Epidemiology Of Enteroviruses Research Articles

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.

The seasonality of nonpolio enteroviruses in the United States: Patterns and drivers

Nonpolio enteroviruses are diverse and common viruses that can circulate year-round but tend to peak in summer. Although most infections are asymptomatic, they can result in a wide range of neurological and other diseases. Many serotypes circulate every year, and different serotypes predominate in different years, but the drivers of their geographical and temporal dynamics are not understood. We use national enterovirus surveillance data collected by the US Centers for Disease Control and Prevention during 1983-2013, as well as demographic and climatic data for the same period, to study the patterns and drivers of the seasonality of these infections. We find that the seasonal pattern of enterovirus cases is spatially structured in the United States and similar to that observed for historical prevaccination poliomyelitis (1931-1954). We identify latitudinal gradients for the amplitude and the timing of the peak of cases, meaning that those are more regularly distributed all year-round in the south and have a more pronounced peak that arrives later toward the north. The peak is estimated to occur between July and September across the United States, and 1 month earlier than that for historical poliomyelitis. Using mixed-effects models, we find that climate, but not demography, is likely to drive the seasonal pattern of enterovirus cases and that the dew point temperature alone explains ∼30% of the variation in the intensity of transmission. Our study contributes to a better understanding of the epidemiology of enteroviruses, demonstrates important similarities in their circulation dynamics with polioviruses, and identifies potential drivers of their seasonality.

Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains

Recombination has been recognized as a major mechanism of evolution in enteroviruses. The Echovirus 30 (E-30) strain Gior was sequenced and phylogenetically compared to all available E-30 sequences to detect recombination events between the 5΄UTR and VP1 genomic regions. The comparison of phylogenetic trees of the 5΄UTR and VP1 revealed incongruences concerning strains, lineages and sub-lineages. Comparative analysis of 62 E-30 sub-genomic sequences revealed six different recombination events that almost all occurred in the same region, having a start point in the 3΄end of the 5΄ UTR and end point in VP4. The only exception was the sub-lineage of Gior for which both borders of recombination were located in the 5΄UTR. These results describe for the first time recombination events in this region in circulating EV-B strains, revealing the exact points of these recombination events, highlighting the impact of such events on the evolution and epidemiology of enteroviruses.

Whole genome sequence analysis of 17 enterovirus 71 strains isolated from children with hand, foot and mouth disease in Guizhou province

Objective To inquire into the molecular epidemiology of enterovirus 71(EV71) in our region by analyzing the whole genome characteristics and genetic evolution of EV 71 strains isolated from Guizhou area. Methods The throat swabs samples of hospitalized children with hand, foot and mouth disease in Guizhou province from 2013 to 2015 were collected, the virus nucleic acid were extracted, then the whole genome of virus were piecewise amplified by reverse transcription polymerase chain reaction(RT-PCR) and sequenced.Sequencing results were edited and spliced by DNAMAN8.0 software, then the viral genome sequences were compared with genome sequences of other EV71 strains in the genebank by Blastn, the phylogenetic tree was constructed by the Neighbor-Joining method in MEGA5.2 software. Results The whole genome sequences of 17 EV71 strains were successfully isolated and amplified, the whole genome length of 17 EV71 isolates was 7 405 base pair, encoded about 2 193 amino acids.The 17 isolates were divided into ten species of amino acid sequences by 12 differences of amino acid among the strains, different sequences and clinical types had not shown regularity and correlation.The nucleotide homology in VP1 region, 5′untranslated region(5′UTR) and 3′ untranslated region (3′UTR) were high among 17 EV71 isolates.The results that the whole genome of 17 EV71 isolates was compared with representative strains of EV71 A, B, C genotype and coxsakievirus A 16 ( CA16) showed that 17 EV71 isolates had higher homology with EV71 C4a subtype, 95.3%-98.1%, and the lowest homology with CA16.The phylogenetic tree was constructed based on nucleotide sequence of the whole genome, VP1 region and 5′untranslated region of 17 isolates showed that the 17 isolates were clustered into one cluster, and were clustered in the same branch with C4a isoforms, the phylogenetic relationships among different regions were different. Conclusion The popular genotype of EV71 strains in Guizhou area for 2013-2015 was C4a subtype, consistenting with the genotype of popular EV71 in other regions of China.EV71 strains hasn′t the antigen transformation and input of a new subtype temporarily, but exist nucleotide and amino acid changes, so need be chronically and dynamically monitored.There is no correlation between the amino acid sequence difference of 17 EV71 isolates and the state of an illness. Key words: Hand, foot, and mouth disease; Enterovirus 71; Genome wide; Homology; Genetic evolution analysis; Virulence,

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.

