSIONS

The herpes consensus PCR for a given virus was more sensitive than the standard, targeted PCR used in our laboratory. The clinical signs presented by patients infected with HSV-1, HSV-2 and CMV were similar to those reported in previous studies. For VZV, we report the possibility of mild, transient cerebral viral reactivation. Our data on the detection of EBV by PCR suggest that the PCR test is of predictive value for cerebral lymphoma in immunocompromised patients. The possible role of HHV-6 in a subacute neurological disorder merits further investigation.

Herpes Consensus PCR test: a useful diagnostic approach to the screening of viral diseases of the central nervous system

BACKGROUND

Infections of the central nervous system (CNS) are a difficult diagnostic problem for both clinicians and microbiologists. Various clinical signs, such as encephalitis, myelitis, meningitis, may be associated with herpesviruses. The use of multiplex 'Herpes Consensus' polymerase chain reaction (HC-PCR) in association with nested PCR (nPCR), in addition to classical techniques, made it possible to optimise the management of cerebrospinal fluid (CSF) and serum samples from patients affected by these viral diseases of the CNS.

OBJECTIVES

To test by HC-PCR by nPCR and cell culture the CSF and sera from patients with viral infections of the CNS.

STUDY DESIGN

We analysed 320 CFS, 154 serum samples and 11 various samples from 286 patients with clinically suspected encephalitis, meningitis or other diseases of the CNS by HC-PCR, nPCR and traditional investigations (cell culture and serological tests).

RESULTS

On molecular analysis with the HC-PCR test, 51 CFS samples (15.9%) were positive for at least one of the six target Herpes viruses: fourteen for Herpes simplex 1 (HSV-1), seven for HSV-2, 12 for Cytomegalovirus (CMV; one of which was from an HIV-positive patient), five for Epstein-Barr virus (EBV; four of which were from HIV-positive patients), three for Varicella-Zoster virus (VZV), five for Human Herpes virus type 6 (HHV-6), three for HSV-1 with HHV-6 co-infection (two cases) and HSV-2 co-infection (one case), and two for HHV-6 with CMV or EBV co-infection (both from patients with immune deficiency). A further 12 samples were positive in nPCR for HHV-7 (8), ADV (1), Enterovirus (1), HSV-1 (1), EBV (1). Of the 154 serum samples, 17 (11.0%) tested positive by HC-PCR for HSV-1 (4), HSV-2 (1), CMV(1), EBV(1), VZV(3) or HHV-6(6), 1 with co-HSV-2/VZV infection. A further five samples tested positive for HHV-7 in nPCR. Culture and tests for antibodies did not supply sufficiently sensitive and specific data.

CONCLUSIONS

Our laboratory experience shows that herpesviruses play a central aetiological role in viral infections of the CNS. PCR analysis, especially the HC-PCR test, have revolutionised the diagnostic approach to such infections, making possible rapid, specific and highly sensitive baseline screening. In this way, microbiological investigations can lead to prompt diagnosis, which was limited in the past to a very small number of cases.

Detection and species identification of four human herpesviruses using polymerase chain reaction coupled with restriction endonuclease analysis

A polymerase chain reaction (PCR) based assay for detection and species identification of four human herpesviruses, including herpes simplex virus types 1 and 2, Epstein-Barr virus, and cytomegalovirus was developed. The detection of the herpesviruses was achieved by seminested PCR with three primers targeting well-conserved regions within the DNA-polymerase gene. Virus species were identified by simple restriction enzyme digestion of the amplified products with TaqI or RsaI. In comparison with mono-specific nested PCR assays the tetra-specific assay demonstrated similar specificity and sensitivity with reference and clinical samples. The tetra-specific assay is sensitive, cost effective, and can be used for examination of clinical samples of different origin.

Multiplex detection of herpesviruses in tear fluid using the "stair primers" PCR method: prospective study of 93 patients

Human herpesviruses can infect the eye and be excreted subsequently in tears. The aim of the present study was to use a multiplex PCR to detect herpesviruses (HSV-1, -2, VZV, CMV, EBV, HHV-6) in tears from normal subjects and from patients with pathological conditions (acute herpes, zoster, papillary conjunctivitis, and dry eye). Schirmer test strips were used to collect tear fluid from 93 patients, sampling both eyes. DNA was then extracted from the 186 samples by chromatography, and viral DNA amplified using a commercialised multiplex "stair primer" method. Thirty-four samples (18.3%) contained Taq inhibitors. The multiplex test gave positive results for HSV and VZV in tear fluid from patients with acute dendritic keratitis (3 patients) and acute ocular zoster (4 patients) and was, therefore, considered effective in testing samples from patients with acute lesions. HSV-1 and HSV-2 were found in two samples from patients with metaherpetic corneal scarring. Among 28 cases of dry eye, two were positive for HHV-6, the latter being associated with EBV in one patient. HHV-6 was also found in 4 out of 54 cases of papillary conjunctivitis. This raised occurrence of HHV-6 in dry eye or papillary conjunctivitis, suggests new clinical patterns for HHV-6 latency or reactivation. Detection of EBV in 1 out of 80 healthy eyes confirms previous evidence that lacrimal glands constitute potentially a site for latent-phase EBV.