Molecular detection and identification of enteroviruses using enzymatic amplification and nucleic acid hybridization

Detection of Enteroviruses and SARS-CoV-2 in Tunisian Wastewater

Monitoring the circulation of enteric viruses in environmental wastewater is a valuable tool for preventing the emergence of waterborne and food-borne diseases in humans. The detection of viruses was performed in five Tunisian wastewater treatment plants, three located in the Grand Tunis City (WWTP 1, WWTP 2, WWTP 3) and two in the Sahel of Tunisia (WWTP 4, WWTP 4), known as very developed and crowded zones, to assess the effectiveness of three biological wastewater treatment procedures namely natural oxidizing lagoons, rotating biodisks procedure, activated sludge procedure, and one tertiary sewage treatment using UV-C254 reactor for this enteric viruses' removal. Thus, 242 sewage samples were collected between June 2019 and May 2020 from different lines of wastewater treatment procedures implemented in the five wastewater treatment plants investigated. SARS-CoV-2 was analyzed using real-time multiplex reverse-transcription polymerase chain reaction (multiplex real-time RT-PCR) and enteroviruses using reverse-transcription polymerase chain reaction (RT-PCR). The enteroviruses detection showed 93% and 73% respective high frequencies only in the two WWTPs of the Grand Tunis (WWTP 1 and WWTP 2). SARS-CoV-2 was detected in 58% of the all wastewater samples collected from the five studied WWTPs with a respective dominance of N gene (47%), S gene (42%), RdRp gene (42%) and at last E gene (20%). These enteroviruses and SARS-CoV-2 detection were revealed in all steps of the wastewater treatment procedures, so poor virological quality is found at the exit of each biological and tertiary step of treatment investigated. For the first time in Tunisia, these results highlighted the enterovirus and SARS-CoV-2 detection with high rates, and the ineffectiveness of the biological and UV-C254 treatment implemented to remove these viruses. The preliminary results of SARS-CoV-2 circulation in Tunisian wastewater confirmed the wide positivity rate underlined by other works worldwide and allowed showing a move towards integrating wastewater as a way for this virus to spread in different areas and environments. So, this last result about SARS-CoV-2 circulation allowed us to caution about the strong probability of diffusion of this hazardous virus through water and sewage; despite its enveloped character and nature, as a labile and sensitive virus in these environments. Thus, establishing a national surveillance strategy is needed to improve the sanitary quality of treated wastewater and prevent public health problems related to these viruses in treated wastewater.

Development of a real-time RT-PCR assay for the detection of pan-human parechoviruses

Background

Parechoviruses (PeV-As), which constitute a new genus within the family Picornaviridae, have been associated with numerous localized outbreaks of serious diseases, such as coryza, pneumonia, maculopapular exanthem, and conjunctivitis. However, to the best of our knowledge, only a few laboratories worldwide conduct tests for the identification of this group of viruses. Therefore, in this study, we aimed to develop and validate a real-time RT-PCR assay for the identification of PeV-As.

Methods

To design and validate a real-time PCR primer–probe targeting the 5′-UTR region of PeV-As, the 5′-UTR sequences of PeV-As available in GenBank were aligned using the MUSCLE algorithm in MEGA v7.0. Thereafter, the highly conserved 5′-UTR region was selected, and its primer–probe sequence was designed using Primer Premier v5.0. This primer–probe sequence was then evaluated for specificity, sensitivity, and repeatability, and for its validation, it was tested using fecal samples from 728 healthy children living in Beijing (China).

Results

The PeV-A real-time RT-PCR assay detected only the RNA-positive standards of PeV-A genotypes (1–8, 14, 17, and 18), whereas 72 serotypes of non-PeV-A EV viruses were undetected. In addition, the VP1 region of these 11 PeV-A genotypes that tested positive were amplified using the primers designed in this study. Typing results indicated that eight, one, and two strains of the 11 were PeV-A1, PeV-A4, and PeV-A6, respectively. We also determined and presented the genetic characterization and phylogenetic analyses results corresponding to these 11 VP1 region sequences. Furthermore, real-time RT-PCR assay showed good sensitivity with LOD of 10² copies/μL. Positive results in eight parallel experiments at each concentration gradient from 10⁷ copies/μL to 10² copies/μL, indicating good repeatability.

Conclusion

Our findings suggested that the real-time RT-PCR assay developed in this study can be applied for routine PeV-A identification. We detected PeV-A1, 4 and 6 genotypes in the 728 faecal samples using this method. Additionally, we believe that our results will serve as a foundation for further studies on PeV-As and facilitate the expansion of the gene sequence information available in GenBank.

Inflammatory dilated cardiomyopathy : Etiology and clinical management

Inflammatory dilated cardiomyopathy (DCMi) is a syndrome, not an etiological disease entity. The infective etiology and the immunopathology can be best determined through endomyocardial biopsy with a complete work-up by light microscopy, immunohistology, and polymerase chain reaction for microbial agents. This review focuses on the methodological advances in diagnosis in the past few years and exemplifies the importance of an etiology-orientated treatment in different case scenarios. In fulminant nonviral myocarditis, immunosuppressive treatment together with hemodynamic stabilization of the patient via mechanical circulatory support (e.g., microaxial pumps, extracorporeal membrane oxygenation, left ventricular assist device) can be life-saving. For viral inflammatory cardiomyopathy, intravenous immunoglobulin treatment can resolve inflammation and often eradicate the virus.

Domain I of the 5' non-translated genomic region in coxsackievirus B3 RNA is not required for productive replication

Domain I is a cloverleaf-like secondary structure at the 5' termini of all enterovirus genomes, comprising part of a cis-acting replication element essential for efficient enteroviral replication. 5' genomic terminal deletions up to as much as 55% of domain I can occur without lethality following coxsackie B virus infections. We report here that the entire CVB structural domain I can be deleted without lethality.

Analysis of formalin-fixed and frozen myocardial autopsy samples for viral genome in childhood myocarditis and dilated cardiomyopathy with endocardial fibroelastosis using polymerase chain reaction (PCR)

Viral infection of the myocardium is implicated in the pathogenesis of myocarditis and dilated cardiomyopathy (DCM). Enteroviruses have been considered the most common viral etiologic agents, based on peripheral culture and serologic methods. Recently, polymerase chain reaction (PCR) has been shown to be useful in the detection of viral genomes from various infected organs and body fluids. In this study, myocardial samples from autopsy specimens (formalin fixed and fresh frozen) were examined for enteroviral and DNA viral (adenovirus, herpes simplex virus [HSV], and cytomegalovirus (CMV]) genome by PCR. The specimens studied were from 58 patients with myocarditis, 28 patients with DCM and endocardial fibroelastosis [EFE], and 22 controls. Viral genome was detectable in 34 of the 58 (59%) autopsy-proven myocarditis samples (18 adenovirus, 12 enterovirus, 2 CMV, 2 HSV) and 6 of the 28 samples from patients with DCM and EFE (6 adenovirus). We conclude that PCR is effective in the rapid amplification of virus from frozen and formalin-fixed myocardial samples and that adenovirus is an important etiologic agent in viral myocarditis as well as DCM with EFE.

