Phylogenetic analysis of Echovirus 30 isolated during the 2005 outbreak in France reveals existence of multiple lineages and suggests frequent recombination events

Enteroviruses: epidemic potential, challenges and opportunities with vaccines

Enteroviruses (EVs) are the most prevalent viruses in humans. EVs can cause a range of acute symptoms, from mild common colds to severe systemic infections such as meningitis, myocarditis, and flaccid paralysis. They can also lead to chronic diseases such as cardiomyopathy. Although more than 280 human EV serotypes exist, only four serotypes have licenced vaccines. No antiviral drugs are available to treat EV infections, and global surveillance of EVs has not been effectively coordinated. Therefore, poliovirus still circulates, and there have been alarming epidemics of non-polio enteroviruses. Thus, there is a pressing need for coordinated preparedness efforts against EVs.This review provides a perspective on recent enterovirus outbreaks and global poliovirus eradication efforts with continuous vaccine development initiatives. It also provides insights into the challenges and opportunities in EV vaccine development. Given that traditional whole-virus vaccine technologies are not suitable for many clinically relevant EVs and considering the ongoing risk of enterovirus outbreaks and the potential for new emerging pathogenic strains, the need for new effective and adaptable enterovirus vaccines is emphasized.This review also explores the difficulties in translating promising vaccine candidates for clinical use and summarizes information from published literature and clinical trial databases focusing on existing enterovirus vaccines, ongoing clinical trials, the obstacles faced in vaccine development as well as the emergence of new vaccine technologies. Overall, this review contributes to the understanding of enterovirus vaccines, their role in public health, and their significance as a tool for future preparedness.

Investigating the virulence of coxsackievirus B6 strains and antiviral treatments in a neonatal murine model

Coxsackievirus B6 (CVB6), a member of the human enterovirus family, is associated with severe diseases such as myocarditis in children. However, to date, only a limited number of CVB6 strains have been identified, and their characterization in animal models has been lacking. To address this gap, in this study, a neonatal murine model of CVB6 infection was established to compare the replication and virulence of three infectious-clone-derived CVB6 strains in vivo. The results showed that following challenge with a lethal dose of CVB6 strains, the neonatal mice rapidly exhibited a series of clinical signs, such as weight loss, limb paralysis, and death. For the two high-virulence CVB6 strains, histological examination revealed myocyte necrosis in skeletal and cardiac muscle, and immunohistochemistry confirmed the expression of CVB6 viral protein in these tissues. Real-time PCR assay also revealed higher viral loads in the skeletal and cardiac muscle than in other tissues at different time points post infection. Furthermore, the protective effect of passive immunization with antisera and a neutralizing monoclonal antibody against CVB6 infection was evaluated in the neonatal mouse model. This study should provide insights into the pathogenesis of CVB6 and facilitate further research in the development of vaccines and antivirals against CVBs.

Inborn errors of TLR3- or MDA5-dependent type I IFN immunity in children with enterovirus rhombencephalitis

Enterovirus (EV) infection rarely results in life-threatening infection of the central nervous system. We report two unrelated children with EV30 and EV71 rhombencephalitis. One patient carries compound heterozygous TLR3 variants (loss-of-function F322fs2* and hypomorphic D280N), and the other is homozygous for an IFIH1 variant (loss-of-function c.1641+1G>C). Their fibroblasts respond poorly to extracellular (TLR3) or intracellular (MDA5) poly(I:C) stimulation. The baseline (TLR3) and EV-responsive (MDA5) levels of IFN-β in the patients’ fibroblasts are low. EV growth is enhanced at early and late time points of infection in TLR3- and MDA5-deficient fibroblasts, respectively. Treatment with exogenous IFN-α2b before infection renders both cell lines resistant to EV30 and EV71, whereas post-infection treatment with IFN-α2b rescues viral susceptibility fully only in MDA5-deficient fibroblasts. Finally, the poly(I:C) and viral phenotypes of fibroblasts are rescued by the expression of WT TLR3 or MDA5. Human TLR3 and MDA5 are critical for cell-intrinsic immunity to EV, via the control of baseline and virus-induced type I IFN production, respectively.

Upsurge in echovirus 30 detections in five EU/EEA countries, April to September, 2018

An upsurge in Echovirus 30 (E30) infections, associated with meningitis/meningoencephalitis, has been observed in Denmark, Germany, the Netherlands, Norway and Sweden in the period April to September 2018, compared with 2015–2017. In total, 658 E30 infections among 4,537 enterovirus infections were detected in 15 countries between January and September 2018 and affected mainly newborns and 26–45 year-olds. National public health institutes are reminded to remain vigilant and inform clinicians of the ongoing epidemic.

