Molecular identification of enteroviruses responsible for an outbreak of aseptic meningitis; implications in clinical practice and epidemiology

Molecular Epidemiology of Enterovirus in Children with Central Nervous System Infections

Limited recent molecular epidemiology data are available for pediatric Central Nervous System (CNS) infections in Europe. The aim of this study was to investigate the molecular epidemiology of enterovirus (EV) involved in CNS infections in children. Cerebrospinal fluid (CSF) from children (0–16 years) with suspected meningitis–encephalitis (ME) who were hospitalized in the largest pediatric hospital of Greece from October 2017 to September 2020 was initially tested for 14 common pathogens using the multiplex PCR FilmArray^® ME Panel (FA-ME). CSF samples positive for EV, as well as pharyngeal swabs and stools of the same children, were further genotyped employing Sanger sequencing. Of the 330 children tested with FA-ME, 75 (22.7%) were positive for EV and 50 different CSF samples were available for genotyping. The median age of children with EV CNS infection was 2 months (IQR: 1–60) and 44/75 (58.7%) of them were male. There was a seasonal distribution of EV CNS infections, with most cases detected between June and September (38/75, 50.7%). EV genotyping was successfully processed in 84/104 samples: CSF (n = 45/50), pharyngeal swabs (n = 15/29) and stools (n = 24/25). Predominant EV genotypes were CV-B5 (16/45, 35.6%), E30 (10/45, 22.2%), E16 (6/45, 13.3%) and E11 (5/45, 11.1%). However, significant phylogenetic differences from previous described isolates were detected. No unusual neurologic manifestations were observed, and all children recovered without obvious acute sequelae. Specific EV circulating genotypes are causing a significant number of pediatric CNS infections. Phylogenetic analysis of these predominant genotypes found genetic differences from already described EV isolates.

Molecular characterization of enteroviruses among hospitalized patients in Greece, 2013-2015

BACKGROUND

There are only sporadic data for the circulation of Enteroviruses (EVs) in Greece with previous studies reporting mainly the presence of Echoviruses (E) and Coxsackie viruses (CV) B.

OBJECTIVES

We carried out a surveillance study for the molecular characterization of EVs detected in hospitalized patients throughout Greece as well as a phylogenetic analysis of the most frequently encountered serotypes.

STUDY DESIGN

Stools, cerebrospinal fluids, throat swabs and blood samples were collected from hospitalized patients with suspicion of EV infection. All samples were tested for EVs by rRT-PCR targeting the 5' untranslated region of EV genome. For positive samples, PCR amplification and sequencing targeting a part of VP1 region was performed.

RESULTS

We examined 831 samples and 209 were positive for EVs with Enterovirus B species being the most frequently amplified. E30, CVB5 and E9 were the most frequent serotypes of Enterovirus B species, whereas CVA6 and EV-A71 the most frequent serotypes of Enterovirus A species. Evs were significantly detected more frequently in stool samples compared to other types of specimens. Phylogenetic analysis revealed that most EV-A71 strains clustered in the subgenogroups C2 whereas all the CVA6 strains belonged to sub-genotype D3. Additionally, two different lineages of E30 and three different clusters of E9 viruses circulated simultaneously in Greece. Our data indicated that most EV strains from Greece were similar to strains circulating throughout Europe during the same period.

CONCLUSIONS

We provide a comprehensive picture of EVs circulating in Greece which can be helpful to interpret trends in EV diseases by associating them with circulating serotypes.

Molecular Pathogenicity of Enteroviruses Causing Neurological Disease

Enteroviruses are single-stranded positive-sense RNA viruses that primarily cause self-limiting gastrointestinal or respiratory illness. In some cases, these viruses can invade the central nervous system, causing life-threatening neurological diseases including encephalitis, meningitis and acute flaccid paralysis (AFP). As we near the global eradication of poliovirus, formerly the major cause of AFP, the number of AFP cases have not diminished implying a non-poliovirus etiology. As the number of enteroviruses linked with neurological disease is expanding, of which many had previously little clinical significance, these viruses are becoming increasingly important to public health. Our current understanding of these non-polio enteroviruses is limited, especially with regards to their neurovirulence. Elucidating the molecular pathogenesis of these viruses is paramount for the development of effective therapeutic strategies. This review summarizes the clinical diseases associated with neurotropic enteroviruses and discusses recent advances in the understanding of viral invasion of the central nervous system, cell tropism and molecular pathogenesis as it correlates with host responses.

