Echovirus 9 genetic diversity detected in whole-capsid genome sequences obtained directly from clinical specimens using next generation sequencing.

Echovirus 9 (E9) has been detected in an increased number of symptomatic patient samples received by the National Enterovirus Reference Laboratory in Hungary during 2018 compared to previously reported years.Formerly identified E9 viruses from different specimen types detected from patients of various ages and showing differing clinical signs were chosen for the detailed analysis of genetic relationships and potential variations within the viral populations. We used next generation sequencing (NGS) analysis of 3,900 nucleotide long amplicons covering the entire capsid coding region of the viral genome without isolation, directly from clinical samples.Compared to the E9 reference strain, the viruses showed about 79% nucleotide and around 93% amino acid sequence similarity. The four new viral genome sequences had 1-20 nucleotide differences between them also resulting in 6 amino acid variances in the coding region, including 3 in the structural VP1 capsid protein. One virus from a patient with hand, foot, and mouth disease had two amino acid changes in the VP1 capsid protein. An amino acid difference was also detected in the non-structural 2C gene of one virus sequenced from a throat swab sample from a patient with meningitis, compared to the faecal specimen taken two days later. Two amino acid changes, one in the capsid protein, were found between faecal samples of meningitis patients of different ages.Sequencing the whole capsid genome revealed several nucleotide and amino acid differences between E9 virus strains detected in Hungary in 2018.

Origin and evolution analysis and genetic characteristics of echovirus 9 in China.

BACKGROUND: Echovirus 9 (E9) is associated with a wide variety of diseases and medical conditions, and the clinical symptoms of sporadic cases caused by E9 often are severe. With a high global prevalence, E9 has caused multiple outbreaks worldwide. However, little is known about the genetic and geographic population dynamics of E9. METHOD: A total of 131 VP1 gene sequences, including15 generated in this study and 116 obtained from GenBank, were used to coestimate time-resolved phylogenies to infer viral evolution and transmission in worldwide. Overlapping fragments representing whole genomes were amplified by reverse transcription polymerase chain reaction (RT-PCR) using specific primers. Then, we reported the genetic characteristics of fifteen E9 strains in the Chinese Mainland. Similarity plots and bootscanning analysis were used to determine recombination patterns of E9. RESULTS: The estimated mean evolutionary rate of global E9 VP1 gene was 4.278 × 10-3 substitutions per site per year (95% confidence interval [CI], 3.822 × 10-3/site/year to 4.710 × 10-3/site/year), and the common ancestor of E9 likely emerged around 1868 (95% CI, 1840 to 1892). The full-length genomic sequences of the fifteen E9 strains showed 76.9-79.6% nucleotide identity and 95.3-95.9% amino acid identity with E9 Barty strain. 11 of 15 E9 whole genome sequence present four recombination patterns, and E9 recombinants have extensive genetic exchanges in the 2C and P3 regions with other Enterovirus B (EV-B) circulated in China. Four of six E9 strains were temperature sensitive, and two were temperature resistant, and a comparative genomics analysis suggested that 411, 865 and 867 amino acid substitution in the P1 region was related to temperature sensitivity. CONCLUSION: This study highlights a persistent transmission network of E9 in worldwide, provides valuable information regarding the molecular epidemiology of E9.

Molecular characterization of echovirus 9 strains isolated from hand-foot-and-mouth disease in Kunming, Yunnan Province, China.

Echovirus 9 (E9) belongs to the species Enterovirus B. So far, 12 whole genome sequences of E9 are available in GenBank. In this study, we determined the whole genomic sequences of five E9 strains isolated from the stools of patients with hand-foot-and-mouth disease in Kunming, Yunnan Province, China, in 2019. Their nucleotide and amino acid sequences shared 80.8-80.9% and 96.4-96.8% identity with the prototype Hill strain, respectively, and shared 99.3-99.9% and 99.1-99.8% mutual identity, respectively. Recombination analyses revealed that intertype recombination had occurred in the 2C and 3D regions of the five Yunnan E9 strains with coxsackieviruses B5 and B4, respectively. This study augmented the whole genome sequences of E9 in the GenBank database and extended the molecular characterization of this virus in China.

Direct next-generation sequencing diagnosis of echovirus 9 meningitis, France.

The prognosis of central nervous system infections caused by enteroviruses partially depends on the viral genotype, which is not provided by current point-of-care diagnostic methods. In this study, next-generation sequencing identified an echovirus 9 directly from the cerebrospinal fluid of a patient presenting with meningitis.

Acute meningoencephalitis associated with echovirus 9 infection in Sri Lanka, 2009.

