Enteroviruses as agents of emerging infectious diseases

Structural basis for a highly conserved RNA-mediated enteroviral genome replication

Enteroviruses contain conserved RNA structures at the extreme 5' end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3' spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3' spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.

Molecular characterization of coxsackievirus A24 variants isolated from an outbreak of acute hemorrhagic conjunctivitis

PURPOSE

Acute Hemorrhagic conjunctivitis (AHC) is associated with CVA24v. Recently there was a severe outbreak of conjunctivitis in months of July and August 2023 in India. This study emphasizes the identification of the distinct mutations in the CVA24v strains, which were isolated during the AHC outbreak and could have potentially played a role in the high transmission of AHC in India during the 2023 outbreak.

METHODS

A total of 71 conjunctivitis patients aged 1-75 years comprising 47 males and 24 females who attended Ophthalmology department of a tertiary care hospital of easternIndia were studied.RNA was extracted from all conjunctival swab samples and converted into cDNA. Subsequently, the viral 5' UTR was amplified and the PCR positive samples were subjected to sequencing. The newly isolated viral 5' UTR sequences were aligned with other worldwide sequences using the Clustal W tool to conduct mutational analysis. A phylogenetic tree was built using the MEGA software for viral genotype identification.

RESULTS

All of the current outbreak strains belonged to genotype IV of CVA24v. The present outbreak strains formed a distinct clade in the phylogenetic tree and were different from previously reported Indian strains. Two persistent mutations, specifically in domain IV (T213C) and domain V (C475T), were exclusively detected within the internal ribosome entry site (IRES) of the 5' UTR of the current strains causing the outbreak. These two alterations have previously been shown to impact the virulence of another enterovirus (CV B3), but they have not been described in CVA24v until now.

CONCLUSION

Finding of the present study highlights the possibility and the significance of the aforementioned two mutations in enhancing the transmissibility of the newer CVA24v strains. Hence, these two distinct mutations should be investigated further for developing antiviral therapies to combat future AHC outbreaks associated with CVA24v.

Non-Polio Enteroviruses Isolated by Acute Flaccid Paralysis Surveillance Laboratories in the Russian Federation in 1998-2021: Distinct Epidemiological Features of Types

More than 100 types of non-polio enteroviruses (NPEVs) are ubiquitous in the human population and cause a variety of symptoms ranging from very mild to meningitis and acute flaccid paralysis (AFP). Much of the information regarding diverse pathogenic properties of NPEVs comes from the surveillance of poliovirus, which also yields NPEV. The analysis of 265 NPEV isolations from 10,433 AFP cases over 24 years of surveillance and more than 2500 NPEV findings in patients without severe neurological lesions suggests that types EV-A71, E13, and E25 were significantly associated with AFP. EV-A71 was also significantly more common among AFP patients who had fever at the onset and residual paralysis compared to all AFP cases. In addition, a significant disparity was noticed between types that were common in humans (CV-A2, CVA9, EV-A71, E9, and E30) or in sewage (CVA7, E3, E7, E11, E12, and E19). Therefore, there is significant evidence of non-polio viruses being implicated in severe neurological lesions, but further multicenter studies using uniform methodology are needed for a definitive conclusion.

A multiplex real-time fluorescence-based quantitative PCR assay for calf diarrhea viruses

Introduction

Calf diarrhea is a significant condition that has a strong effect on the cattle industry, resulting in huge economic losses annually. Bovine torovirus (BToV), bovine enterovirus (BEV), bovine norovirus (BNoV), bovine coronavirus (BCoV), bovine rotavirus (BRV), and bovine viral diarrhea virus (BVDV) are key pathogens that have been implicated in calf diarrhea. Among these viruses, there remains limited research on BToV, BEV, and BNoV, with no available vaccines or drugs for their prevention and control. Although commercial vaccines exist for BCoV, BRV, and BVDV, the prevalence of these diseases remains high.

Methods

To address this issue, we developed a multiplex real-time fluorescence quantitative PCR method for detecting BToV, BEV, BNoV, BCoV, BRV, and BVDV. This method can be used to effectively monitor the prevalence of these six viruses and serve as a reference for future prevention and control strategies. In this study, we specifically designed primers and probes for the BNoV Rdrp, BEV 5'UTR, BToV M, BCoV N, BRV NSP5, and BVDV 5'UTR genes.

Results

This method was determined to be efficient, stable, and sensitive. The lowest detectable levels of plasmids for BNoV, BEV, BToV, BRV, BCoV, and BVDV were 1.91 copies/μL, 96.0 copies/μL, 12.8 copies/μL, 16.4 copies/μL, 18.2 copies/μL, and 65.3 copies/μL, respectively. Moreover, the coefficients of variation for all six detection methods were < 3%; they also exhibited a strong linear relationship (R2 ≥ 0.98), and an amplification efficiency of 90%-110%. A total of 295 fecal and anal swabs were collected from calves with diarrhea in Guangdong, China. The positive rates for BToV, BEV, BNoV, BCoV, BR, and BVDV were determined to be 0.34% (1/295), 6.10% (18/295), 0.68% (2/295), 1.36% (4/295), 10.85% (32/295), and 2.03% (6/295), respectively. Notably, BEV and BRV exhibited the highest prevalence.

Discussion

Additionally, this study identified the occurrence of BToV and BNoV in Guangdong for the first time. In summary, this study successfully established an effective method for detecting several important bovine viruses; ultimately, this holds strong implications for the future development of the cattle industry.

Surveillance, epidemiology, and impact of the coronavirus disease 2019 interventions on the incidence of enterovirus infections in Nanchang, China, 2010-2022

Introduction

Pathogen spectrum of Hand, foot and mouth disease (HFMD) has substantially changed in the past decade in China. Growing evidence has indicated that anti-COVID-19 nonpharmaceutical interventions (NPIs) can support control of various infectious diseases, including intestinal diseases.

Methods

In this study, HFMD cases were enrolled from sentinel hospitals of Nanchang, Jiangxi province, and enteroviruses were genotyped using specific real time RT-PCR. We systematically characterized the epidemiology of HFMD based on the continuous molecular surveillance and estimated the impact of COVID-19 intervention on HFMD incidence using seasonal autoregressive integrated moving average (ARIMA) models.

Results

A total of 10247 HFMD cases were included during 2010-2022, of which 6121 enterovirus (EV)-positive cases (59.7%) were identified by real-time RT-PCR. Over 80% cases were associated with EV-A71 and coxsackievirus A16 (CVA16) during 2010-2012, while the type distribution significantly changed as CVA6 emerged to be dominant, accounting for 22.6%-59.6% during 2013-2022. It was observed that the prevalence patterns of EV-A71 and CVA16 were similar and both of them peaked in the second quarter and then leveled off. However, CVA6 was generally prevalent around the fourth quarter, demonstrating a staggered prevalence during 2010-2019. During the COVID-19 epidemic, the seasonal HFMD epidemic peak was restrained, and the ARIMA analysis indicated that the COVID-19 intervention had mitigated EV transmission during the first COVID-19 outbreak in early 2020. In addition, bivariate Spearman's cross-correlation coefficients were estimated for the major types CVA6, CVA16 and EV-A71. Our analyses indicated the possible existence of correlations among CVA6, CVA16 and EV-A71 prevalence in the epidemiological level.

Discussion

Taken together, the type distribution of HFMD has substantially changed over the last decade and CVA6 and CVA16 are currently the most predominant types co-circulating in Nanchang. The anti-COVID-19 NPIs significantly reduced the incidence of EV infections.

