An international external quality assessment of nucleic acid amplification of herpes simplex virus

Evaluation of the Performance Characteristics of a New POC Multiplex PCR Assay for the Diagnosis of Viral and Bacterial Neuromeningeal Infections

Point-of-care syndromic PCR (POC SPCR) assays are useful tools for the rapid detection of the most common causative agents of community-acquired infections responsible for meningitis and encephalitis infections. We evaluated the performance characteristics of the new QIAstat-Dx® Meningitis/Encephalitis panel (QS) compared to the laboratory reference methods and the POC SPCR Biofire® FilmArray® Meningitis Encephalitis Panel (FA). Viral (Enterovirus, Parechovirus, HSV-1, HSV-2, HHV-6, VZV) and bacterial (E. coli K1, H. influenzae, L. monocytogenes, encapsulated N. meningitidis, M. pneumoniae, S. agalactiae, S. pneumoniae, S. pyogenes) pathogens were suspended at low concentrations and tested with the POC SPCR systems. The reproducibility, analytical specificity, carryover contamination, interferences and clinical samples were evaluated. All samples tested positive with both QS and FA except for those containing the lowest concentrations of Enterovirus-D68-B3, Echovirus-30 and S. agalactiae which were only detected by FA. In terms of analytical specificity, we observed 3 false positive results out of 48 QS tests versus 1 out of 37 FA tests. For the other studied criteria, both QS and FA performed as expected. Our results suggest that the performance characteristics of QS are close to those of FA. A prospective multicenter study would be useful to complete the performances evaluation of QS.

Implementation and Evaluation of a Fully Automated Multiplex Real-Time PCR Assay on the BD Max Platform to Detect and Differentiate Herpesviridae from Cerebrospinal Fluids

A fully automated multiplex real-time PCR assay--including a sample process control and a plasmid based positive control--for the detection and differentiation of herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2) and varicella-zoster virus (VZV) from cerebrospinal fluids (CSF) was developed on the BD Max platform. Performance was compared to an established accredited multiplex real time PCR protocol utilizing the easyMAG and the LightCycler 480/II, both very common devices in viral molecular diagnostics. For clinical validation, 123 CSF specimens and 40 reference samples from national interlaboratory comparisons were examined with both methods, resulting in 97.6% and 100% concordance for CSF and reference samples, respectively. Utilizing the BD Max platform revealed sensitivities of 173 (CI 95%, 88-258) copies/ml for HSV1, 171 (CI 95%, 148-194) copies/ml for HSV2 and 84 (CI 95%, 5-163) copies/ml for VZV. Cross reactivity could be excluded by checking 25 common viral, bacterial and fungal human pathogens. Workflow analyses displayed shorter test duration as well as remarkable fewer and easier preparation steps with the potential to reduce error rates occurring when manually assessing patient samples. This protocol allows for a fully automated PCR assay on the BD Max platform for the simultaneously detection of herpesviridae from CSF specimens. Singular or multiple infections due to HSV1, HSV2 and VZV can reliably be differentiated with good sensitivities. Control parameters are included within the assay, thereby rendering its suitability for current quality management requirements.

Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens

Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here.

Application of RT-Bst to enhance detection of pathogenic viruses of the respiratory tract

Inefficiency of RT-PCR can be associated with the suboptimal process of reverse transcription as only 40-80% of RNA is converted to cDNA. We employed a novel method, RT-Bst, to enrich the concentration of cDNA for subsequent multiplex PCR detection of selected RNA viruses. The RT-Bst method amplifies cDNA through reverse transcription of viral RNA using reverse transcriptase and amplification of cDNA using Bst DNA polymerase. Viral RNA was extracted from 25 nasopharyngeal samples for detection of influenza A, B and C; parainfluenza 1-4; human coronaviruses 229E and OC43; respiratory syncytial virus (RSV) and rhinovirus. Both multiplex one-step RT-PCR and RT-Bst PCR were used to compare their performances for detection of virus sequences. These findings were compared with routine laboratory detection. When using RT-Bst PCR, 28% of samples yielded a viral pathogen compared to 20% with RT-PCR and 12% using routine diagnostic tests. RT-Bst PCR was shown to have particular utility in the detection of RSV RNA as this was present in 20% of the samples studied compared to 8% when using RT-PCR. For one patient, RT-Bst PCR was able to detect RSV five days earlier than conventional hospital diagnostic testing. RT-Bst and RT-Bst PCR can be used as alternative approaches to reverse transcription and one-step RT-PCR, respectively, for sequence-independent amplification of RNA virus sequences and a larger scale analysis of this new diagnostic approach is warranted.

