The role of conformational epitopes in the evolutionary divergence of enterovirus D68 clades: A bioinformatics-based study

Pterostilbene Exhibits Broad-Spectrum Antiviral Activity by Targeting the Enterovirus Capsid, Inactivating Viral Particles, Blocking Viral Binding, and Protecting Mice From Lethal EV-A71 Challenge

Human enteroviruses (EVs) are a major public health issue worldwide owing to their potential to cause respiratory illnesses, hand-foot-and-mouth disease, and severe neurological complications. Currently, no effective drugs or multivalent vaccines are available. Pterostilbene (Pte), a naturally occurring compound found in blueberries and other plants, is a type of stilbene with a similar structure to resveratrol. Pterostilbene exerts antioxidant, anti-inflammatory, and anticancer properties. However, few studies have explored its antiviral activity. This study aimed to investigate the anti-enteroviral effect and mechanisms of Pte against EV-A71 and EV-D68. Cytotoxicity and antiviral assays were performed to assess the safety of Pte to cells and its antiviral effects against enteroviruses. Viral attachment, inactivation assays, cellular receptor binding, western blotting, time-of-addition and time-of-removal assays, particle stability thermal release assay, and molecular docking were performed to elucidate the antiviral mechanisms of Pte. Additionally, we validated the antiviral effects of Pte using in vivo experiments. Among the stilbenes examined, Pte exerted a broad-spectrum inhibitory effect on various enteroviruses, including EV-A71, EV-D68, and coxsackieviruses at 40 μM, without cytotoxicity. Mechanistically, Pte significantly inhibited enteroviral attachment, inactivated viral particles, blocked viral binding to its receptors, and increased virion stability. Molecular docking analysis revealed that Pte occupied a hydrophobic pocket in viral protein 1, indicating a strong binding affinity and acting as an efficient inhibitor. Notably, sequence alignment of multiple enteroviruses indicated that the Pte-interacting residues in VP1 were highly conserved. In vivo studies demonstrated that oral administration of Pte significantly alleviated infection symptoms and reduced mortality in hSCARB2 transgenic mice. Pte possesses potential application as a broad-efficacy antiviral drug against enteroviral infections.

Insights Into Enterovirus D68 Immunology: Unraveling the Mysteries of Host-Pathogen Interactions

BACKGROUND

Enterovirus D68 (EV-D68) has emerged as a significant respiratory and neurological pathogen, particularly affecting children with severe respiratory illnesses and acute flaccid myelitis. Understanding the interaction between EV-D68 and the host immune system is crucial for developing effective prevention and treatment strategies.

OBJECTIVES

This review aims to examine the immune response to EV-D68, its mechanisms of immune evasion, and the current progress in vaccine and antiviral development while identifying gaps in knowledge and future research directions.

METHODS

A comprehensive review of the literature was conducted, focusing on the innate and adaptive immune responses to EV-D68, its strategies for immune evasion, and advancements in therapeutic interventions.

RESULTS

Pattern recognition receptors detect EV-D68 and trigger antiviral defenses, including interferon production and activation of natural killer cells. B cells generate antibodies, while T cells coordinate a targeted response to the virus. EV-D68 employs mechanisms such as antigenic variation and disruption of host antiviral pathways to evade immune detection. Progress in vaccine and antiviral research shows promise but remains in the early stages.

CONCLUSIONS

EV-D68 represents a complex and evolving public health challenge. Although the immune system mounts a robust response, the virus's ability to evade these defenses complicates efforts to control it. Continued research is essential to develop effective vaccines and antivirals and to address gaps in understanding its pathogenesis and immune interactions.

IMPLICATIONS

A multidisciplinary approach is critical to improving diagnostic, preventive, and therapeutic strategies for EV-D68, ensuring better preparedness for future outbreaks.