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

Epidemiology of Hand, Foot, and Mouth Disease and Genetic Evolutionary Characteristics of Coxsackievirus A10 in Taiyuan City, Shanxi Province from 2016 to 2020

In recent years, the prevalence of hand, foot, and mouth disease (HFMD) caused by enteroviruses other than enterovirus A71 (EV-A71) and coxsackievirus A16 (CVA16) has gradually increased. The throat swab specimens of 2701 HFMD cases were tested, the VP1 regions of CVA10 RNA were amplified using RT-PCR, and phylogenetic analysis of CVA10 was performed. Children aged 1–5 years accounted for the majority (81.65%) and boys were more than girls. The positivity rates of EV-A71, CVA16, and other EVs were 15.22% (219/1439), 28.77% (414/1439), and 56.01% (806/1439), respectively. CVA10 is one of the important viruses of other EVs. A total of 52 CVA10 strains were used for phylogenetic analysis based on the VP1 region, 31 were from this study, and 21 were downloaded from GenBank. All CVA10 sequences could be assigned to seven genotypes (A, B, C, D, E, F, and G), and genotype C was further divided into C1 and C2 subtypes, only one belonged to subtype C1 and the remaining 30 belonged to C2 in this study. This study emphasized the importance of strengthening the surveillance of HFMD to understand the mechanisms of pathogen variation and evolution, and to provide a scientific basis for HFMD prevention, control, and vaccine development.

Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody

Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to comprehensively understand the specificities and the immunological characteristic of this serotype. The solved cryo-EM structures of the F-, A-, and E-particles of E3 bound with 6D10 revealed the structural features of the virus-antibody interface. Importantly, the structures of E-particles bound with 6D10 revealed for the first time the nature of the C-terminus of VP1 for HEV-Bs at the structural level. The highly immunogenic nature of this region in the E-particles provides new strategies for vaccine development for HEV-Bs.

Serotype analysis of pediatric enteroviral meningitis in Gwangju, Republic of Korea: Number of annual cases, distribution by age group, and characteristics of each serotype

BACKGROUND

Enteroviral meningitis is a common disease in children; however, serotype data are still lacking, especially for late childhood.

OBJECTIVES

This study analyzed the number of annual cases, distribution by age group, and characteristics of each serotype among children with enteroviral meningitis.

STUDY DESIGN

After the initial screening of 1,009 children (<18 years) with viral meningitis between 2008 and 2021, the data of enteroviral meningitis were retrospectively reviewed. The number of annual cases and serotypes were investigated. The distribution of serotypes across different ages was reviewed. Clinical characteristics of the major serotypes (detected in at least 15 patients) were further examined.

RESULTS

Among the 700 patients with enteroviral meningitis, serotypes were tested in 517 patients (73.9%), which could be typed in 370 patients (71.6%). EV-A71 was the most common serotype detected in 2010, 2012, and 2019. After 2020, enterovirus was rarely detected. The group B coxsackieviruses (CVBs) were commonly detected in neonates (CVB1, 33.3%) and infants (CVB5, 17.4%). The echoviruses were commonly detected beyond infancy; E30 was the most frequently detected in late childhood (14.4%) and adolescents (15.4%). EV-A71 was the most frequently detected in early childhood (17.2%). Between the 11 major serotypes, vomiting, headache, and irritability were more commonly associated with echoviruses (P <0.01). In EV-A71, neurologic symptoms and skin lesions were more common (P <0.01).

CONCLUSION

The CVBs were commonly detected in neonates and infants, whereas the echoviruses were commonly detected beyond infancy and caused vomiting, headache, and irritability. EV-A71 was the most frequently detected in early childhood, frequently causing neurologic and dermatologic problems.

Epidemiology of Echovirus 30 Infections Detected in a University Hospital in Catalonia, Spain, in 1995–2020

There is a growing interest in echovirus 30 (E30), an enterovirus responsible for neurological disease and hospitalization. There are multiple studies of outbreaks, but few that study the epidemiology over long periods of time. Our study aims to describe the clinical, epidemiological and microbiological characteristics of a series of E30 infections detected over 26 years. Data were retrospectively collected from a database of all enterovirus infections identified in our laboratory. They were detected by viral isolation or nucleic acid detection in patients presenting with respiratory or neurological infections, rash, sepsis-like syndrome, or gastroenteritis. Enterovirus genotyping was performed by amplification of the VP1 gene using RT-nested PCR, followed by sequencing and BLAST analysis. Of the 2402 enterovirus infections detected, 1619 were linked to at least one genotype and 173 were caused by E30. Clinical information was available for 158 (91.3%) patients. E30 was associated with neurological infection in 107 (67.8%) cases and it was detected almost every year. Phylogenetic analysis was performed with 67 sequences. We observed that E30 strains circulating in Catalonia from 1996 to 2016 belong to two lineages (E and F), although the majority cluster was in F. In 2018, lineage I emerged as the dominant lineage.

A Journey into the Clinical Relevance of Heme Oxygenase 1 for Human Inflammatory Disease and Viral Clearance: Why Does It Matter on the COVID-19 Scene?

Heme oxygenase 1 (HO-1), the rate-limiting enzyme in heme degradation, is involved in the maintenance of cellular homeostasis, exerting a cytoprotective role by its antioxidative and anti-inflammatory functions. HO-1 and its end products, biliverdin, carbon monoxide and free iron (Fe²⁺), confer cytoprotection against inflammatory and oxidative injury. Additionally, HO-1 exerts antiviral properties against a diverse range of viral infections by interfering with replication or activating the interferon (IFN) pathway. Severe cases of coronavirus disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are characterized by systemic hyperinflammation, which, in some cases, leads to severe or fatal symptoms as a consequence of respiratory failure, lung and heart damage, kidney failure, and nervous system complications. This review summarizes the current research on the protective role of HO-1 in inflammatory diseases and against a wide range of viral infections, positioning HO-1 as an attractive target to ameliorate clinical manifestations during COVID-19.

Surveillance, Epidemiology and Impact of EV-A71 Vaccination on Hand, Foot, and Mouth Disease in Nanchang, China, 2010-2019

After the first national-scale outbreak of Hand, foot, and mouth disease (HFMD) in China, a national surveillance network was established. Here we described the epidemiology and pathogenic profile of HFMD and the impact of EV-A71 vaccination on pathogen spectrum of enteroviruses in the southeastern Chinese city of Nanchang during 2010–2019. A total of 7,951 HFMD cases from sentinel hospitals were included, of which 4,800 EV-positive cases (60.4%) were identified by real-time RT-PCR. During 2010–2012, enterovirus 71 (EV-A71) was the main causative agent of HFMD, causing 63.1% of cases, followed by 19.3% cases associated with coxsackievirus A16 (CV-A16). Since 2013, the proportion of other enteroviruses has increased dramatically, with the sub genotype D3 strain of Coxsackievirus A6 (CV-A6) replacing the dominance of EV-A71. These genetically diverse native strains of CV-A6 have co-transmitted and co-evolved in Nanchang. Unlike EV-A71 and CV-A16, most CV-A6 infections were concentrated in autumn and winter. The incidence of EV-A71 infection negatively correlated with EV-A71 vaccination (r = −0.990, p = 0.01). And severe cases sharply declined as the promotion of EV-A71 vaccines. After 2-year implementation of EV-A71 vaccination, EV-A71 is no longer detected from the reported HFMD cases in Nanchang. In conclusion, EV-A71 vaccination changed the pattern of HFMD epidemic, and CV-A6 replaced the dominance of EV-A71 over time.

A study of drug candidates derived from pleconaril for inhibiting coxsackievirus B3 (Cvb3) by ADMET, molecular docking, molecular dynamics and retrosynthesis

In the light of the serious diseases attributed to it, there is an urgent and inescapable need to hunt for antiviral medications for Coxsackievirus B3 (CVB3).

