Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses

IMPORTANCE

By employing a cost-effective approach for complete genome sequencing, the study has enabled the identification of novel enterovirus strains and shed light on the genetic exchange events during outbreaks. The success rate of genome sequencing and the scalability of the protocol demonstrate its practical utility for routine enterovirus surveillance. Moreover, the study's findings of recombinant strains of EVA71 and CVA2 contributing to epidemics in Malaysia and Taiwan emphasize the need for accurate detection and characterization of enteroviruses. The investigation of the whole genome and upstream ORF sequences has provided insights into the evolution and spread of enterovirus subgenogroups. These findings have important implications for the prevention, control, and surveillance of enteroviruses, ultimately contributing to the understanding and management of enterovirus-related illnesses.

Molecular characterization and pathogenicity evaluation of enterovirus G isolated from diarrheic piglets

IMPORTANCE

Enterovirus G is a species of positive-sense single-stranded RNA viruses associated with several mammalian diseases. The porcine enterovirus strains isolated here were chimeric viruses with the PLCP gene of porcine torovirus, which grouped together with global EV-G1 strains. The isolated EV-G strain could infect various cell types from different species, suggesting its potential cross-species infection risk. Animal experiment showed the pathogenic ability of the isolated EV-G to piglets. Additionally, the EV-Gs were widely distributed in the swine herds. Our findings suggest that EV-G may have evolved a novel mechanism for broad tropism, which has important implications for disease control and prevention.

Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings

Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater andair sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.

Changes in enterovirus epidemiology after easing of lockdown measures

INTRODUCTION

Public health measures aimed at controlling transmission of SARS-CoV-2, otherwise known as "lockdown" measures, had profound effects on circulation of non-SARS viruses, many of which decreased to very low levels.  The interrupted transmission of these viruses may have lasting effects. Some of the influenza clades seem to have disappeared during this period, a phenomenon which is described as a "funnel effect". It is currently unknown if the lockdown measures had any effect on the diversity of circulating viruses, other than influenza. Enteroviruses are especially interesting in this context, as the clinical presentation of an infection with a particular enterovirus-type may be clade-dependent.

METHODS AND MATERIALS

Enteroviruses were detected in clinical materials using a 5'UTR-based detection PCR, and partial VP-1 sequences were obtained, using methods described before. All samples with EV detections from a large part of the Netherlands were included in the study. The samples originated from general practitioners, general hospitals, university hospitals and public health offices.

RESULTS

Five EV-genotypes circulated in significant numbers before and after the lockdown, EV-D68, E-11, CV-A6, CV-B5 and CV-A2. All five genotypes showed decreased genetic diversity after the lockdown, and four indicate a significant number of sequences clustering together with a very high sequence homology. Moreover, children with E-11 and CV-B5 detections were significantly older after the lockdown than before.

CONCLUSIONS

The reduced enterovirus transmission in the Netherlands during the pandemic, seems to have led to a decrease in genetic diversity in the five most commonly detected enterovirus serotypes.

Comparing the Clinical Courses of Children With Human Rhinovirus/Enterovirus to Children With Other Respiratory Viruses in the Outpatient Setting

BACKGROUND

While infections caused by rhinoviruses and enteroviruses are common among children, the entirety of their clinical impact remains elusive. We compared the clinical outcomes of children with rhinovirus/enterovirus infections to other common respiratory viruses in outpatient settings.

METHODS

We conducted a retrospective analysis of nasopharyngeal samples singly positive for human rhinovirus/enterovirus (HRV/ENT), influenza A/B (FLU) or respiratory syncytial virus (RSV) from patients ≤17 years submitted for clinical testing via multiplex polymerase chain reaction between 2016 and 2019. We evaluated the following outpatient outcomes: days of respiratory symptoms before testing; visits for respiratory symptoms; receipt of a breathing treatment; receipt of antibiotics and hospital admission. Statistical analyses were conducted controlling for age and comorbid conditions.