BackgroundHuman 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.AimTo 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.MethodsDuring 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.ResultsHEV 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.ConclusionHEV 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.

Molecular identification of human enteroviruses associated with aseptic meningitis in Yunnan province, Southwest China.

Human enteroviruses (EVs) are the major causative agents of aseptic meningitis. In this study, a total of 524 children were admitted to the children Kunming hospital (continental China) for aseptic meningitis manifestations in 2009 and 2010. An EV infection was diagnosed in 85/524 children (16.2 %) and the viruses detected were assigned to 16 serotypes. Most serotypes belonged to the enterovirus B species. Echovirus 9 was predominant (24.7 %), followed by coxsackievirus B5 (23.5 %) and then echovirus 30 (16.5 %). Echovirus 9 was firstly identified as the predominant serotype in sporadic aseptic meningitis which occurred in Yunnan, Southwest China. This work indicates the need to perform large-scale surveillance to gain a better insight into the epidemiology of enteroviruses associated with aseptic meningitis in China.

Molecular epidemiology of enterovirus in Scotland, January 2013–December 2015

Molecular epidemiology of enterovirus in Scotland, January 2013–December 2015

Molecular epidemiology of enterovirus and parechovirus infections according to patient age over a 4-year period in Spain.

The epidemiology and clinical association of enterovirus (EV) and parechovirus (HPeV) infections, as well as the type-distribution-according-to-age, were determined during a 4-year study period in Spain. During 2010-2013, a total of 21,832 clinical samples were screened for EV and the detection frequency was 6.5% (1,430). Of the total EV-negative samples, only 1,873 samples from 2011 to 2013 were available for HPeV testing. HPeV was detected in 42 (2%) of them. Positive samples were genotyped using PCR and sequencing. EV infections occurred in all age groups of patients: neonates (17%), children 28 days to 2 years (29%), children 2-14 years (40%), and adults (14%). Thirty-four different EV types were identified. HPeV infections were detected exclusively in infants <8 m (70% neonates, P < 0.05). All but one HPeV were HPeV-3. Differences in type frequency detection were found according to age and clinical manifestation. Coxsackievirus (CV)-B4 (61%), CV-B5 (83%), and HPeV-3 (64%) were more frequent in neonates than in older patients (P < 0.05). Echovirus (E)-3 (60%), E-18 (47%), E-25 (62%), CV-A6 (61%), CV-A16 (72%), and EV-71 (75%) were mainly detected in children 28 days to 2 years (P < 0.05), whereas, E-6 (79%), E-20 (88%), and E-30 (85%) were predominant in children >2 years and adults (P < 0.05). Clinically, meningitis was associated with EV (P < 0.01) whereas, encephalitis was more frequent in HPeV-infected patients. CV-B types were associated with myocarditis (90%; P < 0.05) and EV species A with hand-foot-mouth-disease/atypical exanthema (88%; P < 0.05). J. Med. Virol. 89:435-442, 2017. © 2016 Wiley Periodicals, Inc.

Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China

BackgroundAlthough hand, foot, and mouth disease (HFMD) is a major public concern in China, the prevalence and clinical symptoms associated with the different agents of HFMD in this country remain poorly understood. ObjectivesWe investigated the clinical and molecular characteristics of enteroviruses in patients with HFMD from Wenzhou, China. Study designPatients with laboratory-confirmed HFMD admitted to the Yuying Children's Hospital in Wenzhou, China during 2013 were included in this study. Viral RNA sequences were amplified using RT-PCR, determined by sequencing, and compared by phylogenetic analysis. ResultsA total of 955 clinically diagnosed HFMD cases were determined using PCR, with whole viral genomes obtained for each enterovirus type. 14 types of enterovirus belonging to two viral species were identified. Notably, Coxsackievirus A6 (CV-A6) was the most common species detected (77.8%), followed by EV-A71 (8.2%) and CV-A10 (8.1%). Phylogenetic analysis revealed multiple independent introductions of these viruses into Wenzhou. In addition, the enterovirus observed in Wenzhou had a recombinant history, with two or three recombination breakpoints. Although the illness associated with CV-A6 was milder than that of EV-A71, CV-A6 infection caused more widespread rash, larger blisters, and subsequent skin peeling and/or nail shedding. ConclusionOur study revealed the co-circulation of 14 types of enteroviruses in a single location – Wenzhou, China – with CV-A6 virus the predominant agent of HFMD. This work highlights the need to perform larger-scale surveillance to fully understand the epidemiology of enteroviruses in China and the wider Asia-Pacific region.

