Evaluation of real-time PCR versus PCR with liquid-phase hybridization for detection of enterovirus RNA in cerebrospinal fluid

A Longitudinal Study on Enteric Virus Contamination in Bivalves along the Coast of Ibaraki Prefecture, Japan

ABSTRACT

During the 2014 to 2018 seasons, we conducted a longitudinal study involving enteric virus surveillance in bivalves, including natural oysters and clams harvested in Ibaraki Prefecture, Japan. Some norovirus (NoV) contaminations were detected in natural oysters, whereas no enteric virus was found in clams. NoVs detected in oysters were of the genotypes GII.4 and GII.6, both of which are closely related genetically to the NoV strains prevalent in humans. We found low level of enteric virus contamination in bivalves collected along the coast of Ibaraki Prefecture. The possibility of food poisoning caused by these viruses appears low, and few cases of infectious disease have been observed in the surrounding area. The harvest timing was more related to contamination quantity than the harvest area in many enteric viruses. Our results highlight that contamination of bivalves by enteric viruses may depend upon the prevalence of human diarrhea and illness.

HIGHLIGHTS

Digital PCR—An Emerging Technology with Broad Applications in Microbiology

BACKGROUND

The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.

CONTENT

Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.

SUMMARY

dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

Syndrome Evaluation System for Simultaneous Detection of Pathogens Causing Acute Encephalitic Syndrome in India, Part-2: Validation Using Well Characterized Clinical Samples

Diagnosis of the aetiological agent in case of acute encephalitic syndrome (AES) continues to pose a challenge in clinical practice as a variety of pathogens are known to cause AES. Here, we report the validation of a Syndrome Evaluation System (SES) developed for simultaneous detection of multiple AES pathogens using a well characterized set of Cerebrospinal fluid (CSF) samples. The validation of the SES was carried out in two phases. In the first phase, the SES was validated using 51 CSF samples obtained from autopsy proven cases and 50 samples obtained from apparently healthy individuals undergoing spinal anesthesia for minor surgeries served as "controls." The SES detected etilogical agent in 48/51 (94.11 %) samples obtained from autopsy proven AES cases while all the 50 CSF samples obtained from "controls" were negative. In the second phase, the SES was validated using well characterized CSF samples obtained from AES patients fulfilling the WHO case definition of AES (Group I; n = 207) and samples that were collected from patients with non-infectious neurological disorder (Group II; n = 90). All the samples were tested using multiple conventional/serological assays and categorized into various groups. Amongst the AES cases fulfilling WHO case definition, the SES detected AES pathogens in 160/207 (77.29%) cases while conventional serological/molecular assays were able to detect AES pathogens only in 77/207 (37.1%) of cases. Further, in 12/83 CSF samples that were positive by SES and negative by conventional serological/molecular tests, the results were additionally confirmed by sequencing the PCR products to rule out non-specific amplification in the SES. In patients with non-infectious neurological disorders the SES detected latent viruses 12/90 CSF samples. These results indicate that the SES, apart being a rapid, sensitive, specific, and cost-effective method provides the major advantage of simultaneous detection of multiple pathogens using as single specimen of CSF.

Enteroviruses and Parechoviruses

Infections with enteroviruses and human parechoviruses are highly prevalent, particularly in neonates, where they may cause substantial morbidity and mortality. Individuals with B-cell-related immunodeficiencies are at risk for severe enteroviral infections, usually a chronic and fatal meningoencephalitis. In transplant recipients and patients with malignancy, enterovirus infections typically involve the respiratory tract, but cases of severe, disseminated infection have been described. The mainstay of diagnosis for enterovirus and human parechovirus infections involves the use of molecular diagnostic techniques. However, routine nucleic acid-detection methods for enteroviruses will not detect human parechoviruses. Laboratory diagnosis of these viral infections is important in determining a patient's prognosis and guiding clinical management.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

Human parechovirus infection in neonatal intensive care

BACKGROUND

Approximately 5-6% of all infective episodes in neonatal intensive care unit (NICU) are of viral origin. Previous studies suggest that human parechovirus (HPeV) infection presents most commonly in term infants, as a sepsis-like syndrome in which meningoencephalitis is prominent. Our aim was to study the infection rate and associated features of HPeV.

METHODS

Blood samples were taken from NICU babies older than 48 hours, who were being investigated for late onset sepsis. Clinical and laboratory data were collected at the time of the suspected sepsis episode. Samples were tested using universal primers and probe directed at the 5'-untranslated region of the HPeV genome by reverse transcriptase polymerase chain reaction (RT-PCR). Results were confirmed by electrophoresis and DNA sequencing.