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.

Serum Neutralization Assay for the Determination of Antibody Levels Against Non-Polio Enterovirus Strains in Central and Western Greece

Mutations and recombination events have been identified in enteroviruses. Point mutations accumulate with a frequency of 6.3 × 10(-4) per base pair per replication cycle affecting the fitness, the circulation, and the infectivity of enteroviral strains. In the present report, the serological status of the Central and Western Greek population (Larissa and Ioannina, respectively) in the 1-10-year, 11-20-year, 21-30-year, and 31-40-year age groups against six non-polio enterovirus strains, their respective echovirus prototypes, and Sabin 1, 2, and 3 vaccine strains was evaluated, through serum-neutralization assay. In the Western Greek population, antibody levels were detected only for clinical isolates of E30 serotype in all age groups, and for environmental isolate LR61G3 (E6 serotype) only in the 31-40 age group, whereas an immunity level was observed in the Central Greek population, against all strains, except for EIS6B (E3 serotype). Amino acid substitutions were encountered across the structural region of the capsid, between the prototypes and the respective isolates. These substitutions may alter the antigenicity of each strain and may explain the variations observed in the neutralization titers of the different strains. As a consequence, these substitutions severely affect antibody binding and increase the ability of the virus to escape the immune response. It is tempting to assume that changes in the antigenic properties observed in circulating echoviruses represent a selection of viral variants that are less prone to be neutralized by human antibodies. These facts argue for the need of immunological studies to the population to avoid epidemics due to the circulation of highly evolved derivatives.

Detection of Enteroviruses in Influent and Effluent Flow Samples from Wastewater Treatment Plants in Italy

This study evaluated the presence and seasonal distribution of polio and other enteroviruses in four wastewater treatment plants in three cities in Italy, using different treatment systems. Detection of enteroviruses was carried out by virus isolation in cell cultures after concentration of water samples collected at both inlet and outlet of the treatment plants, following the methods described in the WHO guidelines. Viral serotypes isolated before and after water treatment were compared. Forty-eight non-polio enteroviruses were isolated from 312 samples collected at the inlet of the four wastewater treatment plants, 35 of which were Coxsackievirus type B (72.9 %) and 13 Echovirus (27.1 %). After treatment, 2 CVB3, 1 CVB5, and 1 Echo 6 were isolated. CVB3 and Echo 6 serotypes were also detected in samples collected at the inlet of the TP, in the same month and year. The high rate of detection of infectious enteroviruses in inlet sewage samples (30.1 %) indicates wide diffusion of these viruses in the populations linked to the collectors. The incomplete removal of infectious viruses following sewage treatment highlights possible risks for public health relate to treated waters discharge into the environment.

Successful control of an echovirus 6 meningitis outbreak in a neonatal intensive care unit in central Greece

We report an outbreak of echovirus 6 meningitis in a neonatal intensive care unit in central Greece from July to August 2011. The most probable source of the outbreak was a mother; during hospitalization, her neonate was initially infected, followed by 7 more. Stricter infection control measures were implemented, and no other cases have been observed.

Detection of viruses in used ventilation filters from two large public buildings

BACKGROUND

Viral and bacterial pathogens may be present in the air after being released from infected individuals and animals. Filters are installed in the heating, ventilation, and air-conditioning (HVAC) systems of buildings to protect ventilation equipment and maintain healthy indoor air quality. These filters process enormous volumes of air. This study was undertaken to determine the utility of sampling used ventilation filters to assess the types and concentrations of virus aerosols present in buildings.

METHODS

The HVAC filters from 2 large public buildings in Minneapolis and Seattle were sampled to determine the presence of human respiratory viruses and viruses with bioterrorism potential. Four air-handling units were selected from each building, and a total of 64 prefilters and final filters were tested for the presence of influenza A, influenza B, respiratory syncytial, corona, parainfluenza 1-3, adeno, orthopox, entero, Ebola, Marburg, Lassa fever, Machupo, eastern equine encephalitis, western equine encephalitis, and Venezuelan equine encephalitis viruses. Representative pieces of each filter were cut and eluted with a buffer solution.