The aetiology of acute meningoencephalitis in Sri Lankan children and adults is poorly understood. This study was carried out to determine pathogens responsible for meningoencephalitis in Sri Lanka. A hospital-based cross-sectional study was performed using cerebrospinal fluid samples (22 adult and 17 pediatric) collected from August to December 2009 from patients clinically diagnosed with acute meningoencephalitis at two tertiary care hospitals in Sri Lanka. Routine microbiology for bacterial pathogens together with in-house RT-PCR and PCR assays for the detection of dengue viruses, Japanese encephalitis virus, West Nile virus, chikungunya virus, enteroviruses, mumps virus, measles virus, herpes simplex viruses types 1 and 2, and varicella zoster virus were performed. Bacterial pathogens were not isolated from any patient specimens. However, from nine of the paediatric patients aged 1 month to 10 years (mean age 5.2 years) echovirus 9 (E-9; family Picornaviridae, genus Enterovirus,species Enterovirus B ) was detected by RT-PCR. All nine patients presented with fever, six had headache, and seven had vomiting. Neck stiffness indicating meningitis was present in six of the patients. Phylogenetic analysis of partial VP1 and VP4-VP2 genes showed these E-9 strains to be most closely related to E-9 strains detected in CSF from Korea and France in 2005 and 2006. The remaining patients were negative for all other viruses tested. E-9 was the most common cause of acute meningoencephalitis in the tested paediatric population from Sri Lanka in 2009, which likely reflects circulation of this E-9 strain between Europe and Asia over several years.

Rubella virus genotype 1G and echovirus 9 as etiologic agents of exanthematous diseases in Brazil: insights from phylogenetic analysis.

The aim of the present study was to identify the rubella virus (RV) and enterovirus (EV) genotypes detected during the Epidemiological Surveillance on Exanthematic Febrile Diseases (VIGIFEX) study and to perform phylogenetic analysis. Ten RV- and four EV-positive oropharyngeal samples isolated from cell culture were subjected to RT-PCR and sequencing. Genotype 1G and echovirus 9 (E-9) was identified in RV- and EV-positive samples, respectively. The RV 1G genotype has been persisting in Brazil since 2000-2001. No evidence of E-9 being involved in exanthematic illness in Brazil has been reported previously. Differential laboratory diagnosis is essential for management of rash and fever disease.

[Complete genome sequence characteristics of human echovirus 9 strain isolated in Yunnan, China].

To analyze the genomic sequence characteristics of a human Echovirus 9(ECHO-9) strain isolated from a child with Hand-foot-mouth disease (HFMD) in Kunming, Yunnan Province, in 2010. The complete genome sequence of a human echovirus 9 strain, MSH-KM812-2010 was determined. As other human enterovirus, its genome was 7,424 nucleotides (nts) in length and encoded for 2,203 amino acids (aas). In comparison to other human enteroviruses, MSH-KM812-2010 strain had the highest homology with other strains of human echovirus 9 in structural genomic regions and more homologous to other serotypes of B specie than to human echovirus 9 in non-structural genomic regions. Phylogenetic analysis based on complete VP1 gene revealed that the sequences of human echovirus 9 segregated into three distinct clades A, B and C with more than 15. 0% diversity between clades. All Chinese isolates belonged to the same clade. RDP3 and Blast revealed evident recombination in non-structural genomic regions. This report is the first to, describe the complete genome of the human echovirus 9 in China and provide an overview of the diversity of genetic characteristics of a circulating human echovirus 9.

A single amino acid substitution in viral VP1 protein alters the lytic potential of clone-derived variants of echovirus 9 DM strain in human pancreatic islets.

In vitro studies with primary human pancreatic islets suggest that several enterovirus serotypes are able to infect and replicate in beta cells. Some enterovirus strains are highly cytolytic in vitro whereas others show virus replication with no apparent islet destruction. The capability to induce islet destruction is determined only partially by the virus serotype, since strain specific differences have been detected within some serotypes including echovirus 9 (E-9). In this study, the viral genetic factors determining the outcome of islet infection (i.e., destructive vs. benign) were investigated by constructing parallel infectious clones of lytic E-9-DM strain that was isolated from a small child at the clinical onset of type 1 diabetes. The capabilities of these clone-derived viruses to induce islet destruction were monitored and the lytic potential of clones was modified by site-directed mutagenesis. The lytic capabilities of these clone-derived viruses in human pancreatic islets were modified by a single amino acid substitution (T81A) in the capsid protein VP1. The data presented outline the importance of amino acid point mutations in the pathogenetic process leading to islet necrosis. However, although the amino acid substitution (T81A) modifies the lytic capabilities of E-9-DM strain-derived microvariant strains, it is likely that additional viral genetic determinants of pancreatic islet pathogenicity exist in other E-9 strains.

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

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 EV infections in KEPCO Medical Center, Seoul, Korea from July 2006 to September 2010. EV detection and genotype identification 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.

