Retrospective Genotyping of Enteroviruses Using a Diagnostic Nanopore Sequencing Workflow

Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0-4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance.

Rubella virus chronic inflammatory disease and other unusual viral phenotypes in inborn errors of immunity

Infectious susceptibility is a component of many inborn errors of immunity. Nevertheless, antibiotic use is often used as a surrogate in history taking for infectious susceptibility, thereby disadvantaging patients who present with viral infections as their phenotype. Further complicating clinical evaluations are unusual manifestations of viral infections which may be less familiar that the typical respiratory viral infections. This review covers several unusual viral phenotypes arising in patients with inborn errors of immunity and other settings of immune compromise. In some cases, chronic infections lead to oncogenesis or tumor-like growths and the conditions and mechanisms of viral-induced oncogenesis will be described. This review covers enterovirus, rubella, measles, papillomavirus, and parvovirus B19. It does not cover EBV and hemophagocytic lymphohistiocytosis nor lymphomagenesis related to EBV. EBV susceptibility has been recently reviewed. Our goal is to increase awareness of the unusual manifestations of viral infections in patients with IEI and to describe treatment modalities utilized in this setting. Coincidentally, each of the discussed viral infections can have a cutaneous component and figures will serve as a reminder of the physical features of these viruses. Given the high morbidity and mortality, early recognition can only improve outcomes.

Evaluation of enterovirus concentration, species identification, and cerebrospinal fluid parameters in patients of different ages with aseptic meningitis in São Paulo, Brazil

Human enteroviruses (EV) are the most common cause of aseptic meningitis worldwide. Data on EV viral load in cerebrospinal fluid (CSF) and related epidemiological studies are scarce in Brazil. This study investigated the influence of EV viral load on CSF parameters, as well as identifying the involved species. CSF samples were collected in 2018-2019 from 140 individuals at The Hospital das Clínicas, São Paulo. The EV viral load was determined using real-time quantitative polymerase chain reaction, while EV species were identified by 5'UTR region sequencing. Median viral load was 5.72 log10  copies/mL and did not differ by subjects' age and EV species. Pleocytosis was observed in 94.3% of cases, with the highest white blood cell (WBC) counts in younger individuals. Viral load and WBC count were correlated in children (p = 0.0172). Elevated lactate levels were observed in 60% of cases and correlated with the viral load in preteen-teenagers (p = 0.0120) and adults (p = 0.0184). Most individuals had normal total protein levels (70.7%), with higher in preteen-teenagers and adults (p < 0.0001). By sequencing, 8.2% were identified as EV species A and 91.8% as species B. Age-specific variations in CSF characteristics suggest distinct inflammatory responses in each group.

Molecular Epidemiology Reveals the Co-Circulation of Two Genotypes of Coxsackievirus B5 in China

Coxsackievirus B5 (CVB5) is an important enterovirus B species (EV-Bs) type. We used the full-length genomic sequences of 53 viral sequences from the national hand, foot, and mouth disease surveillance network in the Chinese mainland (2001-2021). Among them, 69 entire VP1 coding region nucleotide sequences were used for CVB5 genotyping and genetic evolution analysis. Phylogenetic analysis based on a data set of 448 complete VP1 sequences showed that CVB5 could be divided into four genotypes (A-D) worldwide. Sequences from this study belonged to genotypes B and D, which dominated transmission in the Chinese mainland. Two transmission lineages of CVB5 have been discovered in the Chinese mainland, lineage 2 was predominant. Markov chain Monte Carlo analysis indicated that the tMRCA of CVB5 in the Chinese mainland could be traced to 1955, while the global trend could be traced to 1862, 93 years earlier than China. The evolution rate of CVB5 was higher in the Chinese mainland than worldwide. The spatiotemporal dynamics analysis of CVB5 assessed that virus transportation events were relatively active in Central, Northeast, North and Northwest China. Recombination analysis revealed frequent intertypic recombination in the non-structural region of CVB5 genotypes B and D with the other EV-Bs, revealing eight recombination lineages. Our study showed the molecular evolution and phylogeography of CVB5 that could provide valuable information for disease prevention.

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.