RT-Bst: an integrated approach for reverse transcription and enrichment of cDNA from viral RNA

The synthesis of cDNA from RNA is challenging due to the inefficiency of reverse transcription (RT). In order to address this, an RT-Bst method was developed for sequential RT of RNA and Bst DNA polymerase amplification for enrichment of cDNA in a single-tube reaction. Using genomic RNA from bacteriophage MS2, the yield of cDNA produced by RT alone and RT-Bst were compared by analysis of polymerase chain reaction (PCR)-amplified products. A superior performance was observed when amplifying MS2 cDNA with random primers following RT-Bst compared to RT alone, indicating greater quantities of cDNA were present after RT-Bst. RT-Bst was also compared with RT alone for their relative ability to produce sufficient cDNA to amplify eight target regions spanning the respiratory syncytial virus (RSV) genome. Six out of eight targets were amplified consistently by PCR subsequent to RT-Bst amplification, whereas only three out of eight targets could be amplified after RT alone. The RSV sequences were selectively amplified using RSV-specific primers from a mixed template containing an excess of MS2 RNA without amplifying MS2 sequences. This suggests that RT-Bst can be used to amplify RNA sequences non-specifically using random primers and specifically using sequence-specific primers, and enhances the yield of cDNA when compared to RT alone.

Development and Validation of a Laboratory-Developed Multiplex Real-Time PCR Assay on the BD Max System for Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA in Various Clinical Specimens

A multiplex real-time PCR (quantitative PCR [qPCR]) assay detecting herpes simplex virus (HSV) and varicella-zoster virus (VZV) DNA together with an internal control was developed on the BD Max platform combining automated DNA extraction and an open amplification procedure. Its performance was compared to those of PCR assays routinely used in the laboratory, namely, a laboratory-developed test for HSV DNA on the LightCycler instrument and a test using a commercial master mix for VZV DNA on the ABI7500fast system. Using a pool of negative cerebrospinal fluid (CSF) samples spiked with either calibrated controls for HSV-1 and VZV or dilutions of a clinical strain that was previously quantified for HSV-2, the empirical limit of detection of the BD Max assay was 195.65, 91.80, and 414.07 copies/ml for HSV-1, HSV-2, and VZV, respectively. All the samples from HSV and VZV DNA quality control panels (Quality Control for Molecular Diagnostics [QCMD], 2013, Glasgow, United Kingdom) were correctly identified by the BD Max assay. From 180 clinical specimens of various origins, 2 CSF samples were found invalid by the BD Max assay due to the absence of detection of the internal control; a concordance of 100% was observed between the BD Max assay and the corresponding routine tests. The BD Max assay detected the PCR signal 3 to 4 cycles earlier than did the routine methods. With results available within 2 h on a wide range of specimens, this sensitive and fully automated PCR assay exhibited the qualities required for detecting simultaneously HSV and VZV DNA on a routine basis.

Clinical application of viral cerebrospinal fluid PCR testing for diagnosis of central nervous system disorders: a retrospective 11-year experience

The cerebrospinal fluid (CSF) polymerase chain reaction (PCR) is the gold standard to detect cerebral viral activity. As positive findings do not prove an impact on the neurological disorder, data interpretation is difficult. To better assess the impact of positive CSF PCR findings in different neurological diseases and to identify coherences facilitating CSF PCR data interpretation, we performed this retrospective analysis of CSF PCR data of 481 pediatric and 2604 adult patients, including herpes simplex virus (HSV), varicella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpesvirus 6 (HHV-6), and enteroviruses (EV). Nucleic acid of EBV was detected in 1.6% (39/2449), of VZV in 1.3% (34/2624), of HSV in 1.24% (37/2994), of EV in 0.4% (10/2364), of HHV-6 in 0.17% (4/2417), and of CMV in 0.2% (5/2514) of the patients. Newborns and elderly people showed highest infection rates. HSV, VZV, and EV prevailed in typical infectious central nervous system (CNS) diseases; EBV, in further inflammatory neurological diseases; HSV and EBV, in immunocompromised patients; and EBV, HSV, and HHV-6, in further non-inflammatory neurological diseases. Analysis of successive PCR studies revealed delayed viral detection for EBV (6/147) and HSV (1/217), respectively. Rapid viral clearance was typical for HSV, VZV, CMV, and EV infections, although the maximum duration of viral detection was 15days for HSV and 12days for VZV, respectively. This suggests that the detection of HSV, VZV, CMV, and EV strongly indicates symptomatic viral CNS disease. Secondary viral reactivation mostly underlies positive EBV and HHV-6 findings. Their detection does not rule out clinical impact but recommends searching for additional underlying conditions.