RESULTS

Attempts were made to detect viruses by inoculation of these eluates in cell cultures (Vero, MDCK, and RK-13) and specific pathogen-free embryonated chicken eggs. Two passages of eluates in cell cultures or these eggs did not reveal the presence of any live virus. The eluates were also examined by polymerase chain reaction or reverse-transcription polymerase chain reaction to detect the presence of viral DNA or RNA, respectively. Nine of the 64 filters tested were positive for influenza A virus, 2 filters were positive for influenza B virus, and 1 filter was positive for parainfluenza virus 1.

CONCLUSION

These findings indicate that existing building HVAC filters may be used as a method of detection for airborne viruses. As integrated long-term bioaerosol sampling devices, they may yield valuable information on the epidemiology and aerobiology of viruses in air that can inform the development of methods to prevent airborne transmission of viruses and possible deterrents against the spread of bioterrorism agents.

Molecular detection and identification of enteroviruses in children admitted to a university hospital in Greece

Although enteroviral infections occur frequently during childhood, the circulation of particular serotypes has never been studied in Greece. The objectives of the present report were molecular detection and identification of human enteroviruses in children admitted with nonspecific febrile illness or meningitis to a university hospital during a 22-month period. A one-step Real-Time RT-PCR protocol was used for rapid enterovirus detection in genetic material extracted directly from clinical samples, and a sensitive reverse transcription-semi-nested PCR targeting part of the VP1-coding region was used for genotypic identification of the different serotypes. Twenty-one enterovirus strains were detected and identified in 20 stool samples, one cerebrospinal fluid (CSF) sample, one whole blood sample and one throat swab from 21 out of 134 febrile patients (15.7%). Ten strains belonged to Human Enterovirus Species B (HEV-B) (six serotypes) and eleven to HEV-A (four serotypes). Most of the strains were closely associated with virulent strains circulating in Europe and elsewhere. Detection of the emerging pathogen enterovirus 71 for a first time in Greece was particularly important.

Full-genome sequence analysis of a multirecombinant echovirus 3 strain isolated from sewage in Greece

An echovirus 3 (Echo3) strain (strain LR31G7) was isolated from a sewage treatment plant in Greece in 2005. Full-genome molecular, phylogenetic, and SimPlot analyses were conducted in order to reveal the evolutionary pathways of the isolate. Nucleotide and phylogenetic analyses of part of the VP1 genomic region revealed that the isolated strain correlates with Echo3 strains isolated during the same year in France and Japan, implying that the same virus circulated in Europe and Asia. LR31G7 was found to be a recombinant that shares the 3' part of its genome with an Echo25 strain isolated from asymptomatic infants in Norway in 2003. Nucleotide and SimPlot analyses of the VP1-2A junction, where the recombination was located, revealed the exact recombination breakpoint (nucleotides 3357 to 3364). Moreover, there is evidence that recombination events had occurred in 3B-3D region in the evolutionary history of the isolate. Our study indicates that recombination events play major roles in enterovirus evolution and that the circulation of multirecombinant strains with unknown properties could be potentially dangerous for public health.

Direct extraction and molecular characterization of enteroviruses genomes from human faecal samples

Routine diagnosis of acute flaccid paralysis (AFP) is still based on classical virological procedures. Several enteroviruses serotypes are not easily isolated in cell cultures system used and routinely more than one passage in cell culture is performed. A total of 54 archived faecal samples were examined. The heterogeneous nature of faecal samples may contribute to variations in the yields of viral nucleic acids with different extraction methods and specimen types. PCR inhibitors are frequently encountered in stool specimens. From the three methods initially compared for extraction of viral RNA, QIAamp Viral RNA Mini Kit was retained as it yielded the highest amount of viral RNA without the interference of RT-PCR inhibitors. Evaluation of 54 archived stool specimens by RT-PCR and cell culture resulted in a higher frequency of detection by RT-PCR. With the use of RT-PCR we were able to detect two additional samples otherwise considered negative for enterovirus isolation if only the cell culture standard methodology was employed. RNA extraction with QIAamp Viral RNA Mini Kit coupled with RT-PCR in the 5'NCR (subgrouping into distinct genetic clusters of all enteroviruses) and VP1 (reliable serotyping by sequencing) is a rapid and sensitive technique of direct poliovirus/non-polio enteroviruses recovery and molecular characterization from human faecal specimens without further passage in cell culture, which may select for genetic variants that may not accurately reflect the virus composition in the original specimen.