Impact of Enterovirus Molecular Assay Turnaround Time on Hospitalization Length During an Echovirus 30 Meningitis Outbreak, France, Fall 2014

Background:

The impact of Enterovirus Real Time-Polymerase Chain Reaction assay (EV RT-PCR) on hospitalization lengths of patients with aseptic meningitis has been investigated but the impact of early EV RT-PCR results released on time before patient discharge remains unclear during Echovirus meningitis outbreaks.

Objective:

To assess a potential correlation between EV RT-PCR turn-around time and hospitalization lengths during an Echovirus meningitis outbreak.

Method:

Eighteen patients demonstrating a positive EV RT-PCR assay performed on Cerebrospinal Fluid (CSF) samples collected between October 1st 2014 and December 31st 2014 were retrospectively included. Viral protein 1 (VP1) gene region was amplified and sequenced using a classical Sanger sequencing reaction. Clinical data were retrospectively collected from patient’s records. Quantitative variables expressed as median values and ranges were compared using Mann Whitney U test. Correlations were performed using simple regression analysis.

Results:

Phylogenetic VP1 sequence analyses identified that the outbreak was related to an Echovirus 30 strain in 7 out of the 10 cases with available sequencing data. The three remaining sequences analyses evidenced Echovirus 14, 9 and 7 strains. Hospitalization length was statistically shorter in children without comorbidity (n=5) than in adult patients (n=10) or neonates and children with comorbidity (n=3) (p=0.003 and 0.01 respectively), whereas EV RT-PCR turnaround time was not statistically different between these groups. Correlation between hospitalization length and EV RT-PCR turnaround time was poor (R2=0.06), especially in adults (R2=0.01)

Conclusion:

Our data indicated that EV RT-PCR turnaround time was not correlated to hospitalization length during a short Echovirus meningitis outbreak.

Poliovirus and Other Enteroviruses from Environmental Surveillance in Italy, 2009-2015

Within the initiatives for poliomyelitis eradication by WHO, Italy activated an environmental surveillance (ES) in 2005. ES complements clinical Acute Flaccid Paralysis (AFP) surveillance for possible polio cases, detects poliovirus circulation in environmental sewage, and is used to monitor transmission in communities. In addition to polioviruses, the analyses comprised: (i) the monitoring of the presence of non-polio enteroviruses in sewage samples and (ii) the temporal and geographical distribution of the detected viruses. From 2009 to 2015, 2880 sewage samples were collected from eight cities participating in the surveillance. Overall, 1479 samples resulted positive for enteroviruses. No wild-type polioviruses were found, although four Sabin-like polioviruses were detected. The low degree of mutation found in the genomes of these four isolates suggests that these viruses have had a limited circulation in the population. All non-polio enteroviruses belonged to species B and the most frequent serotype was CV-B5, followed by CV-B4, E-11, E-6, E-7, CV-B3, and CV-B2. Variations in the frequency of different serotypes were also observed in different seasons and/or Italian areas. Environmental surveillance in Italy, as part of the 'WHO global polio eradication program', is a powerful tool to augment the polio surveillance and to investigate the silent circulation or the re-emergence of enteroviruses in the population.

Echovirus 30 detection in an outbreak of acute myalgia and rhabdomyolysis, Brazil 2016-2017

OBJECTIVES

To describe an outbreak of acute myalgia accompanied by elevated levels of muscle enzymes that occurred in the northeast region of Brazil from December 2016 through to May 2017.

METHODS

Clinical data were analysed and laboratory tests were performed in 86 specimens obtained from 52 individuals with suspected acute myalgia. A broader reactive enterovirus real-time RT-PCR followed by a semi-nested PCR amplification of partial VP1 gene were performed to identify the causative agent.

RESULTS

Eighty-six clinical samples were received in our laboratory during the myalgia outbreak. Median age of individuals was 39 years. Sudden acute myalgia and dark urine were the most common symptoms. Creatine phosphokinase levels were elevated with mean value ∼16 893 U/L. Human enterovirus was detected in 67% (58/86) of the patient's specimens (urine, serum, faeces and rectal swab). The enterovirus positivity per patient was 82.7% (43/52). Echovirus 30 (E-30) (82% of the typed specimens, 18/22; 76.4% (13/17) of the typed specimens per patient) was the main enterovirus identified. In addition to E-30, CV-A16 (1/22) and E-6 (3/22) were detected in 4% and 14% of the typed specimens, respectively. No deaths occurred.

CONCLUSION

The 2016-2017 outbreak of acute myalgia that occurred in the northeast region of Brazil can be associated with E-30. Despite the clinical manifestations, a favourable outcome was observed for all patients.

