Analysis of enterovirus genotypes using single-strand conformation polymorphisms of polymerase chain reaction products

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.

Differences in replication capacity between enterovirus 71 isolates obtained from patients with encephalitis and those obtained from patients with herpangina in Taiwan

The cellular-tropism and biological characteristics of enterovirus 71 (EV71) isolates in Taiwan (TW) were studied. Growth curve experiments were conducted using cell lines that were possibly exhibited pathogenesis, and RT-PCR and sequencing tests were undertaken to amplify the 5' non-coding region (5'-NCR). The encephalitis isolate EV71 TW98NTU2078 was PBMC-tropic, temperature-resistant (Tr) at 40 degrees C, and easier to replicate in HTB-14 (astrocytoma) than the herpangina isolate EV71 TW98NTU1186 (The viral yields were 100-fold higher than those of the herpangina isolate EV71 TW98NTU1186 at 96 hr post infection.). The herpangina isolate EV71 TW98NTU1186 was non-PBMC-tropic, and temperature-sensitive (Ts) at 40 degrees C. The replication of EV71 TW98NTU1186 in HTB-14 was lower. No EV71 isolate infected HTB-37 (human colon adenocarcinoma cells). The encephalitis EV71 isolate exhibited better replication and transmission in PBMCs and astrocytes than did the EV71 isolate without CNS involvement.

Human enterovirus isolates from an outbreak typed using heteroduplex mobility analysis

Genotyping and serotyping of enteroviruses is important for epidemiological, prognostic, and therapeutic reasons. In this study clinical isolates of enterovirus 71 during an outbreak of childhood meningoencephalitis in Sydney, Australia were identified using heteroduplex mobility analysis (HMA) of products from RT-PCR amplification of the 5' untranslated region. Five enterovirus 71 isolates shared identical heteroduplex patterns and nucleotide sequences in the 5' untranslated region. A sixth isolate exhibited minor differences in heteroduplex pattern and sequencing confirmed the isolate varied by 1% at the nucleotide level. The use of multiple reference strains and the analysis of heteroduplex patterns increased the confidence of isolate identification, and allowed identification of strain variation which could be subsequently further analyzed using sequencing. HMA can be used to accurately distinguish identical and variant isolates derived from sporadic cases and clustered infections with enteroviruses, including those causing serious infections.

Genotyping of human cytomegalovirus using non-radioactive single-strand conformation polymorphism (SSCP) analysis

Genetic variation in the glycoprotein B (gB) gene may play a role in human cytomegaloviruses (HCMVs) pathogenesis. Using restriction analysis of the gB gene product (PCR-RFLP), amplified by the nested polymerase chain reaction, the HCMV strains can be compared and classified into at least four HCMV groups. PCR single-strand conformation polymorphism (PCR-SSCP) is one of the techniques used to identify a mutant sequence or a polymorphism in a known gene. SSCP analysis has the advantage over RFLP analysis on detection of DNA polymorphisms and point mutations at a variety of positions in DNA fragments. However, the original SSCP protocols using the incorporation of radioactive label and polyacrylamide gel electrophoresis for detection are labour intensive and time-consuming. A simplified SSCP protocol is described to identify HCMV strains and the gB genotype, allowing the detection of sequence variations not residing in the endonuclease recognition sites.

Coxsackie B virus infection in idiopathic dilated cardiomyopathy: clinical and pharmacological implications

Idiopathic dilated cardiomyopathy (IDC) is a myocardial disease characterised by ventricular dilatation, impaired contractility, and the symptoms of congestive heart failure. Although the causes of IDC remain uncertain, much interest has been focused on the enteroviral infection in the myocardium in the pathogenesis of this disease. Enteroviral RNA has been demonstrated in the myocardium at all stages of IDC. Recent studies using sequence analysis of enteroviral polymerase chain reaction (PCR) products have shown that the viruses detected in hearts of patients with IDC are coxsackie B. In addition, active coxsackieviral RNA replication in the myocardium has been demonstrated by strand-specific detection of viral RNA. Viral antigen has also been found in hearts with IDC by immunohistochemical techniques. In tissue culture experiments and transgenic mice, it has been shown that restricted coxsackieviral RNA replication, and not infectious virus progeny, in the myocardium can impair cardiac contractile function and lead to dilated cardiomyopathy. Coxsackieviral RNA in the myocardium can be a marker of a poor clinical outcome after partial left ventriculectomy, and might influence prognosis after heart transplantation. Therefore, there is a therapeutic need to detect replicating coxsackieviral RNA in the myocardium, and a specific therapy for coxsackie B viruses is indicated in the management of patients with virus-positive IDC.