RESULTS

There were 1355 positive samples included in this analysis (HRV/ENT: n = 743, FLU: n = 303 and RSV: n = 309). Compared to HRV/ENT, children with FLU had 28% fewer days of respiratory symptoms (β: -0.32; 95% confidence interval: -0.46 to -0.18; P < 0.001), fewer visits for respiratory symptoms, and significantly decreased odds of receiving a breathing treatment or antibiotics, and admission to the hospital. Children with RSV had a similar number of days of respiratory symptoms, outpatient visits and odds of hospital admission, but significantly increased odds of receiving a breathing treatment and antibiotics compared to those with HRV/ENT.

CONCLUSION

Clinicians should have a high level of vigilance when managing children with positive respiratory viral testing for HRV/ENT given the potential for clinical outcomes similar to and, in some instances, worse than known highly pathogenic viruses.

Emerging concerns of atypical hand foot and mouth disease caused by recombinant Coxsackievirus A6 variants in Henan, China

An increasing number of studies have reported that atypical hand, foot, and mouth disease (HFMD) is becoming a new concern for children's health. At present, there is no official definition for atypical HFMD, but some studies have defined that it occurs at anatomic sites not listed in the definition of HFMD issued by the World Health Organization. Several pathogens have been reported to cause atypical HFMD, such as Coxsackievirus (CV)A6. As one of the most prevalent enteroviruses in the world, CVA6 seems to affect a wider range of children and causes more severe and prolonged illness than other enteroviruses. The early lesions of atypical HFMD are very similar to the clinical presentations of other diseases, such as eczema, which poses a challenge for clinicians aiming to identify and diagnose HFMD in a timely manner. Here, we report on six atypical HFMD patients caused by recombinant CVA6 variants, and the atypical manifestations include eczema coxsackium, large herpes, rice-like red papules and herpes, purpuric rash, and onychomadesis, as well as and large red herpes on scalp, perianal, testicles, shoulders and neck, and other atypical eruption sites, hoping to draw the attention of other pediatricians. This study will provide scientific guidance for timely diagnosis of HFMD to prevent serious complications.

The Emergence and Widespread Circulation of Enteric Viruses Throughout the COVID-19 Pandemic: A Wastewater-Based Evidence

Growing evidence shed light on the importance of wastewater-based epidemiology (WBE) during the pandemic, when the patients rarely visited the clinics despite the fact that the infections were still prevalent in the community as before. The abundance of infections in the community poses a constant threat of the emergence of new epidemic strains. Herein, we investigated enteric viruses in raw sewage water (SW) from Japan's Tohoku region and compared them to those from the Kansai region to better understand the circulating strains and their distribution across communities during the COVID-19 pandemic. Raw SW was collected between 2019 and 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major AGE viruses by RT-PCR. Sequence-based analyses were used to assess genotypes and evolutionary relationships. The most commonly detected enteric virus was rotavirus A (RVA) at 63.8%, followed by astrovirus (AstV) at 61.1%, norovirus (NoV) GII and adenovirus (AdV) at 33.3%, sapovirus (SV) at 25.0%, enterovirus (EV) at 19.4%, and NoV GI at 13.9%. The highest prevalence (46.0%) was found in the spring. Importantly, enteric viruses did not decline during the pandemic. Rather, several strains like NoV GII.2, DS-1-like human G3 (equine) RVA, MLB1 AstV, and different F41 HAdV emerged throughout the pandemic and spread widely over the Tohoku and Kansai regions. Tohoku's detection rate remained lower than that of the Kansai area (36 vs 58%). This study provides evidence for the emergence and spread of enteric viruses during the pandemic.