Environmental Surveillance of Non-polio Enteroviruses in Poland, 2011.

The aim of this study was to apply environmental surveillance to evaluate circulation of non-polio enteroviruses (NPEVs) in sewage in Poland. Samples of raw sewage were collected in 14 sewage disposal systems from January to December, 2011. Sewage samples were concentrated prior to analysis by RT-PCR and isolation in cells (RD, L20B and Caco-2). Out of the 165 analysed samples, 127 (77%) were positive for enteroviruses using RT-PCR and 109 (66%) were positive for enteroviruses using cell culture methods and the highest detection rate was observed in the summer and autumn. In total, 141 enteroviruses were identified using neutralization test (107 NPEVs and 34 polioviruses). Accounting for 52% of all the detected NPEVs, E11 and E3 were the predominant serotypes identified in raw sewage. Retrospectively, E11 was the known aetiology for the past aseptic meningitis outbreaks in Poland, as E3 being rarely associated with any outbreak prior to 2013. In conclusion, the environmental surveillance provides data which may help in understanding the epidemiology of enteroviruses in humans.

Recombination among human non-polio enteroviruses: implications for epidemiology and evolution.

Human enteroviruses (EV) belong to the Picornaviridae family and are among the most common viruses infecting humans. They consist of up to 100 immunologically and genetically distinct types: polioviruses, coxsackieviruses A and B, echoviruses, and the more recently characterized 43 EV types. Frequent recombinations and mutations in enteroviruses have been recognized as the main mechanisms for the observed high rate of evolution, thus enabling them to rapidly respond and adapt to new environmental challenges. The first signs of genetic exchanges between enteroviruses came from polioviruses many years ago, and since then recombination has been recognized, along with mutations, as the main cause for reversion of vaccine strains to neurovirulence. More recently, non-polio enteroviruses became the focus of many studies, where recombination was recognized as a frequent event and was correlated with the appearance of new enterovirus lineages and types. The accumulation of multiple inter- and intra-typic recombination events could also explain the series of successive emergences and disappearances of specific enterovirus types that could in turn explain the epidemic profile of circulation of several types. This review focuses on recombination among human non-polio enteroviruses from all four species (EV-A, EV-B, EV-C, and EV-D) and discusses the recombination effects on enterovirus epidemiology and evolution.

Molecular epidemiology of enterovirus B77 isolated from non polio acute flaccid paralytic patients in Pakistan during 2013

Human enteroviruses are associated with various clinical syndromes and severe neurological disorders. The aim of this study was to determine the molecular epidemiology of non polio enteroviruses and their correlation with acute flaccid paralysis (AFP) patients living in Khyber Pakhtunkhwa (KP) and Federally Administered Tribal Areas (FATA) of Pakistan. The stool samples collected from these patients were used for isolation of non polio enteroviruses (NPEVs). Out of 38 samples, 29 (76.3%) were successfully typed by microneutralization assay into eleven serotypes including echovirus (E)-3 (5.3%), E-7 (2.6%), E-11 (13.2%), E-12 (7.9%), E-13 (10.5%), E-20 (7.9%), E-27 (5.3%), E-29 (10.5%), E-30 (7.9%), E-33 (2.6%), coxsackievirus (CV) B5 (2.6%) and nine isolates (23.7%) remained untyped which were confirmed as NPEVs by real time RT-PCR. Complete VP1 genetic sequencing data characterized untypeable isolates into enterovirus B77 (EV-B77). Moreover, molecular phylogenetic analysis classified these viruses into two new genotypes having high genetic diversity (at least 17.7%) with prototype.This study provides valuable information on extensive genetic diversity of EV-B77 genotypes. Although, its association with neurological disorder has not yet been known but isolation of nine EV-B77 viruses from AFP cases highlights the fact that they may have a contributing role in the etiology of AFP. In addition, it is needed to establish enterovirus surveillance system and laboratory diagnostic facilities for early detection of NPEVs that may cause poliomyelitis like paralysis especially in the situation when we are at the verge of polio eradication.

Epidemic Trends of Enterovirus Infections From Pediatric Patients in Cheonan, Korea.

