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

Progress in etiological diagnosis of viral meningitis

In recent years, with the rapid development of molecular biology techniques such as polymerase chain reaction and molecular biochip, the etiological diagnosis of viral encephalitis has a very big step forward. At present, the etiological examination of viral meningitis mainly includes virus isolation, serological detection and molecular biological nucleic acid detection. This article reviews the progress in etiological diagnosis of viral meningitis.

Highly sensitive and rapid identification of coxsackievirus A16 based on reverse transcription multiple cross displacement amplification combined with nanoparticle-based lateral flow biosensor assay

Introduction

One of the main pathogens responsible for human hand, foot, and mouth disease (HFMD), coxsackievirus A16, has put young children’s health at danger, especially in countries in the Asia-Pacific region. Early quick identification is essential for the avoidance and control of the disorder since there are no vaccinations or antiviral medications available to prevent and manage CVA16 infection.

Methods

Here, we describe the creation of an easy, speedy, and accurate CVA16 infection detection approach using lateral flow biosensors (LFB) and reverse transcriptionmultiple cross displacement amplification (RT-MCDA). A group of 10 primers was developed for the RT-MCDA system in order to amplify the genes in an isothermal amplification device while targeting the highly conserved region of the CVA16 VP1 gene. Then, without requiring any extra tools, RT-MCDA amplification reaction products might well be detected by visual detection reagent (VDR) and LFB.

Results

The outcomes showed that 64°C within 40 min was the ideal reaction setting for the CVA16-MCDA test. Target sequences with <40 copies might be found using the CVA16-MCDA. There was no cross-reaction among CVA16 strains and other strains. The findings demonstrated that the CVA16-MCDA test could promptly and successfully identify all of the CVA16-positive (46/220) samples identified by the traditional real-time quantitative polymerase chain reaction (qRT-PCR) assays for 220 clinical anal swab samples. The whole process, such as the processing of the sample (15 min), the MCDA reaction (40 min), and the documenting of the results (2 min), could be finished in 1 h.

Conclusion

The CVA16-MCDA-LFB assay, which targeted the VP1 gene, was an efficient, simple, and highly specific examination that might be used extensively in rural regions’ basic healthcare institutions and point-of-care settings.

Genetic diversity of the enteroviruses detected from cerebrospinal fluid (CSF) samples of patients with suspected aseptic meningitis in northern West Bank, Palestine in 2017

BACKGROUND

Human enterovirus genus showed a wide range of genetic diversity.

OBJECTIVES

To investigate the genetic diversity of the enteroviruses isolated in 2017 in northern West Bank, Palestine.

STUDY DESIGN

249 CSF samples from aseptic meningitis cases were investigated for HEV using two RT-PCR protocols targeting the 5' NCR and the VP1 region of the HEV genome. The phylogenetic characterization of the sequenced VP1 region of Echovirus18 (E18) and Coxsackievirus B5 (CVB5) isolated in Palestine along with 27 E18 and 27 CVB5 sequences available from the Genbank were described.

RESULTS

E18 and CVB5 account for 50% and 35% of the successfully HEV types, respectively. Phylogenetic tree of E18 and CVB5 showed three main clusters, with all Palestinian isolates uniquely clustering together with those from China and from different countries, respectively. Cluster I of E18, with 13 Palestinian and 6 Chinese isolates, showed the lowest haplotype-to-sequence ratio (0.6:1), haplotype diversity (Hd), nucleotide diversity (π), and number of segregating sites (S) compared to clusters II and III. Furthermore, cluster I showed negative Tajima's D and Fu-Li'sF tests with statistically significant departure from neutrality (P<0.01). In both E18 and CVB5 populations, high haplotype diversity, but low genetic diversity was evident. Inter-population pairwise genetic distance (Fst) and gene flow (Nm) showed that the Palestinian E18 and CVB5 clusters were highly differentiated from the other clusters.

CONCLUSIONS

The study divulged close genetic relationship between Palestinian HEV strains as confirmed by population genetics and phylogenetic analyses.

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTube^TM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTube^TM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.

Molecular detection and genotyping of enteroviruses from CSF samples of patients with suspected sepsis-like illness and/or aseptic meningitis from 2012 to 2015 in West Bank, Palestine

BACKGROUND

Human enteroviruses (HEVs) are the most frequently reported cause of aseptic meningitis with or without CSF pleocytosis in childhood. Rapid detection and genotype of HEVs is essential to determine the causative agent and variant causing sepsis-like illness and/or aseptic meningitis.