Detections of rare enterovirus C105 linked to an emerging novel clade, Spain, 2019 to 2024

Enterovirus (EV)-C105 is a rare genotype not previously detected in Spain. Between 2019 and 2024, we detected EV-C105 in respiratory samples of five patients, through routine EV surveillance. Three cases had respiratory illness and two were hospitalised for neurological illness. Four of the five sequenced strains belonged to an emerging clade (C1), defined by four novel nonsynonymous mutations in key antigenic epitopes. We recommend reinforced clinical awareness and EV genomic surveillance, including respiratory samples, even when symptoms are neurological.

A self-amplifying RNA vaccine prevents enterovirus D68 infection and disease in preclinical models

The recent emergence and rapid response to severe acute respiratory syndrome coronavirus 2 was enabled by prototype pathogen and vaccine platform approaches, driven by the preemptive application of RNA vaccine technology to the related Middle East respiratory syndrome coronavirus. Recently, the National Institutes of Allergy and Infectious Diseases identified nine virus families of concern, eight enveloped virus families and one nonenveloped virus family, for which vaccine generation is a priority. Although RNA vaccines have been described for a variety of enveloped viruses, a roadmap for their use against nonenveloped viruses is lacking. Enterovirus D68 was recently designated a prototype pathogen within the family Picornaviridae of nonenveloped viruses because of its rapid evolution and respiratory route of transmission, coupled with a lack of diverse anti-enterovirus vaccine approaches in development. Here, we describe a proof-of-concept approach using a clinical stage RNA vaccine platform that induced robust enterovirus D68-neutralizing antibody responses in mice and nonhuman primates and prevented upper and lower respiratory tract infections and neurological disease in mice. In addition, we used our platform to rapidly characterize the antigenic diversity within the six genotypes of enterovirus D68, providing the necessary data to inform multivalent vaccine compositions that can elicit optimal breadth of neutralizing responses. These results demonstrate that RNA vaccines can be used as tools in our pandemic-preparedness toolbox for nonenveloped viruses.

Enterovirus-D68 - A Reemerging Non-Polio Enterovirus that Causes Severe Respiratory and Neurological Disease in Children

The past decade has seen the global reemergence and rapid spread of enterovirus D68 (EV-D68), a respiratory pathogen that causes severe respiratory illness and paralysis in children. EV-D68 was first isolated in 1962 from children with pneumonia. Sporadic cases and small outbreaks have been reported since then with a major respiratory disease outbreak in 2014 associated with an increased number of children diagnosed with polio-like paralysis. From 2014-2018, major outbreaks have been reported every other year in a biennial pattern with > 90% of the cases occurring in children under the age of 16. With the outbreak of SARS-CoV-2 and the subsequent COVID-19 pandemic, there was a significant decrease in the prevalence EV-D68 cases along with other respiratory diseases. However, since the relaxation of pandemic social distancing protocols and masking mandates the number of EV-D68 cases have begun to rise again - culminating in another outbreak in 2022. Here we review the virology, pathogenesis, and the immune response to EV-D68, and discuss the epidemiology of EV-D68 infections and the divergence of contemporary strains from historical strains. Finally, we highlight some of the key challenges in the field that remain to be addressed.

Clinical and molecular epidemiology of enterovirus D68 from 2013 to 2020 in Shanghai

Enterovirus D68 (EV-D68) is an emerging pathogen that has caused outbreaks of severe respiratory disease worldwide, especially in children. We aim to investigate the prevalence and genetic characteristics of EV-D68 in children from Shanghai. Nasopharyngeal swab or bronchoalveolar lavage fluid samples collected from children hospitalized with community-acquired pneumonia were screened for EV-D68. Nine of 3997 samples were EV-D68-positive. Seven of nine positive samples were sequenced and submitted to GenBank. Based on partial polyprotein gene (3D) or complete sequence analysis, we found the seven strains belong to different clades and subclades, including three D1 (detected in 2013 and 2014), one D2 (2013), one D3 (2019), and two B3 (2014 and 2018). Overall, we show different clades and subclades of EV-D68 spread with low positive rates (0.2%) among children in Shanghai between 2013 and 2020. Amino acid mutations were found in the epitopes of the VP1 BC and DE loops and C-terminus; similarity analysis provided evidence for recombination as an important mechanism of genomic diversification. Both single nucleotide mutations and recombination play a role in evolution of EV-D68. Genetic instability within these clinical strains may indicate large outbreaks could occur following cumulative mutations.