Clinical assessment of assays for diagnosis of herpes simplex infection

It is becoming increasingly clear that the herpes simplex viruses (HSVs) 1 and 2 constitute a major, global, public health problem, particularly as genital herpes is implicated in the causation of a significant percentage of onwards transmission of the HIV virus. A major factor in the transmission of HSV is that most carriers are unaware of their diagnosis. In the last few years, the development of nucleic acid amplification technology and type-specific antibody serology to test for HSV-1 and -2 has contributed significantly to the accurate diagnosis of these infections. Despite guidance to the contrary, there is still much use of less sensitive tests such as viral culture and antibody testing based on crude antigen. It is essential that we use the most sensitive and specific diagnostic tests if we are to curb this epidemic.

Nucleic acid amplification technology for the diagnosis of genital herpes infection

Nucleic acid amplification technologies are well-characterized methods for the rapid and sensitive diagnosis of a wide variety of infectious diseases. Herpes simplex virus amplification is no exception, demonstrating as much as a ninefold enhancement in sensitivity over viral culture in some settings. Currently, there are no US Food and Drug Administration-approved systems for herpes simplex virus amplification; hence, most laboratories utilize in-house-developed PCR-based systems. Unfortunately, the utilization of herpes simplex virus amplification has been confined to the investigations of suspected herpes simplex virus encephalitis, largely due to cost and the need for appropriately trained technical staff. Recent methodological advances will help to render herpes simplex virus nucleic acid amplification technologies more applicable to routine practice. However, the use of nucleic acid amplification technologies for the diagnosis of genital herpes infection remains highly controversial.

Laboratory diagnosis of viral infection

Since the last Handbook of Clinical Neurology volume on this topic, viral diagnosis has made tremendous strides, moving from the margin to the mainstream of clinical care. For many years, conventional virus isolation was the mainstay of viral diagnosis since it was sensitive and “open-minded.” However, growth in conventional cell culture entails an inherent delay that limits its clinical impact. Although rapid culture and viral antigen methods detect fewer pathogens and are less sensitive than conventional culture, both require less expertise and have greatly reduced time to result. Polymerase chain reaction has ushered in a new era in virology, especially in the diagnosis of neurologic diseases. Molecular amplification methods are rapid, highly sensitive, can be automated, quantitative, and detect viruses not amenable to routine culture. User-friendly, walk-away tests with results in an hour, as well as multiplex tests that can detect 20 viruses in a single reaction, are now a reality. As the variety of test methods and commercial products proliferate, the challenges for clinicians and laboratories are selecting which tests to utilize in which clinical scenarios, and understanding how to interpret the results. The advantages and limitations of each method are discussed in this chapter, with special attention to neurologic disease.

Amp-PCR: combining a random unbiased Phi29-amplification with a specific real-time PCR, performed in one tube to increase PCR sensitivity

In clinical situations where a diagnostic real-time PCR assay is not sensitive enough, leading to low or falsely negative results, or where detection earlier in a disease progression would benefit the patient, an unbiased pre-amplification prior to the real-time PCR could be beneficial. In Amp-PCR, an unbiased random Phi29 pre-amplification is combined with a specific real-time PCR reaction. The two reactions are separated physically by a wax-layer (AmpliWax®) and are run in sequel in the same sealed tube. Amp-PCR can increase the specific PCR signal at least 100×10⁶-fold and make it possible to detect positive samples normally under the detection limit of the specific real-time PCR. The risk of contamination is eliminated and Amp-PCR could replace nested-PCR in situations where increased sensitivity is needed e.g. in routine PCR diagnostic analysis. We show Amp-PCR to work on clinical samples containing circular and linear viral dsDNA genomes, but can work well on DNA of any origin, both from non-cellular (virus) and cellular sources (bacteria, archae, eukaryotes).