AIM

To investigate the molecular epidemiology of enteroviruses (EVs) among patients with sepsis-like illness and/or aseptic meningitis admitted to three major hospitals in West Bank, Palestine from 2012 to 2015.

METHODS

During the study period, 356 CSF samples were collected from patients with sepsis-like illness and/or aseptic meningitis. Two RT-nested PCR assays targeting a partial part of 5'UTR for direct diagnosis and the VP1 region for genotyping by sequence analysis of the viral genome were used.

RESULTS

HEV RNA was detected in 66 of 356 (18.5%) of CSF samples. Age distribution showed that 64% (42/66) were infants (<1 year), 18% were children between 1 and 5 years old, 12% were children between 5 and 10 years old, and 6% were more than 10 years old. Of the 66 EV cases, 12 were successfully genotyped. Five different EV genotypes were identified. All of them belonged to HEV-B species. The study showed that echovirus 6 genotype accounted for 42% of the sequenced cases. The HEV infections in the present study tended to show slight seasonal pattern with more cases occurring during spring and summer, yet still significant numbers were also reported in fall and winter seasons.

CONCLUSION

HEV was isolated from a significant number of children with sepsis-like illness and/or aseptic meningitis. In addition, the molecular method utilized for direct diagnosis and genotyping of HEV from CSF revealed that more than one HEV type circulated in the West Bank, Palestine during the study period.

Confirmed viral meningitis with normal CSF findings

An 18-year-old woman presented with a progressively worsening headache, photophobia feverishness and vomiting. Three weeks previously she had returned to the UK from a trip to Peru. At presentation, she had clinical signs of meningism. On admission, blood tests showed a mild lymphopenia, with a normal C reactive protein and white cell count. Chest X-ray and CT of the head were normal. Cerebrospinal fluid (CSF) microscopy was normal. CSF protein and glucose were in the normal range. MRI of the head and cerebral angiography were also normal. Subsequent molecular testing of CSF detected enterovirus RNA by reverse transcriptase PCR. The patient's clinical syndrome correlated with her virological diagnosis and no other cause of her symptoms was found. Her symptoms were self-limiting and improved with supportive management. This case illustrates an important example of viral central nervous system infection presenting clinically as meningitis but with normal CSF microscopy.

A new factor influencing pathogen detection by molecular assay in children with both mild and severe hand, foot, and mouth disease

This study aimed to find novel information concerning pathogen detection and some probable coinfection factors in hand, foot, and mouth disease (HFMD). In this study, 1104 clinically diagnosed HFMD patients were included. Enterovirus 71 (EV71), coxsackievirus A16 (CA16), and 14 different respiratory pathogens were examined from nasopharyngeal swabs using polymerase chain reaction (PCR) or reverse transcriptase PCR (RT-PCR). To evaluate the immune activation in HFMD patients, 8 cytokines and IgM antibodies to EV71 and CA16 from mild and severe patients were detected. Our results indicated that the severity of HFMD may affect the pathogen detection. The lower positive rates of enterovirus and respiratory viruses in severe HFMD cases by RT-PCR were probably related to stronger immune response. Therefore, immunological tests such as ELISA are essential supplements to PCR or RT-PCR in order to increase pathogen diagnosis in HFMD, especially in severe cases.

Enteroviral central nervous system infections in children of the region of monastir, Tunisia: diagnosis, laboratory findings of cerebrospinal fluid and clinical manifestations

Human enteroviruses (HEV) are one of the major causes of central nervous system (CNS) infections in pediatrics. A prospective study was conducted to assess the epidemiological, clinical, and laboratory characteristics of enterovirus (EV) infections of the CNS in children under 15-years-old, suspected of having viral CNS infections and admitted to the Pediatric Department of Monastir University Hospital, Tunisia. Enteroviral RNA was detected by 5' NCR nested RT-PCR assay in 33 % (20 out of 60) of cerebrospinal fluid specimens, whereas only six samples (10 %) were EV positive in cell culture. EV-positive patients were clustered according to their clinical manifestations, predominantly diagnosed as aseptic meningitis (65 %) and meningoencephalitis (20 %). Fever, headache, vomiting, and neck stiffness were the most pronounced symptoms. Pleocytosis with the predominance of lymphocytes was observed in 60 % of EV positive specimens. Although patients suffering from EV infections were encountered throughout the year, most occurred during spring and summer months. Using VP1-2A nested RT-PCR and sequence analysis, three of the 20 positive HEV were identified as Echovirus (E)-9. This is the first report of a cluster of aseptic meningitis cases caused by E-9 in Monastir.