A norovirus oyster-related outbreak in a nursing home in France, January 2012

The presence of norovirus in shellfish is a public health concern in Europe. Here, we report the results of an investigation into a norovirus gastroenteritis outbreak following a festive lunch which affected 84 (57%) residents and staff members of a nursing home in January 2012 in France. Individuals who had eaten oysters had a significantly higher risk of developing symptoms in the following 2·5 days than those who had not, the risk increasing with the amount eaten [relative risk 2·2 (1·0-4·6) and 3·3 (1·6-6·6) for 3-4 and 5-12 oysters, respectively]. In healthy individuals during those days, 29 (32%) subsequently became ill, most of whom were staff members performing activities in close contact with residents. Genogroup II noroviruses were detected in faecal samples, in a sample of uneaten oysters and in oysters from the production area. Identifying a norovirus's infectious dose may facilitate the health-related management of contaminated shellfish.

Classification and histological, immunohistochemical, and molecular diagnosis of inflammatory myocardial disease

In the WHO 1996 classification of cardiomyopathies, myocarditis is defined as an "inflammatory disease of the myocardium associated with cardiac dysfunction" and is listed among "specific cardiomyopathies". Myocarditis is diagnosed on endomyocardial biopsy (EMB) by established histological, immunological, and immunohistochemical criteria, and molecular techniques are recommended to identify viral etiology. Infectious, autoimmune, and idiopathic forms of inflammatory cardiomyopathy are recognized that may lead to dilated cardiomyopathy. According to Dallas criteria, myocarditis is diagnosed in the setting of an "inflammatory infiltrate of the myocardium with necrosis and/or degeneration of adjacent myocytes, not typical of ischemic damage associated with coronary artery disease". The majority of experts in the field agree that an actual increase in sensitivity of EMB has now been reached by using immunohistochemistry together with histology. A value of >14 leukocytes/mm(2) with the presence of T lymphocytes >7 cells/mm(2) has been considered a realistic cut off to reach a diagnosis of myocarditis. The development of molecular biological techniques, particularly amplification methods like polymerase chain reaction (PCR) or nested-PCR, allows the detection of low copy viral genomes even from an extremely small amount of tissue such as in EMB specimens. Positive PCR results obtained on EMB should always be accompanied by a parallel investigation on blood samples collected at the time of the EMB. According to the recent Association for European Cardiovascular Pathology guidelines, optimal specimen procurement and triage indicates at least three, preferably four, EMB fragments, each 1-2 mm in size, that should immediately be fixed in 10 % buffered formalin at room temperature for light microscopic examination. In expected focal myocardial lesions, additional sampling is recommended. Moreover, one or two specimens should be snap-frozen in liquid nitrogen and stored at -80 °C or alternatively stored in RNA-later for possible molecular tests or specific stains. A sample of peripheral blood (5-10 ml) in EDTA or citrate from patients with suspected myocarditis allows molecular testing for the same viral genomes sought in the myocardial tissue.

Early-onset neonatal sepsis

Early-onset sepsis remains a common and serious problem for neonates, especially preterm infants. Group B streptococcus (GBS) is the most common etiologic agent, while Escherichia coli is the most common cause of mortality. Current efforts toward maternal intrapartum antimicrobial prophylaxis have significantly reduced the rates of GBS disease but have been associated with increased rates of Gram-negative infections, especially among very-low-birth-weight infants. The diagnosis of neonatal sepsis is based on a combination of clinical presentation; the use of nonspecific markers, including C-reactive protein and procalcitonin (where available); blood cultures; and the use of molecular methods, including PCR. Cytokines, including interleukin 6 (IL-6), interleukin 8 (IL-8), gamma interferon (IFN-γ), and tumor necrosis factor alpha (TNF-α), and cell surface antigens, including soluble intercellular adhesion molecule (sICAM) and CD64, are also being increasingly examined for use as nonspecific screening measures for neonatal sepsis. Viruses, in particular enteroviruses, parechoviruses, and herpes simplex virus (HSV), should be considered in the differential diagnosis. Empirical treatment should be based on local patterns of antimicrobial resistance but typically consists of the use of ampicillin and gentamicin, or ampicillin and cefotaxime if meningitis is suspected, until the etiologic agent has been identified. Current research is focused primarily on development of vaccines against GBS.

Frequency of enterovirus detection in blood samples of neonates admitted to hospital with sepsis-like illness in Kuwait

This study investigated the role of enteroviruses in sepsis-like illness among neonates in Kuwait. Serum samples from 139 consecutive neonates presenting with sepsis-like illness during a three and a half-year-period whose blood cultures were negative for bacterial pathogens were tested. Enterovirus RNA was detected by single-step reverse-transcription PCR (RT-PCR). Specific genotypes were identified by direct DNA sequencing of enteroviral genome. Serotype-specific antibodies in serum samples from some selected patients were detected by virus neutralization test using coxsackievirus B types (CBVs). All 139 neonates presented with sepsis-like illness and blood samples were uniformly negative for aerobic/anaerobic bacterial cultures. Fifty-six (40%) neonates had further complications of sepsis including carditis (n = 34) and multi-organ involvement (n = 22). Enterovirus RNA was detected by RT-PCR in 34 of 139 (24%) serum samples which is among the highest frequency reported so far in non-epidemic settings. Genotyping identified CBVs as most common enteroviruses, causing 19 of 34 (56%) enteroviral sepsis episodes in neonates. Of 34 carditis cases, 18 were positive for CBVs by serotyping including all 10 enterovirus RNA-positive samples. Only one fatality was observed due to liver failure in a neonate with hepatitis. Our data showed that enteroviruses are responsible for 24% of neonatal sepsis cases due to non-bacterial causes in Kuwait. The data indicate that enteroviruses should be considered in the differential diagnosis of sepsis-like illness among neonates, particularly those with negative blood cultures for bacterial pathogens.

Human rhinovirus species C infection in young children with acute wheeze is associated with increased acute respiratory hospital admissions

RATIONALE

Human rhinovirus species C (HRV-C) is the most common cause of acute wheezing exacerbations in young children presenting to hospital, but its impact on subsequent respiratory illnesses has not been defined.

OBJECTIVES

To determine whether acute wheezing exacerbations due to HRV-C are associated with increased hospital attendances due to acute respiratory illnesses (ARIs).

METHODS

Clinical information and nasal samples were collected prospectively from 197 children less than 5 years of age, presenting to hospital with an acute wheezing episode. Information on hospital attendances with an ARI before and after recruitment was subsequently obtained.

MEASUREMENTS AND MAIN RESULTS

HRV was the most common virus identified at recruitment (n = 135 [68.5%]). From the 120 (88.9%) samples that underwent typing, HRV-C was the most common HRV species identified, present in 81 (67.5%) samples. Children with an HRV-related wheezing illness had an increased risk of readmission with an ARI (relative risk, 3.44; 95% confidence interval, 1.17-10.17; P = 0.03) compared with those infected with any other virus. HRV-C, compared with any other virus, was associated with an increased risk of a respiratory hospital admission before (49.4% vs. 27.3%, respectively; P = 0.004) and within 12 months (34.6% vs. 17.0%; P = 0.01) of recruitment. Risk for subsequent ARI admissions was further increased in atopic subjects (relative risk, 6.82; 95% confidence interval, 2.16-21.55; P = 0.001). Admission risks were not increased for other HRV species.

CONCLUSIONS

HRV-C-related wheezing illnesses were associated with an increased risk of prior and subsequent hospital respiratory admissions. These associations are consistent with HRV-C causing recurrent severe wheezing illnesses in children who are more susceptible to ARIs.