Global proficiency study of human papillomavirus genotyping

Internationally comparable quality assurance of Human Papillomavirus (HPV) DNA detection and typing methods is essential for evaluation of HPV vaccines and effective monitoring and implementation of HPV vaccination programs. Therefore, the World Health Organization (WHO) HPV Laboratory Network (LabNet) designed an international proficiency study. Following announcement at the WHO website, the responding laboratories performed HPV typing using one or more of their usual assays on 43 coded samples composed of titration series of purified plasmids of 16 HPV types (HPV6, -11, -16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, and -68). Detection of at least 50 IU of HPV16 or HPV18 DNA and of 500 genome equivalents (GE) of the other 14 HPV types (in samples with single and multiple HPV types) was considered proficient. Fifty-four laboratories worldwide submitted a total of 84 data sets. More than 21 HPV-genotyping assays were used. Commonly used methods were Linear Array, Lineblot, InnoLiPa, Clinical Array, type-specific real-time PCR, PCR-Luminex and microarray assays. The major oncogenic HPV types (HPV16 and -18) were detected in 89.7% (70/78) and 92.2% (71/77) of the data sets, respectively. HPV types 56, 59, and 68 were the least commonly detected types (in less than 80% of the data sets). Twenty-eight data sets reported multiple false-positive results and were considered nonproficient. In conclusion, we found that international proficiency studies, traceable to international standards, allow standardized quality assurance for different HPV-typing assays and enable the comparison of data generated from different laboratories worldwide.

Monitoring of herpes simplex virus DNA types 1 and 2 viral load in cerebrospinal fluid by real-time PCR in patients with herpes simplex encephalitis

A quantitative polymerase chain reaction (PCR) assay was evaluated retrospectively on 92 cerebrospinal fluid (CSF) samples from 29 patients with herpes simplex virus (HSV) encephalitis with the aim to study if the concentration of HSV genomes can be used as a prognostic marker and for monitoring of antiviral therapy. The results were compared to those obtained previously by nested PCR, and the numbers of HSV genomes/ml were evaluated in correlation to patient outcome and treatment. The aims were to compare the sensitivity of a conventional nested PCR to a quantitative PCR, to investigate the range of HSV genome concentration in initial samples and to evaluate possible relationships between the HSV DNA concentrations in CSF, neopterin levels, and outcome of disease. The 29 initial samples contained between 2 x 10(2) and 42 x 10(6) HSV genomes/ml. There was no apparent correlation between the amount of HSV DNA in the initial samples and income status, initial neopterin levels, or prognosis. The number of HSV genomes/ml declined after treatment in all patients, but HSV DNA was still detectable after day 20 in 3 out of 16 patients. A long duration of genome detectability was found to correlate with poor outcome. There was no difference in sensitivity between the nested PCR and the quantitative PCR. While the quantitative PCR is more rational than a nested PCR, the quantitation of HSV genomes does not seem very useful as a prognostic marker in HSV encephalitis.

Interlaboratory comparison of cytomegalovirus viral load assays

To assess interlaboratory variability in qualitative and quantitative cytomegalovirus (CMV) viral load (VL) testing, we distributed a panel of samples to 33 laboratories in the USA, Canada and Europe who performed testing using commercial reagents (n = 17) or laboratory-developed assays (n = 18). The panel included two negatives, seven samples constructed from purified CMV nucleocapsids in plasma (2.0-6.0 log(10) copies/mL) and three clinical plasma samples. Interlaboratory variation was observed in both actual (range, 2.0-4.0 log(10) copies/mL) and self-reported lower limits of detection (range, 1.0-4.0 log(10) copies/mL). Variation observed in reported results for individual samples ranged from 2.0 log(10) (minimum) to 4.3 log(10) (maximum)(.) Variation was greatest at low VLs. Assuming +/- 0.5 log(10) relative to the expected result represents an acceptable result, 57.6% of results fell within this range. Use of commercially available reagents and procedures was associated with less variability compared with laboratory-developed assays. Interlaboratory variability on replicate samples was significantly greater than intralaboratory variability (p < 0.0001). The significant interlaboratory variability in CMV VL observed may be impacting patient care and limiting interinstitutional comparisons. The creation of an international reference standard for CMV VL assay calibration would be an important step in quality improvement of this laboratory tool.

False negative PCR despite high levels of JC virus DNA in spinal fluid: Implications for diagnostic testing

Genome amplification methods such as polymerase chain reaction (PCR) have revolutionized our ability to detect viruses in spinal fluids of patients with neurologic diseases. It is not as well appreciated among clinicians that PCR protocols, quality assurance, and technical expertise vary significantly among laboratories. In a multi-laboratory blinded study of herpes simplex virus PCR, the most widely used and best validated CSF PCR assay, low-level positives were often missed and false positives were not uncommon [Schloss L, van Loon AM, Cinque P, Cleator G, Echevarria JM, Falk KI, et al. An international external quality assessment of nucleic acid amplification of herpes simplex virus. J Clin Virol 2003;28(2):175-85]. In addition, genome variability and mutations, which are increasingly recognized for a number of different viruses, can lead to falsely low or negative results. Both clinicians and laboratories must recognize the limitations of PCR, since misleading results may have serious consequences. We present here a case of a rapidly progressive, fatal neurologic illness in a young mother, whose CSF JCV DNA PCR at a reference laboratory was falsely negative. Ultimately, brain biopsy established the diagnosis of progressive multifocal leukoencephalopathy (PML). Repeat PCR testing of the same CSF targeting a different region of the genome yielded a high positive result.