Comparison of quantitative RT-PCR with cell culture to detect viral hemorrhagic septicemia virus (VHSV) IVb infections in the Great Lakes

Viral hemorrhagic septicemia virus (VHSV) is an important pathogen of cultured and wild fish in marine and freshwater environments. A new genotype, VHSV IVb, was isolated from a fish collected from the Great Lakes in 2003. Since the first isolation, VHSV IVb has been confirmed in 28 species, signaling the early invasion and continued spread of this Office International des Epizooties-reportable agent. For surveillance of this virus in both wild and experimental settings, we have developed a rapid and sensitive one-step quantitative real-time polymerase chain reaction (qRT-PCR) assay that amplifies a 100-base-pair conserved segment from both the genomic negative strand and the mRNA positive strand of the nucleoprotein (N) gene of VHSV IVb. This assay is linear over seven orders of magnitude, with an analytical capability of detecting a single copy of viral RNA and reproducibility at 100 copies. The assay is approximately linear with RNA input from 50 to 1000 ng per assay and works equally well with RNA prepared from a column-based or phenol-chloroform-based method. In wild-caught fish, 97% of the cases were found to be more than three orders of magnitude more sensitive using qRT-PCR than using cell culture. Of the 1,428 fish from the Great Lakes region tested in 2006 and 2007, 24% were positive by qRT-PCR whereas only 5% were positive by cell culture. All of the fish that were positive by cell culture were also positive by qRT-PCR. Importantly, qRT-PCR sensitivity is comparable to that of cell culture detection when comparing VHSV viral RNA levels with viral titer stocks, confirming that the high qRT-PCR signals obtained with diagnostic samples are due to the accumulation of N gene mRNA by transcriptional attenuation. The qRT-PCR assay is particularly valuable for rapid and high-throughput prescreening of fish before confirmatory testing by cell culture or sequencing tissue-derived amplicons and especially in detecting infection in fish that do not show clinical signs of VHS.

Enterovirus meningitis in Greece from 2003-2005: diagnosis, CSF laboratory findings, and clinical manifestations

Enteroviruses (EVs) are the most commonly identified cause of aseptic meningitis. Rapid detection and characterization of EV meningitis is essential in making decisions for patient management and treatment. A total of 52 cases of acute aseptic meningitis that occurred from March 2003 to April 2005 were investigated for EVs using viral culture and/or molecular methods directly in the cerebrospinal fluid (CSF). EVs were detected in 21 out of 52 (40.4%) patients using reverse transcription-PCR (RT-PCR) and/or tissue culture. EVs were isolated from six out of 37 (16.2%) cultured specimens, while 20 out of 52 (38.4%) specimens yielded positive results when 5'non-coding region (5'NCR) RT-PCR assay was used. One specimen that was culture-positive was RT-PCR-negative. Using the VP1-2A RT-PCR and sequence analysis, 14 of the 21 positive EVs were identified as: four strains of Coxsackie virus B5, five echovirus 11, two echovirus 9, one echovirus 5, one echovirus 14, and one Coxsackie virus A9. Fever, headache, vomiting, and stiff neck were the most pronounced symptoms. Pleocytosis with the predominance of lymphocytes and mild elevated protein levels characterized the CSF specimens. Coxsackie virus B5 and echovirus 11 were the predominant serotypes during the study period. Although there was seasonal enteroviral activity (April-November), cases also occurred in the cold months. The 5'NCR and VP1-2A RT-PCR with sequence analysis were found to be superior to conventional methods for direct diagnosis and the typing of EVs.

Real-time PCR for mumps diagnosis on clinical specimens--comparison with results of conventional methods of virus detection and nested PCR

BACKGROUND

Since November 2003, the UK has seen a dramatic rise in the number of mumps cases, resulting in increasing demands on virology laboratories to confirm mumps infection in a timely and efficient manner. Traditional mumps virus detection methods are often insensitive, lengthy, and cumbersome. Some laboratories in the UK now use molecular methods that are based on nested polymerase chain reaction (PCR). Early serological diagnosis often relies on detection of anti-mumps IgM, which may be absent in the first 10 days of illness.