Molecular epidemiology and recombination of enterovirus D68 in China

Enterovirus D68 (EV-D68), a member of Enterovirus genus of the Picornaviridae family, mainly causes respiratory system-related diseases as well as neurological complications in some patients. At present, there is no effective vaccine or treatment for the virus. The aim of this research was to systematically analyse the molecular epidemiology, recombination and changes in the epitope of EV-D68 in China from 2008 to 2022. Through phylogenetic analysis based on VP1 sequences, it was found that there was limited information about EV-D68 infection before 2011 and that EV-D68 infection was dominated by the A2 gene subtype from 2011 to 2013 and the B3 genotype from 2014 to 2018, during which A2 and B3 were coprevalent and alternately prevalent. We also constructed a phylogenetic tree using the EV-D68 full-length genome sequences, and the genotype of each sequence was consistent with that of the VP1 sequence evolutionary tree. Recombination analysis showed that MH341715 underwent intertypic recombination with the A2 genotype MH341729 at the 5' untranslated region (5'UTR) and that P1-P3 underwent recombination with the B3 genotype MH341712. The capsid protein VP1 is one of the most important structural proteins. In VP1, the BC-loop (89-105 amino acids) and DE-loop (140-152 amino acids) are the most variable domains on the surface of the virus and are associated with epitopes. In this study, it was found that the dominant amino acid composition of the BC-loop and DE-loop continued to change with the epidemic of the virus; the amino acid composition also differed in different regions of the same genotypes. The ongoing genomic and molecular epidemiology of EV-D68 remains important for predicting emergence of new viruses and preventing major outbreaks of respiratory diseases.

Insights into the molecular evolution of enterovirus D68

Enterovirus D68 (EV-D68) is a respiratory virus that primarily affects children and has been associated with sporadic outbreaks of respiratory illness worldwide. In the present study, temporal spreading and molecular evolution of EV-D68 clades (A1, A2, B, B1, B2, B3, and C) were evaluated. Bayesian coalescent analysis was performed to study viral evolution. Data from 976 whole-genome sequences (WGSs) collected between 1977 and 2022 were evaluated. For A1, the most recent common ancestor was dated to 2005-04-17 in the USA; for A2 it was 2003-12-23 in China; for B, it was 2003-07-06 in China; for B1, it was 2010-03-21 in Vietnam; for B2, it was 2006-11-25 in Vietnam; for B3, it was 2011-01-15 in China; and for C, it was 2000-06-27 in the USA. The molecular origin of EV-D68 was in Canada in 1995, and later it was disseminated in France in 1997, the USA in 1999, Asia in 2008, the Netherlands in 2009, New Zealand in 2010, Mexico in 2014, Kenya in 2015, Sweden in 2016, Switzerland in 2018, Spain in 2018, Belgium in 2018, Australia in 2018, and Denmark in 2019. In 2022, this virus circulated in the USA. In conclusion, EV-D68 originated in Canada in the 1990s and spread to Europe, Asia, Oceania, Latin America, and Africa.

Complete genome analysis of echovirus 30 strains isolated from hand-foot-and-mouth disease in Yunnan province, China

BACKGROUND

Echovirus 30 is prone to cause hand-foot-and-mouth disease in infants and children. However, molecular epidemiologic information on the spread of E30 in southwestern China remains limited. In this study, we determined and analyzed the whole genomic sequences of E30 strains isolated from the stools of patients with hand-foot-and-mouth disease in Yunnan Province, China, in 2019.

METHODS

E30 isolates were obtained from fecal samples of HFMD patients. The whole genomes were sequenced by segmented PCR and analyzed for phylogeny, mutation and recombination. MEGA and DNAStar were used to align the present isolates with the reference strains. The VP1 sequence of the isolates were analyzed for selection pressure using datamonkey server.