Complete genome sequence characteristics of human echovirus 9 strain isolated in Yunnan, China / 病毒学报

To analyze the genomic sequence characteristics of a human Echovirus 9(ECHO-9) strain isolated from a child with Hand-foot-mouth disease (HFMD) in Kunming, Yunnan Province, in 2010. The complete genome sequence of a human echovirus 9 strain, MSH-KM812-2010 was determined. As other human enterovirus, its genome was 7,424 nucleotides (nts) in length and encoded for 2,203 amino acids (aas). In comparison to other human enteroviruses, MSH-KM812-2010 strain had the highest homology with other strains of human echovirus 9 in structural genomic regions and more homologous to other serotypes of B specie than to human echovirus 9 in non-structural genomic regions. Phylogenetic analysis based on complete VP1 gene revealed that the sequences of human echovirus 9 segregated into three distinct clades A, B and C with more than 15. 0% diversity between clades. All Chinese isolates belonged to the same clade. RDP3 and Blast revealed evident recombination in non-structural genomic regions. This report is the first to, describe the complete genome of the human echovirus 9 in China and provide an overview of the diversity of genetic characteristics of a circulating human echovirus 9.

Viral meningitis: which patients can be discharged from the emergency department?

BACKGROUND: Even in an era when cases of viral meningitis outnumber bacterial meningitis by at least 25:1, most patients with clinical meningitis are hospitalized. OBJECTIVE: We describe the clinical characteristics of an unusual outbreak of viral meningitis that featured markedly elevated cerebrospinal fluid white blood cell counts (CSF WBC). A validated prediction model for viral meningitis was applied to determine which hospital admissions could have been avoided. METHODS: Data were collected retrospectively from patients presenting to our tertiary care center. Charts were reviewed in patients with CSF pleocytosis (CSF WBC > 7 cells/mm(3)) and a clinical diagnosis of meningitis between March 1, 2003 and July 1, 2003. Cases were identified through hospital infection control and by surveying all CSF specimens submitted to the microbiology laboratory during the outbreak. RESULTS: There were 78 cases of viral meningitis and 1 case of bacterial meningitis identified. Fifty-eight percent of the viral meningitis cases were confirmed by culture or polymerase chain reaction to be due to Enterovirus. Mean CSF WBC count was 571 cells/mm(3), including 20 patients with a CSF WBC count > 750 cells/mm(3) (25%) and 11 patients with values > 1000 cells/mm(3) (14%). Sixty-four of 78 patients (82%) were hospitalized. Rates of headache, photophobia, nuchal rigidity, vomiting, and administration of intravenous fluids in the Emergency Department were no different between admitted and discharged patients. Only 26/78 (33%) patients with viral meningitis would have been admitted if the prediction model had been used. CONCLUSIONS: Although not all cases of viral meningitis are necessarily suitable for outpatient management, use of a prediction model for viral meningitis may have helped decrease hospitalization by nearly 60%, even though this outbreak was characterized by unusually high levels of CSF pleocytosis.

Prolonged viral RNA detection in the central nervous system of one-week-old Swiss albino mice following coxsackievirus B4 and echovirus 9 infection.

OBJECTIVES: Type B coxsackieviruses (CV-B), together with echoviruses (E), are among the most common pathogens encountered in aseptic meningitis and meningoencephalitis. They frequently infect the central nervous system (CNS). The mechanisms of virus spreading in the CNS are poorly understood. In the present study, we investigated CV-B4 and E-9 spreading and neurotropism within intraperitoneally inoculated one-week-old Swiss albino mice. METHODS: Seminested RT-PCR and virus isolation were used to assay viral distribution. RESULTS: Viral RNA was present in various organs: brain, spinal cord, spleen and heart at various times post-infection (p.i.); ranging from 1 day p.i. up to 30, 60 and 90 days p.i, respectively, for CV-B4-JVB-, E-9 Barty- and CV-B4-E2-infected mice. Organs became negative for virus isolation after 5 days p.i., except for brain and heart from CV-B4 E2-infected mice, which remained positive for up to 10 and 15 days p.i., respectively. Negative viral RNA strand was detected mainly in brain and spinal cord of infected mice until 30 and 60 days p.i. CONCLUSION: This is the first report on the persistence of CV-B4 and E-9 in the CNS of intraperitoneally inoculated mice.

Enteroviral meningitis and concurrent peripheral motor axonal polyneuropathy.

Enteroviral infections can cause acute flaccid paralysis resulting from anterior myelitis, but the occurrence of axonal polyneuropathy is not well described. We report an 8-year-old boy who presented with symmetric, ascending flaccid paralysis and was diagnosed with concurrent echovirus type 9 viral meningitis.

Synthesis and in vitro study of antiviral and virucidal activity of novel 2-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamide derivatives.