DNA methylation and single-nucleotide polymorphisms in DDX58 are associated with hand, foot and mouth disease caused by enterovirus 71

BACKGROUND

This research aimed to explore the association between the RIG-I-like receptor (RIG-I and MDA5 encoded by DDX58 and IFIH1, respectively) pathways and the risk or severity of hand, foot, and mouth disease caused by enterovirus 71 (EV71-HFMD). In this context, we explored the influence of gene methylation and polymorphism on EV71-HFMD.

METHODOLOGY/PRINCIPAL FINDINGS

60 healthy controls and 120 EV71-HFMD patients, including 60 mild EV71-HFMD and 60 severe EV71-HFMD patients, were enrolled. First, MiSeq was performed to explore the methylation of CpG islands in the DDX58 and IFIH1 promoter regions. Then, DDX58 and IFIH1 expression were detected in PBMCs using RT-qPCR. Finally, imLDR was used to detect DDX58 and IFIH1 single-nucleotide polymorphism (SNP) genotypes. Severe EV71-HFMD patients exhibited higher DDX58 promoter methylation levels than healthy controls and mild EV71-HFMD patients. DDX58 promoter methylation was significantly associated with severe HFMD, sex, vomiting, high fever, neutrophil abundance, and lymphocyte abundance. DDX58 expression levels were significantly lower in mild patients than in healthy controls and lower in severe patients than in mild patients. Binary logistic regression analysis revealed statistically significant differences in the genotype frequencies of DDX58 rs3739674 between the mild and severe groups. GeneMANIA revealed that 19 proteins displayed correlations with DDX58, including DHX58, HERC5, MAVS, RAI14, WRNIP1 and ISG15, and 19 proteins displayed correlations with IFIH1, including TKFC, IDE, MAVS, DHX58, NLRC5, TSPAN6, USP3 and DDX58.

CONCLUSIONS/SIGNIFICANCE

DDX58 expression and promoter methylation were associated with EV71 infection progression, especially in severe EV71-HFMD patients. The effect of DDX58 in EV71-HFMD is worth further attention.

A Different Epidemiology of Enterovirus A and Enterovirus B Co-circulating in Korea, 2012-2019

BACKGROUND

Enteroviruses (EVs) occur frequently worldwide and are known to be associated with a broad spectrum of clinical manifestations from mild syndromes to neurological disease. To understand the epidemiology of EV in Korea, we characterized EV-infected cases during 2012-2019 based on national surveillance.

METHODS

We collected specimens from patients with suspected EV infections and analyzed the data using real-time reverse-transcription polymerase chain reaction and VP1 gene sequencing.

RESULTS

Among the 18 261 specimens collected, EVs were detected in 6258 (34.3%) cases. Although the most common EV types changed annually, EV-A71, echovirus 30, coxsackievirus B5, coxsackievirus A6, and coxsackievirus A10 were commonly identified. Among the human EVs, the case numbers associated with the 2 major epidemic species (EV-A and EV-B) peaked in the summer. While EV-A species affected 1-year-old children and were associated with herpangina and hand, foot, and mouth disease, EV-B species were mostly associated with neurologic manifestations. The highest incidence of EV-B species was observed in infants aged <12 months. Feces and respiratory specimens were the most predictive of EV infection. Specimens collected within 5 days of symptom onset allowed for timely virus detection.

CONCLUSIONS

EV-A and EV-B species co-circulating in Korea presented different epidemiologic trends in clinical presentation, affected subjects, and seasonality trends. This study could provide information for the characterization of EVs circulating in Korea to aid the development of EV antivirals and vaccines, as well as public health measures to control enteroviral diseases.

World-Wide Prevalence and Genotype Distribution of Enteroviruses

Enteroviruses (EVs) are highly prevalent viruses world-wide, causing a wide range of diseases in both children and adults. Insight in the global prevalence of EVs is important to define their clinical significance and total disease burden, and assists in making therapeutic decisions. While many studies have been conducted to describe epidemiology of EVs in specific (sub)populations and patient cohorts, little effort has been made to aggregate the available evidence. In the current study, we conducted a search in the PubMed and Embase (Ovid) databases to identify articles reporting EV prevalence and type distribution. We summarized the findings of 153 included studies. We found that EVs are highly prevalent viruses in all continents. Enterovirus B was the most detected species worldwide, while the other species showed continent-specific differences, with Enterovirus C more detected in Africa and Enterovirus A more detected in Asia. Echovirus 30 was by far the most detected type, especially in studies conducted in Europe. EV types in species Enterovirus B-including echovirus 30-were often detected in patient groups with neurological infections and in cerebrospinal fluid, while Enterovirus C types were often found in stool samples.