Advanced detection strategies for cardiotropic virus infection in a cohort study of heart failure patients

The prevalence and contribution of cardiotropic viruses to various expressions of heart failure are increasing, yet primarily underappreciated and underreported due to variable clinical syndromes, a lack of consensus diagnostic standards and insufficient clinical laboratory tools. In this study, we developed an advanced methodology for identifying viruses across a spectrum of heart failure patients. We designed a custom tissue microarray from 78 patients with conditions commonly associated with virus-related heart failure, conditions where viral contribution is typically uncertain, or conditions for which the etiological agent remains suspect but elusive. Subsequently, we employed advanced, highly sensitive in situ hybridization to probe for common cardiotropic viruses: adenovirus 2, coxsackievirus B3, cytomegalovirus, Epstein-Barr virus, hepatitis C and E, influenza B and parvovirus B19. Viral RNA was detected in 46.4% (32/69) of heart failure patients, with 50% of virus-positive samples containing more than one virus. Adenovirus 2 was the most prevalent, detected in 27.5% (19/69) of heart failure patients, while in contrast to previous reports, parvovirus B19 was detected in only 4.3% (3/69). As anticipated, viruses were detected in 77.8% (7/9) of patients with viral myocarditis and 37.5% (6/16) with dilated cardiomyopathy. Additionally, viruses were detected in 50% of patients with coronary artery disease (3/6) and hypertrophic cardiomyopathy (2/4) and in 28.6% (2/7) of transplant rejection cases. We also report for the first time viral detection within a granulomatous lesion of cardiac sarcoidosis and in giant cell myocarditis, conditions for which etiological agents remain unknown. Our study has revealed a higher than anticipated prevalence of cardiotropic viruses within cardiac muscle tissue in a spectrum of heart failure conditions, including those not previously associated with a viral trigger or exacerbating role. Our work forges a path towards a deeper understanding of viruses in heart failure pathogenesis and opens possibilities for personalized patient therapeutic approaches.

Genomic surveillance of enterovirus associated with aseptic meningitis cases in southern Spain, 2015-2018

New circulating Enterovirus (EV) strains often emerge through recombination. Upsurges of recombinant non-polio enteroviruses (NPEVs) associated with neurologic manifestations such as EVA71 or Echovirus 30 (E30) are a growing public health concern in Europe. Only a few complete genomes of EVs circulating in Spain are available in public databases, making it difficult to address the emergence of recombinant EVs, understand their evolutionary relatedness and the possible implication in human disease. We have used metagenomic (untargeted) NGS to generate full-length EV genomes from CSF samples of EV-positive aseptic meningitis cases in Southern Spain between 2015 and 2018. Our analyses reveal the co-circulation of multiple Enterovirus B (EV-B) types (E6, E11, E13 and E30), including a novel E13 recombinant form. We observed a genetic turnover where emergent lineages (C1 for E6 and I [tentatively proposed in this study] for E30) replaced previous lineages circulating in Spain, some concomitant with outbreaks in other parts of Europe. Metagenomic sequencing provides an effective approach for the analysis of EV genomes directly from PCR-positive CSF samples. The detection of a novel, disease-associated, recombinant form emphasizes the importance of genomic surveillance to monitor spread and evolution of EVs.

Neurodevelopmental Outcomes of Infants Younger Than 90 Days Old Following Enterovirus and Parechovirus Infections of the Central Nervous System

Enteroviruses (EVs) and human parechoviruses (HPeVs) are a major cause of central nervous system (CNS) infection in young infants. They have been implicated in neurodevelopmental delay, however limited data are available. The aim of this study is to describe the clinical outcome of young infants and to assess and compare the medium-term neurodevelopment following CNS infections caused by EV and HPeV. A multicentre observational ambispective study was conducted between May 2013 and March 2018. Children under 3 months of age with EV or HPeV CNS infection excluding encephalitis were included. Infants were contacted 1 year after the acute infection and their neurological development was evaluated using the Ages and Stages Questionnaire-3 (ASQ-3). If any area assessed was abnormal during the first round of tests, a second round was completed 6 to 12 months later. Forty-eight young infants with EV and HPeV CNS infection were identified: 33 (68.8%) were positive for EV and 15 (31.3%) for HPeV. At first assessment 14 out of 29 EV (48.3%) and 3 out of 15 HPeV (20%) positive cases presented some developmental concern in the ASQ-3 test. EV-positive infants showed mild and moderate alteration in all domains analyzed and HPeV-positive infants showed mild alterations only in gross and fine motor domains. Significant alterations in communication were observed in EV-positive but not in HPeV-positive infants (31 vs. 0%, p = 0.016). At second assessment 4 out of 13 EV-positive patients (30.8%) showed mild to moderate concerns in communication and gross motor function domains and 3 out of 13 (23.1%) showed significant concern in fine motor function. Although CNS infections without associated encephalitis are generally assumed to be benign our study shows that at a median age of 18 months almost half of the EV-infected infants (48.3%) and 20% of HPeV-positive infants presented some developmental concern in the ASQ-3 test. We recommend monitor the neurological development of infants during the first years of life after HPeV CNS infection and especially after EV CNS infection, even in mild cases, for an early intervention and stimulation of psychomotor development if necessary.

Enterovirus D: A Small but Versatile Species

Enteroviruses (EVs) from the D species are the causative agents of a diverse range of infectious diseases in spite of comprising only five known members. This small clade has a diverse host range and tissue tropism. It contains types infecting non-human primates and/or humans, and for the latter, they preferentially infect the eye, respiratory tract, gastrointestinal tract, and nervous system. Although several Enterovirus D members, in particular EV-D68, have been associated with neurological complications, including acute myelitis, there is currently no effective treatment or vaccine against any of them. This review highlights the peculiarities of this viral species, focusing on genome organization, functional elements, receptor usage, and pathogenesis.

Reviewing Antiviral Research Against Viruses Causing Human Diseases - A Structure Guided Approach

The littlest of all the pathogens, viruses have continuously been the foremost strange microorganisms to consider. Viral Infections can cause extreme sicknesses as archived by the HIV/AIDS widespread or the later Ebola or Zika episodes. Apprehensive framework distortions are too regularly watched results of numerous viral contaminations. Besides, numerous infections are oncoviruses, which can trigger different sorts of cancer. Nearly every year a modern infection species rises debilitating the world populace with an annihilating episode. Subsequently, the need of creating antivirals to combat such rising infections. In any case, from the innovation of to begin with antiviral medicate Idoxuridine in 1962 to the revelation of Baloxavir marboxil (Xofluza) that was FDA-approved in 2018, the hone of creating antivirals has changed significantly. In this article, different auxiliary science strategies have been described that can be referral for therapeutics innovation.

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Ocular Infections

The variety and complexity of ocular infections have increased significantly in the last decade since the publication of Cumitech 13B, Laboratory Diagnosis of Ocular Infections (L. D. Gray, P. H. Gilligan, and W. C. Fowler, Cumitech 13B, Laboratory Diagnosis of Ocular Infections, 2010). The purpose of this practical guidance document is to review, for individuals working in clinical microbiology laboratories, current tools used in the laboratory diagnosis of ocular infections. This document begins by describing the complex, delicate anatomy of the eye, which often leads to limitations in specimen quantity, requiring a close working bond between laboratorians and ophthalmologists to ensure high-quality diagnostic care. Descriptions are provided of common ocular infections in developed nations and neglected ocular infections seen in developing nations. Subsequently, preanalytic, analytic, and postanalytic aspects of laboratory diagnosis and antimicrobial susceptibility testing are explored in depth.

The role of Th17 cells in viral infections

The present review provides an overview of recent advances regarding the function of Th17 cells and their produced cytokines in the progression of viral diseases. Viral infections alone do not lead to virus-induced malignancies, as both genetic and host safety factors are also involved in the occurrence of malignancies. Acquired immune responses, through the differentiation of Th17 cells, form the novel components of the Th17 cell pathway when reacting with viral infections all the way from the beginning to its final stages. As a result, instead of inducing the right immune responses, these events lead to the suppression of the immune system. In fact, the responses from Th17 cells during persistent viral infections causes chronic inflammation through the production of IL-17 and other cytokines which provide a favorable environment for tumor growth and its development. Additionally, during the past decade, these cells have been understood to be involved in tumor progression and metastasis. However, further research is required to understand Th17 cells' immune mechanisms in the vast variety of viral diseases. This review aims to determine the roles and effects of the immune system, especially Th17 cells, in the progression of viral diseases; which can be highly beneficial for the diagnosis and treatment of these infections.