This study was performed to investigate the epidemiology of enterovirus (EV) infections in children at a single hospital during recent 5 years. This study was preformed from December 2008 to November 2013. We subjected 1,067 cerebrospinal fluid (CSF) specimens from 1,053 patients and 678 stool specimens from 665 patients using real-time reverse-transcription polymerase chain reaction tests that could detect EV. The data were analyzed according to seasonality and patient age and sex. During this period, 176 of the total 1,053 patients (16.81%) were positive for EV in CSF. The highest rate of EV-positive samples occurred in children less than 1 year of age (114/176, 64.77%), and the most prevalent month was June. The results for CSF and stool specimens were concordant in 545 (80.38%) of 678 cases. We described the epidemiological analytic data of the EV in the population of Cheonan, South Korea. The combination of the CSF and stool specimen enhances the diagnostic yield. There is a need for continuous study of EV infections and its clinical manifestations.

Molecular epidemiology of enterovirus 71 strains isolated from children in Yamagata, Japan, between 1990 and 2013.

Enterovirus 71 infections have become a major public issue in the Asia-Pacific region due to the large number of fatal cases. To clarify the longitudinal molecular epidemiology of enterovirus 71 (EV71) in a community, we isolated 240 strains from children, mainly with hand-foot-and-mouth diseases, between 1990 and 2013 in Yamagata, Japan. We carried out a sequence analysis of the VP1 region (891 bp) using 223 isolates and identified six subgenogroups (B2, B4, B5, C1, C2 and C4) during the study period. Subgenogroups C1 and B2 were found only between 1990 and 1993 and have not reappeared since. In contrast, strains in subgenogroups C2, C4 and B5 appeared repeatedly with genomic variations. Recent reports from several local communities in Japan have suggested that identical predominant subgenogroup strains, which have also been found in the Asia-Pacific region, have been circulating in a wide area in Japan. However, it is likely that there is a discrepancy between the major subgenogroups circulating in the Asia-Pacific region and those in Europe. It is necessary to continue the analysis of the longitudinal epidemiology of EV71 in local communities, as well as on regional and global levels, to develop strategies against severe EV71 infections.

Coxsackieviruses in Ontario, January 2005 to December 2011

In 2010, there was an increase in enterovirus meningitis in the province of Ontario, Canada. Concurrently, there was also an increase in coxsackievirus A9-positive specimens in Alberta, Canada. This study aimed to describe the results of an investigation into the increase in coxsackievirus (A9 serotype) in 2010 in Ontario. For the purpose of this study, we report on specimens tested by viral culture at Public Health Ontario Laboratory as part of routine laboratory testing from January 1, 2005 to December 31, 2011. Coxsackieviruses represented more than one third of enteroviruses detected, with A9 being the serotype most commonly identified. The most common specimen source in which A9 was isolated was cerebrospinal fluid, followed by nasopharyngeal swabs and stool. Patients in whom A9 was detected were older than individuals with any other coxsackievirus serotype. The increase in enterovirus meningitis in Ontario in 2010 was likely due to an increase in A9 circulation. A9 was most commonly identified among children; however A9 may cause severe illness in both children and adults. Monitoring the circulation and epidemiology of enteroviruses can inform clinicians about circulating pathogens to optimize clinical testing and antibiotic use.

Molecular epidemiology of enteroviruses associated with acute encephalitis syndrome in India

Molecular epidemiology of enteroviruses associated with acute encephalitis syndrome in India

Molecular epidemiology of enterovirus 71, coxsackievirus A16 and A6 associated with hand, foot and mouth disease in Spain

Hand, foot and mouth disease (HFMD) is a childhood illness frequently caused by genotypes belonging to the enterovirus A species, including coxsackievirus (CV)-A16 and enterovirus (EV)-71. Between 2010 and 2012, several outbreaks and sporadic cases of HFMD occurred in different regions of Spain. The objective of the present study was to describe the enterovirus epidemiology associated with HFMD in the country. A total of 80 patients with HFMD or atypical rash were included. Detection and typing of the enteroviruses were performed directly in clinical samples using molecular methods. Enteroviruses were detected in 53 of the patients (66%). CV-A6 was the most frequent genotype, followed by CV-A16 and EV-71, but other minority types were also identified. Interestingly, during almost all of 2010, CV-A16 was the only causative agent of HFMD but by the end of the year and during 2011, CV-A6 became predominant, while CV-A16 was not detected. In 2012, however, both CV-A6 and CV-A16 circulated. EV-71 was associated with HFMD symptoms only in three cases during 2012. All Spanish CV-A6 sequences segregated into one major genetic cluster together with other European and Asian strains isolated between 2008 and 2011, most forming a particular clade. Spanish EV-71 strains belonged to subgenogroup C2, as did most of the European sequences circulated. In conclusion, the recent increase of HFMD cases in Spain and other European countries has been due to a larger incidence of circulating species A enteroviruses, mainly CV-A6 and CV-A16, and the emergence of new genetic variants of these viruses.