Distribution of species enterovirus B in patients with central nervous system infections in São Paulo State, Brazil

Enteroviruses (EV) are most common cause of central nervous system (CNS) infection, mainly aseptic meningitis. In Brazil, data available concerning the distribution of EV types are scarce. The aim of this study was to describe of types EV in patients with infection of the CNS in São Paulo State. This retrospective study was conducted in clinical samples collected from patients with infections of the CNS from 2004 to 2014. We investigated the presence of EV by virus isolation in cell culture. The samples that showed cytopathic effect in the cell culture were submitted by indirect immunofluorescence assay, reverse transcription polymerase chain reaction and VP1 partial sequencing to identification of EV isolated. A total of 176 EV isolated in cell culture was detected and typed in 14.5% (n = 176/1215) of clinical samples analyzed; corresponding to 71.0% of AM, and 19.3% of encephalitis and meningoencephalitis. Echoviruses (E) were isolated most frequently, with 155 strains (88.1%), Coxsackievirus B (CV-B), with 20 cases (11.4%), CV-A, with 01 case (0.6%). E-6 was the most commonly identified followed in decreasing order by E-30; E-18; CV-B5; E-4; E-11; CV-B2 and E-9; E-7; CV-A9, CV-B1, CV-B3, CV-B4, E-13, E-14, and E-21. EV detected were classified as belonging to the species enterovirus B. EV were detected in all the period of the year with the highest rate in the spring and summer months. Data obtained in this study contribute to the knowledge about EV circulation implicated in CNS infections over a 11-year period in São Paulo State, Brazil.

Prevalence of Eleven Infectious Viruses Causing Diarrhea in Korea

Rotavirus and norovirus are well-known causes of viral infectious diarrhea. There are few reports on diarrhea caused by other viruses in Korea, although cases of gastroenteritis attributable to other viruses are increasing worldwide. The aims of this study were to detect various causes of viral diarrhea and to investigate their prevalence. A total of 801 fecal specimens submitted to a clinical microbiology laboratory for the detection of diarrheal viruses were included. We sought to detect rotavirus A/B/C, adenovirus, astrovirus, norovirus GI/GII, sapovirus, Aichi virus, human parechovirus, enterovirus, human cosavirus, human bocavirus, and Saffold virus using multiplex reverse transcription polymerase chain reaction (RT-PCR). At least one diarrheal virus was detected in 223 (27.8%) fecal specimens. Among them, two viruses were detected in 11 specimens. Rotavirus A was most common (17.1%; N = 137), followed by norovirus GII (5.0%; N = 40), enterovirus (4.2%; N = 34), adenovirus (1.0%; N = 8), astrovirus (1.0%; N = 8), human parechovirus (0.6%; N = 5), and human bocavirus (0.2%; N = 2). Rotaviruses B and C, norovirus GI, sapovirus, Aichi virus, human cosavirus, and Saffold virus were not detected. We confirmed that various diarrheal viruses can be detected in fecal specimens. We must consider the possibility of viruses other than rotavirus and norovirus being present in cases of diarrhea.

Sequence analysis of the first B5 subgenogroup strain of enterovirus 71 isolated in Korea

Enterovirus A71 (EV71), the main etiological agent of handfoot- mouth disease (HFMD), circulates in many areas of the world and has caused large epidemics since 1997, especially in the Asia-Pacific region. In this study, we determined the full-genome sequence of CMC718, a newly isolated EV71 strain in Korea. The CMC718 genome was 7,415 nucleotides in length and was confirmed by whole-genome phylogenetic analysis to belong to the B5 genotype. In particular, CMC718 demonstrated maximum identity with strain M988 of the B5 genotype and numerous amino acid variants were detected in the 3D domain of the viral protein P3, which is consistent with the mutation pattern of a B5 strain isolated in 2012–2013. Comparison of the CMC718 sequence with other EV71 reference strains confirmed the relationship and genetic variation of CMC718. Our study was a full-genome sequence analysis of the first EV71 strain of the B5 genotype isolated in South Korea. This information will be a valuable reference for the development of methods for the detection of recombinant viruses, the tracking of infections, and the diagnosis of EV71.