Application value of EV/EV71/CA16-SAT detection in children with hand-foot-mouth disease

The objective of this work was to explore the application value of a new type of fluorescent nucleic acid isothermal amplification (SAT) to detect EV/EV71/CA16-SAT in children with hand-foot-mouth disease (HFMD). For this purpose, from March 2017 to September 2019, Chengdu Children's Specialized Hospital collected throat swabs from children with clinical manifestations of hand, foot and mouth disease, and used SAT technology to screen and detect universal enterovirus (EV) nucleic acid (There were 1860 children with EV-RNA) positive. Patients who are EV-RNA positive at any time: first use the same throat swab specimen to detect EV71/CA16-RNA; secondly, collect venous blood and use the colloidal gold method to detect IgM antibodies in EV71/CA16 serum. The patients with positive EV71/CA16-RNA or EV71/CA16-IgM (or both) were repeated the above two methods 2 weeks and 4 weeks after standard treatment for review and comprehensive analysis. Results showed that 763 cases were enrolled for the first time: 59.76% were male and 40.24% were female; the age ranged from 1 month to 13 years, of which 69.06% were from 1 to 4 years old; CA16-RNA positive 56.23%, EV71-RNA positive 21.89%, CA16/EV71 -RNA were all positive in 1.57%; CA16-IgM was positive in 64.48%, EV71-IgM was positive in 54.26%, and CA16/EV71-IgM were both positive in 18.74%. After 2 weeks, 722 cases were reexamined: 26.73% were positive for CA16-RNA, 7.89% were positive for EV71-RNA, 0.28% were both positive for CA16/EV71-RNA; 66.21% were positive for CA16-IgM, 51.52% were positive for EV71-IgM, and IgM were all positive in 17.73%. Four weeks later, 489 cases were reexamined: among them, CA16-RNA positive 5.73% of which were positive for EV71 color RNA (0.005%), and 12.68% of them were all positive for EV71lym. The strategy of combining SAT technology and colloidal gold method to detect EV/EV71/CA16 nucleic acid (RNA) and serum IgM antibody in children HFMD can improve the early detection rate and accuracy of HFMD; According to the comprehensive analysis of the detection results of children with HFMD at the early stage, 2 weeks and 4 weeks of the present study, it is suggested that EV/EV71/CA16-SAT nucleic acid detection can be used to judge the prognosis, follow-up treatment, set isolation time, return students to school, and community management in children with HFMD. and prevention and control have more clinical application value.

Molecular Epidemiology and Evolution of Coxsackievirus A14

As the proportion of non-enterovirus 71 and non-coxsackievirus A16 which proportion of composition in the hand, foot, and mouth pathogenic spectrum gradually increases worldwide, the attention paid to other enteroviruses has increased. As a member of the species enterovirus A, coxsackievirus A14 (CVA14) has been epidemic around the world until now since it has been isolated. However, studies on CVA14 are poor and the effective population size, evolutionary dynamics, and recombination patterns of CVA14 are not well understood. In this study, 15 CVA14 strains were isolated from HFMD patients in mainland China from 2009 to 2019, and the complete sequences of CVA14 in GenBank as research objects were analyzed. CVA14 was divided into seven genotypes A-G based on an average nucleotide difference of the full-length VP1 coding region of more than 15%. Compared with the CVA14 prototype strain, the 15 CVA14 strains showed 84.0-84.7% nucleotide identity in the complete genome and 96.9-97.6% amino acid identity in the encoding region. Phylodynamic analysis based on 15 CVA14 strains and 22 full-length VP1 sequences in GenBank showed a mean substitution rate of 5.35 × 10-3 substitutions/site/year (95% HPD: 4.03-6.89 × 10-3) and the most recent common ancestor (tMRCA) of CVA14 dates back to 1942 (95% HPD: 1930-1950). The Bayesian skyline showed that the effective population size had experienced a decrease-increase-decrease fluctuation since 2004. The phylogeographic analysis indicated two and three possible migration paths in the world and mainland China, respectively. Four recombination patterns with others of species enterovirus A were observed in 15 CVA14 strains, among which coxsackievirus A2 (CVA2), coxsackievirus A4 (CVA4), coxsackievirus A6 (CVA6), coxsackievirus A8 (CVA8), and coxsackievirus A12 (CVA12) may act as recombinant donors in multiple regions. This study has filled the gap in the molecular epidemiological characteristics of CVA14, enriched the global CVA14 sequence database, and laid the epidemiological foundation for the future study of CVA14 worldwide.