Viral meningitis: an overview

Meningitis is a serious condition that affects the central nervous system. It is an inflammation of the meninges, which is the membrane that surrounds both the brain and the spinal cord. Meningitis can be caused by bacterial, viral, or fungal infections. Many viruses, such as enteroviruses, herpesviruses, and influenza viruses, can cause this neurological disorder. However, enteroviruses have been found to be the underlying cause of most viral meningitis cases worldwide. With few exceptions, the clinical manifestations and symptoms associated with viral meningitis are similar for the different causative agents, which makes it difficult to diagnose the disease at early stages. The pathogenesis of viral meningitis is not clearly defined, and more studies are needed to improve the health care of patients in terms of early diagnosis and management. This review article discusses the most common causative agents, epidemiology, clinical features, diagnosis, and pathogenesis of viral meningitis.

Seroprevalence of group B Coxsackieviruses: Retrospective study in an Italian population

Group B Coxsackieviruses (CVB) include six serotypes (B1-6) responsible for a wide range of clinical diseases. Since no recent seroepidemiologic data are available in Italy, the study aim was to investigate CVB seroprevalence in a wide Italian population. The study retrospectively included 2459 subjects referring to a large academic hospital in Rome (Italy) in the period 2004-2016. Seroprevalence rates and neutralizing antibodies (nAb) titers were evaluated in relation to years of observation and subjects' characteristics. Positivity for at least one serotype was detected in 69.1% of individuals. Overall, the prevalent serotype was B4, followed by B3 (33.3%), B5 (26.2%), B1 (12.7%), B2 (11.0%), and B6 (1.7%). For B2, a significant decrease in seroprevalence over years was observed. Positivity to at least one virus was 25.2% in children aged 0 to 2 years, but significantly increased in preschool (3-5 years) (50.3%) and school (6-10 years) children (70.4%). Higher nAb responses for B3 and B4 were observed in children aged 3 to 5 years. A high overall CVB prevalence was found. Type-specific variations in prevalence over time probably reflect the fluctuations in circulation typical of Enteroviruses. Children are at greater risk for CVB infection given the high number of seronegative subjects aged 0 to 10 years.

Enteroviruses from Humans and Great Apes in the Republic of Congo: Recombination within Enterovirus C Serotypes

Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including non-human primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N = 24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N = 38) living around and within these parks. Enteroviruses were detected in 29.4% of gorilla and 13.15% of human feces, including wild and human-habituated gorillas, local humans and eco-guards. Two identical strains were isolated from two humans coming from two remote regions. Their genomes were similar and all genes showed their close similarity to coxsackieviruses, except for the 3C, 3D and 5′-UTR regions, where they were most similar to poliovirus 1 and 2, suggesting recombination. Recombination events were found between these strains, poliovirus 1 and 2 and EV-C99. It is possible that the same EV-C species circulated in both humans and apes in different regions in the Congo, which must be confirmed in other investigations. In addition, other studies are needed to further investigate the circulation and genetic diversity of enteroviruses in the great ape population, to draw a definitive conclusion on the different species and types of enteroviruses circulating in the Republic of Congo.

Molecular characterization of non-polio enteroviruses isolated from children with acute flaccid paralysis in IRAN, 2015-2018

In addition to polioviruses, non-polio enteroviruses (NPEVs) are frequently isolated from patients with acute flaccid paralysis (AFP) worldwide. In polio-free countries, there have been expectations that with disappearing wild poliovirus from the community, the rate of AFP would decrease, but the increasing number of AFP cases proved this notion to be wrong. There are speculations that NPEVs might be the cause of increasing AFP rate. The aim of this study was to investigate frequency, genetic diversity, circulation patterns of NPEVs isolated from AFP cases in Iran from 2015 to 2018. Fifty-three NPEVs were isolated from stool specimens of AFP cases during four years of AFP surveillance. Nested PCR and VP1 sequencing revealed 20 NPEV types in which Echovirus 3 (13.2%), Echovirus 6 (13.2%), Echovirus 7 (7.5%), Echovirus 13 (7.5%) and Echovirus 21 (7.5%) were the most frequent. Coxsackie B viruses were isolated for the first time in AFP cases in Iran. The phylogenetic analysis of Echovirus 3 and Echovirus 6 revealed that Iranian echovirus strains belonged to the same cluster, indicating these viruses have been circulating in Iran for a long time. Compared to global Echovirus 3 and Echovirus 6 references, Echovirus 3 and Echovirus 6 strains detected in this study were closely related to Indian and Malaysia strains, respectively. The results of this study demonstrated a wide variety of NPEV types in Iranian patients, some of which had not been reported in previous studies. Moreover, this study highlights the need for NPEV surveillance in AFP cases.

Detection and molecular characterisation of bovine Enterovirus in Brazil: four decades since the first report

It is suggested that bovine enteroviruses (BEV) are involved in the aetiology of enteric infections, respiratory disease, reproductive disorders and infertility. In this study, bovine faecal samples collected in different Brazilian states were subjected to RNA extraction, reverse transcription-polymerase chain reaction analysis and partial sequencing of the 5′-terminal portion of BEV. One hundred and three samples were tested with an overall positivity of 14.5%. Phylogenetic analysis clustered these BEV Brazilian samples into the Enterovirus F clade. Our results bring an important update of the virus presence in Brazil and contribute to a better understanding of the distribution and characterisation of BEV in cattle.

Relationship Between Inactivation and Genome Damage of Human Enteroviruses Upon Treatment by UV254, Free Chlorine, and Ozone

Quantitative PCR (qPCR) is a convenient tool for monitoring virus concentrations in water and wastewater treatment trains, though it only informs about virus presence, but not infectivity. This limitation can be overcome if the relationship between infectivity loss and genome decay induced by a given disinfectant is known. Here, we performed inactivation experiments using two human enteroviruses, Coxsackievirus B5 and Echovirus 11, with three disinfection methods: low-pressure ultraviolet light (UV₂₅₄), free chlorine (FC), and ozone. We compared the inactivation rates as measured by culturing to the decay rates of the whole genome, to evaluate the extent of qPCR-measurable genome damage as a function of inactivation. To determine genome damage, we used an approach that estimates damage across the full viral genome from the measured decay of multiple amplicons distributed across the viral genome. Correlations between inactivation and genome decay were observed for all viruses and all disinfection treatments, but results showed that even among closely related viruses, disinfection methods can damage the viral genome to different extents and that genome damage does not necessarily translate to inactivation. For both viruses, UV₂₅₄ treatment had the closest relationship between inactivation and genome decay and with ozone, the rate of genome decay exceeded the inactivation rate. Finally, for FC, the ratios between methods were vastly different between viruses. This work provides the basis to relate qPCR measurements to infectivity loss and enables the establishment of molecular monitoring tools for assessing enterovirus inactivation during disinfection treatments of water and wastewater.

Virucidal activity and the antiviral mechanism of acidic polysaccharides against Enterovirus 71 infection in vitro

Enterovirus 71 (EV71) is the predominant pathogen for severe hand, foot, and mouth disease (HFMD) in children younger than 5 years, and currently no effective drugs are available for EV71. Thus, there is an urgent need to develop new drugs for the control of EV71 infection. In this study, LJ04 was extracted from Laminaria japonica using diethylaminoethyl cellulose-52 with 0.4 mol/l NaCl as the eluent, and its virucidal activity was evaluated based on its cytopathic effects on a microplate. LJ04 is composed of fucose, galactose, and mannose and mainly showed good virucidal activity against EV71. The antiviral mechanisms of LJ04 were the direct inactivation of the virus, the blockage of virus binding, disruptions to viral entry, and weak inhibitory activity against the nonstructural protein 3C. The two most important findings from this study were that LJ04 inhibited EV71 proliferation in HM1900 cells, which are a human microglia cell line, and that LJ04 can directly inactivate EV71 within 2 hr at 37°C. This study demonstrates for the first time the ability of a polysaccharide from L. japonica to inhibit viral and 3C activity; importantly, the inhibition of 3C might have a minor effect on the antiviral effect of LJ04. Consequently, our results identify LJ04 as a potential drug candidate for the control of severe EV71 infection in clinical settings.