Herpes Simplex Virus Type 1 infection: overview on relevant clinico-pathological features

Herpes Simplex Virus Type 1 (HSV-1) is a nuclear replicating enveloped virus, usually acquired through direct contact with infected lesions or body fluids (typically saliva). The prevalence of HSV-1 infection increases progressively from childhood, the seroprevalence being inversely related to socioeconomic background. Primary HSV-1 infections in children are either asymptomatic or following an incubation period of about 1 week gives rise to mucocutaneous vesicular eruptions. Herpetic gingivostomatitis typically affects the tongue, lips, gingival, buccal mucosa and the hard and soft palate. Most primary oro-facial HSV infection is caused by HSV-1, infection by HSV-2 is increasingly common. Recurrent infections, which occur at variable intervals, typically give rise to vesiculo-ulcerative lesions at mucocutaneous junctions particularly the lips (herpes labialis). Recurrent HSV-1 infection within the mouth is uncommon in otherwise healthy patients, although in immunocompromised patients, recurrent infection can be more extensive and/or aggressive. The diagnosis of common herpetic infection can usually be based upon the clinical history and presenting features. Confirmatory laboratory diagnosis is, however, required when patients are, or may be, immunocompromised.

External quality assessment of cytomegalovirus DNA detection on dried blood spots

BACKGROUND

Testing for viral DNA in neonatal blood dried on paper (DBS) has proved a valid means of diagnosing congenital CMV infection with both clinical and epidemiological relevance. To assess the quality of the detection of CMV-DNA on DBS in laboratories performing this test a proficiency panel consisting of nine samples with two blood spots on each filter paper was produced and distributed. Six samples were derived from whole blood, negative for CMV DNA and antibody, and spiked with cell-grown CMV Towne in various concentrations (7.3 x 102 - 9.6 x 105 copies/ml), one was a CMV positive clinical specimen (3.9 x 106 copies/ml), and two samples were CMV-negative whole blood.

RESULTS

The 27 responding laboratories from 14 countries submitted 33 datasets obtained by means of conventional PCR (n = 5) or real-time PCR (n = 28) technologies. A correct positive result was reported in at least 91% of datasets in samples with a viral load of 8.8 x 104 copies/ml or higher. However only 59% and 12% identified the 9.4 x 103 and 7.3 x 102 copies/ml samples, respectively, correctly as positive. False positive results were reported by 9% of laboratories and in 11% of datasets.

CONCLUSION

These results indicate a clear need for improvement of methods as sensitivity and false-positivity still appear to be a major problem in a considerable number of laboratories.

Quantitative detection of herpes simplex virus DNA in the lower respiratory tract

Quantitation of herpes simplex virus (HSV) DNA in bronchoalveolar lavage specimens could indicate an infectious role in the lower respiratory tract. The aim of this study was to compare quantitative HSV DNA results from adult bronchoalveolar lavage specimens to clinical outcome. Quantitative real-time PCR assays targeting HSV and other herpes viruses were performed on adult bronchoalveolar lavage specimens obtained from a largely immunocompromised population during a 1-year period. The results were compared to patient characteristics and outcome. HSV DNA was detected in 11 (19%) of 57 bronchoalveolar lavage specimens with a mean viral level of 5.6 log genome equivalents/ml (range, 2.9-8.1 log). A threshold of HSV DNA levels equal or higher than 5.0 log (n = 7) was associated with mortality within 28 days following hospital admission (odds ratio [OR], 6.8; 95% confidence interval [CI], 1.2-39.2). A threshold level of 5.5 log was associated with mortality within 28 days of sampling (OR 8.5; 95% CI 1.2-62.1), only after excluding patients receiving specific antiviral medication. Patients with HSV DNA levels equal or higher than 7.5 log had severe respiratory failure. Viral pneumonia was histologically proven in one patient with 8.0 log at autopsy. No patient with HSV DNA levels below 5.5 log (n = 5) or DNA levels higher than 5.0 log of cytomegalovirus (CMV) (n = 3), Epstein-Barr virus (EBV) (n = 9), varicella-zoster virus (VZV) (n = 1), or human herpesvirus 6 (HHV-6) (n = 0) died within 28 days of hospital admission. We conclude that quantitative detection of HSV DNA in bronchoalveolar lavage fluid is a potential diagnostic tool for detection of relevant viral infection of the lower respiratory tract.