Enterovirus Meningitis without Pleocytosis: a Retrospective Observational Study in Adults

Reverse-transcription polymerase chain reaction (RT-PCR)-confirmed enterovirus (EV) meningitis without pleocytosis has only been previously reported in children. In this study, we examined the frequency of EV meningitis without pleocytosis in adults and compared its clinical features. We retrospectively analyzed the data of adult patients with EV meningitis confirmed using cerebrospinal fluid (CSF) RT-PCR. Among the 17 patients included in this study, 58.8% showed no pleocytosis. The median age and clinical symptoms did not differ between the pleocytosis and non-pleocytosis groups. There were no statistically significant differences in seasonal variation or time from the onset of meningitis symptoms to lumbar puncture. The peripheral white blood cell (WBC) count in patients with pleocytosis was significantly higher than that in patients without pleocytosis. The median CSF pressure showed a higher trend in the non-pleocytosis group. Patients with CSF pressures higher than normal were more common in the non-pleocytosis group. The median CSF protein values were higher than the normal values in both groups. We confirmed the high frequency of EV meningitis without pleocytosis in adults. Accurate diagnosis using RT-PCR is necessary when meningitis symptoms are prominent during an EV epidemic, and CSF protein levels and pressure are high, even if the CSF WBC count is normal.

Molecular epidemiology and phylodynamic analysis of enterovirus 71 in Beijing, China, 2009-2019

BACKGROUND

Enterovirus 71(EV71)-associated hand, foot and mouth disease (HFMD) decreased dramatically in Beijing from 2009 to 2019. This study was to investigate the epidemiological characteristics, evolutionary dynamics, geographic diffusion pathway, and other features of EV71 in Beijing, China.

METHODS

We conducted a retrospective study of EV71-associated HFMD and its causative agent in Beijing, China, from 2009 to 2019. Phylogenetic and phylogeographic methods based on the EV71 genome were used to determine the evolution features, origin, and spatiotemporal dynamics. Positive selection sites in the VP1 gene were identified and exhibited in the tertiary structure. Bayesian birth-death skyline model was used to estimate the effective reproductive number (Re).

RESULTS

EV71-associated HFMD decreased greatly in Beijing. From 2009 to 2019, EV71 strains prevalent in Beijing shared high homology in each gene segment and evolved with a rate of 4.99*10- 3 substitutions per site per year. The genetic diversity of EV71 first increased and peaked in 2012 and then decreased with fluctuations. The time to the most recent common ancestor (TMRCA) of EV71 in Beijing was estimated around 2003 when the EV71 strains were transmitted to Beijing from east China. Beijing played a crucial role in seeding EV71 to central China as well. Two residues (E145Q/G, A293S) under positive selection were detected from both the VP1 dataset and the P1 dataset. They were embedded within the loop of the VP1 capsid and were exposed externally. Mean Re estimate of EV71 in Beijing was about 1.007.

CONCLUSION

In recent years, EV71 was not the primary causative agent of HFMD in Beijing. The low Re estimate of EV71 in Beijing implied that strategies for preventing and controlling HFMD were performed effectively. Beijing and east China played a crucial role in disseminating EV71 to other regions in China.