RESULTS

HPeV was detected in 11 of 84 samples (13%). These infants had a mean [interquartile range (IQR)] gestational age of 28.9 (26.9-30.6) weeks and mean birth weight of 1.26 (SD = 0.72) kg. The median day of presentation was 16 (IQR: 11-27). These characteristics were similar to the infants without positive viral detection. Six infants presented with respiratory signs. One infant presented with signs of meningitis. Six of the 11 episodes of HPeV infection occurred during the winter months (December to February). No HPeV positive infants had abnormal findings on their 28-day cranial ultrasound examination.

CONCLUSIONS

We found an HPeV infection rate of 13% in infants being tested for late onset sepsis. HPeV should be considered as a possible cause of sepsis-like symptoms in preterm infants.

Design and validation of a real-time RT-PCR for the simultaneous detection of enteroviruses and parechoviruses in clinical samples

Human enteroviruses (EVs) and parechoviruses (HPeVs) are important etiological agents causing infections such as meningitis, encephalitis and sepsis-like disease in neonates and young children. We have developed a real-time RT-PCR for simultaneous detection of EV and HPeV in clinical samples. Primers and probe sets were designed from the conserved 5'-noncoding region of the genomes. The sensitivity, specificity and reproducibility of the technique were measured using a set of 25 EV and 6 HPeV types. All EVs but no HPeVs were detected with the EV primers-probe set. The HPeV primers-probe set detected only the 6 HPeV types. The lower detection limit was found to be 4 and 40CCID50/ml for HPeV and EV respectively, demonstrating high sensitivity of the technique for both viruses. The threshold cycle values were highly reproducible on repeat testing of positive controls among assay runs. The assay was evaluated in 53 clinical samples of suspected meningitis, sepsis or febrile syndromes from children under 3 years. In 11 of these (21%) EVs were detected, while 4, i.e. 7.5%, were HPeV positive. Molecular typing was carried out for 73% of the viruses. In summary, the RT-PCR method developed demonstrated effectively both EV and HPeV detection, which can cause similar clinical symptoms in infants.

Viral diagnostics in the era of digital polymerase chain reaction

Unlike quantitative polymerase chain reaction (qPCR), digital PCR (dPCR) achieves sensitive and accurate absolute quantitation of a DNA sample without the need for a standard curve. A single PCR reaction is divided into many separate reactions that each have a positive or negative signal. By applying Poisson statistics, the number of DNA molecules in the original sample is directly calculated from the number of positive and negative reactions. The recent availability of multiple commercial dPCR platforms has led to increased interest in clinical diagnostic applications, such as low viral load detection and low abundance mutant detection, where dPCR could be superior to traditional qPCR. Here we review current literature that demonstrates dPCR's potential utility in viral diagnostics, particularly through absolute quantification of target DNA sequences and rare mutant allele detection.

Detecting respiratory viruses in asymptomatic children

BACKGROUND

Viral respiratory infections are among the most common reasons for hospitalization of children in the United States. Our objective was to compare molecular and conventional methods in a cohort of hospitalized children with and without symptoms of respiratory viral illness (RVI).

METHODS

We conducted a retrospective cohort study of infants and toddlers hospitalized between December 2007 and March 2008 at Johns Hopkins Hospital. Five hundred sixty-nine of 641 patient visits (89%) were tested on admission. Conventional tests (immunochromatography, direct fluorescent antibody, shell vial and tube culture) were performed on all patients and nucleic acid tests (NATs) were performed on available samples (n = 306). Viruses were grouped into those routinely (group 1) and those not routinely (group 2) detected by conventional methods.

RESULTS

In children with RVI symptoms (n = 148), NATs identified a virus in 83% of specimens compared with 49% by conventional methods (P < 0.001), but detected a similar percentage of specimens with group 1 viruses (48.6% and 55.4%; P = 0.13) compared with conventional tests. In children without RVI symptoms (n = 158), NATs identified a virus in 41.7% of specimens compared with 4.4% by conventional tests (P < 0.001) and identified more group 1 viruses (9.5% and 4.4%; P = 0.03) compared with conventional tests. Group 2 viruses were identified by NATs in a similar percentage of symptomatic and asymptomatic patients (25% and 32.3%; P = 0.20).

CONCLUSIONS

Molecular assays may have several advantages over conventional methods for detecting respiratory viruses, including improved sensitivity and rapid detection, but given the high prevalence of positive results in children without RVI symptoms, results should be interpreted cautiously.