OBJECTIVES

We compared a one-step real-time RT-PCR with an established nested PCR (SH-PCR) and virus detection by culture and antigen detection, and assessed the clinical usefulness of mumps real-time PCR for diagnosis from CSF.

STUDY DESIGN

In total, 280 clinical samples were investigated by real-time PCR, nested PCR and a combination of traditional virus detection methods (antigen detection on oral samples, cell culture on all samples). Furthermore, 88 CSF samples submitted for diagnosis of possible viral meningitis were analysed by real-time PCR.

RESULTS

The real-time PCR detected the highest number of positive oral samples (119/180) compared to SH-PCR (92/180) and combined virus culture and antigen detection procedures (90/180). Sensitivity of mumps virus detection in urine was poor for all three methods: 34.0% (traditional detection), 29.8% (real-time PCR) and 2.1% (SH-PCR), respectively. Real-time PCR on 88 CSF samples identified five patients with mumps meningitis, significantly increasing viral diagnosis in this cohort.

CONCLUSION

Real-time PCR on oral samples is the investigation of choice for mumps infection. Mumps virus detection in urine by any of the PCRs used was clearly less successful. Real-time PCR on CSF samples seems a promising adjunct for diagnosis of mumps meningitis, especially in an age group with high incidence of mumps.

Clinical and diagnostic findings of an echovirus meningitis outbreak in the north west of England

INTRODUCTION

An outbreak of echovirus meningitis occurred in the north west of England in 2001. This paper reviewed the clinical features and the role of different diagnostic methods.

METHODS

This was a prospective study of adults admitted to a regional infectious disease unit with a probable diagnosis of meningitis, March to August 2001.

RESULTS

Half the 40 cases were male; median age was 28 (range 16-51) years. Fifteen of 38 (39.5%) were smokers, and 20 of 24 (83.3%) had close contact with children. Median (range) duration of symptoms was 1.1 (0.25-7) days. Symptoms included headache (100%), photophobia (87.5%), and nausea (67.5%), and severity ranged from minimal signs to those consistent with a meningoencephalitis. The diagnosis was confirmed virologically in 29 of 40 (72%); echovirus 30 was isolated from six. Cerebrospinal fluid (CSF) enterovirus polymerase chain reaction (PCR) was positive in 26 of 32 (81%), and CSF virus culture in 3 of 16 (19%). Thirty one per cent of CSF samples had a neutrophil predominance, and 3 of 29 (10%) virologically confirmed cases had normal CSF microscopy and biochemistry.

CONCLUSION

CSF microscopy may be normal or suggest bacterial meningitis in a substantial minority of cases of echovirus meningitis. CSF PCR for enterovirus seems to be more sensitive than virus culture of CSF, although PCR does not yield information on circulating virus type. Early and accurate diagnosis could reduce both use of parenteral antibiotics and length of hospital stay with both morbidity and cost implications. Close contact with children may be a risk factor, particularly if good hygiene measures are not practised.

Human parechovirus types 1, 2 and 3 infections in Canada

These infections are associated with a variety of clinical syndromes, in part related to specific serotype.

A new reverse transcription–polymerase chain reaction assay was developed for identification of 28 Canadian human parechovirus (HPeV) isolates, including 20 HPeV-1, 3 HPeV-2, and 5 HPeV-3, recovered from 1985 to 2004. All HPeV-1 isolates but 1 were genetically distinct from the Harris reference strain. One HPeV-2 isolate was related to the Williamson strain; the other 2 were related to the Connecticut strain. HPeV-3 isolates clustered together. Seventy-five percent of isolates were recovered during the typical enterovirus season. All patients but 1 were children with a mean age of 14.6 months, 6.3 months, and 0.7 months for HPeV-1, HPeV-2, and HPeV-3 patients, respectively. All HPeV-2– and HPeV-3–infected children were hospitalized with a diagnosis of viremia or sepsis. HPeV-1–infected children had bronchiolitis diagnosed in 50% of the cases, with few cases of pneumonia and enteritis. Two infected patients (1 child with leukemia and a 78-year-old woman) died of septic shock and severe pneumonia, respectively.