The Upf1 protein restricts EV-A71 viral replication

Enterovirus A71 (EV-A71) is transmitted through the respiratory tract, gastrointestinal system, and fecal-oral routes. The main symptoms caused by EV-A71 are hand, foot, and mouth disease (HFMD) or vesicular sore throat. Upf1 (Up-frameshift protein 1) was reported to degrade mRNA containing early stop codons, known as nonsense-mediated decay (NMD). Upf1 is also involved in the NMD mechanism as a host factor detrimental to viral replication. In this study, we dissected the potential roles of Upf1 in the EV-A71-infected cells. Upf1 was virulently down-regulated in three different EV-A71-infected cells, RD, Hela, and 293T, implying that Upf1 is a host protein unfavorable for EV-A71 replication. Knockdown of Upf1 protein resulted in increased viral RNA expression and production of progeny virus, and conversely, overexpression of Upf1 protein resulted in decreased viral RNA expression and production of progeny virus. Importantly, we observed increased RNA levels of asparagine synthetase (ASNS), one of the indicator substrates for the NMD mechanism, which indirectly suggests that EV-A71 infection of cells suppresses NMD activity in the host. The results shown in this study are useful for subsequent analysis of the relationship between the NMD/Upf1 mechanism and other picornaviruses, which may lead to the development of anti-picornavirus drugs.

Molecular epidemiology of hand, foot, and mouth disease in Karnataka, India in 2022

BACKGROUND

Hand, foot, and mouth disease (HFMD) is an enteroviral disease that occurs as outbreaks and sporadic cases in India. In this study, we investigated and characterized the aetiology of HFMD cases that occurred in Karnataka, South India from April to October 2022.

METHODS

Throat swabs, vesicular swabs, urine, and blood samples from suspected cases were analysed by reverse transcription polymerase chain reaction (RT-PCR) for the detection of enteroviruses. Molecular typing of the enterovirus-positive samples was carried out by amplifying the partial virion protein 1(VP1) gene sequence, followed by sequencing and phylogenetic analysis.

RESULTS

Out of the 187 samples received from 82 cases, 93 (50%) tested positive (55/82 cases, 67%) for enteroviruses, with the majority of the HFMD cases reported in paediatric population of less than 5 years (36/55, 65.4%), while 3 cases (3/55, 5.4%) were adults. Out of the 55 enterovirus-positive cases, 31 showed partial VP1 region amplification and 19 of these cases were typed as coxsackievirus A16 (CV-A16) (13/19, 68.4%) and CV-A6 (6/19, 31.6%). The CV-A16 strains identified belonged to subclade B1c while two CV-A6 strains belonged to subclade E2. On molecular testing for other viruses causing fever-rash symptoms, 4/27 (15%) enterovirus-negative cases were detected as herpes simplex virus (1 case) and varicella zoster virus (3 cases) positive.

CONCLUSION

The main causative agent of HFMD in Karnataka in 2022 was CV-A16, followed by CV-A6. Apart from the common paediatric HFMD cases, adult cases were also reported during this period. Further studies involving laboratory and clinical investigations are essential for monitoring and managing HFMD in the community.

Trends of Enterovirus D68 Concentrations in Wastewater, California, USA, February 2021-April 2023

In this retrospective study, we measured enterovirus D68 (EV-D68) genomic RNA in wastewater solids longitudinally at 2 California, USA, wastewater treatment plants twice per week for 26 months. EV-D68 RNA was undetectable except when concentrations increased from mid-July to mid-December 2022, which coincided with a peak in confirmed EV-D68 cases.

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.

SIRT-1 is required for release of enveloped enteroviruses

Enterovirus D68 (EV-D68) is a re-emerging enterovirus that causes acute respiratory illness in infants and has recently been linked to Acute Flaccid Myelitis. Here, we show that the histone deacetylase, SIRT-1, is essential for autophagy and EV-D68 infection. Knockdown of SIRT-1 inhibits autophagy and reduces EV-D68 extracellular titers. The proviral activity of SIRT-1 does not require its deacetylase activity or functional autophagy. SIRT-1's proviral activity is, we demonstrate, mediated through the repression of endoplasmic reticulum stress (ER stress). Inducing ER stress through thapsigargin treatment or SERCA2A knockdown in SIRT-1 knockdown cells had no additional effect on EV-D68 extracellular titers. Knockdown of SIRT-1 also decreases poliovirus and SARS-CoV-2 titers but not coxsackievirus B3. In non-lytic conditions, EV-D68 is primarily released in an enveloped form, and SIRT-1 is required for this process. Our data show that SIRT-1, through its translocation to the cytosol, is critical to promote the release of enveloped EV-D68 viral particles.