A neonatal murine model of coxsackievirus A4 infection for evaluation of vaccines and antiviral drugs

Coxsackievirus A4 (CVA4) infection can cause hand, foot and mouth disease (HFMD), an epidemic illness affecting neonatal and paediatric cohorts, which can develop to severe neurological disease with high mortality. In this study, we established the first ICR mouse model of CVA4 infection for the evaluation of inactivated vaccines and antiviral drug screening. The CVA4 YT226R strain was selected to infect the neonatal mice and three infectious factors were optimized to establish the infection model. The 3-day-old neonatal mice exhibited clinical symptoms such as hind limb paralysis and death. The severe inflammatory reactions were closely related to the abnormal expression of the acute phase response proinflammatory cytokine IL-6 and an imbalance in the IFN-γ/IL-4 ratio. Importantly, the inactivated CVA4 whole-virus vaccine induced humoral immune responses in adult females and the maternal antibodies afforded mice complete protection against lethal dose challenges of homologous or heterologous CVA4 strains. Both IFN-α2a and antiserum inhibited the replication of CVA4 and increased the survival rates of neonatal mice during the early stages of infection. This neonatal murine model of CVA4 infection will be useful for the development of prophylactic and therapeutic vaccines and for screening of antiviral drugs targeting CVA4 to decrease morbidity and mortality.

Recombination Events and Conserved Nature of Receptor Binding Motifs in Coxsackievirus A9 Isolates

Coxsackievirus A9 (CVA9) is an enterically transmitted enterovirus and one of the most pathogenic type among human enteroviruses. CVA9 isolates use a distinctive RGD (Arg-Gly-Asp) motif within VP1 capsid protein that defines its ability to bind to integrin receptor(s) for cellular entry. To investigate CVA9 evolution and pathogenicity, genetic relationships and recombination events were analyzed between 54 novel clinical isolates of CVA9, as well as 21 previously published full length CVA9 sequences from GenBank. Samples were investigated by partial sequencing of the novel VP1 and 3Dpol genes, as well as including the corresponding areas from GenBank sequences. Phylogenetic analyses were combined with clinical data in a further attempt to analyze whether sequence evolution reflects CVA9 pathogenicity in the phylogenies. Furthermore, VP1 gene was also analyzed for receptor binding sites including the RGD motif and the putative heparan sulfate (HS) site. Analysis of the 559-nucleotide-long VP1 sequences identified six clades. Although most of the strains within each clade showed geographical clustering, the grouping pattern of the isolates in the analysis of the VP1 gene was strikingly different from grouping of 3Dpol, which suggests that recombination events may have occurred in the region encoding the nonstructural proteins. Inclusion of clinical data did not provide any evidence of symptom based phylogenetic clustering of CVA9 isolates. Amino acid sequence analysis of the VP1 polypeptide demonstrated that the RGD motif was fully conserved among the isolates while the putative HS binding site was only found in one isolate. These data suggest that integrin binding is essential for virus tropism, but do not explain the symptom repertoire.

Infectious Myelopathies

PURPOSE OF REVIEW

This article reviews bacterial, viral, fungal, and parasitic pathogens associated with myelopathy. Infectious myelopathies may be due to direct infection or parainfectious autoimmune-mediated mechanisms; this article focuses primarily on the former.

RECENT FINDINGS

Some microorganisms exhibit neurotropism for the spinal cord (eg, enteroviruses such as poliovirus and flaviviruses such as West Nile virus), while others are more protean in neurologic manifestations (eg, herpesviruses such as varicella-zoster virus), and others are only rarely reported to cause myelopathy (eg, certain fungal and parasitic infections). Individuals who are immunocompromised are at increased risk of disseminated infection to the central nervous system. Within the last few years, an enterovirus D68 outbreak has been associated with cases of acute flaccid paralysis in children, and emerging Zika virus infection has been concurrent with cases of acute flaccid paralysis due to Guillain-Barré syndrome, although cases of myelitis have also been reported. Associated pathogens differ by geographic distribution, with myelopathies related to Borrelia burgdorferi (Lyme disease) and West Nile virus more commonly seen in the United States and parasitic infections encountered more often in Latin America, Southeast Asia, and Africa. Characteristic CSF and MRI patterns have been identified with many of these infections.

SUMMARY

A myriad of pathogens are associated with infectious myelopathies. Host factors, geographic distribution, clinical features, CSF profiles, and MRI findings can assist in formulating the differential diagnosis and ultimately guide management.

Recent advances on the role of host factors during non-poliovirus enteroviral infections

Non-polio enteroviruses are emerging viruses known to cause outbreaks of polio-like infections in different parts of the world with several cases already reported in Asia Pacific, Europe and in United States of America. These outbreaks normally result in overstretching of health facilities as well as death in children under the age of five. Most of these infections are usually self-limiting except for the neurological complications associated with human enterovirus A 71 (EV-A71). The infection dynamics of these viruses have not been fully understood, with most inferences made from previous studies conducted with poliovirus.Non-poliovirus enteroviral infections are responsible for major outbreaks of hand, foot and mouth disease (HFMD) often associated with neurological complications and severe respiratory diseases. The myriad of disease presentations observed so far in children calls for an urgent need to fully elucidate the replication processes of these viruses. There are concerted efforts from different research groups to fully map out the role of human host factors in the replication cycle of these viral infections. Understanding the interaction between viral proteins and human host factors will unravel important insights on the lifecycle of this groups of viruses.This review provides the latest update on the interplay between human host factors/processes and non-polio enteroviruses (NPEV). We focus on the interactions involved in viral attachment, entry, internalization, uncoating, replication, virion assembly and eventual egress of the NPEV from the infected cells. We emphasize on the virus- human host interplay and highlight existing knowledge gaps that needs further studies. Understanding the NPEV-human host factors interactions will be key in the design and development of vaccines as well as antivirals against enteroviral infections. Dissecting the role of human host factors during NPEV infection cycle will provide a clear picture of how NPEVs usurp the human cellular processes to establish an efficient infection. This will be a boost to the drug and vaccine development against enteroviruses which will be key in control and eventual elimination of the viral infections.

Genetic landscape and macro-evolution of co-circulating Coxsackieviruses A and Vaccine-derived Polioviruses in the Democratic Republic of Congo, 2008-2013