Contamination with PCR detectable virus in a virus isolation quality assurance panel

External quality control schemes are an essential part of the quality assurance of all diagnostic virology laboratories. There are a few providers of nucleic acid detection quality control panels. Consequently, diagnostic laboratories may test panels that are developed specifically for virus isolation by nucleic acid detection methods. Here, we report on a recent simulated eye swab panel from a National external quality assessment service, which was meant for virus isolation but which we tested by polymerase chain reactions assays. The results suggest that the samples had been contaminated at source leading to difficulty in interpretation of the panel and a poor score.

Infection-associated encephalopathies: their investigation, diagnosis, and treatment

Reduced level of consciousness is a common clinical finding in acutely sick patients. In the majority of cases a cause for the encephalopathy is readily identifiable,whilst in a minority the aetiology is more difficult to ascertain. Frequently the onset of encephalopathy is associated with, or follows, infection. The mechanisms through which infection leads to encephalopathy are diverse. They range from direct microbial invasion of the brain or its supporting structures, to remote, infection-triggered mechanisms such as acute disseminated encephalomyelitis. Most common however, is the encephalopathy caused through a remote effect of systemic sepsis-septic encephalopathy. This article discusses the clinical presentation and underlying pathogeneses of the acute encephalopathies associated with infection, aiming to aid both their recognition and treatment.

Infectious pathogen detection arrays: viral detection in cell lines and postmortem brain tissue

A unique array-based pathogen chip has been developed for the detection of viral RNA or DNA relevant to pathologies of the central nervous system. A total of 715 unique oligonucleotides (60-mer) representing approximately 100 pathogens were designed based on open reading frames (ORFs) from highly conserved and heterogenic regions within viral families. In addition, viral genes reflecting different stages of pathogen infection were also included to potentially define the stage of the viral infection. Viruses (double-stranded DNA, double- or single-stranded RNA, delta, retroid), parasites, and bacteria were included. Test samples labeled with Cy5 were examined by cohybridization with a reference RNA, labeled with Cy3, to the pathogen microarray chip. Good reproducibility of experiments was observed, based on data generated from duplicate hybridizations and duplicate spots on the microarray platform. A viral transcript detection sensitivity of 1 x 10(3) plaque-forming units (pfus) was achieved using selected cell lines and viruses. These findings suggest that the array-based platform described here is capable of detecting a broad spectrum of viruses in a single assay with relatively high sensitivity, specificity, and reproducibility. This method may be used to provide evidence of viral infection in postmortem tissue from psychiatric patients as well as a wide range of other diagnostic categories.

Results of the first World Health Organization international collaborative study of detection of human papillomavirus DNA

Twenty-nine laboratories in 12 countries participated in a study to assess the performance of various human papillomavirus (HPV) detection assays through the use of a recombinant HPV DNA standard reagent panel. The panel was designed by a group of HPV experts, and samples were prepared and distributed by the World Health Organization International Laboratory for Standards and Biologicals in The Netherlands. Each panel consisted of 24 coded samples including a dilution series for HPV types 16 and 18, alone or in combination with five other high-risk (HR) HPV types including HPV types 31, 33, 35, 45, and 52, the low-risk HPV type 6, and a negative control. Qualitative assays were generally consistent across laboratories, and most invalid results reflected a lack of HPV test sensitivity. The combined data sets had a proficiency for HPV 16 of 62.5% (15/24) and for HPV 18 of 73.9% (17/23). HPV 31 was the least accurately detected by participating laboratories. Approximately half of participating laboratories failed to detect high concentrations of HPV 31 and, to a lesser extent, to detect HPV types 35, 52, and 6. The panel sample materials offer a source of renewable and reproducible material that could be used in the future development of international standard reagents for calibration of HPV DNA assays and kits.

Polymerase chain reaction and Goldmann-Witmer coefficient analysis are complimentary for the diagnosis of infectious uveitis

PURPOSE

To determine the relative contribution of the analysis of intraocular antibody production and the polymerase chain reaction (PCR) in aqueous humor (AH) to the diagnosis of infectious uveitis.