Variability in molecular typing of Coxsackie A viruses by RFLP analysis and sequencing

The aim of the present study was to develop an assay capable of classifying the Coxsackie A virus (CAV) prototype strains on the basis of restriction fragment length polymorphism (RFLP) analysis of 5'-UTR-derived reverse transcription polymerase chain reaction (RT-PCR) amplicons, and to determine how these data could be used for typing wild-type CAV isolates. Moreover, sequencing of the amplified genomic fragments of the clinical isolates, and comparison with all the published sequences of the respective genomic region of enterovirus reference and wild-type strains were attempted for typing of the isolates. Twenty-four prototype CAV strains from the 23 currently recognized serotypes were studied; most of them were successfully differentiated with the aid of four restriction endonucleases: HaeIII, HpaII, DdeI, and StyI. It was not possible to differentiate between CAV5, 7, and 16, or between CAV15 and 18 in this way, but the members of each of these two groups were satisfactorily differentiated with the aid of single-strand conformational polymorphism (SSCP) analysis of their RT-PCR amplicons. Fifteen clinical isolates, 13 of them of known CAV serotype, were also studied with the same four endonucleases and the results were compared with the data obtained from the RFLP analysis of the reference strains. The experimental results showed that only two clinical samples of previously known identity had an identical restriction pattern with the respective prototype strains. The sequences of the amplicons of the clinical isolates had the greatest percentage of alignment with enterovirus strains of a different serotype, indicating variability in the 5'-UTR and the inability to use the whole sequence of the amplicons for typing CAVs. The significance of the findings in relation to the possible usefulness of the RFLP-based method is discussed.

Myocardial inflammatory cell infiltrates in cases of dilated cardiomyopathy as a determinant of outcome following partial left ventriculectomy

Partial left ventriculectomy (PLV) can be used to treat refractory congestive heart failure caused by dilated cardiomyopathy (DCM). In order to understand the relationship between the underlying myocardial injury and early clinical outcomes after PLV, histopathologic, immunohistochemical and virologic studies of the resected myocardium were performed. The posterolateral left ventricular walls from 27 patients with idiopathic DCM were examined. Cardiomyocyte diameter, degree of myocardial fibrosis, degree of cardiomyocyte degeneration, and degree of inflammatory cell infiltration were compared with mortality rates. Polymerase chain reaction was performed to detect enterovirus genome in the myocardium. Some patients had inflammatory cell infiltrates with focal accumulations of lymphocytes and macrophages, including both cytotoxic/suppressor T-cells and helper/inducer T-cells. The number of inflammatory cells (activated lymphocytes plus macrophages/mm2) was significantly greater in patients who died of cardiac insufficiency after surgery (27.8 +/- 5.7; n = 7) than in the survivors (11.1 +/- 2.5; n = 15). There was no significant difference in the degree of myocardial fibrosis, cardiomyocyte diameter or degree of cardiomyocyte degeneration between the 2 groups. Enterovirus genome was detected in the myocardium of 9 (38%) of 24 patients examined and 5 of these enterovirus-positive hearts had severe inflammatory cell infiltrates (37.9 +/- 2.5/mm2). Early survival in patients undergoing PLV for DCM is significantly affected by the degree of myocardial inflammation, so patients with more severe or ongoing inflammation may have poor clinical outcomes. Chronic myocarditis may play an important role in the etiology and pathophysiology of idiopathic DCM.