Optimization of a combined human parechovirus-enterovirus real-time reverse transcription-PCR assay and evaluation of a new parechovirus 3-specific assay for cerebrospinal fluid specimen testing

Human parechoviruses (HPeVs), particularly type 3 (HPeV3), are known central nervous system (CNS) pathogens, causing serious infections in infants similar to those caused by enteroviruses (EVs). The primary aim of this study was to combine and validate HPeV and EV real-time reverse transcription-PCR (RT-PCR) detection assays with the best available RT-PCR reagents and conditions for parallel detection of HPeV and EV on a single platform. The secondary aim was to develop and validate a newly developed HPeV3-specific real-time RT-PCR assay. Five commercially available RT-PCR kits were evaluated with the pan-HPeV and EV assays in one-step and two-step RT-PCRs. Two-step RT-PCR with the AgPath ID RT-PCR (AGP) kit performed best for both pan-HPeV and EV assays. The pan-HPeV-specific assay performed best with the AGP kit in a one-step RT-PCR. Frozen aliquots of 145 (for HPeV, n = 70; for EV, n = 75) previously characterized cerebrospinal fluid (CSF) specimens were tested by EV-, pan-HPeV-, and HPeV3-specific (HPeV specimens only) assays. The pan-HPeV and EV assays demonstrated 100% analytical sensitivity and specificity compared to historic results, while the HPeV3-specific assay demonstrated 97% sensitivity and 100% specificity. We propose a real-time pan-HPeV, EV two-step RT-PCR algorithm for simultaneous detection of HPeV and EV from CSF specimens on a single platform. The HPeV3-specific one-step RT-PCR assay can be used as a rapid and cost-effective assay to detect and identify HPeV3 in pan-HPeV RT-PCR assay-positive CSF specimens.

Viral diagnostics in the era of digital polymerase chain reaction

Unlike quantitative polymerase chain reaction (qPCR), digital PCR (dPCR) achieves sensitive and accurate absolute quantitation of a DNA sample without the need for a standard curve. A single PCR reaction is divided into many separate reactions that each have a positive or negative signal. By applying Poisson statistics, the number of DNA molecules in the original sample is directly calculated from the number of positive and negative reactions. The recent availability of multiple commercial dPCR platforms has led to increased interest in clinical diagnostic applications, such as low viral load detection and low abundance mutant detection, where dPCR could be superior to traditional qPCR. Here we review current literature that demonstrates dPCR's potential utility in viral diagnostics, particularly through absolute quantification of target DNA sequences and rare mutant allele detection.

Diagnostic performance of two highly multiplexed respiratory virus assays in a pediatric cohort

Background

Rapid detection of respiratory viruses is important for management and infection control in hospitalized patients. Multiplex nucleic acid tests (NATs) have begun to replace conventional methods as gold standards for respiratory virus detection.

Objective

To compare the performance of two large multiplex NATS, ResPlex II (RPII) and Respiratory Virus Surveillance kit with electrospray ionization mass spectrometry (RVS/MS) using nasopharyngeal aspirates (NPAs) from hospitalized children who had been tested previously with conventional methods.

Study design

Stored residual NPAs (N = 306) were tested concomitantly by RPII and RVS/MS. Alternate NATs were used to adjudicate discordant results.

Results

More viruses were detected with multiplex NATs (RPII, 110; RVS/MS, 109) than conventional assays (86); diagnostic gain was primarily for fastidious viruses (coronaviruses and enteroviruses [EVs]/human rhinoviruses [HRVs]). Total positive and negative agreement between the multiplex NATs for all viruses detected was quite high (86% positive agreement, 99% negative agreement). Most individual viruses were detected with fairly equivalent accuracy by the multiplex NATs, except for adenoviruses (RPII sensitivity 40%) and human metapneumovirus (RVS/MS sensitivity 42%). RPII had the advantage of detecting EVs and HRVs, however, it demonstrated considerable EV/HRV cross-reactivity (29 HRV-positive specimens by real-time PCR were positive for EV by RPII and 21 specimens positive for HRV only by RT-PCR were dual positive for EV/HRV by RPII). RPII also had reduced sensitivity for HRV detection (in 36 specimens, HRV was detected by RT-PCR but not by RPII).

Conclusions

Both multiplex NATs were promising, but had notable limitations.

An open-label phase I trial of a live attenuated H2N2 influenza virus vaccine in healthy adults

Please cite this paper as: Talaat et al. (2012) An open‐label phase I trial of a live attenuated H2N2 influenza virus vaccine in healthy adults. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750‐2659.2012.00350.x.

Background  Live attenuated influenza vaccines (LAIV) against a variety of strains of pandemic potential are being developed and tested. We describe the results of an open‐label phase I trial of a live attenuated H2N2 virus vaccine.

Objectives  To evaluate the safety, infectivity, and immunogenicity of a live attenuated H2N2 influenza virus vaccine.

Participants/methods  The A/Ann Arbor/6/60 (H2N2) virus used in this study is the attenuated, cold‐adapted, temperature‐sensitive strain that provides the genetic backbone of seasonal LAIV (MedImmune). We evaluated the safety, infectivity, and immunogenicity of two doses of 10⁷ TCID₅₀ of this vaccine administered by nasal spray 4 weeks apart to normal healthy seronegative adults.