Enteroviruses (EVs) are among the most common viruses infecting humans worldwide but only a few Non-Polio Enterovirus (NPEV) isolates have been characterized in the Democratic Republic of Congo (DR Congo). Moreover, circulating vaccine-derived polioviruses (PVs) [cVDPVs] isolated during multiple outbreaks in DR Congo from 2004 to 2018 have been characterized so far only by the sequences of their VP1 capsid coding gene. This study was carried to i) investigate the circulation and genetic diversity of NPEV and polio vaccine isolates recovered from healthy children and Acute Flaccid Paralysis (AFP) patients, ii) evaluate the occurrence of genetic recombination among EVs belonging to the Enterovirus C species (including PVs) and iii) identify the virological factors favoring multiple emergences of cVDPVs in DR Congo. The biological material considered in this study included i) a collection of 91 Sabin-like PVs, 54 cVDPVs and 150 NPEVs isolated from AFP patients between 2008 and 2012 in DR Congo and iii) a collection of 330 stool specimens collected from healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. Studied virus isolates were sequenced in four distinct sub-genomic regions 5’-UTR, VP1, 2C^ATPase and 3D^pol. Resulting sequences were compared through comparative phylogenetic analyses. Virus isolation showed that 19.1% (63/330) healthy children were infected by EVs including 17.9% (59/330) of NPEVs and 1.2% (4/330) of type 3 Sabin-like PVs. Only one EV-C type, EV-C99 was identified among the NPEV collection from AFP patients whereas 27.5% of the 69 NPEV isolates typed in healthy children belonged to the EV-C species: CV-A13 (13/69), A20 (5/69) and A17 (1/69). Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences in at least one of the targeted non-structural regions of their genomes: 5’UTR, 2C^ATPase and 3D^pol. Some of these non-vaccine sequences of the recombinant cVDPVs were strikingly related to homologous sequences from co-circulating CV-A17 and A20 in the 2C^ATPase region as well as to those from co-circulating CV-A13, A17 and A20 in the 3D^pol region. This study provided the first evidence uncovering CV-A20 strains as major recombination partners of PVs. High quality AFP surveillance, sensitive environmental surveillance and efficient vaccination activities remain essential to ensure timely detection and efficient response to recombinant cVDPVs outbreaks in DR Congo. Such needs are valid for any epidemiological setting where high frequency and genetic diversity of Coxsackieviruses A13, A17 and A20 provide a conducive viral ecosystem for the emergence of virulent recombinant cVDPVs.

The strategy of the Global Polio Eradication Initiative is based on the surveillance of patients suffering from Acute Flaccid Paralysis (AFP) and mass vaccination with live-attenuated vaccine strains of polioviruses (PVs) in endemic areas. However, vaccine strains of PVs can circulate and replicate for a long time when the vaccine coverage of the population is low. Such prolonged circulation and replication of vaccine strains of PVs can result to the emergence of circulating vaccine-derived polioviruses [cVDPVs] that are as virulent as wild PVs. In this study, we performed the molecular characterization of a large collection of 377 virus isolates recovered from paralyzed patients between 2008 and 2012 in DR Congo and healthy children in 2013 in the Kasai Oriental and Maniema provinces of DR Congo. We found that the genetic diversity of enteroviruses of the species Enterovirus C is more important than previously reported. Interestingly, 50 of the 54 cVDPVs featured recombinant genomes containing exogenous sequences of the 2C ATPase and/or 3D polymerase coding genes acquired from co-circulating Coxsackieviruses A13, A17 and A20. Coxsackieviruses A20 strains were identified for the first time as major partners of genetic recombination with co-circulating live-attenuated polio vaccine strains.

Our findings highlight the need to reinforce and maintain high quality surveillance of PVs and efficient immunization activities in order to ensure early detection and control of emerging cVDPVs in all settings where high frequency and diversity of Coxsackieviruses A13, A17 and A20 have been documented.

Hand, foot, and mouth disease associated with coxsackievirus A10: more serious than it seems

INTRODUCTION

Hand, foot, and mouth disease (HFMD) is a common viral childhood illness, that has been a severe public health concern worldwide, particularly in the Asia-Pacific region. According to epidemiological data of HFMD during the past decade, the most prevalent causal viruses were enterovirus (EV)-A71, coxsackievirus (CV)-A16, CV-A6, and CV-A10. The public health burden of CV-A10-related diseases has been underestimated as their incidence was lower than that of EV-A71 and CV-A16 in most HFMD outbreaks. However, cases of CV-A10 infection are more severe, and its genome is more variable, which has alerted the research community worldwide. Areas covered: In this paper, studies on the epidemiology, laboratory diagnosis, clinical manifestations, molecular epidemiology, seroepidemiology, animal models of CV-A10, and vaccines and antiviral strategies against this genotype are reviewed. In addition, the genetic evolution of circulating strains was analyzed. Expert opinion: Multivalent vaccines against EV-A71, CV-A16, CV-A6, and CV-A10 should be a next-step HFMD vaccine strategy.

Transcriptomic analysis reveals that enterovirus F strain SWUN-AB001 infection activates JNK/SAPK and p38 MAPK signaling pathways in MDBK cells

Background

Enteroviruses (Picornaviridae family) have been widely detected in the feces from cattle with diarrhea. However, the mechanisms responsible for the pathogenicity of enteroviruses in cattle remain unclear. Recently, we isolated a novel EV-F7 strain called SWUN-AB001 from diarrheal yak (Bos grunniens) feces. To explore the pathogenic mechanisms of this novel virus, we used a transcriptomics approach to find genes with differential expression patterns in Madin-Darby bovine kidney (MDBK) cells during infection with SWUN-AB001 over time.

Results

MDBK cells were sampled at 12 and 24 h post-infection (hpi) to represent the early and late stages of a SWUN-AB001 infection. Compared with the non-infected cells, 19 and 1050 differentially expressed genes (DEGs) were identified at 12 and 24 hpi, respectively. These DEGs were associated with disease, signal transduction, cellular process and cytokine signaling categories. At 24 hpi, the pathway enrichment analysis revealed that signal pathways such as c-Jun NH2-terminal kinase/ stress-activated protein kinase (JNK/SAPK) and mitogen-activated protein kinase (MAPK) pathways and cytokine-cytokine receptor interactions were associated with the interactions occurring between EV-F7 and MDBK cells. Our additional western blot analysis showed that the phosphorylation levels of JNK/SAPK and p38 MAPK proteins increased significantly in the MDBK cells at 24 hpi. The result indicated that infection with EV-F7 could activate JNK/SAPK and p38 MAPK pathways in MDBK cells, and possibly trigger large-scale cytokine production.

Conclusion

Our transcriptome analysis provides useful initial data towards better understanding of the infection mechanisms used by EV-F7, while highlighting the potential molecular relationships occurring between the virus and the host’s cellular components.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1721-8) contains supplementary material, which is available to authorized users.

A systematic review of evidence that enteroviruses may be zoonotic

Enteroviruses infect millions of humans annually worldwide, primarily infants and children. With a high mutation rate and frequent recombination, enteroviruses are noted to evolve and change over time. Given the evidence that human enteroviruses are commonly found in other mammalian species and that some human and animal enteroviruses are genetically similar, it is possible that enzootic enteroviruses may also be infecting human populations. We conducted a systematic review of the English and Chinese literature published between 2007 and 2017 to examine evidence that enteroviruses may be zoonotic. Of the 2704 articles screened for inclusion, 16 articles were included in the final review. The review of these articles yielded considerable molecular evidence of zooanthroponosis transmission, particularly among non-human primates. While there were more limited instances of anthropozoonosis transmission, the available data support the biological plausibility of cross-species transmission and the need to conduct periodic surveillance at the human–animal interface.

Molecular characteristics of hand, foot, and mouth disease for hospitalized pediatric patients in Yunnan, China

Hand, foot, and mouth disease (HFMD) is a common infectious disease caused by multiple enteroviruses (EVs) in China. To better define the etiologic agents and clinical characteristics of HFMD, we conducted this study in Yunnan, China.In this study, 1280 stool specimens were collected from pediatric patients hospitalized for treatment of HFMD in 2010. EV was detected with nested reverse transcription polymerase chain reaction and directly genotyped by gene sequencing of the viral protein 1 (VP1) region. Phylogenetic analysis was performed based on the VP1 partial gene and the clinical characteristics were analyzed using SPSS Software.Of 1280 specimens, 1115 (87.1%) tested positive for EV. Seventeen different EV serotypes were detected. Coxsackievirus A16 (CA16) was the most frequently detected serotype (615/1115 cases, 55.1%), followed by enterovirus 71 (EV71; 392/1115, 35.2%), CA10 (45/1115, 4.0%), and CA4 (23/1115, 2.1%). Among the 709 severe cases, CA16, EV71, CA10, and CA4 accounted for 48.0%, 42.0%, 3.5%, and 2.3%, respectively. Of the 26 critical cases, 13 were caused by EV71, 9 by CA16, 2 by CA4, and 1 each were the result of CA10 and E9, respectively. All EV71, CA16, CA10, and CA4 isolates were highly homologous to the strains isolated from mainland China, and belonged to the C4a, B1a, G, and C genotypes, respectively.Our study showed that EV71 and CA16 were the main causative agents for severe and critical HFMD, but other serotypes can also cause severe and critical cases.