Development and assay of RNA transcripts of enterovirus species A to D, rhinovirus species a to C, and human parechovirus: assessment of assay sensitivity and specificity of real-time screening and typing methods

Nucleic acid amplification methods such as the PCR have had a major impact on the diagnosis of viral infections, often achieving greater sensitivities and shorter turnaround times than conventional assays and an ability to detect viruses refractory to conventional isolation methods. Their effectiveness is, however, significantly influenced by assay target sequence variability due to natural diversity and rapid sequence changes in viruses that prevent effective binding of primers and probes. This was investigated for a diverse range of enteroviruses (EVs; species A to D), human rhinoviruses (HRVs; species A to C), and human parechovirus (HPeV) in a multicenter assay evaluation using a series of full-length prequantified RNA transcripts. RNA concentrations were quantified by absorption (NanoDrop) and fluorescence methods (RiboGreen) prior to dilution in buffer supplemented with RNase inhibitors and carrier RNA. RNA transcripts were extremely stable, showing minimal degradation after prolonged storage at temperatures between ambient and -20°C and after multiple freeze-thaw cycles. Transcript dilutions distributed to six referral laboratories were screened by real-time reverse transcriptase PCR assays using different primers and probes. All of the laboratories reported high assay sensitivities for EV and HPeV transcripts approaching single copies and similar amplification kinetics for all four EV species. HRV detection sensitivities were more variable, often with substantially impaired detection of HRV species C. This could be accounted for in part by the placement of primers and probes to genetically variable target regions. Transcripts developed in this study provide reagents for the ongoing development of effective diagnostics that accommodate increasing knowledge of genetic heterogeneity of diagnostic targets.

Comparison of human parechovirus and enterovirus detection frequencies in cerebrospinal fluid samples collected over a 5-year period in edinburgh: HPeV type 3 identified as the most common picornavirus type

Human enteroviruses (EVs) and more recently parechoviruses (HPeVs) have been identified as the principal viral causes of neonatal sepsis-like disease and meningitis. The relative frequencies of specific EV and HPeV types were determined over a 5-year surveillance period using highly sensitive EV and HPeV PCR assays for screening 4,168 cerebrospinal fluid (CSF) specimens collected from hospitalized individuals between 2005 and 2010 in Edinburgh. Positive CSF samples were typed by sequencing of VP1. From the 201 EV and 31 HPeV positive (uncultured) CSF samples on screening, a high proportion of available samples could be directly typed (176/182, 97%). Highest frequencies of EV infections occurred in young adults (n = 43; 8.6%) although a remarkably high proportion of positive samples (n = 98; 46%) were obtained from young infants (<3 months). HPeV infections were seen exclusively in children under the age of 3 months (31/1,105; 2.8%), and confined to spring on even-numbered years (22% in March 2006, 25% in April 2008, and 22% in March 2010). In contrast, EV infections were distributed widely across the years. Twenty different EV serotypes were detected; E9, E6, and CAV9 being found most frequently, whereas all but one HPeVs were type 3. Over this period, HPeV3 was identified as the most prevalent picornavirus type in CNS-related infections with similarly high incidences of EV infection frequencies in very young children. The highly sensitive virus typing methods applied in this study will assist further EV and HPeV screening of sepsis and meningitis cases as well as in future molecular epidemiological studies and population surveillance.

Development of a highly sensitive real-time one step RT-PCR combined complementary locked primer technology and conjugated minor groove binder probe

Background

Enterovirus (EV) infections are commonly associated with encephalitis and meningitis. Detection of enteroviral RNA in clinical specimens has been demonstrated to improve the management of patients, by ruling out other causes of disease.

Method

To develop a sensitive and reliable assay for routine laboratory diagnosis, we developed a real-time one step reverse transcription polymerase chain reaction (RT-PCR) assay with minor groove binder probes and primers modified with complementary locked primer technology (TMC-PCR). We checked the sensitivity of the developed assay by comparing it to a previously published TaqMan probe real-time one-step RT-PCR (TTN-PCR) procedure using enteroviral isolates, Enterovirus Proficiency panels from Quality Control on Molecular Diagnostics (QCMD-2007), and clinical specimens from patients with suspected EV infections.

Results

One hundred clinical specimens from 158 suspected viral meningitis cases were determined to be positive by the TMC-PCR assay (63.29%), whereas only 60 were found to be positive by the TTN-PCR assay (37.97%). The positive and negative agreements between the TMC-PCR and TTN-PCR assays were 100% and 59.2%, respectively.

Conclusion

This data suggest that the TMC-PCR assay may be suitable for routine diagnostic screening from patient suspected EV infection.

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.

Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo

AIMS

To characterize major enteric viruses (enterovirus, rotavirus, norovirus, astrovirus and adenovirus) in the sewage of Greater Cairo and to compare the results with clinical data collected during the same period.

METHODS AND RESULTS

Seventy-two sewage samples from two waste water treatment plants were collected from April 2006 through February 2007. Enteroviruses, noroviruses (NoVs) and rotaviruses (RVs) were detected by RT-PCR in 22%, 18% and 8.3% of the samples, respectively. No adenovirus and astrovirus was detected. G2P[8], G9P[8], G1P[8], G2P[4] and rare G12 RV isolates were detected in the environment as well as a bovine RV. The environmental NoV strains mostly belonged to genogroup I (84%). Rotaviruses and some of the NoVs were similar to those found in the clinical samples at the same time.

CONCLUSIONS

The comparison of environmental and clinical data suggests that similar RV and NoV isolates were circulating in the environment and in the population during the same period.

SIGNIFICANCE AND IMPACT OF THE STUDY

Few studies have investigated the prevalence and the epidemiology of RVs and NoVs in Cairo. This work is the first to establish a correlation between viral gastroenteritis and the concomitant presence of enteric viruses in the environment for Greater Cairo where combined environmental and clinical surveys should help to prevent infections caused by these major pathogens.

Improvement of a real-time RT-PCR assay for the detection of enterovirus RNA

We describe an improvement of an earlier reported real-time RT-PCR assay for the detection of enterovirus RNA, based on the 5' exonuclease digestion of a dual-labeled fluorogenic probe by Taq DNA polymerase. A different extraction method, real-time RT-PCR instrument and primer set were evaluated. Our data show that the optimized assay yields a higher sensitivity and reproducibility and resulted in a significant reduced hands-on time per sample.

Molecular evaluation of enteroviruses in the pathogenesis of idiopathic dilated cardiomyopathy

BACKGROUND

There is great disparity in the literature as to the presence and relevance of enterovirus in heart tissue from patients with dilated cardiomyopathy (DCM). Published estimates of enteroviral positive tissue in DCM range from 0 to 50%. Very little sequence information is so far available on those samples which are positive.

HYPOTHESIS

Re-examination of fresh biopsy material from patients previously tested, plus 13 new cases of DCM, and sequencing the products would yield information on the validity of the technique and on the type of virus being detected.

METHODS

RNA from biopsy or explant tissue was tested for the presence of enterovirus using reverse transcriptase polymerase chain reaction (PCR). The nucleotide sequences of all positive PCR products were determined by direct sequencing.

RESULTS

Positive PCR signals were found in 10% of samples from patients with DCM and in 16% of control tissues. Two DCM and 12 control samples gave the same nucleotide sequence, which was different from the CB3 used as a positive control. The other 4 DCM samples all produced multiple bands on sequencing.

CONCLUSION

The results do not support a major role for enterovirus in DCM. There is need for some caution, however, as a review of the literature shows that studies using single biopsies, such as this one, produce consistently lower estimates for enterovirus than do those wherein multiple biopsies are examined.