Molecular detection and identification of an enterovirus during an outbreak of aseptic meningitis

Stool samples from sixteen cases of children with meningitis originating from four different and geographically isolated parts of Greece were investigated for enteroviruses. The conventional method of cell culture in four different cell lines was initially used for the isolation of enteroviruses. The results showed a cytopathic effect (CPE) in all cases after two, or even more successive passages in only one cell line (RD), although a less-than-satisfactory CPE was obtained in many cases. Seroneutralization with RIVM mixed hyperimmune antisera followed and the isolates were typed as Coxsackie B viruses. The method of RT-PCR with enterovirus-specific primers targeted to the highly conserved 5'-UTR of the genome was initially used for the detection of enteroviruses from the inoculated cell cultures. A positive RT-PCR result was obtained for all of the clinical samples rapidly and accurately and the isolates were further characterized with the aid of Restriction Fragment Length Polymorphism (RFLP) analysis and Single Strand Conformation Polymorphism analysis (SSCP) of the amplicons. The RFLP analysis showed first of all that the isolates had an identical restriction pattern with Coxsackie B5 Faulkner reference strain with 4 out of 5 restriction enzymes and secondly, both RFLP and SSCP analysis indicated the epidemiological association of the isolates. The speed of the molecular methodology that was used in comparison with the conventional methods and its possible significance for the description of virus evolution and circulation in the populations is discussed.

Evaluation of viral infection in the myocardium of patients with idiopathic dilated cardiomyopathy

OBJECTIVES

The aim of this study was to evaluate the viral etiology of idiopathic dilated cardiomyopathy (DCM).

BACKGROUND

The demonstration of enteroviral genome in hearts with DCM has reinforced the importance of enteroviruses in the pathogenesis of DCM. However, there is uncertainty about the character and activity of enteroviruses detected in the myocardium. Recently, the association of hepatitis C virus or adenovirus with DCM has been reported.

METHODS

Myocardial specimens from 26 patients with idiopathic DCM, which were obtained at partial left ventriculectomy (PLV), were examined virologically. Strand-specific detection of enteroviral RNA was performed to differentiate active viral replication from latent persistence. Polymerase chain reaction was used to detect genomic sequences of hepatitis C virus, adenovirus, cytomegalovirus, influenza viruses, mumps virus, herpes simplex viruses, varicella-zoster virus and Epstein-Barr virus.

RESULTS

Plus-strand enteroviral RNA was detected in 9 (35%) of the 26 patients. Minus-strand enteroviral RNA was determined in seven (78%) of these nine plus-strand RNA-positive patients. Sequence analysis revealed that the enteroviruses detected were coxsackie B viruses, such as coxsackievirus B3 and B4. However, genetic material from other viruses was not detected. Six (86%) of seven minus-strand enteroviral RNA-positive patients died of cardiac insufficiency within the first six months after PLV.

CONCLUSIONS

Coxsackie B viruses were seen in hearts with idiopathic DCM. Active viral RNA replication appeared to be present in a significant proportion of these cases. Minus-strand coxsackieviral RNA in the myocardium can be a marker for poor clinical outcome after PLV. There was no evidence of persistent infection by other viruses in hearts with DCM.

Methods for subtyping and molecular comparison of human viral genomes

The development over the past two decades of molecular methods for manipulation of RNA and DNA has afforded molecular virologists the ability to study viral genomes in detail that has heretofore not been possible. There are many molecular techniques now available for typing and subtyping of viruses. The available methods include restriction fragment length polymorphism analysis, Southern blot analysis, oligonucleotide fingerprint analysis, reverse hybridization, DNA enzyme immunoassay, RNase protection analysis, single-strand conformation polymorphism analysis, heteroduplex mobility assay, nucleotide sequencing, and genome segment length polymorphism analysis. The methods have certain advantages and disadvantages which should be considered in their application to specific viruses or for specific purposes. These techniques are likely to become more widely used in the future for epidemiologic studies and for investigations into the pathophysiology of virus infections.