Results  Twenty‐one participants received a first dose of the vaccine; 18 participants received a second dose. No serious adverse events occurred during the trial. The most common adverse events after vaccination were headache and musculoskeletal pain. The vaccine was restricted in replication: 24% and 17% had virus detectable by culture or rRT‐PCR after the first and second dose, respectively. Antibody responses to the vaccine were also restricted: 24% of participants developed an antibody response as measured by either hemagglutination‐inhibition assay (10%), or ELISA for H2 HA‐specific serum IgG (24%) or IgA (16%) after either one or two doses. None of the participants had a neutralizing antibody response. Vaccine‐specific IgG‐secreting cells as measured by enzyme‐linked immunospot increased from a mean of 0·5 to 2·0/10⁶ peripheral blood mononuclear cells (PBMCs); vaccine‐specific IgA‐secreting cells increased from 0·1 to 0·5/10⁶ PBMCs.

Conclusions  The live attenuated H2N2 1960 AA ca vaccine demonstrated a safety profile consistent with seasonal trivalent LAIV but was restricted in replication and minimally immunogenic in healthy seronegative adults.

Rapid simultaneous detection of enterovirus and parechovirus RNAs in clinical samples by one-step real-time reverse transcription-PCR assay

Enteroviruses (EVs) are recognized as the major etiological agent in meningitis in children and young adults. The use of molecular techniques, such as PCR, has substantially improved the sensitivity of enterovirus detection compared to that of virus culture methods. PCR-based methods also can detect a much wider range of EV variants, including those within species A, as well as human parechoviruses (HPeVs) that often grow poorly in vitro and which previously have been underdiagnosed by traditional methods. To exploit these developments, we developed a real-time one-step reverse transcription-PCR (RT-PCR) for the rapid and sensitive detection of EV and HPeV in clinical specimens. Two commercially available RT-PCR kits were used (method I, Platinum one-step kit; method II, Express qPCR one-step kit) with primers and probes targeting the EV and HPeV 5'-untranslated regions (5'UTR). Amplification dynamics (threshold cycle [C(T)]values and efficiencies) of absolutely quantified full-length RNA transcripts representative of EV species A to D and HPeV were similar, demonstrating the effectiveness of both assays across the range of currently described human EV and HPeV variants. Probit analysis of multiple endpoint replicates demonstrated comparable sensitivities of the assays for EV and HPeV (method I, approximately 10 copies per reaction for both targets; method II, 20 copies per reaction). C(T) values were highly reproducible on repeat testing of positive controls within assays and between assay runs. Considering the sample turnaround time of less than 3 h, the multiplexed one-step RT-PCR method provides rapid diagnostic testing for EV and HPeV in cases of suspected central nervous system infections in a clinically relevant time frame.

An open label Phase I trial of a live attenuated H6N1 influenza virus vaccine in healthy adults

BACKGROUND

We describe the results of an open label Phase I trial of a live attenuated H6N1 influenza virus vaccine (ClinicalTrials.gov Identifier: NCT00734175).

METHODS AND FINDINGS

We evaluated the safety, infectivity, and immunogenicity of two doses of 10(7) TCID(50) of the H6N1 Teal HK 97/AA ca vaccine, a cold-adapted and temperature sensitive live, attenuated influenza vaccine (LAIV) in healthy seronegative adults. Twenty-two participants received the first dose of the vaccine, and 18 received the second dose of vaccine 4 weeks later. The vaccine had a safety profile similar to that of other investigational LAIVs bearing avian hemagglutinin (HA) and neuraminidase (NA) genes. The vaccine was highly restricted in replication: two participants had virus detectable by rRT-PCR beyond day 1 after each dose. Antibody responses to the vaccine were also restricted: 43% of participants developed a serum antibody response as measured by any assay: 5% by hemagglutination-inhibition assay, 5% by microneutralization assay, 29% by ELISA for H6 HA-specific IgG and 24% by ELISA for H6 HA specific IgA after either 1 or 2 doses. Following the second dose, vaccine specific IgG and IgA secreting cells as measured by ELISPOT increased from a mean of 0.6 to 9.2/10(6) PBMCs and from 0.2 to 2.2/10(6) PBMCs, respectively.

CONCLUSION

The H6N1 LAIV had a safety profile similar to that of LAIV bearing other HA and NA genes, but was highly restricted in replication in healthy seronegative adults. The H6N1 LAIV was also not as immunogenic as the seasonal LAIV.

Assessment of mitochondrial toxicity by analysis of mitochondrial protein expression in mononuclear cells

BACKGROUND

Real-time PCR has quantified decreased mitochondrial DNA levels in association with nucleoside reverse transcriptase inhibitor (NRTI) therapy of HIV-infected populations. However, real-time PCR is best suited to distinguish log differences in an analyte. In an effort to monitor individuals in more detail, we developed a flow cytometric assay to gauge mitochondrial function.

METHODS

Flow cytometric quantification of a mitochondrial DNA-encoded mitochondrial protein (cytochrome c oxidase subunit I (COX-I)) and a nuclear DNA-encoded mitochondrial protein [ATP synthase subunit D (Sub-D)] was optimized and validated.