Inhibition of enterovirus 71 replication and viral 3C protease by quercetin

BACKGROUND

Enterovirus 71 (EV71) is one of the major causative agents of hand, foot, and mouth disease (HFMD), which is sometimes associated with severe central nervous system disease in children. There is currently no specific medication for EV71 infection. Quercetin, one of the most widely distributed flavonoids in plants, has been demonstrated to inhibit various viral infections. However, investigation of the anti-EV71 mechanism has not been reported to date.

METHODS

The anti-EV71 activity of quercetin was evaluated by phenotype screening, determining the cytopathic effect (CPE) and EV71-induced cells apoptosis. The effects on EV71 replication were evaluated further by determining virus yield, viral RNA synthesis and protein expression, respectively. The mechanism of action against EV71 was determined from the effective stage and time-of-addition assays. The possible inhibitory functions of quercetin via viral 2Apro, 3Cpro or 3Dpol were tested. The interaction between EV71 3Cpro and quercetin was predicted and calculated by molecular docking.

RESULTS

Quercetin inhibited EV71-mediated cytopathogenic effects, reduced EV71 progeny yields, and prevented EV71-induced apoptosis with low cytotoxicity. Investigation of the underlying mechanism of action revealed that quercetin exhibited a preventive effect against EV71 infection and inhibited viral adsorption. Moreover, quercetin mediated its powerful therapeutic effects primarily by blocking the early post-attachment stage of viral infection. Further experiments demonstrated that quercetin potently inhibited the activity of the EV71 protease, 3Cpro, blocking viral replication, but not the activity of the protease, 2Apro, or the RNA polymerase, 3Dpol. Modeling of the molecular binding of the 3Cpro-quercetin complex revealed that quercetin was predicted to insert into the substrate-binding pocket of EV71 3Cpro, blocking substrate recognition and thereby inhibiting EV71 3Cpro activity.

CONCLUSIONS

Quercetin can effectively prevent EV71-induced cell injury with low toxicity to host cells. Quercetin may act in more than one way to deter viral infection, exhibiting some preventive and a powerful therapeutic effect against EV71. Further, quercetin potently inhibits EV71 3Cpro activity, thereby blocking EV71 replication.

Th17 cytokine profiling of colorectal cancer patients with or without enterovirus 71 antigen expression

OBJECT

Th17 cytokines have been identified in several types of human cancers. In this pilot study, the expression of Th17 cytokines profiling in enteroviruses 71 (EV71) associated colorectal cancer (CRC) were explored.

METHODS

66 patients with CRC were enrolled in this study; immune- histochemical analyses were performed on cancerous tissues and adjacent non- cancerous tissues of the patients. Serum Th17 cytokines of CRC patients and healthy controls were measured using a Luminex 200 analyzer.

RESULTS

Cancerous tissues had more positive EV71 antigen expression than adjacent non- cancerous tissues. In TNM II-III CRC, 59.9% of cancerous tissues were observed to be EV71 positive; on the contrary, 65.2% of the adjacent non- cancerous epithelium was EV71 negative. In TNM I CRC, all adjacent non- cancerous epithelium was virus negative, but in TNM IV, half of adjacent non- cancerous tissues were virus positive. Serum IL-10 were significantly higher in CRC patients than in healthy controls, and IL-10 concentrations in the EV71 positive group were higher than those of the EV71 negative group, with the highest IL-10 levels being observed in CRC patients with strong positive group (P < 0.05). Similar results were found for IL-21 and IL-23. IL-17 levels were higher in CRC patients than in healthy controls, there was no significant difference in IL-17 between the viral positive and viral negative groups (P > 0.05).

CONCLUSION

Persistent existing EV71 viral antigens in intestinal tissues are positively associated with TNM III/IV CRC. EV71 latent infection recruits Th17 cells in the colorectal tumor site, stimulating Th17 cytokine production that closely associated with CRC carcinogenesis.

Non-neutralizing Antibody Responses against VP1 in Enterovirus A, B, C and Rhinovirus A species among Infants and Children in Shanghai

The overall non-neutralizing antibody responses against EV infections among infants and children remain unknown. The non-neutralizing antibody responses against VP1 of EV-A species (Enterovirus 71 (EV71), Coxsackievirus A16 (CA16)), EV-B species (Coxsackievirus B3 (CB3)), EV-C species (Poliovirus 1 (PV1)) and RV-A species (Rhinovirus A N13 (RV13)) were detected and analyzed using a novel evolved immunoglobulin-binding molecule (NEIBM)-based ELISA among infants and children aged 1 day to 6 years in Shanghai. The anti-VP1 reactivity against these EVs changed similarly in an age-related dynamic: being high level in the 1-28-day age group, declining to the lowest level in the 1-12-month age group, gradually increasing to the peak level in the 13-60-month age group, and remarkably declining in the 61-72-month age group, which reflects the conversion from maternally-derived to primary antibody responses. The anti-RV13 VP1 antibodies were demonstrated at the highest level, with anti-CB3 and PV1 VP1 antibodies at the second highest level and anti-CA16 and EV71 VP1 antibodies at the lowest level. These findings are the first to describe the overall non-neutralizing antibody responses against VP1 of the EV-A, B, C and RV-A viruses among the infants and children and could be helpful for further understanding the ubiquitous EV infections among children.

Induction of a high-titered antibody response using HIV gag-EV71 VP1-based virus-like particles with the capacity to protect newborn mice challenged with a lethal dose of enterovirus 71

Enterovirus 71 (EV71) is the most frequently detected causative agent in hand, foot, and mouth disease (HFMD) and is a serious threat to public health in the Asia-Pacific region. Many EV71 vaccines are under development worldwide, and although both inactivated virus vaccines and virus-like particles (VLPs) are considered to be effective, the main focus has been on inactivated EV71vaccines. There have been very few studies on EV71 VLPs. In this study, using a strategy based on HIV gag VLPs, we constructed a gag-VP1 fusion gene to generate a recombinant baculovirus expressing the EV71 structural protein VP1 together with gag, which was then used to infect TN5 cells to form VLPs. The VLPs were characterized using transmission electron microscopy, electrophoresis and staining with Coomassie blue, and Western blotting. Mice immunized with gag-VP1 VLPs showed strong humoral and cellular immune responses. Finally, immunization of female mice with gag-VP1 VLPs provided effective protection of their newborn offspring against challenge with a lethal dose EV71. These results demonstrate a successful approach for producing EV71 VP1 VLPs based on the ability of HIV gag to self-assemble, thus providing a good foundation for producing high-titered anti-EV71 antibody by immunization with VLP-based gag EV71 VP1 protein.

Identification and whole-genome characterization of a recombinant Enterovirus B69 isolated from a patient with Acute Flaccid Paralysis in Niger, 2015

Enterovirus B69 (EV-B69) is a rarely reported type and till date, only the full-length genome sequence of the prototype strain is available. Besides the prototype strain, only limited VP1 sequences of this virus from Africa and India are available in GenBank. In this study, we analyzed the full-length genome sequence of an EV-B69 strain recovered from a patient with acute flaccid paralysis in Niger. Compared with the EV-B69 prototype strain, it had 79.6% and 76.3% nucleotide identity in the complete genome and VP1 coding region, respectively. VP1 sequence analyses revealed also high variation in nucleotide similarity (68.9%-82.8%) with previously isolated EV-B69 strains in India and Africa. The great genetic divergence among EV-B69 strains indicates that this type is not a newly emergent virus, but has circulated for many years at low epidemic strength. Phylogenetic incongruity between structural and non-structural regions and similarity plot analyses revealed that multiple recombination events occurred during its evolution. This study expands the number of EV-B69 whole genome sequences which would help genomic comparison for future studies to understand the biological and pathogenic properties of this virus, assess its potential public health impact and comprehend the role of recombination in the evolution of enteroviruses.