Molecular evolutionary dynamics of enterovirus A71, coxsackievirus A16 and coxsackievirus A6 causing hand, foot and mouth disease in Thailand, 2000-2022

Hand, foot and mouth disease (HFMD) is a public health threat worldwide, particularly in the Asia-Pacific region. Enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), and CVA6 are the major pathogens causing HFMD outbreaks in several countries, including Thailand. We retrieved 385 VP1 nucleotide sequences, comprising 228 EV-A71, 33 CVA16, and 124 CVA6, deposited in the databases between 2000 and 2022 for molecular evolutionary characterization using Bayesian phylogeny. All EV-A71 identified belonged to genotype B, subgenotypes B4, and B5, and to genotype C, subgenotypes C1, C2, C4a, C4b, and C5. The analyzes demonstrated these viruses' co-circulation and subgenotypic changes throughout the past two decades. The CVA16 was grouped in genotype B1, predominantly subgenotype B1a, and the CVA6 was grouped in subgenotype D3, clades 1-4. The tMRCA of EV-A71 genotypes B and C, CVA16 B1, and CVA6 D3 dated 1993.79, 1982.62, 1995.86, and 2007.31, respectively, suggesting that the viruses were likely introduced and cryptically circulated in Thailand before the HFMD cases were recognized. We demonstrated these viruses' fluctuation and cyclical pattern throughout the two decades of observation. This study provided insight into evolutionary dynamics concerning molecular epidemiology and supported the selection of current genotype-matched vaccines, vaccine development, and implementation.

Enhanced detection of viruses for improved water safety

Human viruses pose a significant health risk in freshwater environments, but current monitoring methods are inadequate for detecting viral presence efficiently. We evaluated a novel passive in-situ concentration method using granular activated carbon (GAC). This study detected and quantified eight enteric and non-enteric, pathogenic viruses in a freshwater recreational lake in paired grab and GAC passive samples. The results found that GAC passive sampling had a higher detection rate for all viruses compared to grab samples, with adenovirus found to be the most prevalent virus, followed by respiratory syncytial virus, norovirus, enterovirus, influenza A, SARS-CoV-2, and rotavirus. GAC in-situ concentration allowed for the capture and recovery of viral gene copy targets that ranged from one to three orders of magnitude higher than conventional ex-situ concentration methods used in viral monitoring. This simple and affordable sampling method may have far-reaching implications for reducing barriers associated with viral monitoring across various environmental contexts.

First description and phylogenetic analysis of coxsackie virus A non-polio enteroviruses and parechoviruses A in South Sudanese children

Enteroviruses (EV) and parechoviruses A (PeV-A) are commonly circulating viruses able to cause severe disease. Surveillance studies from sub-Saharan Africa are limited and show high but variable infection rates and a high variation in genotypes. This is the first study to describe EV and PeV-A circulation in children in South Sudan. Of the fecal samples collected, 35% and 10% were positive for EV and PeV-A, respectively. A wide range of genotypes were found, including several rarely described EV and PeV-A types. Coxsackie virus A (CVA) EV-C types, particularly CVA13, were the most dominant EV types. The CVA13 types had a high diversity with the majority belonging to four different previously described clusters. PeV-A1 and -A14 were the most common PeV-A genotypes. A lack of representative data from our and other studies from sub-Saharan Africa demonstrates the need for more systematic surveillance of non-polio EV and PeV-A types in this region.