RESULTS

Intra-assay and interassay variability was low using peripheral blood mononuclear cells (PBMCs) (CV of 6.15% for COX-I and 7.11% Sub-D, and 9.38% and 9.83% for COX-I and Sub-D, respectively). Mitochondrial protein depletion was evident with in vitro treatment of cells with ethidium bromide (EtBr) and zalcitabine (ddC). Mitochondrial protein expression in 40 healthy adults clustered tightly. Depletion of mitochondrial protein, however, was neither detected in cryopreserved PBMC from NRTI-treated children (n = 9) nor in adults with a history of symptoms consistent with mitochondrial toxicity or ongoing treatment with didanosine (ddI) or stavudine (d4T) (n = 51).

CONCLUSIONS

A validated flow cytometric assay allows simultaneous detection of mitochondrial DNA and nuclear DNA encoded proteins at the single cell level, offering a method to monitor for mitochondrial function. Prospective studies are required to evaluate whether mitochondrial protein loss is observed in at-risk patients prior to the onset of symptoms from mitochondrial dysfunction.

Development and implementation of a molecular diagnostic platform for daily rapid detection of 15 respiratory viruses

Acute respiratory tract infections are caused by a large number of viruses. Diagnostic methods have until recently been available only for a limited number of these viruses. With the objective to achieve sensitive assays for all respiratory viruses, a rational workflow in the laboratory, and a short turn-around time, a real-time PCR diagnostic platform for daily rapid detection of 15 respiratory viruses was developed. The system was evaluated on 585 stored nasopharyngeal aspirates from hospitalized children. Previous analysis by immunofluorescence and virus isolation identified viruses in 37% of the samples while the new PCR diagnostic panel detected 57% virus positive samples. The new platform was introduced in the laboratory in October 2007 and has then fully replaced the standard immunofluorescence assay for rapid detection of viruses and virus isolation.

Detection of respiratory viruses by molecular methods

SUMMARY

Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.

An enterovirus epidemic in infants in the summer and fall of 2006

The aim of this study was to evaluate the diagnostic procedures in infants presenting with febrile illness in the summer and fall of 2006. Infants younger than 90 days presenting with febrile illness were included. A sepsis evaluation was performed. Stool and/or cerebrospinal fluid were tested for enterovirus (polymerase chain reaction [PCR]). Twenty-four infants were included, with a median age of 36 days (range 5-87). Nineteen infants (79%) were diagnosed with enterovirus infection. In nine infants, both stool and cerebrospinal fluid were tested for enterovirus; both specimens were positive in three infants. In seven infants, only the stool and in three infants, only the cerebrospinal fluid was tested. The five infants without enterovirus infection were only partly tested; in four infants, only the stool and in one infant, only the cerebrospinal fluid was tested. Three infants (13%) were diagnosed with a urinary tract infection, one of which tested positive for enterovirus as well. Twenty-three infants received antibiotic treatment. The median duration of antibiotic treatment of infants without bacterial infection was 3.2 days. Thorough diagnostic evaluation for enterovirus in different specimens is important, as, often, only one specimen is positive for enterovirus. When enterovirus is diagnosed, patient management may be influenced.

Development of multiplexed real-time quantitative polymerase chain reaction assay for detecting human adenoviruses

Adenoviruses (AdVs) have been associated with a wide variety of human disease and are increasingly recognized as viral pathogens that can cause significant morbidity and mortality in immunocompromised patients. Early detection of AdV DNA in plasma and sterile fluids has been shown to be useful for identifying patients at risk for invasive AdV disease. Because of the large number of existing Adv types, few real-time quantitative AdV polymerase chain reaction (PCR) assays published effectively cover all AdV types. We designed a series of AdV PCR primers and probes and empirically multiplexed them into 2 separate real-time PCR assays to quantitatively detect all 49 serotypes of human AdV (types 1-49) available from American Type Culture Collection. We then subsequently multiplexed all the primers and probes into 1 reaction. The sensitivity of these assays was determined to be less than 10 copies per reaction (500 copies/mL plasma). In a retrospective evaluation, we detected all 84 clinical AdV isolates isolated in cell culture from patients undergoing hematopoietic stem cell transplantation between 1981 and 1987. Prospective analysis of 46 consecutive clinical samples submitted for AdV testing showed greater sensitivity and equal specificity of the AdV PCR than viral culture. This real-time PCR assay allows rapid, sensitive, and specific quantification of all currently defined AdVs into either 2 or 1 multiplex assay for clinical samples.

Performance of the GeneXpert enterovirus assay for detection of enteroviral RNA in cerebrospinal fluid

BACKGROUND

The GeneXpert Dx System allows for automated extraction, processing, amplification and real-time detection of target nucleic acids.

OBJECTIVES

To evaluate the performance of the Cepheid Xpert enterovirus (EV) assay for detection of EV RNA compared to a nucleic acid sequence based amplification (NASBA) assay and a user-developed TaqMan RT-PCR assay.