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

BACKGROUND AND OBJECTIVES

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

STUDY DESIGN AND RESULTS

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

CONCLUSIONS

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

Aseptic meningitis in children: analysis of 506 cases

BACKGROUND

Non-polio human enteroviruses are the leading cause of aseptic meningitis in children. The role of enterovirus PCR for diagnosis and management of aseptic meningitis has not been fully explored.

METHODOLOGY/PRINCIPAL FINDINGS

A retrospective study was conducted to determine the epidemiological, clinical, and laboratory characteristics of aseptic meningitis and to evaluate the role of enterovirus PCR for the diagnosis and management of this clinical entity. The medical records of children who had as discharge diagnosis aseptic or viral meningitis were reviewed. A total of 506 children, median age 5 years, were identified. The annual incidence rate was estimated to be 17/100,000 children less than 14 years of age. Most of the cases occurred during summer (38%) and autumn (24%). The dominant clinical symptoms were fever (98%), headache (94%) and vomiting (67%). Neck stiffness was noted in 60%, and irritation in 46% of the patients. The median number of CSF cell count was 201/mm(3) with polymorphonuclear predominance (>50%) in 58.3% of the cases. Enterovirus RNA was detected in CSF in 47 of 96 (48.9%) children tested. Children with positive enterovirus PCR had shorter hospitalization stay as compared to children who had negative PCR or to children who were not tested (P = 0.01). There were no serious complications or deaths.

CONCLUSIONS

Enteroviruses accounted for approximately one half of cases of aseptic meningitis. PCR may reduce the length of hospitalization and plays important role in the diagnosis and management of children with aseptic meningitis.

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.

Genetic variation of coxsackie virus B5 strains associated with aseptic meningitis in Greece

In order to explore the genetic relationships among coxsackie virus B5 strains in Greece, the nucleotide sequences of the partial VP1 gene in strains isolated from aseptic cases of meningitis were determined and compared with those of strains isolated from other countries. Phylogenetic analysis showed a high degree of divergence (25%) among Greek strains isolated in different years, which clustered with high bootstrap values in a different subgroup of viruses, suggesting that enterovirus types vary with time rather than geographical distribution. A non-synonymous mutation present in the strains of this study was not observed in other coxsackie virus B5 strains.

Evaluation of a method to re-use electropositive cartridge filters for concentrating viruses from tap and river water

Electropositively charged filters are frequently used for concentrating enteric viruses from large volumes of water. A major disadvantage to the use of these filters, however, is that they are not cost-effective. At US$ 150-180 per filter, routine viral monitoring of water is cost-prohibitive. This study describes the development of a method which allows a filter to be used up to three times, achieving comparable recoveries to new filters. Zetapor 1MDS and N66 Posidyne electropositive filters were tested. The method was analyzed using tap water and Ohio River water that was spiked with poliovirus. Tap water recoveries averaged 32% for new filters, 30% for filters used twice, and 38% for filters used three times. River water recoveries averaged 68% for new filters, 83% for filters used twice, and 100% for filters used three times. RT-PCR and dot-blot hybridization were performed on sample concentrates to ensure that all viral nucleic acid from the previous test had been removed from the filters by the treatment process.

Evaluation of seroneutralization and molecular diagnostic methods for echovirus identification

In this study we compared the identification results of 41 echovirus clinical isolates using RIVM pools (National Institute for Public Health and the Environment RIVM, Bilthoven, The Netherlands) and reverse transcription-polymerase chain reaction (PCR) assays. Primer pair UG52-UC53 amplified a 433-bp segment in the 5' untranslated region. Restriction enzyme HpaII was used for subgrouping of our isolates into 2 different genetic clusters. Amplification of 315 bp that is located in 5' end of VP1 gene as well as of a long genomic fragment (1452 bp) including the VP1 3' end, the entire coding sequence of 2A, 2B, and the 5' moiety of the 2C-coding region was achieved by the application of PCR protocols with primers 292-222 and EUG2a, 2b, 2c-EUC2, respectively. Phylogenetic trees were constructed for the 5' end as well as for the 3' end of VP1 gene using nucleotide sequences derived from sequencing of clinical isolates and homologous sequences of all echovirus serotypes. The phylogenetic grouping pattern of the clinical isolates revealed a correlation of serotype and genotype either in the 5' or in the 3' end of the VP1 gene that was investigated in the present study claiming that they can be either used for molecular typing of echoviruses.