DESIGN

Retrospective case-control study.

METHODS

Paired AH and serum samples from 230 patients suspected of infectious uveitis were examined for intraocular antibody production against herpes simplex virus (HSV), varicella zoster virus (VZV), and Toxoplasma gondii by calculating the Goldmann-Witmer coefficient (GWC). In addition, AH samples were investigated by real-time PCR to determine the presence of microbial DNA.

RESULTS

Positive results were obtained in 54 cases (23%): 13 HSV (24%), 16 VZV (30%), and 25 T gondii (46%). Of these, 23 (43%) were positive for both GWC and PCR, 26 (48%) only for GWC, and 5 (9%) only for PCR. With PCR as the sole diagnostic approach, a correct diagnosis of the infectious etiology would have been missed in 34% of cases for the herpes viruses and in 64% for T gondii. Analysis of the relationship between a positive laboratory diagnosis and the time of sampling after onset of ocular disease demonstrated that intraocular antibody production was found throughout the course of the diseases. Viral DNA was more readily detected early in infection. In contrast, T gondii nucleic acid was not detected until 3 weeks after onset of ocular disease.

CONCLUSIONS

Analysis of intraocular antibody production contributed considerably to the etiological diagnosis of infectious uveitis, most notably of ocular toxoplasmosis early after onset of disease. Therefore, both PCR and GWC determination might be performed for comprehensive diagnosis of intraocular infections.

Stability of lyophilised specimens for the molecular detection of viral DNA/RNA

BACKGROUND

The range of nucleic acid-based technologies for the molecular detection of pathogens has grown rapidly in recent years. The influx of new testing methods into the clinical laboratory, demands for evaluation and standardisation of methods, interpretation of results and evaluation of laboratory performance have highlighted the need for internal and External Quality Assessment (EQA) systems more than ever before. External Quality Assessment panels demand reproducible, stable specimens of consistent form, suitable for transportation.

OBJECTIVES

To determine the stability of freeze-dried viral specimens in terms of molecular detection.

STUDY DESIGN

When EQA specimens are prepared, they undergo long-term storage and testing as part of the quality control (QC) process. The frequency and nature of testing is dependent on the resources and methodologies available at the time. A range of virus preparations used for EQA was monitored over a period of months to years in a retrospective study; the available quality monitoring data for the five viruses, including storage temperature and method of detection were analysed.

RESULTS

The nucleic acid (DNA or RNA) of the freeze-dried viruses included in the study was readily detectable over a long period of time. Quantitative analysis indicated that detectable concentrations of nucleic acid post-freeze drying were similarly maintained. Storage temperature was an important factor in the stability of HCV, but other viruses were unaffected by storage at different temperatures.

CONCLUSIONS

In summary, the molecular detection of nucleic acid (DNA or RNA) in freeze-dried specimens of HSV1, HSV2, HBV, HCV and HIV is possible even after prolonged storage, in some cases at a range of temperatures. Freeze drying allows large-scale production of viral specimens of high quality for EQA, which are stable in varying storage and shipment conditions. Furthermore, detection of each virus was possible with a range of commonly used molecular diagnostic methods.

Infectious Complications of Cancer Therapy

Advances in the management of cancer, particularly the development of new chemotherapeutic agents, have greatly improved the survival and outcome of patients with hematologic malignancies and solid tumors; overall 5-year survival rates in cancer patients have improved from 39% in the 1960s to 60% in the 1990s.1 However, infection, caused by both the underlying malignancy and cancer chemotherapy, particularly myelosuppressive chemotherapy, remains a persistent challenge.

Reduced PCR sensitivity due to impaired DNA recovery with the MagNA Pure LC total nucleic acid isolation kit

The increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. In the present study, we evaluated the performance of the MagNA Pure LC total nucleic acid isolation kit (M extraction) in comparison with the manual method (Si extraction) according to Boom et al. (R. Boom, C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990) for the detection of viral DNA by competitive quantitative PCR. Reconstruction experiments with HindIII-digested phage lambda DNA and HaeIII-digested phiX174 DNA showed that the recovery of DNA from phosphate-buffered saline, cerebrospinal fluid, EDTA-anticoagulated plasma, and EDTA-anticoagulated whole blood by M extraction is, on average, 6.6-fold lower compared to Si extraction. PCR signals of spiked PCR control DNAs for Epstein-Barr virus and varicella-zoster virus were also between 1.9- and 14.2-fold lower after M extraction compared to Si extraction, also suggesting impaired DNA recovery. M extraction of spiked cytomegalovirus strain AD 169 in whole blood showed a 5- to 10-fold reduction in PCR sensitivity compared to Si extraction. This reduction of PCR sensitivity was also observed when clinical whole blood samples were processed by M extraction. Before implementing M extraction, the clinical consequences of the reduced recovery should first be considered, especially when maximal sensitivity is required.