Epidemiological study of non-polio enterovirus neurological infections in children in the region of Monastir, Tunisia

The epidemiological, virological, and clinical syndromes of 86 children younger than 13 years suspected of having neurological diseases and admitted to Fattouma Bourguiba Hospital of Monastir from January 2002 to November 2003 were analyzed. The presence of enterovirus was studied in cerebrospinal fluid (CSF) samples by reverse transcription-polymerase chain reaction (RT-PCR) and by isolation on cell culture. Sixty-one (71%) specimens were positive by RT-PCR, whereas 45 (52.3%) were detected by cell culture. Eighty percent (n = 36) of cultured enteroviruses were identified, whereas 20% were untyped. Echoviruses were isolated most frequently, with 32 cases (71.1%) in children. Echovirus 6 was the most commonly identified serotype (22.2%), followed by echovirus 13 (20%). The highest incidence on neurological infection (19.6%) occurred in children less than 6 months of age. The infected children were predominantly male (62.3%). Enteroviruses were detected in all the period of the year with the highest rate in the spring and summer months. Aseptic meningitis was the most commonly diagnosed disease (49%).

Detection of human picornaviruses by multiplex reverse transcription-PCR and liquid hybridization

A qualitative multiplex reverse transcription (RT)-PCR and liquid hybridization assay for the detection of human enteroviruses, rhinoviruses, parechoviruses, and Aichi virus was developed. Furthermore, a separate assay for the recognition of hepatitis A virus was established to complement the test pattern so that all human picornaviruses were covered. The amplicons, which represented the 5' untranslated regions of the viral RNA genomes, were identified in liquid hybridization reactions with genus-specific digoxigenin-labeled oligonucleotide probes. The sensitivity of the multiplex RT-PCR and liquid hybridization assay was 10 to 100 picornavirus genome equivalents for representatives of each picornavirus genus. The hepatitis A virus assay exhibited a sensitivity of 10 genome copies. Both the uniplex and the multiplex tests were highly specific for the target viruses. Twenty-three clinical samples, including cerebrospinal fluid, serum, and nasopharyngeal swab specimens, were used for clinical evaluation of the multiplex RT-PCR assay. The results obtained were consistent with the results of routine virus diagnostic assays. Furthermore, the assay was used to screen 68 stool specimens for the presence of parechoviruses and Aichi virus. One sample was found to contain parechovirus RNA, whereas no Aichi virus was detected. The assay described here can be applied for the efficient identification of human enteroviruses and rhinoviruses in clinical specimens and simultaneously enables the collection of information on the epidemiology and clinical outcomes of infections caused by the currently poorly known human parechoviruses and Aichi virus.

Identification of enteroviral infection among infants and children admitted to hospital with acute gastroentritis in Ho Chi Minh City, Vietnam

A total of 276 fecal specimens collected from infants and children admitted to hospital with acute gastroenteritis in Ho Chi Minh City, Vietnam from October 2002 to September 2003, were tested for the presence of enteroviruses by RT-PCR and virus isolation. Enteroviruses were detected in 27 patients by RT-PCR corresponding to 9.8%. However, only four enterovirus strains could be isolated by cell culture with two different cell lines CaCo2 and Vero, showing specific cytopathic effect (CPE). The results clearly indicate that RT-PCR is a sensitive, specific assay to investigate the true burden of acute gastroenteritis due to enteroviruses in clinical fecal specimens. In the present study, enteroviruses were identified throughout the year except in May and the highest number was in December. Enteroviruses were subjected to molecular analysis by sequencing. It was found that enterovirus strains detected were classified further into two distinct genetic clusters (I, II) and demonstrated the great genetic diversity among them. Based on genetic analysis, 5' noncoding region (5' NCR) sequences suggested the predominant presence of Vietnamese enteroviruses with the greatest similarities to coxsakieviruses (51.9%) and echoviruses (29.6%). Interestingly, two of the sequenced specimens of enteroviruses were similar to a new strain called enterovirus 74. This report is the first detection of enteroviral infection in feces from infants and children admitted to hospital with acute gastroenteritis in Vietnam.

Viral meningitis

Viruses probably account for most cases of acute meningitis. Viral meningitis is often assumed to be a largely benign disease. For the commonest pathogens causing meningitis, enteroviruses, this is usually the case; however, for many of the other pathogens causing viral meningitis, and for common pathogens in the immunocompromised or infants, viral meningitis is frequently associated with substantial neurological complications and a significant mortality. Diagnostic methods for rapid and accurate identification of pathogens have improved over recent years, permitting more precise and earlier diagnoses. There have been fewer developments in therapies for viral meningitis, and there remain no effective therapies for most pathogens, emphasising the importance of prevention and early diagnosis. This review focuses on the presentation, diagnosis and management of viral meningitis and also covers the prevention of meningitis for pathogens where effective vaccines are available.