Laboratory diagnosis and genetic analysis of a family clustering outbreak of aseptic meningitis due to echovirus 30

Echovirus 30 (E30) is a major pathogen associated with aseptic meningitis. In the summer of 2014, a family clustering aseptic meningitis outbreak occurred in urban-rural fringe of Ningbo city in Zhejiang Province in China. To identify the etiologic agent, specimens were tested by cell culture and reverse transcriptase-polymerase chain reaction. Pathogenic examination confirmed that the outbreak is caused by E30. The first case is a 6-year-old child, who studied in kindergarten in local, suffered from headache and fever. Same symptoms appeared in his parents, aunts, and other six relatives continuously. Meanwhile, vomiting occurred in majority of the patients and diarrhea in parts of them. White blood cells in cerebrospinal fluid (CSF) exceeded normal range in all patients. Protein levels in CSF were above normal range in half of the patients. Glucose levels in CSF were within normal range in all patients. We isolated six strains E30 in the stool specimens of patients, and carried out sequencing analysis to VP1 region. Sequencing results showed that 100% sequence identity was seen in both nucleotide and amino acid levels. Phylogenetic analysis discovered that isolate in this study was grouped into sublineage D2 together with sequences isolated from other areas of China in the 2000s and 2010s. Our study is the first family clustering outbreak of aseptic meningitis caused by E30 in Zhejiang Province in China. It is essential to establish an enterovirus molecular surveillance system in China to prevent mass outbreaks in Zhejiang.

Molecular characterization of echovirus 30 isolates from Poland, 1995-2015

Echovirus 30 (E30) is one of the most frequently identified enterovirus and a major cause of meningitis in children and adults. To investigate the genetic variability and relationship of E30 isolated from specimens of aseptic meningitis cases that occurred in Poland over a period of 20 years, sequences of VP1 gene were determined and genetic analysis was performed. From 1995 to 2015, 124 E30 were isolated using RD cells, and 58 isolates were sequenced and characterized by phylogenetic analysis of partial VP1 region (793 nt). In general, nucleotide sequence divergence in pairwise comparisons among Polish E30 isolates ranged from 0.0 to 15.0 %. The phylogenetic analysis revealed that E30 circulating in Poland since 1995 belong to two unique groups: Group I, characterized by high divergence (up to 13.1 %), segregated in four subgroups, and showed strong temporal circulation of E30. Group II, detected in Poland in 2013-2014, was closely correlated with two meningitis outbreaks and formed a separate genetically homogeneous group. Phylogenetic analysis revealed that strains from Poland had the closest genetic relationship with not only the isolates previously identified in Europe (Belarus, France, Germany, Italy, Russia) but also those in other parts of the world (Australia, China). Sequences of outbreak isolates were grouped in group II together with those from Russia and China isolated during 2010-2013. The identification of five distinct viral lineages during 1995-2015 confirmed the high E30 genetic diversity which may be an essential precondition for the emergence of new strains responsible for further potential aseptic meningitis outbreaks.

Sporadic isolation of sabin-like polioviruses and high-level detection of non-polio enteroviruses during sewage surveillance in seven Italian cities, after several years of inactivated poliovirus vaccination

Sewage surveillance in seven Italian cities between 2005 and 2008, after the introduction of inactivated poliovirus vaccination (IPV) in 2002, showed rare polioviruses, none that were wild-type or circulating vaccine-derived poliovirus (cVDPV), and many other enteroviruses among 1,392 samples analyzed. Two of five polioviruses (PV) detected were Sabin-like PV2 and three PV3, based on enzyme-linked immunosorbent assay (ELISA) and PCR results. Neurovirulence-related mutations were found in the 5'noncoding region (5'NCR) of all strains and, for a PV2, also in VP1 region 143 (Ile>Thr). Intertypic recombination in the 3D region was detected in a second PV2 (Sabin 2/Sabin 1) and a PV3 (Sabin 3/Sabin 2). The low mutation rate in VP1 for all PVs suggests limited interhuman virus passages, consistent with efficient polio immunization in Italy. Nonetheless, these findings highlight the risk of wild or Sabin poliovirus reintroduction from abroad. Non-polio enteroviruses (NPEVs) were detected, 448 of which were coxsackievirus B (CVB) and 294 of which were echoviruses (Echo). Fifty-six NPEVs failing serological typing were characterized by sequencing the VP1 region (nucleotides [nt] 2628 to 2976). A total of 448 CVB and 294 Echo strains were identified; among those strains, CVB2, CVB5, and Echo 11 predominated. Environmental CVB5 and CVB2 strains from this study showed high sequence identity with GenBank global strains. The high similarity between environmental NPEVs and clinical strains from the same areas of Italy and the same periods indicates that environmental strains reflect the viruses circulating in the population and highlights the potential risk of inefficient wastewater treatments. This study confirmed that sewage surveillance can be more sensitive than acute flaccid paralysis (AFP) surveillance in monitoring silent poliovirus circulation in the population as well as the suitability of molecular approaches to enterovirus typing.

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.