Epidemiological and molecular characterization of Coxsackievirus A6 causing hand, foot, and mouth disease in the Philippines, 2012-2017

Coxsackievirus A6 (CVA6) is emerging as the dominant serotype among enteroviruses (EVs) responsible for hand, foot, and mouth disease (HFMD) outbreaks in multiple countries. However, details regarding this serotype in the Philippines are limited. In this study, we investigated the epidemiological and molecular characteristics of laboratory-confirmed CVA6 HFMD cases in the Philippines between 2012 and 2017. Data collected from case report forms submitted to the National Reference Laboratory for Poliovirus and other Enteroviruses were used to determine the distribution and clinical findings of laboratory-confirmed CVA6 HFMD. Phylogenetic analyses of the complete viral protein 1 (VP1) and partial 3D polymerase (3Dpol) gene sequences were performed to determine the genotype and recombinant (RF) form of the selected samples. An increase in the detection rate of CVA6 among enterovirus-positive HFMD cases was observed from 61.9% (140/226) in 2012 to 88.1% (482/587) in 2017, with most cases coming from the Luzon island group. Among the detected cases, the majority were children, with a median age of 2 years old (interquartile range: 1.17-3.40). Respiratory-related morbidities were the commonly reported complications (7.9%; 72/907). Based on the VP1 and 3Dpol gene sequence analysis, the CVA6 strains in this study were classified as genotype D3b and RF-A group, respectively. This study elucidated that CVA6 was the most prevalent enterovirus serotype causing HFMD in the Philippines in 2012-2017, with genotype D3b/RF-A circulating within this period. This study highlights the importance of viral surveillance and molecular epidemiological analysis to broaden our understanding of HFMD in the Philippines.

VP2 residue N142 of coxsackievirus A10 is critical for the interaction with KREMEN1 receptor and neutralizing antibodies and the pathogenicity in mice

Coxsackievirus A10 (CVA10) has recently emerged as one of the major causative agents of hand, foot, and mouth disease. CVA10 may also cause a variety of complications. No approved vaccine or drug is currently available for CVA10. The residues of CVA10 critical for viral attachment, infectivity and in vivo pathogenicity have not been identified by experiment. Here, we report the identification of CVA10 residues important for binding to cellular receptor KREMEN1. We identified VP2 N142 as a key receptor-binding residue by screening of CVA10 mutants resistant to neutralization by soluble KREMEN1 protein. The receptor-binding residue N142 is exposed on the canyon rim but highly conserved in all naturally occurring CVA10 strains, which provides a counterexample to the canyon hypothesis. Residue N142 when mutated drastically reduced receptor-binding activity, resulting in decreased viral attachment and infection in cell culture. More importantly, residue N142 when mutated reduced viral replication in limb muscle and spinal cord of infected mice, leading to lower mortality and less severe clinical symptoms. Additionally, residue N142 when mutated could decrease viral binding affinity to anti-CVA10 polyclonal antibodies and a neutralizing monoclonal antibody and render CVA10 resistant to neutralization by the anti-CVA10 antibodies. Overall, our study highlights the essential role of VP2 residue N142 of CVA10 in the interactions with KREMEN1 receptor and neutralizing antibodies and viral virulence in mice, facilitating the understanding of the molecular mechanisms of CVA10 infection and immunity. Our study also provides important information for rational development of antibody-based treatment and vaccines against CVA10 infection.