Use of base excision sequence scanning for detection of genetic variations in St. Louis encephalitis virus isolates

Twenty-two isolates of St. Louis encephalitis (SLE) virus of various geographical origins (Brazil, Argentina, Panama, Texas, Missouri, Maryland, California, and Florida) were examined for genetic variation by the base excision sequence scanning (BESS T-scan) method. A fragment was amplified in the envelope gene with the forward primer labeled in the PCR. The BESS T-scan method determined different clusters according to the profiles generated for the isolates and successfully grouped the isolates according to their geographical origins. Two major clusters, the North American cluster (cluster A) and the South and Central American cluster (cluster B), were defined. Two subgroups, the Texas-California subgroup (subgroup A1) and the Missouri-Maryland-Florida subgroup (subgroup A2), were distinguished within group A. Similarly, group B strains were subclustered to a South American subgroup (subgroup B1) and a Central American subgroup (subgroup B2). These results were consistent with those obtained by DNA sequencing analysis. The ability of the BESS T-scan method to discriminate between strains that present with high degrees of nucleotide sequence similarity indicated that this method provides reliable results and multiple applications for other virus families. The method has proven to be suitable for phylogenetic comparison and molecular epidemiology studies and may be an alternative to DNA sequencing.

Differentiation and characterization of enteroviruses by computer-assisted viral protein fingerprinting

We have developed and standardized a computerized method for the typing and characterization of enteroviruses with radiolabeled viral protein fingerprints. Enteroviral proteins were radiolabeled with [35S]methionine during growth in cell culture and were then separated by polyacrylamide gel electrophoresis. The dried gel was scanned, and from the resulting computer image (which resembled an autoradiogram) protein patterns were computer extracted and stored in a database. The enterovirus database contained community and prototype strains belonging to 20 different enteroviral serotypes. Each serotype has a discrete protein pattern, and the most important pattern differences for determining each type are in the region of the viral capsid proteins VP1, VP2, and VP3. When the database was challenged with 148 clinical enterovirus strains, 144 (97%) were correctly identified by using the correlation coefficient as a quantitative measure of relatedness between two patterns. This method can identify a type in a single test and represents a practical alternative to virus neutralization because it is less expensive, is much faster (3 rather than 10 days), and does not rely on any virus-specific reagents. The results also show that most of the strains currently isolated from the community have protein patterns different from those of their older prototype strains. Viral protein fingerprinting is an evolving, dynamic system for the typing and characterization of enteroviruses. The method is appropriate for use in clinical virology and reference laboratories for the typing of enteroviruses, for the study of the epidemiology of enteroviruses, and for surveillance of enteroviruses.

Molecular typing of enteroviruses: current status and future requirements. The European Union Concerted Action on Virus Meningitis and Encephalitis

Human enteroviruses have traditionally been typed according to neutralization serotype. This procedure is limited by the difficulty in culturing some enteroviruses, the availability of antisera for serotyping, and the cost and technical complexity of serotyping procedures. Furthermore, the impact of information derived from enterovirus serotyping is generally perceived to be low. Enteroviruses are now increasingly being detected by PCR rather than by culture. Classical typing methods will therefore no longer be possible in most instances. An alternative means of enterovirus typing, employing PCR in conjunction with molecular genetic techniques such as nucleotide sequencing or nucleic acid hybridization, would complement molecular diagnosis, may overcome some of the problems associated with serotyping, and would provide additional information regarding the epidemiology and biological properties of enteroviruses. We argue the case for developing a molecular typing system, discuss the genetic basis of such a system, review the literature describing attempts to identify or classify enteroviruses by molecular methods, and suggest ways in which the goal of molecular typing may be realized.

Molecular detection and differentiation of enteroviruses in endomyocardial biopsies and pericardial effusions from dilated cardiomyopathy and myocarditis

Enteroviruses (EVs), especially group B coxsackieviruses, have been implicated in the pathogenesis of myocarditis and dilated cardiomyopathy (DCM). To determine whether a specific type of EV is present in DCM hearts, we examined the genotypes of EVs detected in endomyocardial biopsies and pericardial effusions by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis. Positive PCR results were obtained from biopsies in 6 (19 percent) of 31 patients with DCM, 5 (18 percent) of 28 with myocarditis, 5 (22 percent) of 23 with other cardiac diseases, and from pericardial effusions in 4 (57 percent) of 7 patients with pericarditis. SSCP profiles of most of the clinical samples were different and were not identical to any of the standard group B coxsackie viruses. Our findings suggest that EV genomes are involved in the myocardium of patients with various cardiac conditions and that a particular type of EV is not present in DCM hearts.