2-[(4-Methyl-4H-1,2,4-triazol-3-yl)sulfanyl]acetamide derivatives were synthesized and their structures were confirmed by 1H NMR, IR, and elemental analysis. Cytotoxicity of the compounds towards HEK-293 and GMK cells was evaluated. Moreover, the antiviral and virucidal activities of these compounds against human adenovirus type 5 and ECHO-9 virus were assessed. Some of the newly synthesized derivatives have the potential to reduce the viral replication of both tested viruses.

[Molecular genetic echovirus 9 variants identified in patients with aseptic meningitis in Russia in 2007-2009].

In 2009 echovirus 9 caused a higher seasonal incidence of enterovirus infection (EVI) and its several outbreaks in a number of regions of Russia. Analysis of the partial VP1 coding region differentiated 4 phylogenetic lineages of echoviruses 9 variants identified in patients with aseptic meningitis and EVI in 2007-2009. One variant of echovirus 9 was most commonly encountered in 2009. Echoviruses 9 identified in different areas, which had a high (98.2-100%) homology of nucleotide sequences of the partial VP1 coding region, varied in the amino acid sequences within the B-C loop.

Clinical features of echovirus 6 and 9 infections in children.

BACKGROUND: Clinical features of echovirus 6 and 9 infections in children have not been comprehensively evaluated, particularly for sporadic cases. OBJECTIVE: To describe the clinical features of children with echovirus 6 or 9 infections. STUDY DESIGNS: From 2000 to 2008, 199 children with culture-proven echovirus 6 or 9 infections identified in a university-affiliated hospital were included. Data extracted from 174 inpatients were further analyzed. RESULTS: Age ranged from 4 days to 15 years with a mean of 4.7 years. 123 (62%) were male. The disease spectrums were similar for echovirus 6 (n=100) and 9 (n=74) infections, with aseptic meningitis (49% and 51%, respectively) being the most common syndrome, followed by meningismus, upper respiratory tract infection, pneumonia, and herpangina. All 174 inpatients had fever but the duration of fever was significantly longer in patient with echovirus 9 infection than those with echovirus 6 infections (6.0 days vs. 3.8 days, p<0.001). The rate of leukocytosis (leukocyte count>15,000/µL) were significantly higher in patients with echovirus 6 infections than those with echovirus 9 infection (p<0.001). One neonate with echovirus 6 infection died from hepatic necrosis with coagulopathy, and one infant with echovirus 6 infection and one child with echovirus 9 infection died from brain involvement. Two children had long-term sequelae of seizure disorder. The remaining 169 children (97%) recovered uneventfully. CONCLUSION: For children with echovirus 6 or 9 infections requiring hospitalization, aseptic meningitis was the most common manifestation and fatal outcome or long-term sequel, though rare, might occur.

Epidemiologic and Clinical features of Enteroviral Infections in Children, a Single Center Study in Korea: 2009 / 소아감염

PURPOSE: Enteroviral infection is a common viral illness in children. We undertook this study in attempt to comprehend the epidemiologic and clinical features of enteroviral infections, particularly EV71 in children. METHODS: We enrolled 63 children with enteroviral infection at Severance Children's Hospital in Seoul between May and August 2009. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed from stool or cerebrospinal fluid samples, which were then tested for enteroviral infection. Viral isolation and serotype identification also were performed by RT-PCR. RESULTS: A total of 63 patients with clinical diagnosis of enteroviral infections were enrolled; of those, 38 (60%) were positive for enterovirus. The mean age of the patients was 2 years and 7 months and the sex ratio of male to female was 0.9:1. Their clincal manifestations included aseptic meningitis (21 cases, 55%), HFMD (16 cases, 42%), herpangina (5 cases, 13%), neonatal fever (2 cases, 5%), encephalitis (1 case, 3%), and myocarditis (1 case, 3%). Serotypes of isolated enteroviruses were EV71 (8 cases, 21%), coxsackievirus B1 (8 cases, 21%), coxsackievirus A16 (2 cases, 6%), coxsakievirus A2 (1 case, 3%), coxsakievirus A5 (1 case, 3%), and echovirus 9 (1 case, 3%). Clinical symptoms of EV71 infection included HFMD (5 cases, 63%), aseptic meningitis (3 cases, 38%), encephalitis (1 case, 13%), and myocarditis (1 case, 13%). A positive rate of C-reactive protein in EV71 was higher than those in other enterviral infections. However, there was no statistically significant difference in other laboratory findings. CONCLUSION: We reported on identified enteroviruses, including EV71, during a period of 3 months in the summer of 2009. In this study, EV71 infection frequently occurred in male and clinical manifestation caused by EV71 was a more severe disease than that due to other enterviral infections. There is a need for continuous surveillance of enteroviral infection and its clinical manifestations for diagnosis and treatment of enteroviral infection.