STUDY DESIGN

Assays were evaluated using a 12-member proficiency panel and up to 138 CSF specimens. Samples in which EV RNA was detected by two or more assays were considered true positives.

RESULTS

The GeneXpert, NASBA, and TaqMan assays correctly identified 10, 8, and 7 of 12 proficiency panel members, respectively. For detection of EV RNA in CSF, the sensitivities of the GeneXpert, NASBA, and TaqMan were 100%, 87.5%, and 96%, respectively. There were no false positives. Two samples tested by GeneXpert and NASBA yielded indeterminate or invalid results and could not be resolved.

CONCLUSIONS

The Xpert EV assay is a sensitive and specific method for detection of EV RNA in CSF specimens. The ease of use, random access capability, and minimal hands-on time with the automated GeneXpert system affords laboratories with little molecular diagnostics expertise an opportunity to complete a clinically useful testing within 2.5 h.

Rapid routine detection of enterovirus RNA in cerebrospinal fluid by a one-step real-time RT-PCR assay

BACKGROUND AND OBJECTIVES

This study provides a one-step transcription/real-time (TaqMan probe) PCR assay (TM-PCR) with new consensus primer and probe sequences for generic detection of human pathogenic enteroviruses including difficult to detect ones like for instance Echovirus 30. The amplicon included parts of domain IV and V of the highly conserved internal ribosomal entry site. Generic detection was confirmed by testing a panel of 41 prototypes representing all five human enterovirus/poliovirus species.

STUDY DESIGN AND RESULTS

The 95% detection limit was found to be 100 copies per run using in vitro transcribed coxsackievirus B3 RNA. TM-PCR was compared to an in house nested-PCR assay implemented in detecting enterovirus RNA from CSF samples of patients suffering from meningitis and encephalitis. Concordant results were obtained in all samples (11 positive, 101 negative). Specificity was confirmed with laboratory strains of other neurotropic viruses, and by testing 76 CSF samples of patients with encephalomyelitis disseminata, which all gave negative results.

CONCLUSIONS

The new TM-PCR is a convincing alternative to conventional PCR protocols for the diagnosis of enterovirus meningitis. The one-step strategy limits hands on time and cross contamination risk combined with accelerated assay procedure of only 100 min.

Enterovirus, cytomegalovirus, and Epstein-Barr virus infection screening in idiopathic sudden sensorineural hearing loss

Sudden sensorineural hearing loss (SSNHL) is frequently classified as 'idiopathic' since the causative factor is not identified in most cases. In the present study we determined whether SSNHL is associated with common viral infections, namely enterovirus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV). Between April 2004 and March 2005, we conducted a prospective cohort study on 48 unselected patients with unilateral idiopathic SSNHL. Plasma samples obtained at presentation were analyzed for the presence of enterovirus RNA by reverse-transcription polymerase chain reaction (RT-PCR). Recent occurrence of CMV and EBV infection was determined by serological tests. Among 23 men and 25 women aged 18-84 years (mean age 51.67 years), none presented with clinical symptoms of a viral infection compatible with preceding or concurrent viral infection. One patient (2.08%) had evidence of enterovirus infection by RT-PCR, 3 patients (6.25%) had EBV IgM, and none were positive for CMV IgM. The majority of SSNHL patients (91.67%) did not have evidence of any of the three common viral infections upon presentation. The present study failed to identify recent or concurrent systemic viral infections among SSNHL patients, except for a small proportion who demonstrated recent viral infection. Therefore the theory that viral infection is a factor in SSNHL pathogenesis is not supported by this study. Further studies in larger patient populations and different epidemiological settings are required in order to verify the true role of viral infections in SSNHL.

Multicenter beta trial of the GeneXpert enterovirus assay

The GeneXpert Dx system (Cepheid, Sunnyvale, CA) is a fully integrated and automated nucleic acid sample preparation, amplification, and real-time detection system. It consists of an instrument, a personal computer, and disposable fluidic cartridges. The analytical sensitivity and specificity of the GeneXpert enterovirus assay (GXEA) were determined with a panel of 63 different enterovirus serotypes and 24 other microorganisms, respectively. The potential for blood, hemoglobin, white blood cells, and excess protein to interfere with the assay was also assessed. The performance parameters of the GXEA were determined at three sites with 102 cerebrospinal fluid (CSF) samples obtained from patients with suspected meningitis. All samples were tested for enterovirus RNA with locally developed reverse transcription-PCR (RT-PCR) assays at the trial sites and with a seminested RT-PCR and an analyte-specific reagent (Cepheid) at a reference laboratory. The 5' nontranslated region was the target for all of the PCR assays except the seminested RT-PCR, which amplified a VP1 sequence. The VP1 amplicon was sequenced to identify the enterovirus types. Consensus reference laboratory RT-PCR results were used to classify cases of enteroviral meningitis. The GXEA detected all of the enterovirus serotypes and none of the other microorganisms tested except rhinovirus 16. The assay was unaffected by moderate amounts of blood or blood components. Thirty-six (35%) of the CSF samples tested had at least one positive PCR result. Eleven different enterovirus serotypes were identified in the positive samples. The GXEA had a sensitivity of 97.1% (95% confidence interval [CI], 84.7 to 99.9%) and a specificity of 100% (95% CI, 94.6 to 100%) for the diagnosis of enteroviral meningitis.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Comparative evaluation of three commercial systems for nucleic acid extraction from urine specimens