RESULTS

The complete genome sequences of four E30 were obtained from this virus isolation. Significant homologous recombination signals in the P2-3'UTR region were found in all four isolates with other serotypes. Phylogenetic analysis showed that the four E30 isolates belonged to lineage H. Comparison of the VP1 sequences of these four isolates with other E30 reference strains using three selection pressure analysis models FUBAR, FEL, and MEME, revealed a positive selection site at 133rd position.

CONCLUSIONS

This study extends the whole genome sequence of E30 in GenBank, in which mutations and recombinations have driven the evolution of E30 and further improved and enriched the genetic characteristics of E30, providing fundamental data for the prevention and control of diseases caused by E30. Furthermore, we demonstrated the value of continuous and extensive surveillance of enterovirus serotypes other than the major HFMD-causing viruses.

In silico epitope prediction and evolutionary analysis reveals capsid mutation patterns for enterovirus B

Enterovirus B (EVB) is a common species of enterovirus, mainly consisting of Echovirus (Echo) and Coxsackievirus B (CVB). The population is generally susceptible to EVB, especially among children. Since the 21st century, EVB has been widely prevalent worldwide, and can cause serious diseases, such as viral meningitis, myocarditis, and neonatal sepsis. By using cryo-electron microscopy, the three-dimensional (3D) structures of EVB and their uncoating receptors (FcRn and CAR) have been determined, laying the foundation for the study of viral pathogenesis and therapeutic antibodies. A limited number of epitopes bound to neutralizing antibodies have also been determined. It is unclear whether additional epitopes are present or whether epitope mutations play a key role in molecular evolutionary history and epidemics, as in influenza and SARS-CoV-2. In the current study, the conformational epitopes of six representative EVB serotypes (E6, E11, E30, CVB1, CVB3 and CVB5) were systematically predicted by bioinformatics-based epitope prediction algorithm. We found that their epitopes were distributed into three clusters, where the VP1 BC loop, C-terminus and VP2 EF loop were the main regions of EVB epitopes. Among them, the VP1 BC loop and VP2 EF loop may be the key epitope regions that determined the use of the uncoating receptors. Further molecular evolution analysis based on the VP1 and genome sequences showed that the VP1 C-terminus and VP2 EF loop, as well as a potential "breathing epitope" VP1 N-terminus, were common mutation hotspot regions, suggesting that the emergence of evolutionary clades was driven by epitope mutations. Finally, footprints showed mutations were located on or near epitopes, while mutations on the receptor binding sites were rare. This suggested that EVB promotes viral epidemics by breaking the immune barrier through epitope mutations, but the mutations avoided the receptor binding sites. The bioinformatics study of EVB epitopes may provide important information for the monitoring and early warning of EVB epidemics and developing therapeutic antibodies.

EV-D68 virus-like particle vaccines elicit cross-clade neutralizing antibodies that inhibit infection and block dissemination

Enterovirus D68 (EV-D68) causes severe respiratory illness in children and can result in a debilitating paralytic disease known as acute flaccid myelitis. No treatment or vaccine for EV-D68 infection is available. Here, we demonstrate that virus-like particle (VLP) vaccines elicit a protective neutralizing antibody against homologous and heterologous EV-D68 subclades. VLP based on a B1 subclade 2014 outbreak strain elicited comparable B1 EV-D68 neutralizing activity as an inactivated viral particle vaccine in mice. Both immunogens elicited weaker cross-neutralization against heterologous viruses. A B3 VLP vaccine elicited more robust neutralization of B3 subclade viruses with improved cross-neutralization. A balanced CD4⁺ T helper response was achieved using a carbomer-based adjuvant, Adjuplex. Nonhuman primates immunized with this B3 VLP Adjuplex formulation generated robust neutralizing antibodies against homologous and heterologous subclade viruses. Our results suggest that both vaccine strain and adjuvant selection are critical elements for improving the breadth of protective immunity against EV-D68.