Echovirus type 9 is an important cause of viral encephalitis among infants and young children in Kuwait

BACKGROUND

The role of enteroviruses in encephalitis is not fully established.

OBJECTIVE

This study determined the role of enteroviruses in encephalitis in neonates, infants and young children in Kuwait.

STUDY DESIGN

Cerebrospinal fluid (CSF) samples obtained from 147 patients presenting with 'severe encephalitis' (n=60), 'mild encephalitis' (n=43), and febrile seizures (n=44) over a 3.5-year period, were analyzed. Enteroviral RNA was detected by one-step reverse transcription-PCR (RT-PCR) assay and specific enteroviruses were identified by sequencing a variable region of the enteroviral genome.

RESULTS

Enteroviral RNA was detected in 29 of 103 (28%) samples obtained from encephalitis patients but only in 8 of 44 (18%) samples from patients with febrile seizures. Echovirus type 9 (E9) was detected in 24 of 29 (83%) while E30 was found in 5 of 29 (17%) of enterovirus-positive encephalitis cases. Two of 8 (25%) cases of febrile seizures were infected with E9. The E9 viral load was higher in patients with 'severe encephalitis' than in patients with 'mild encephalitis' or in patients with febrile seizures. All but one enteroviral encephalitis case had a complete recovery.

CONCLUSIONS

Enteroviruses, especially E9 are an important cause of encephalitis among neonates, infants and young children in Kuwait.

5' terminal deletions in the genome of a coxsackievirus B2 strain occurred naturally in human heart

Enteroviruses can induce human myocarditis, which can be modeled in mice inoculated with group B coxsackieviruses (CVB) and in which CVB evolve to produce defective, terminally deleted genomes. The 5' non-translated region (NTR) was enzymatically amplified from heart tissue of a fatal case of enterovirus-associated myocarditis in Japan in 2002. While no intact 5' viral genomic termini were detected, 5' terminal deletions ranged in size from 22 to 36 nucleotides. Sequence of the 5' third of this viral genome is of a modern strain, closely related to CVB2 strains isolated in Japan in 2002. A CVB3 chimera containing the 5' NTR with a 22 nt deletion produced progeny virus upon transfection of HeLa cells. When the 5' 22 nucleotide deletion was repaired, the virus induced myocarditis in mice and replicated like wild type virus in murine heart cells. This is the first report of these naturally-occurring defective enteroviral genomes in human myocarditis.

Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients

Aichi virus has been proposed as a causative agent of gastroenteritis. A total of 457 stool specimens from children hospitalized with acute diarrhea and 566 stool specimens from adults and children involved in 110 gastroenteritis outbreaks were screened for the presence of Aichi virus by reverse transcription-PCR (RT-PCR) amplification of the genomic region of the 3C and 3D (3CD) nonstructural proteins. Our results show a low incidence of Aichi virus in pediatric samples and the existence of mixed infections with other microbiological agents in some cases. From the outbreak survey, it appears that the presence of Aichi virus is an indicator of mixed infections causing gastroenteritis outbreaks and that it could be involved in half of the oyster-associated outbreaks. A second RT-PCR was developed to amplify a part of the VP1 gene. The phylogenetic analysis showed a good correlation between the two classifications based on 3CD and VP1 gene sequences and revealed the prevalence of genotype A in France. It also allowed us to partially describe an Aichi virus strain that could represent a new genotype, thus suggesting the existence of a certain diversity.

Basic rationale, current methods and future directions for molecular typing of human enterovirus

Enterovirus is a genus of the Picornaviridae family including more than 80 serotypes belonging to four species designed Human enterovirus A to D. The antigens of the structural proteins support the subdivision of enteroviruses into multiple serotypes. Comparative phylogeny based on molecular typing methods has been of great help to classify former and new types of enterovirus, and to investigate the diversity of enteroviruses and the evolutionary mechanisms involved in their diversity. By now, molecular typing methods of enterovirus rely mainly on the sequencing of an amplicon targeting a variable part of the region coding for the capsid proteins (VP1 and, alternatively, VP2 or VP4), either from a strain recovered by cell culture or, more recently, by direct amplification of a clinical or environmental specimen. In the future, microarrays are thought to play a major role in enterovirus typing and in the analysis of the determinants of virulence that support the puzzling diversity of the pathological conditions associated with human infection by these viruses.

A large multi-pathogen waterborne community outbreak linked to faecal contamination of a groundwater system, France, 2000

A large waterborne outbreak of infection that occurred during August 2000 in a local community in France was investigated initially via a rapid survey of visits to local physicians. A retrospective cohort study was then conducted on a random cluster sample of residents. Of 709 residents interviewed, 202 (28.5%) were definite cases (at least three liquid stools/day or vomiting) and 62 (8.7%) were probable cases (less than three liquid stools/day or abdominal pain). Those who had drunk tap water had a three-fold increased risk for illness (95% CI 2.4-4.0). The risk increased with the amount of water consumed (chi-square trend: p < 0.0001). Bacteriological analyses of stools were performed for 35 patients and virological analyses for 24 patients. Campylobacter coli, group A rotavirus and norovirus were detected in 31.5%, 71.0% and 21% of samples, respectively. An extensive environmental investigation concluded that a groundwater source to this community had probably been contaminated by agricultural run-off, and a failure in the chlorination system was identified. This is the first documented waterborne outbreak of infection involving human C. coli infections. A better understanding of the factors influencing campylobacter transmission between hosts is required.

High-throughput, sensitive, and accurate multiplex PCR-microsphere flow cytometry system for large-scale comprehensive detection of respiratory viruses

Human respiratory viruses are a diverse group of pathogens composed of hundreds of virus strains, and this presents a major challenge for diagnostic laboratories. To efficiently detect numerous viruses in a large epidemiologic study, we developed a fast, multitarget, sensitive, and specific assay named the Respiratory MultiCode-PLx Assay (RMA). The RMA utilizes improved multiplex PCR chemistry (EraGen MultiCode-PLx technology) coupled with high-throughput microsphere flow cytometry (Luminex). Eighteen sets of virus-specific multiplex PCR primers were developed based on the conserved sequences of all available respiratory-virus sequences for eight distinct groups: human rhinovirus (HRV), respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus (InfV), metapneumovirus, adenovirus (Ad), coronavirus, and enterovirus. Each primer set detected 20 cDNA copies of the intended target per sample and had no reaction with 60,000 copies of human genomic DNA. The accuracy and sensitivity of the RMA for detecting respiratory viruses in human samples were tested with two sets of clinical specimens. First, 101 nasal-wash specimens that were positive for HRV, RSV, InfV, PIV, or Ad by traditional techniques were reanalyzed by RMA, and all target viruses were detected with an overall sensitivity of 94% and specificity of 99%. Second, 103 nasal-wash samples from 5-year-old children with asthma and respiratory symptoms were analyzed; RMA detected viruses in 74 specimens (71.8%) compared to only 24 (23.3%) by traditional culture and immunofluorescent-staining techniques. These results show that RMA is an accurate, sensitive, and practical test for respiratory-virus infections.

An outbreak of aseptic meningitis due to echovirus 30 associated with attending school and swimming in pools

OBJECTIVES

To identify the risk factors of an outbreak of meningitis associated with echovirus 30-infection that occurred in Rome, Italy, in late 1997 among children from two different schools.