A nucleic acid extraction system that can handle small numbers of specimens with a short test turnaround time and short hands-on time is desirable for emergent testing. We performed a comparative validation on three systems: the MagNA Pure compact system (Compact), the NucliSens miniMAG extraction instrument (miniMAG), and the BioRobot EZ1 system (EZ1). A total of 75 urine specimens submitted for polyomavirus BK virus detection were used. The human beta-actin gene was detected on 75 (100%), 75 (100%), and 72 (96%) nucleic acid extracts prepared by the miniMAG, EZ1, and Compact, respectively. The miniMAG produced the highest quantity of nucleic acids and the best precision among the three systems. The agreement rate was 100% for BKV detection on nucleic acid extracts prepared by the three extraction systems. When a full panel of specimens was run, the hands-on time and test turnaround time were 105.7 and 121.1 min for miniMAG, 6.1 and 22.6 min for EZ1, and 7.4 and 33.7 min for Compact, respectively. The EZ1 and Compact systems processed automatic nucleic acid extraction properly, providing a good solution to the need for sporadic but emergent specimen detection. The miniMAG yielded the highest quantity of nucleic acids, suggesting that this system would be the best for specimens containing a low number of microorganisms of interest.

Development and evaluation of a real-time RT-PCR assay on the LightCycler for the rapid detection of enterovirus in cerebrospinal fluid specimens

BACKGROUND

Detection of enteroviral nucleic acid in cerebrospinal fluid (CSF) specimens has been demonstrated to improve the management of patients with aseptic meningitis.

OBJECTIVE

To develop on the LightCycler (LC) instrument a real-time RT-PCR assay based on TaqMan technology for the detection of enteroviruses (EV) in cerebrospinal fluid (CSF) specimens.

STUDY DESIGN

After evaluation of the analytical performances, seventy-four CSF samples collected prospectively from patients who have been suspected for a clinical diagnosis of meningitis were evaluated by two LC real-time RT-PCR assays and one conventional RT-PCR assay.

RESULTS

Our assay detected all 30 different EV species tested, whereas no reactivity was observed with other neurotropic viruses. The analytical sensitivity of both LC RT-PCR real-time assays was 1 TCID50 for LC one-step and two-step RT-PCR assays. Results for LC one-step and LC two-step RT-PCR were compared to results of the conventional RT-PCR: of the 74 CSF specimens tested, 11 were positive and 56 were negative by all methods. Four other specimens were positive for EV by at least two of the methods (including the LC two-step RT-PCR and the conventional RT-PCR), two other CSF specimens were positive by the LC two-step RT-PCR assay only, and another one CSF specimen was positive by the LC one-step RT-PCR assay only. No CSF specimens were negative by the LC two-step RT-PCR assay and positive by the conventional RT-PCR assay. The sensitivity, specificity, positive and negative predictive values of both LC RT-PCR assays by using conventional RT-PCR as the "gold standard" were, respectively, 73.3, 98.3, 91.7, 93.5% for the LC one-step RT-PCR and 100, 96.6, 88.2, 100% for the LC two-step RT-PCR. There was substantial agreement between the three assays (k=0.80).

CONCLUSIONS

The LC two-step RT-PCR assay is a rapid, sensitive and reliable method which can be routinely performed with CSF samples for diagnosis of EV infection and is an important improvement for optimal patient management.

Real-time nucleic acid sequence-based amplification using molecular beacons for detection of enterovirus RNA in clinical specimens

Real-time nucleic acid sequence-based amplification (NASBA) using molecular beacon technology (NASBA-beacon) was compared to standard NASBA with postamplification hybridization using electrochemiluminescently labeled probes (NASBA-ECL) for detection of enteroviruses (EV) in 133 cerebrospinal fluid and 27 stool samples. NASBA-ECL and NASBA-beacon were similar in sensitivity, detecting 55 (100%) and 52 (94.5%) EV-positive samples, respectively. There were no false positives. Both NASBA assays were significantly more sensitive than culture. Real-time NASBA-beacon reagents and equipment rental were more expensive than those for NASBA-ECL; however, time to result was shortened by 1.5 h, hands-on time was reduced by 25 min, and the assay was much simpler for technologists to learn and perform.

QIAamp MinElute virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs

Background

Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids.

Study design

A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits.

Results

There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein–Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2 h to 50–55 min.

Conclusions

Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory.