Molecular evolution of types in non-polio enteroviruses

Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10^-2 to 3.07×10^-2 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.

Multiple transmission chains of coxsackievirus A4 co-circulating in China and neighboring countries in recent years: Phylogenetic and spatiotemporal analyses based on virological surveillance

Coxsackievirus A4 (CV-A4) has been reported frequently in association with many infectious diseases and cases of hand, foot, and mouth disease potentially associated with CV-A4 infection are also identified. This study summarized the Shandong CV-A4 strains isolated from 25years acute flaccid paralysis surveillance, with an emphasis on exploring the phylogenetic analyses and spatiotemporal dynamics of CV-A4 at the global scale. We sampled 43 CV-A4 isolates and utilized VP1 gene to construct phylogenetic trees. Further extensive Bayesian phylogeographic analysis was carried out to investigate the evolution of CV-A4 and understand the spatiotemporal diffusion around the world using BEAST and SPREAD software. Phylogenetic trees showed that CV-A4 emerged to be more active in recent decades and multiple transmission chains were co-circulating. The molecular clock analysis estimated a mean evolutionary rate of 6.4×10^-3 substitutions/site/year, and the estimated origin of CV-A4 around 1944. The phylogeographic analyses suggested the origin of CV-A4 could be in the USA, however regional dissemination was mainly located around the Asia-Europe region. The spatiotemporal dynamics of CV-A4 exhibited frequent viral traffic among localities, and virus from Shandong province seemed to have played a central role in spreading around China and neighboring countries. Our phylogenetic description and phylogeographic analyses indicate the importance of large spatial- and temporal-scale studies in understanding epidemiological dynamics of CV-A4, particularly the diffusion routes will be of great importance to global control efforts.

Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea

Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.

Detection of negative and positive RNA strand of poliovirus Sabin 1 and echovirus E19 by a stem-loop reverse transcription PCR

In this report a strand specific RT-PCR was established for the detection of the replicative negative RNA strand of poliovirus sabin 1 (Sabin1) and Echovirus 19 (E19) strains. The key for the successful conduction of the assay was the use of a specific reverse transcription primer targeting the 5'-UTR of enteroviruses that consisted of a stem-loop structure at the 5'-end and an enteroviral-specific sequence at the 3'-end. The stem loop RT-PCR was found to be an accurate and sensitive method, detecting even 10^-2 CCID₅₀ of poliovirus sabin 1 (Sabin1) and E19 strains 6 h postinfection (p.i.), while CPE appeared 3 days later. This assay was also validated in SiHa and Caski cell lines that are not used for the detection of enteroviruses. The negative RNA strand was detected 6 h and 12 h p.i. in SiHa and Caski cells, when these cell lines were inoculated with 10⁵ and 1 CCID₅₀ respectively, whereas CPE was observed 5 days p.i for SiHa cells and 8 days p.i for Caski cells and that only at 10⁵ CCID₅₀ . The results show that this approach may be used for replacing the time-consuming cell cultures in order to detect the active replication of enteroviruses.

SIGNIFICANCE AND IMPACT OF THE STUDY

Enteroviruses are positive stranded RNA viruses that may cause severe diseases. The conventional method for detection of active viral replication involves virus isolation in sensitive cell cultures followed by titration and seroneutralization. In this report, we describe the use of a stem-loop secondary structured oligonucleotide in RT-PCR assay for the detection of the replicative negative strand of the positive-stranded RNA of poliovirus sabin 1 and E19 strains. This approach proved to be a useful tool that may be used for replacing the time-consuming cell culture assays in order to detect the active replication of enteroviruses.

Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin

Ultraviolet light in the UVC range is a commonly used disinfectant to control viruses in clinical settings and water treatment. However, it is currently unknown whether human viral pathogens may develop resistance to such stressor. Here, we investigate the adaptation of an enteric pathogen, human echovirus 11, to disinfection by UVC, and characterized the underlying phenotypic and genotypic changes. Repeated exposure to UVC lead to a reduction in the UVC inactivation rate of approximately 15 per cent compared to that of the wild-type and the control populations. Time-series next-generation sequencing data revealed that this adaptation to UVC was accompanied by a decrease in the virus mutation rate. The inactivation efficiency of UVC was additionally compromised by a shift from first-order to biphasic inactivation kinetics, a form of 'viral persistence' present in the UVC resistant and control populations. Importantly, populations with biphasic inactivation kinetics also exhibited resistance to ribavirin, an antiviral drug that, as UVC, interferes with the viral replication. Overall, the ability of echovirus 11 to adapt to UVC is limited, but it may have relevant consequences for disinfection in clinical settings and water treatment plants.

Identification and molecular characterization of non-polio enteroviruses from children with acute flaccid paralysis in West Africa, 2013-2014

Besides polioviruses, non-polio enteroviruses (NPEVs) may also be associated with acute flaccid paralysis (AFP). Because poliomyelitis is on the verge of eradication, more attention should be paid to study NPEVs from non-polio AFP cases and their epidemic patterns. In West African countries the epidemiology of NPEVs remains largely unexplored. We investigated the genetic diversity, frequency, circulation patterns, and molecular epidemiology of NPEVs in seven West African countries by analyzing retrospectively a panel of 3195 stool samples from children with AFP collected through routine poliomyelitis surveillance activities between 2013 and 2014. VP1 sequencing and typing on 201 isolates revealed 39 NPEV types corresponding to EV-A (6.9%), EV-B (90.5%), EV-C (2%) and EV-D (0.5%) species. Echoviruses were isolated most frequently with 138 cases (68.6%), followed by coxsackievirus group B with 35 cases (17.4%). No single NPEV type was remarkably dominant. Interestingly, several rarely described types with limited detection worldwide were identified (EVA76, EVA119, EVB75, EVB77, EVB97, EVC99, CVA20, CVA21 and EVD94). This study demonstrates the extensive diversity and diverse circulation patterns of NPEVs from AFP surveillance and highlights the need to formulate effective long-term strategies to monitor NPEV circulations in West Africa.

Evolution of selective-sequencing approaches for virus discovery and virome analysis

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Description of virus enrichment techniques for metagenomics based virome analysis.

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Usefulness of recently developed virome capture sequencing techniques.

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Perspective on negative and positive selection approaches for virome analysis.

Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis.

Evaluation of the enterovirus laboratory surveillance system in Denmark, 2010 to 2013

The primary aim of the Danish enterovirus (EV) surveillance system is to document absence of poliovirus infection. The conflict in Syria has left many children unvaccinated and movement from areas with polio cases to Europe calls for increased awareness to detect and respond to virus-transmission in a timely manner. We evaluate the national EV laboratory surveillance, to generate recommendations for system strengthening. The system was analysed for completeness of viral typing analysis and clinical information and timeliness of specimen collection, laboratory results and reporting of clinical information. Of 23,720 specimens screened, 2,202 (9.3%) were EV-positive. Submission of cerebrospinal fluid and faecal specimens from primary diagnostic laboratories was 79.5% complete (845/1,063), and varied by laboratory and patient age. EV genotypes were determined in 68.5% (979/1,430) of laboratory-confirmed cases, clinical information was available for 63.1% (903/1,430). Primary diagnostic results were available after a median of 1.4 days, typing results after 17 days, detailed clinical information after 33 days. The large number of samples typed demonstrated continued monitoring of EV-circulation in Denmark. The system could be strengthened by increasing the collection of supplementary faecal specimens, improving communication with primary diagnostic laboratories, adapting the laboratory typing methodology and collecting clinical information with electronic forms.