METHODS

A case-control study was carried out. A case was defined as a child from either of the two schools, A or B, who presented meningitis-like (fever, headache and vomiting), diarrhea, or respiratory tract symptoms. All asymptomatic students were included in the analysis as controls.

RESULTS

Among 446 pupils (80%) who answered the questionnaire, 68 met the case definition. Twenty pupils developed a meningitis-like illness. Echovirus 30 was isolated from cerebrospinal fluid (CSF) in four and from stools in six. Forty-eight pupils reported other symptoms. The attack rate was 10.8% in school A and 0.8% in school B for meningitis-like illness; it was 12% and 10%, respectively, for other enterovirus-like illnesses. The risk of meningitis-like illness was higher among children attending school A (crude OR = 14.9; 95% CI = 4.3-52.1), among children using any public pool (OR = 3.8; 95% CI = 1.5-9.9) and those using an outside swimming pool X (OR=13.4; 95% CI=2.7-65.8 versus no swimming pool and OR = 8.3; 95% CI = 1.1-62.6 versus other pools). The epidemic curve appears to suggest a person-to-person transmission.

CONCLUSIONS

The epidemic occurred by person-to-person transmission in a number of classrooms and at swimming pool X.

Myocarditis and inflammatory cardiomyopathy: histomorphological diagnosis

Myocarditis is a non-ischemic inflammatory disease of the myocardium associated with cardiac dysfunction. It most often results from infectious agents, hypersensitivity responses, or immune-related injury. In spite of the development of various diagnostic modalities, early and definite diagnosis of myocarditis still depends on the detection of inflammatory infiltrates in endomyocardial biopsy specimens according to Dallas criteria. Routine application of immunohistochemistry (for characterization of inflammatory cell infiltration) and Polymerase Chain Reaction PCR analysis (for identification of infective agents) has become an essential part of the diagnostic armamentarium for a more precise biopsy report. A new morphological classification is advanced to overcome the limits of Dallas criteria. A semiquantitative assessment of myocyte damage/inflammation (grading) as well as of fibrosis (staging) is indicated, thus providing histopathological diagnosis useful to the clinician for more appropriate patient risk stratification and for the application of new therapies. Consequently, the final diagnosis of myocarditis should be mainly based on three features: etiology, grade, and stage of the disease.

Sporadic amyotrophic lateral sclerosis: a hypothesis of persistent (non-lytic) enteroviral infection

Because of recently reported reverse transcriptase polymerase chain reaction evidence of enterovirus in sporadic amyotrophic lateral sclerosis (SALS) and because of newly available anti-enteroviral drugs binding enteroviral capsids, it is reasonable to re-formulate an enteroviral hypothesis of SALS using recent advances in molecular virology. Viral persistence is non-lytic and non-cytopathic infection that evades host's immune surveillance. Enteroviruses are known to cause persistent as well as lytic infection both in vitro and in vivo. Both virion as well as host factors modulate between persistent and lytic infection. Apoptosis, or programmed cell death, is a process of active non-necrotic cell death. It has complex interplay with viruses and may be either promoted or opposed by them. Apoptosis is a major factor in motor neuron death in SALS. Viral tropism is the process by which viruses select and propagate to target cells. It is controlled by capsid conformation and surface receptors on host cells. Enteroviruses have a region on their capsids known as the canyon which docks on such receptors. Docking induces conformational changes of the capsid and genome release. Poliovirus, tropic for motor neurons, docks on the poliovirus receptor, about which much is known. The virus penetrates the motor system focally after crossing either the blood-muscle or the blood-brain barriers. It propagates bidirectionally along axons and synapses to contiguous motor neurons, upper as well as lower, which sequester infection and create avenues for spread over long distances. If chronic and persistent rather than acute and lytic, such viruses trafficking in a finite system of non-dividing cells and inducing apoptosis would cause cell death that summates linearly rather than exponentially. Taken together, these explain signature clinical features of SALS - focal onset weakness, contiguous or regional spread of weakness, confinement to upper and lower motor neurons, and linear rates of progression. The hypothesis predicts the following testable investigations: 1) viral detection may be possible by applying amplification technology to optimally acquired nervous tissue processed by laser microdissection; 2) genetic susceptibility factors such as cell surface receptor polymorphisms may combine with sporadic exposure and chance penetration of the motor system in SALS; 3) a transgenic animal model might be created by inserting such genetic factors into an animal host and inoculating intramuscularly rather than intracerebrally biochemical fractions of SALS motor neurons at vulnerable periods in the developmental life cycle of the transgenic host; and 4) continual long-term administration of anti-enteroviral agents called capsid-binding compounds which stabilize capsids and prevent genome release might be efficacious.

Detection of Coxsackievirus B3 RNA in mouse myocarditis by nested polymerase chain reaction

BACKGROUND

A majority of cases of viral myocarditis are associated with group B Coxsackieviruses (CVB) and the persistence of these viruses in the myocardium is associated with the progression of acute myocarditis to chronic dilated cardiomyopathy. A highly sensitive nested polymerase chain reaction (NPCR) is required to study the mechanisms of viral persistence in the myocardium.

OBJECTIVES

To develop an enterovirus group-specific NPCR system, to compare it to the reverse-transcription PCR (RT-PCR) plus Southern hybridisation and to investigate the dynamics of viral RNA in a murine model of myocarditis induced by CVB3.

STUDY DESIGN

Primers corresponding to the conserved sequences in the 5'-nontranslated region of enteroviruses were designed to ensure a broad specificity. The specificity of PCR products was confirmed by Southern hybridisation. The sensitivity of RT-PCR or NPCR was assessed using reconstructed infected muscle samples. The myocardial samples of the SWR murine model of CVB3-myocarditis were collected from day 1 to 30 after infection. The presence of viral RNA was detected by the RT-PCR or NPCR and infectious virus was isolated by cell culture.

RESULTS

Both RT-PCR and NPCR could detect all 11 representative enteroviruses. The NPCR could detect as few as 0.01 plaque forming unit of virus, 100 times more sensitive than the RT-PCR. Virus was isolated from the myocardium in acute phase, but was no longer recoverable after 9 days. Viral RNA was detected by the NPCR technique throughout the studied period.

CONCLUSIONS

An enterovirus group-specific NPCR system was developed and was much more sensitive than the RT-PCR technique. It can replace the Southern hybridisation of RT-PCR products. The presence of viral RNA in the myocardium after acute phase indicates a possibility of CVB3 shifting to persistent infection in the SWR mice.

Enteroviruses in Tunisia: virological surveillance over 12 years (1992-2003)

This report is an overview of enterovirus epidemiology in Tunisia during a 12-year period from 1992 to 2003. A total of 4700 clinical samples were collected as part of the national poliovirus surveillance programme and the routine diagnostic programme for aseptic meningitis. Enterovirus detection was performed by isolation on cell culture according to World Health Organization recommended protocols. Serotype identification was performed by seroneutralization of the cytopathic effect using pools of specific antisera and sequencing in the VP1 region of the genome. Poliovirus isolates were assessed for their wild or vaccine-related origin by standard World Health Organization recommended methods (PCR, probe hybridization and ELISA). The results confirm the interruption of wild poliovirus circulation since 1995. A total of 236 non-polio enterovirus (NPEV) strains were isolated; seroneutralization allowed typing of 93 % (219 out of 236) of them. The antisera used allowed the identification of the most common enterovirus serotypes. The remaining 17 isolates were sequenced; 16 of them belonged to enterovirus serotypes that were not targeted by the antisera pools used. A total of 29 different serotypes of NPEV were detected in the country during the study period. Echoviruses of serotypes 6, 11 and 30 were the most frequently isolated, almost every year; other serotypes had a cyclic occurrence and others were detected during a limited period with very few isolates. The NPEV isolation rate varied from year to year but was steadily under 10 %, suggesting a relatively low prevalence of these viruses in comparison to that in other developing countries. A seasonal variation was also noted; the high transmission period starts in March and peaks in September-November. This study is the first report of the epidemiology of NPEV in Tunisia. These viruses are associated with various diseases and epidemiological data may help to clarify their impact on human health.