Whole-genome sequencing and phylogenetic analysis of coxsackievirus-A16 strains causing hand, foot and mouth disease (HFMD) in India

Hand, foot and mouth disease (HFMD) is a common childhood infectious disease, caused by enteroviruses (EVs), which can present with typical or atypical lesions. The illness is self-limiting, but it can also have serious complications. Since 1997, HFMD infections have become endemic and have increased to epidemic proportions across the Asia Pacific region, including India. Coxsackievirus-A16 (CV-A16) outbreaks occurred in India from 2005 onwards, although the clinical symptoms were noticeably different during this period. Understanding the population dynamics of enteroviruses that cause HFMD is crucial in the post-polio era because one of the circulating strain may replace another as the dominant strain. The aim of this study is to describe the genetic features of the CV-A16 strains isolated from hand, foot and mouth disease (HFMD) patients in India. Reverse transcription PCR (RT-PCR) and cell-culture-based isolation of CV-A16 was done from the 55 clinical samples. The entire genome of the CV-A16 isolate was performed from the seven isolates. After the sequences were analysed, a phylogenetic tree was created using bioinformatics tools. The total genomic length obtained was 7411 base pairs (bp). Nucleotide similarity across various regions, including 5'UTR, P1, P2 and 3'UTR, ranged from 87.0-97.9 %, 77.0-95.4 %, 80.3-96.9 %, and 77.9-96.2 %, respectively. Correspondingly, similarities in the VP1 region's nucleotide and amino acid sequences were 91.4-96.4 % and 99.3-99.7 %, respectively. Phylogenetic analysis highlighted that CV-A16 strains identified in Pune, Maharashtra, were grouped within the same cluster. The analysed CV-A16 isolates in this study aligned with subgenotype B1c. These findings have far-reaching implications for the surveillance, prevention and management of HFMD and CV-A16. Monitoring the dynamics of CV-A16 strains, informed by the genetic characteristics identified here, will significantly impact strategies aimed at tackling HFMD and its associated public health challenges.

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CDpro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CDpro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem-loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

Reporter Coxsackievirus A5 Expressing iLOV Fluorescent Protein or Luciferase Used for Rapid Neutralizing Assay in Cells and Living Imaging in Mice

Coxsackievirus A5 (CV-A5) is a re-emerging enterovirus that causes hand, foot, and mouth disease in children under five years of age. CV-A5-M14-611 is a mouse-adapted strain that can infect orally and lead to the death of 14-day-old mice. Here, recombinants based on CV-A5-M14-611 were constructed carrying three reporter genes in different lengths. Smaller fluorescent marker proteins, light, oxygen, voltage sensing (iLOV), and nano luciferase (Nluc) were proven to be able to express efficiently in vitro. However, the recombinant with the largest insertion of the red fluorescence protein gene (DsRed) was not rescued. The construction strategy of reporter viruses was to insert the foreign genes between the C-terminus of VP1 and the N-terminus of 2A genes and to add a 2A protease cleavage domain at both ends of the insertions. The iLOV-tagged or Nluc-tagged recombinants, CV-A5-iLOV or CV-A5-Nluc, exhibited a high capacity for viral replication, genetic stability in cells and pathogenicity in mice. They were used to establish a rapid, inexpensive and convenient neutralizing antibody assay and greatly facilitated virus neutralizing antibody titration. Living imaging was performed on mice with CV-A5-Nluc, which exhibited specific bioluminescence in virus-disseminated organs, while fluorescence induced by CV-A5-iLOV was weakly detected. The reporter-gene-tagged CV-A5 can be used to study the infection and mechanisms of CV-A5 pathogenicity in a mouse model. They can also be used to establish rapid and sensitive assays for detecting neutralizing antibodies.

Increased reports of severe myocarditis associated with enterovirus infection in neonates, United Kingdom, 27 June 2022 to 26 April 2023

Enteroviruses are a common cause of seasonal childhood infections. The vast majority of enterovirus infections are mild and self-limiting, although neonates can sometimes develop severe disease. Myocarditis is a rare complication of enterovirus infection. Between June 2022 and April 2023, twenty cases of severe neonatal enteroviral myocarditis caused by coxsackie B viruses were reported in the United Kingdom. Sixteen required critical care support and two died. Enterovirus PCR on whole blood was the most sensitive diagnostic test. We describe the initial public health investigation into this cluster and aim to raise awareness among paediatricians, laboratories and public health specialists.