Molecular Epidemiology of Enterovirus 71 Infection in the Central Region of Taiwan from 2002 to 2012

Enterovirus 71 (EV71), a causative agent of hand, foot, and mouth disease can be classified into three genotypes and many subtypes. The objectives of this study were to conduct a molecular epidemiological study of EV71 in the central region of Taiwan from 2002–2012 and to test the hypothesis that whether the alternative appearance of different EV71 subtypes in Taiwan is due to transmission from neighboring countries or from re-emergence of pre-existing local strains. We selected 174 EV71 isolates and used reverse transcription-polymerase chain reaction to amplify their VP1 region for DNA sequencing. Phylogenetic analyses were conducted using Neighbor-Joining, Maximum Likelihood and Bayesian methods. We found that the major subtypes of EV71 in Taiwan were B4 for 2002 epidemic, C4 for 2004–2005 epidemic, B5 for 2008–2009 epidemic, C4 for 2010 epidemic and B5 for 2011–2012 epidemic. Phylogenetic analysis demonstrated that the 2002 and 2008 epidemics were associated with EV71 from Malaysia and Singapore; while both 2010 and 2011–2012 epidemics originated from different regions of mainland China including Shanghai, Henan, Xiamen and Gong-Dong. Furthermore, minor strains have been identified in each epidemic and some of them were correlated with the subsequent outbreaks. Therefore, the EV71 infection in Taiwan may originate from pre-existing minor strains or from other regions in Asia including mainland China. In addition, 101 EV71 isolates were selected for the detection of new recombinant strains using the nucleotide sequences spanning the VP1-2A-2B region. No new recombinant strain was found. Analysis of clinical manifestations showed that patients infected with C4 had significantly higher rates of pharyngeal vesicles or ulcers than patients infected with B5. This is the first study demonstrating that different EV 71 genotypes may have different clinical manifestations and the association of EV71 infections between Taiwan and mainland China.

Molecular Epidemiology of Enteroviruses Associated with Hand, Foot, and Mouth Disease in the Mainland of China

Molecular Epidemiology of Enteroviruses Associated with Hand, Foot, and Mouth Disease in the Mainland of China

Epidemiology and Clinical Characteristics of Enterovirus Infections in Children: A Single Center Analysis from 2006 to 2010

† , Jecheon Myongji Hospital, Jecheon-si, Chungbuk, Korea Purpose:This study was performed to investigate the epidemiology of enterovirus (EV) infections in children at a secondary hospital during recent 5 years. Methods:We collected the cerebrospinal fluid, stool and throat swab samples from the pediatric patients with suspected EVinfections in KEPCO Medical Center, Seoul, Korea from July 2006 to September 2010. EVdetection and genotype identi- fication were performed by RT-PCR at Korea Centers for Disease Control and Prevention. Results:A total of 386 samples were collected from 277 patients during study period. Ninety-eight patients (35.4%) were diagnosed with EV infections. The RT-PCR positive rate was the highest in throat swab samples (48.3%). The median age of patient was 4.7 years (range, 0.1-12.5 years). Aseptic meningitis (50, 51.0%) was the most common clinical manifestation; herpangina (22, 22.4%) and hand-foot-mouth disease (18, 18.4%). One hundred EVs were isolated from 98 patients and 20 genotypes of EV were identified; Echovirus 30 (28 cases, 28%), Enterovirus 71 (12 cases, 12%), Echovirus 25 (10 cases, 10%), Echovirus 9 (9 cases, 9%) and Coxsackievirus A6 (8 cases, 8%). Aseptic meningitis caused by Echovirus 30 was the most common manifestation in 2008. There was no complicated case caused by Enterovirus 71. Conclusion:This study showed the epidemiology of confirmed EV infection in children from 2006 to 2010. There is a need for continuous surveillance of EV infections and its clinical manifestations. (Korean J Pediatr Infect Dis 2013;20:81-88)