DNA microarrays for virus detection in cases of central nervous system infection

A low-density, high-resolution diagnostic DNA microarray comprising 38 gene targets for 13 viral causes of meningitis and encephalitis was constructed. The array has been used for the detection of multiplex PCR-amplified viruses in cerebrospinal fluid (CSF) and non-CSF specimens. A total of 41 clinical specimens were positive for echoviruses (23 samples), herpes simplex virus type 2 (4 samples), varicella-zoster virus (4 samples), human herpesvirus 7 (1 sample), human herpesvirus 6A (1 sample) and 6B (2 samples), Epstein-Barr virus (three samples), polyomavirus JC (1 sample), and cytomegalovirus (2 samples). Probes for herpes simplex virus type 1, polyomavirus BK, and mumps and measles viruses were also included on the array. Three samples were false negative by the microarray assay due to discordant results between the multiplex PCR for all 13 viruses simultaneously and the virus-specific PCR alone. Fifteen CSF specimens were true negative. The clinical sensitivity, specificity, and negative and positive predictive values of the assay were 93, 100, 100, and 83%, respectively, when the results were compared to those of the single-virus PCR, which was used as the "gold standard." The microarray-based virus detection assay is qualitative and provides a single-format diagnostic tool for the detection of panviral CNS infections.

Detection of enteric viruses, Giardia and Cryptosporidium in two different types of drinking water treatment facilities

In this study, two types of drinking water treatment facilities (two conventional drinking water treatment plants (DWTPs) and two compact units (Cus)) were compared referring to their production capacity. Water samples were collected from three main points: (a) different water treatment steps (b) washings of sand filters and (c) distribution system at different distances from the water treatment plants. Both viruses and protozoa were concentrated from each water sample by adsorption and accumulation on the same nitrocellulose membrane filters (0.45 microm pore size). Enteroviruses were detected by plaque infectivity assay in BGM cells and HAV, HEV and Norovirus were detected by RT-PCR. Giardia and Cryptosporidium were detected by conventional staining methods and PCR. The results revealed that enterovirus load at the intake ranged between 10-15 PFU/L for the two compact units and between 4.5 and 75 PFU/L for the two conventional DWTPs. The virus load in distribution system of the first type DWTPs at 1 km from the plant was the same as that of the intake. Viruses in the other type of treatment plants CUs at 1, 5 and 7 km, were much reduced. Investigation of raw water sediments of the two DWTPs showed enterovirus counts between 12 and 17.5 PFU/L. Virus count was reduced in sand of filters after washing. Giardia cysts were equally detected by microscopy and PCR in only intake samples of EL-Hawamdia CU (33.3%) and Meet Fares DWTP (50%). Cryptosporidium oocysts were equally detected by microscopy and PCR in intake samples of Abo EL-Nomros CU (100%), EL-Hawamdia CU (66.7%) and Fowa DWTP (50%). At Meet Fares DWTP three positive intake samples for Cryptosporidium were detected by PCR, compared with only two positive samples by microscopy. Giardia cysts and Cryptosporidium oocysts were detected in raw water sediment and sand of filters before washing. Only one sample from Meet Fares DWTP sand of filters after washing was positive for both Giardia and Cryptosporidium. It can be concluded that the poor microbial quality of the water may be due to improper operational skills and management of the various water treatment plants (especially at the two high capacity treatment plants).

Development of a simple restriction fragment length polymorphism assay for subtyping of coxsackie B viruses

Coxsackie B viruses (genus, Enterovirus; family, Picornaviridae) can cause aseptic meningitis, encephalitis, pleurodynia, myocarditis and are implicated in the pathogenesis of dilated cardiomyopathy. The differentiation of the group B coxsackieviruses into their subtypes has potential clinical and epidemiological implications. In the present study, a simple restriction fragment length polymorphism (RFLP) assay was developed for typing of group B coxsackieviruses into subtypes 1-6. It is a two step process, first, virus isolation and identification by virus neutralization assay, using pools of polyclonal antisera, second, the reverse transcription polymerase chain reaction (RT-PCR) using a single primer pair selected from the conserved 5'-untranslated region (5'-UTR) of enterovirus genome followed by RFLP. A 440 bp product was amplified from the reference strains of each subtype of group B coxsackievirus and 29 clinical isolates (positive for group B coxsackieviruses by neutralization assay). The amplified products were subjected to restriction endonuclease digestion by enzyme BsaJI. The assay was able to distinguish all six serotypes of coxsackie B viruses. The results were comparable to serotyping and showed that due to the relatively conserved nature of 5'-UTR in enterovirus genome, this region can be used for subgeneric molecular identification of enteroviruses.

Highly sensitive assay for detection of enterovirus in clinical specimens by reverse transcription-PCR with an armored RNA internal control

The objective of the present study was the development of a diagnostic reverse transcription (RT)-PCR for the specific detection of enterovirus (EV) RNA in clinical specimens controlled by an internal control (IC) RNA. The IC RNA contains the same primer binding sites as EV RNA but has a different probe region. The IC RNA was packaged into an MS2 phage core particle (armored) and was added to the clinical sample to allow monitoring of both extraction efficiency and RT-PCR efficiency. Serial dilutions of the IC RNA were made, and the detection limit of the RT-PCR was tested in a background of EV RNA-negative cerebrospinal fluid. The sensitivity and specificity of the RT-PCR assay were tested by using all 64 known EV serotypes, several non-EV serotypes, and two Quality Control for Molecular Diagnostics (QCMD) Program EV proficiency panels from 2001 and 2002. In total, 322 clinical specimens were tested by RT-PCR, and to establish the clinical utility of the RT-PCR, a comparison of the results of viral culture and RT-PCR was done with 87 clinical specimens. The lower limit of sensitivity was reached at about 150 copies of IC RNA/ml. All 64 EV serotypes were positive, while all non-EV serotypes were negative. All culture-positive samples of the 2001 QCMD proficiency panel (according to the 50% tissue culture infective doses per milliliter) were positive by RT-PCR. Invalid results, i.e., negativity for both EV RNA and IC RNA, due to inhibition of RT-PCR were observed for 33.3% of the members of the 2002 QCMD proficiency panel and 3.1% of the clinical specimens. Inhibition of RT-PCR could be relieved by the addition of 400 ng of bovine alpha-casein per microl to both the RT reaction mixture and the PCR mixture. With this optimized protocol, the results for all samples of the 2002 QCMD proficiency panel and all clinical specimens except one fecal sample (0.3%) were valid. Evaluation of the clinical samples demonstrated that EV infection could be detected in 12 of 87 samples (13.8%) by RT-PCR, while viral culture was negative. Our data show that the RT-PCR with armored IC RNA offers a very reliable and rapid diagnostic tool for the detection of EV in clinical specimens and that the addition of bovine alpha-casein relieved inhibition of the RT-PCR for 99.7% of clinical specimens.