Detection of enterovirus RNA in cerebrospinal fluid (CSF) using NucliSens EasyQ Enterovirus assay

Rapid detection of enterovirus (EV) infections is essential in the management of aseptic meningitis. Molecular approaches have opened the way to such rapid, but also specific and sensitive, diagnostic tests. The aim of this study was to compare the performance of the CE marked NucliSens EasyQ Enterovirus assay with an in-house two-step RT-PCR assay using cerebrospinal fluid (CSF) and throat swab samples. In addition, specificity was tested with clinical isolates positive for viruses with clinical importance in CSF samples. For nucleic acid extraction, the NucliSens miniMAG and NucliSens magnetic extraction reagents were used. Subsequently real-time nucleic acid sequence-based amplification (NASBA) RNA amplification was performed using NucliSens EasyQ basic kit reagents and NucliSens EasyQ Enterovirus reagents. An EV-specific internal homologous control (IC) RNA was used to monitor the entire NucliSens EasyQ procedure at the individual sample level. No IC but an external inhibition control was available for the RT-PCR method. For the NucliSens EasyQ procedure, amplification and real-time detection reactions were carried out in the NucliSens EasyQ analyzer. The real-time NASBA enterovirus detection was based on NASBA amplification and real-time molecular beacon technology. Data were analyzed using the manufacturer's software on the NucliSens EasyQ analyzer. For the in-house assay, RT-PCR amplicons were detected using agarose gel analysis. The analysis of clinical samples positive for HSV-1, HSV-2, adenovirus, CMV, VZV, mumps and rhinovirus were all negative by NucliSens EasyQ Enterovirus assay. Three rhinovirus samples were, however, strongly positive in RT-PCR. A total of 141 clinical samples were retrospectively tested, including 126 cerebrospinal fluid (CSF) samples and 15 throat swabs. The 91 CSF samples were negative by both methods, 31 CSF samples and 14 throat swab samples were positive by both methods. The four CSF samples were positive by RT-PCR only. One throat swab sample was negative in NucliSens EasyQ but positive in RT-PCR. The sensitivity and specificity of both methods seem to be more or less comparable. However, the in-house RT-PCR assay appears to amplify some rhinovirus strains and should therefore not be used for throat swab samples. NucliSens EasyQ Enterovirus assay gave more invalid results than the in-house RT-PCR, which is obvious taken into account the difference in quality control between the CE marked NucliSens EasyQ Enterovirus assay and the in-house enterovirus assay. The NucliSens EasyQ procedure can be completed within 5h versus 9.5h for the RT-PCR. NucliSens EasyQ Enterovirus assay showed to be a standardized, rapid, specific, sensitive and reliable procedure for the detection of enterovirus RNA.

Real-time Fluorescent PCR Techniques to Study Microbial-Host Interactions

This chapter describes how real-time polymerase chain reaction (PCR) performs and how it may be used to detect microbial pathogens and the relationship they form with their host. Research and diagnostic microbiology laboratories contain a mix of traditional and leading-edge, in-house and commercial assays for the detection of microbes and the effects they impart upon target tissues, organs, and systems. The PCR has undergone significant change over the last decade, to the extent that only a small proportion of scientists have been able or willing to keep abreast of the latest offerings. The chapter reviews these changes. It discusses the second-generation of PCR technology-kinetic or real-time PCR, a tool gaining widespread acceptance in many scientific disciplines but especially in the microbiology laboratory.

Comparison of two real-time quantitative assays for detection of severe acute respiratory syndrome coronavirus

The new severe acute respiratory syndrome (SARS) coronavirus (CoV), described in February 2003, infected a total of 8,439 people. A total of 812 people died due to respiratory insufficiency. Close contact with symptomatic patients appeared to be the main route of transmission. However, potential transmission by blood transfusion could not be definitely excluded. Two real-time SARS-specific PCR assays were assessed for their sensitivities, agreement of test results, and intra-assay variabilities. Both assays rely on reverse transcription and amplification of extracted RNA. Dilutions of gamma-irradiated cell culture supernatants of SARS CoV-infected Vero E6 cells were prepared to determine the precisions, linear ranges, and accuracies of the assays. The linear range for the Artus RealArt HPA-Coronavirus assay (Artus assay) was 1 x 10(2) to 1 x 10(7) copies/ml, and that for the Roche LightCycler SARS CoV Quantification kit (Roche assay) was 1 x 10(4) to 2 x 10(8) copies/ml. The detection limit of the Roche assay was 3,982.1 copies/ml, whereas that of the Artus assay was 37.8 copies/ml. Detection limits were calculated with a standard preparation that was recommended for use by the World Health Organization. However, quantification of CoV in this preparation may be imprecise. In summary, both assays are suitable for quantitative measurement of SARS CoV at the high concentrations expected in sputum samples. The Artus assay is also suitable for detection of SARS CoV at the low concentrations found in serum samples.