Incidence and pathogenesis of clinical relapse after herpes simplex encephalitis in adults

OBJECTIVES

To study the occurrence of relapse of herpes simplex encephalitis (HSE) and to find out whether soluble activity markers in cerebrospinal fluid (CSF) indicate direct viral or immune- mediated events.

METHODS

A consecutive series of 32 adult survivors of HSE were followed to determine the incidence of clinical relapse of HSE. Four patients had neurological deterioration interpreted as relapsing HSE. Four non-relapsing HSE cases were selected as matched controls. Fifty nine batched, paired CSF and serum samples from the eight HSE patients were analysed for soluble activity markers, predominantly cytokines and mediators (interferon-gamma, soluble CD8, tumour necrosis factor-alpha, and interleukin-10), amount of HSV-DNA and markers of glial and neuronal destruction (neurofilament protein, glial fibrillary acidic protein, S-100-beta, and neuron specific enolase).

RESULTS

Relapse of HSE was diagnosed in 3 of 26 (12 %) acyclovir-treated patients (5 episodes during 6.1 years of followup) and in 1 of 6 vidarabine-recipients. All relapses occurred from 1 to 4 months after acute HSE, except for a second relapse after 3.3 years in one patient. Computer tomography at relapses revealed few abnormalities apart from those found during the primary disease. Intravenous acyclovir and corticosteroids were given for 7-21 days in all the relapse patients. All relapse patients seemed to recover to the pre-relapse condition. HSV-DNA was demonstrated in CSF in all patients during the acute stage but not in any of 13 CSF samples taken during relapse phases. The HSV viral load during the acute stage of HSE was not higher or of longer duration in the relapsing patients than in the non-relapsing HSE controls. The levels of sCD8 were increased in nearly all CSF samples tested with peaks of sCD8 at one month of acute HSE. In all episodes of relapse, sCD8 peaks were detected during the first week at high levels. CSF levels of neuron-specific enolase, S-100 and glial fibrillary acidic protein were markedly lower at relapse than at the acute stage of HSV-1 encephalitis.

CONCLUSION

The lack of demonstrable HSV DNA in CSF, the lack of acute CSF signs and the lack of signs of neural and glia cells destruction indicate that a direct viral cytotoxicity is not the major pathogenic mechanism in relapse. Instead, the pronounced CSF proinflammatory immunological response and the relative lack of CSF anti-inflammatory cytokine IL-10 response suggest immunologically-mediated pathogenicity.

A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses

Objectives

To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories.

Study design

Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected.

Results

All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory.

Conclusions

The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics.

Factors influencing PCR detection of viruses in cerebrospinal fluid of patients with suspected CNS infections

BACKGROUND

Polymerase chain reaction (PCR) is used to detect viruses in the cerebrospinal fluid (CSF) of patients with neurological disease. However, data to assist its use or interpretation are limited.

OBJECTIVE

We investigated factors possibly influencing viral detection in CSF by PCR, which will also help clinicians interpret positive and negative results.

METHODS

CSF from patients with was tested for human herpesviruses types 1-6, JC virus, enteroviruses, and Toxoplasma gondii. The likelihood of central nervous system (CNS) infection was classified as likely, possible, or unlikely. PCR findings in these categories were compared using single variable and logistic regression analysis.

RESULTS

Of 787 samples tested, 97 (12%) were PCR positive for one or more viruses. Of episodes likely to be CNS viral infections, 30% were PCR positive compared to 5% categorised as unlikely. The most frequent positive findings were Epstein Barr virus (EBV), enteroviruses, and herpes simplex virus (HSV). Enteroviruses and HSV were found predominantly in the likely CNS viral infection group, whereas EBV was found mainly in the unlikely group. Positive PCR results were more likely when there were 3-14 days between symptom onset and lumbar puncture, and when CSF white cell count was abnormal, although a normal CSF did not exclude a viral infection.

CONCLUSIONS

The diagnostic yield of PCR can be maximised by using sensitive assays to detect a range of pathogens in appropriately timed CSF samples. PCR results, in particular EBV, should be interpreted cautiously when symptoms cannot readily be attributed to the virus detected.