A sensitive and quantitative single-tube real-time reverse transcriptase-PCR for detection of enteroviral RNA

BACKGROUND

Enteroviruses (EVs) are significant human pathogens. Rapid and sensitive diagnostic techniques are desirable.

OBJECTIVES

To develop a quantitative single-tube real-time reverse transcription-polymerase chain reaction (RT-PCR) for human enterovirus ribonucleic acid (RNA) (QPCR), with protection against amplimer contamination.

STUDY DESIGN

The method was evaluated with serial dilutions of EV, 62 cerebrospinal fluid (CSF) specimens from meningitis patients, and the third and fourth European Union Concerted Action Enterovirus Proficiency Panels. A commercial EV PCR test was run in parallel.

RESULTS

Optimisation included RNA extraction procedure, design and concentrations of primers and probes from the 5' non-coding region as well as recombinant Thermus thermophilus polymerase (rTth), Mn(OAc)(2) and thermolabile UNG concentrations. Of 62 CSF samples from cases of meningitis submitted for QPCR testing, 34 (76%) and 21 (47%) were positive by QPCR and a commercial EV RNA detection kit, respectively. The detection limit of QPCR was 0.001 TCID(50)/ml (50% tissue culture-infective dose per millilitre) for a coxsackievirus B2 preparation and <10 copies of a plasmid containing coxsackievirus B2 complementary deoxyribonucleic acid (cDNA). The relation between threshold cycle (C(t)) and amount of virus was linear (r = 0.99) over a range of 10(-3) to 10(4) TCID(50)/ml of coxsackievirus B2.

CONCLUSIONS

The QPCR method allows a large number of samples to be screened rapidly. Its sensitivity, simplicity, and reproducibility make it a suitable tool for the routine laboratory.

Laboratory diagnosis of enteroviral infections of the central nervous system by using a nested RT-polymerase chain reaction (PCR) assay

Enteroviruses are the most common pathogens identified in infants hospitalized for suspected aseptic meningitis. Rapid detection of enterovirus infection is essential in taking the decision for treatment with antiviral agents and applying infection control measures in hospitalized pediatric patients. The purpose of this study was to compare the results of conventional virus isolation with those of enteroviral RNA detection by reverse transcription (RT)-PCR method in identical specimens from cases of suspected aseptic meningitis. Cerebrospinal fluid (CSF) samples were collected for viral examination from 68 pediatric patients with suspected aseptic meningitis from 1999 to 2002. These samples were inoculated in HeLa, Hep-2 and RD cell culture. The viral RNA was investigated by in-house RT-PCR method. The isolated viruses were typed by neutralization test. 36 of the 68 specimens were detected to be enterovirus positive by culture method, while 43 of them yielded positive results when RT-PCR method is used. Discrepancies occurred between the two methods in 15 specimens. While 11 specimens were positive by RT-PCR, these are found to be culture-negative. The isolated viruses were typed as Echovirus 30 (n: 30), Group B coxsackievirus (n: 5) and one isolate could not be typed by neutralization. Because of higher sensitivity and rapidity of RT-PCR, it is superior (p = 0.016) to virus culture of CSF for the diagnosis of enterovirus meningitis. Although the clinical usefulness of viral culture from CSF is limited, the final laboratory identification needs cultural techniques.

Molecular diagnosis of viral infections of the central nervous system

The development of techniques for the amplification of DNA and RNA opened the way for the creation of extremely specific, sensitive, and rapid diagnostic tests for the detection of viral infections of the central nervous system. Polymerase chain reaction (PCR) and reverse transcription PCR diagnostic assays have revolutionized the approach to the diagnosis of important viral pathogens--in particular, enteroviruses (EVs), herpes viruses, and JC virus (JCV). These molecular approaches to diagnosis have led to improvements in clinical outcome and patient care. Additionally, their use has permitted a better understanding of the natural history and clinical spectrum of the syndromes caused by these important human pathogens. This article summarizes the current understanding with regard to the available, molecularly based, diagnostic assays for the detection of EVs, herpes viruses, and JCV.

An echovirus type 33 winter outbreak in New Zealand

Echovirus type 33 (E33) is a relatively uncommon enterovirus. An E33 outbreak during the winter of 2000 in New Zealand led to 75 virologically-confirmed cases of E33 infection (2.6 cases per 100,000 individuals). Sixty-six (88%) of the 75 patients were aged <30 years, with the highest rates of infection recorded in Maori and Pacific ethnic groups. Overall, 47 (84%) of 56 patients whose cases were analyzed had either aseptic meningitis or encephalitis. Central nervous system involvement was more common after infancy (43 of 45 non-infant patients vs. 4 of 11 infants [relative risk, 2.6; 95% CI, 1.5-4.3]). Two infants died, including a neonate with fulminant hepatitis. Independent of symptom duration, neutrophil-predominant pleocytosis was detected in 17 (41%) of 41 cerebrospinal fluid specimens. Virus isolates could not be definitively typed by antibody neutralization testing but were identified as E33 by partial sequencing of the VP-1 capsid gene. The isolates were closely related to strains from Australia and Oman. Molecular typing, together with a serotype-specific E33 PCR, improved the speed and effectiveness of the outbreak investigation.

Comparison of automated and manual nucleic acid extraction methods for detection of enterovirus RNA

Automated nucleic acid extraction is an attractive alternative to labor-intensive manual methods. We compared two automated methods, the BioRobot M48 instrument (Qiagen, Inc.) and MagNA Pure (Roche Applied Sciences) methods, to two manual methods, the QIAamp Viral RNA Mini kit (Qiagen) and TRIzol (Invitrogen), for the extraction of enterovirus RNA. Analytical sensitivity was assessed by dilution analysis of poliovirus type 2 Sabin in cerebrospinal fluid. The sensitivity of PCR was equivalent after RNA extraction with QIAamp, BioRobot M48, and MagNA Pure. All 18 replicates of 100 PFU/ml were detected after extraction by the four methods. Fewer replicates of each successive dilution were detected after extraction by each method. At 10(-1) PFU/ml, 17 of 18 replicates were positive by QIAamp, 15 of 18 replicates were positive by BioRobot M48, and 12 of 18 replicates were positive by MagNA Pure; at 10(-2) PFU/ml, 4 of 17 replicates were positive by QIAamp, 2 of 18 replicates were positive by BioRobot M48, and 0 of 18 replicates were positive by MagNA Pure. At 10(-3) PFU/ml, no replicates were detected. Evaluation of TRIzol was discontinued after nine replicates due to a trend of lower sensitivity (at 10(-3) PFU/ml eight of nine replicates were positive at 100 PFU/ml, four of nine replicates were positive at 10(-1) PFU/ml, and zero of nine replicates were positive at 10(-2) PFU/ml). Concordant results were obtained in 24 of 28 clinical specimens after extraction by all methods. No evidence of contamination was observed after extraction by automated instruments. The data indicate that the sensitivity of enterovirus PCR is largely similar after extraction by QIAamp, BioRobot M48, and MagNA Pure; a trend of decreased sensitivity was observed after TRIzol extraction. However, the results of enterovirus PCR were largely concordant in patient samples, indicating that the four extraction methods are suitable for detection of enteroviruses in clinical specimens.