Complete genome sequence analysis of human echovirus 30 isolated during a large outbreak in Guangdong Province of China, in 2012

In May and June 2012, an outbreak of aseptic meningitis caused by Echovirus 30 (E30) occurred on a large scale in Luoding, Guangdong Province, China. Our team successfully isolated one subtype, strain 2012EM161, and its complete genome was sequenced. The phylogenetic tree of viral protein (VP) 1 gene sequences showed that the viral isolate was similar to the E30 strain prevalent in Fujian (2011), with identity of 98.05–99.32 % and 98.63–99.32 % for nucleotides and amino acids respectively. Whole genome-based phylogenetic analysis indicated that 2012EM161 contained the most proximate consensus to DQ246620 (Zhejiang, 2003) and FDJS03 (AY948442, Jiangsu, 2005), with nucleotide homogeneity of 87.09 % and 86.98 % respectively. The RDP4.16 and Simplot analysis showed that the newly discovered 2012EM161 was probably a recombinant, which was closely related to the strain of E30 (DQ246620) in the first half of the genome and the strain of E6 (JX976771) in genomic P3 region. The whole genome sequence of 2012EM161 will allow further study of the origin, evolution, and the molecular epidemiology of E30 strains.

Molecular epidemiology of Echovirus 30 in Fujian, China between 2001 and 2011

Echovirus 30 (E-30) was responsible for an outbreak of aseptic meningitis between April 1 and June 2, 2011 in Fujian Province, China. A molecular epidemiology study of 115 E-30 strains was performed to characterize the genetic features of the etiologic agent of the 2011 aseptic meningitis outbreak. The phylogenetic trees of the complete VP1 gene (876 bp) from 74 of 115 isolates and 50 reference sequences were analyzed. Three lineages (E-30_h, i, and j) were detected that had co-circulated in Fujian in the last decade, of which E-30_j was new. The other 72 Fujian strains and 16 representative strains from other provinces of China all belong to E-30_h and E-30_i. Two distinct E-30 clusters including virus isolates obtained during adult surveillance were associated with the 2011 outbreak and differed from Fujian isolates prior to 2011, suggesting that the viruses may vary and adult infections play an important role in viral transmission. Thus, the multiple lineages of E-30 in Fujian and variant viruses enhanced transmissibility, which may be related to the epidemic activity of E-30.

Molecular typing and epidemiology of enteroviruses in Cyprus, 2003-2007

Human enteroviruses (HEVs) are responsible for a wide spectrum of clinical diseases. Even though usually associated with non-specific febrile illness, they are the most common cause of viral meningitis and pose a serious public-health problem, especially during outbreaks. Rapid detection and identification of HEV serotypes in clinical specimens are important in appropriate patient management and epidemiological investigation. A 5 year study (2003-2007) of clinical specimens from patients with viral meningitis and/or symptoms of enteroviral infection was carried out in Cyprus to determine the underlying enteroviral aetiology. Reverse transcription, followed by a sequential PCR strategy targeting the 5' non-coding region and VP1 region, was used for typing the isolated enteroviruses. The serotype of each isolate was determined by blast search of the VP1 amplicon sequence against GenBank. Clinical specimens from a total of 146 patients were diagnosed as enterovirus-positive. Twenty-two different serotypes were identified. The main strains identified were echovirus 18 and echovirus 30, followed by coxsackievirus B5, echovirus 9, echovirus 6, coxsackievirus A10 and coxsackievirus B2. However, rapid changes in serotype frequency and diversity were observed over time. Serotype distribution corresponded essentially with observations reported from other European countries in the same period. The present report demonstrates the epidemiology of enteroviruses in Cyprus from 2003 to 2007.

A large Finnish echovirus 30 outbreak was preceded by silent circulation of the same genotype

An outbreak of echovirus 30 (E-30) in 2009 was confirmed by both frequent isolation of the virus from sewage as well as from patient samples in Finland. Over the last 10 years E-30 had only been isolated sporadically in Finland. We here study the phylogenetic relationships of the strains from the outbreak in the context of E-30 circulation over the last 20 years. The analyzed region comprised 276 nucleotides in the 5' end of VP1 (nucleotides 132-407 in the VP1 of the E-30 Bastianni strain). The Finnish strains were clustered into at least four distinct genogroups, with seven clusters exceeding the genotype demarcation of 12% and the 2009 epidemic strains forming the largest genogroup VII. Moreover, we detected largely divergent genotypes in 2007 and 2009. Interestingly, close genetic relatives of the epidemic strains had already been isolated a few years before the outbreak. Phylodynamic analysis estimated 8.9 years (95% highest posterior density intervals 7.0-11.0) as the age of genogroup VII, indicating a probable origin and evolutionary history prior to its introduction and epidemic expansion in Finland. Finally, the most recent common ancestor for the current E-30 diversity dates back to 1939 (95% highest posterior density intervals 1913-1956).