Detection of enteric viruses in municipal sewage sludge by a combination of the enzymatic virus elution method and RT-PCR

Pathogenic enteric viruses can be retained in municipal sewage sludge as has been reported by many researchers. Although the RT-PCR technique has been extensively employed for the virus detection from various environmental samples, the application of RT-PCR to the detection of viruses in sewage sludge has the difficulty because of inhibitory substances to the gene amplification. However, a combination of the enzymatic virus elution (EVE) method with RT-PCR made it possible to effectively detect viruses in sewage sludge. The enzymatic breakdown of sludge flocs in the EVE method enhanced the virus elution from poliovirus 1 (PV1)-inoculated sewage sludge, and the detection of PV1 was performed by RT-PCR without any inhibitions. On the contrary, the application of RT-PCR to the viral assay in the US EPA method using the 10% beef extract solution was not practical because of inhibitions to the viral gene amplification. The combination of the EVE method using lysozyme (polysaccharide-degrading enzyme), papain (protease), and chymotrypsin (protease) with RT-PCR resulted in a virus recovery efficiency of 31%, but a synergistic effect of these enzymes on the virus recovery efficiency was not observed. The EVE method using lysozyme or papain could be a promising procedure for the virus elution from sewage sludge in detecting these viruses with RT-PCR.

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

A LightCycler and two TaqMan real-time PCR assays were evaluated against an older PCR with liquid-phase hybridization method for the detection of enterovirus RNA in 74 patient samples. The two-step LightCycler and the two-step TaqMan formats correlated well with each other (r(2) = 0.90) and were equally sensitive compared to the liquid-phase hybridization method, whereas the one-step recombinant Tth DNA polymerase format was rather insensitive, detecting enterovirus RNA in only about one-half of those patient samples previously positive by liquid-phase hybridization. The two-step TaqMan method was optimized utilizing 10 micro l of cDNA and demonstrated the highest degree of analytical sensitivity among the methods evaluated in our study, being able to reproducibly quantify down to 510 copies of enteroviral RNA/ml of cerebrospinal fluid. This new assay can be performed in 4 h, is much less labor intensive, and showed less cross-reactivity with rhinovirus than the liquid-phase hybridization assay. Thus, the two-step TaqMan assay should prove useful in the diagnosis of enteroviral meningitis versus bacterial meningitis, thereby resulting in timely and appropriate clinical management that can amount to significant cost savings to the patient and health care system.

Viral causes of cardiac inflammation

Over the past year there have been few significant breakthroughs in the understanding of the etiologies of viral myocarditis or dilated cardiomyopathy (DCM). One interesting trend has been the increasing number of reports of myocarditis associated with parvovirus B19 infection. Whether this is simply a result of improved diagnostics, or reflects an underlying change in the etiology is unclear. However, studies of the underlying mechanisms of these disorders have resulted in several reports linking the acquired and viral forms. Over the past few years the cytoarchitecture has been a focus of study for familial DCM. During the last year, one key molecule, dystrophin, has been shown to be disrupted in patients with end-stage cardiomyopathy, irrespective or etiology, mutated in patients with sporadic forms of disease and identified as a potential susceptibility gene for viral infection of the myocardium. The shared cellular receptor, the Coxsackievirus B-Adenovirus receptor (CAR), for the two most common viral agents associated with acquired myocarditis and DCM, was shown to be up-regulated in patients with DCM, potentially making the expression of this protein a marker of susceptibility to virus infection. However, a study of the CAR gene in patients with DCM or myocarditis did not identify any genetic mutations in these patients. Finally a receptor for viral double stranded RNA (TLR-3) was identified. The role of this receptor in the innate immune response against cardiotropic viruses has yet to be elucidated.

New PCR test that recognizes all human prototypes of enterovirus: application for clinical diagnosis

We describe a new PCR test (Penter RT-PCR) that recognizes all 64 prototypes of enterovirus. Sixty clinical samples were analyzed in parallel with this Penter RT-PCR and previously described PCR tests: 34 and 32 samples tested positive, respectively. This assay is suitable for use in clinical diagnosis, and its ability to amplify all known serotypes makes it more useful than other consensus PCR tests.

Determination of enterovirus serotype inferred from sequence analysis of PCR products

BACKGROUND

Enterovirus infections are common in neonates. Virus isolation is the only diagnostic method to confirm enterovirus serotype infections, however, is not always successful.

OBJECTIVES

A new approach for the diagnosis of enterovirus infections was performed, using the reference strain inferred from sequence analysis of PCR products.

STUDY DESIGN

Virus isolation, enterovirus RT-PCR and sequence analysis were performed from clinical samples or stored sera from two neonates with fever and rash. Neutralizing test (NT) antibodies against prototype reference virus were measured in paired sera.

RESULTS

Virus isolation was negative in both patients but the enterovirus genome was amplified in the acute phase sera obtained from the two patients. From the results of sequence analysis of 109 nucleotides located in the 5'-noncoding of the conserved region of enteroviruses, a high homology to echovirus types 25 and 30 was found. More than a 4-fold increase in NT antibodies against reference viruses was demonstrated in the acute and convalescent phase sera. They were confirmed as echovirus type 25 and 30 infection, respectively.

CONCLUSIONS

These virological examinations are practical and useful for clinical settings for a diagnosis of enterovirus infections because of an insufficient positive rate in virus isolation.

Molecular sub-grouping of enterovirus reference and wild type strains into distinct genetic clusters using a simple RFLP assay

RFLP analysis and sequencing of RT-PCR amplicons in previous studies revealed the existence of intra-serotypic variability in the 5'-UTR of human enteroviruses, complicating the use of this method to serotype isolates. During the present study, the available sequences of many enterovirus reference and wild type strains were analysed in an attempt to discover restriction sites that would rapidly and reliably aid the classification of human enteroviruses into specific sub-groups on the basis of their 5'-UTR for diagnostic and/or epidemiological purposes. Despite intratypic genetic variability in the 5'-UTR, the results of the sequence analysis, as well as data from the RFLP analysis of 61 enterovirus reference strains from 60 different serotypes and 123 clinical isolates showed that one restriction endonuclease, HpaII, may contribute to a reliable sub-classification of CAVs and the rest of enteroviruses, on the basis of 5'-UTR, into five genetic groups, which could be particularly useful in clinical and epidemiological studies. Although more sequence data from enterovirus reference and wild type strains may be required for the elaboration of a precise molecular identification system, the more possible genotypic classification into distinct clusters, as shown with the restriction enzyme HpaII, and the determination of the biological significance of this grouping (pathogenesis, epidemiology) might constitute an alternative means of enterovirus identification against conventional classification into distinct serotypes.

Evaluation of integrated cell culture-PCR (C-PCR) for virological analysis of environmental samples

AIMS

The aims of this study were to establish an integrated culture-polymerase chain reaction (C-PCR) method for detection of enteric viruses in environmental samples, and to evaluate it for sensitivity, speed and provision of virus infectivity data.

METHODS AND RESULTS

C-PCR, direct reverse transcription (RT)-PCR, PCR and plaque assay methods were used to detect enteroviruses and adenoviruses in seeded and naturally contaminated environmental samples. Using C-PCR, infectious enterovirus presence was confirmed in 3 d and adenovirus presence in 5 d, compared with up to 10 d required by conventional cell culture methods.

CONCLUSIONS

C-PCR was the preferred method for detection of enteric viruses in environmental samples containing high viral concentrations. It was less successful for samples with low viral concentrations or containing toxic materials or inhibitors.

SIGNIFICANCE AND IMPACT OF THE STUDY

C-PCR provides sensitive, specific results within 2-5 d and is useful as a rapid screen for environmental samples of low toxicity.