Chromogranin A provides additional prognostic information in children with severe hand, foot, and mouth disease: A prospective observational study

OBJECTIVE

Severe hand, foot, and mouth disease (HFMD) is associated with high mortality in children, and persistent sympathetic activation is a common presentation. The aim of this study was to prospectively investigate serum chromogranin A (CHGA) levels and their prognostic role in this condition.

METHODS

Serum CHGA, creatine kinase myocardial band (CK-MB), serum D-dimer, norepinephrine, blood glucose, lactate, and C-reactive protein levels, white blood cell (WBC) counts, usage of vasopressors, pediatric risk of mortality Ⅲ (PRISM-Ⅲ) scores, and viral etiology were measured upon pediatric intensive care unit (PICU) admission. The correlation between clinical outcomes and the indicators listed above were analyzed, and the ability of CHGA as a biomarker to predict mortality was evaluated.

RESULTS

Serum CHGA levels were higher in the non-survivors group than in the survivors group (median (interquartile range): 434.8 (374.3-502.4) vs 183.3 (131.9-246.9) μg/l; p < 0.001) and were correlated with norepinephrine (r = 0.37. p < 0.001), blood glucose (r = 0.32, p = 0.001), lactate (r = 0.25, p = 0.009), WBC (r = 0.20, p = 0.039), and PRISM-Ⅲ scores (r = 0.748, p < 0.0001). Patients suffering neurogenic pulmonary edema, those infected with enterovirus A71, and those requiring more vasopressors had higher serum CHGA levels (median (interquartile range): 385 (239.9-488.8) vs 161 (115.6-222.9), 340.6 (190.6-436.0) vs 150.5 (112.1-210.0), 395.6 (209.1-487.0) vs 167.7 (110.5-240.5) μg/l, respectively; p < 0.0001). The CHGA level upon PICU admission in severe HFMD could be an independent risk factor for mortality (adjusted odds ratio 2.459, 95% confidence interval 1.054-5.906, p = 0.038) with high specificity (87.5%) and sensitivity (82.6%) (cut-off value at 339.6 μg/l).

CONCLUSIONS

The CHGA level in severe HFMD was found to be associated with cardiopulmonary failure. If measured upon PICU admission, CHGA may provide additional prognostic information in this disease.

The History of Enterovirus A71 Outbreaks and Molecular Epidemiology in the Asia-Pacific Region

Enterovirus A71 (EV-A71) is one of the common causative pathogens for hand foot and mouth disease (HFMD) affecting young children. HFMD outbreak can result in a substantial pediatric hospitalization and burden the healthcare services, especially in less-developed countries. Since the initial epidemic of predominantly EV-A71 in California in 1969, the high prevalence of HFMD in the Asia-pacific region and elsewhere around the world represents a significant morbidity in this age group. With the advent of rapid and accurate diagnostic tools, there has been a dramatic increase in the number of laboratory-confirmed EV-A71 infection over the past two decades. The population, cultural, and socioeconomic diversity among countries in the Asia-Pacific region all influence the transmission and morbidity associated with HFMD. This review summarizes the current state of epidemiology of EV-A71 in Asia-Pacific countries based on the most recent epidemiological data and available information on the prevalence and disease burden. This knowledge is important in guiding the prevention, control and future research on vaccine development of this highly contagious disease of significant socioeconomic implications in public health.

Comparison of Nonpolio Enteroviruses in Children With Herpangina and Hand, Foot and Mouth Disease in Taiwan

BACKGROUND

Nonpolio enterovirus (NPEV) infections are often present with herpangina (HA) and hand, foot and mouth disease (HFMD). Most countries sample NPEVs in HFMD cases, targeting enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) that are associated with outbreaks and severe complications. HA is also monitored in Taiwan and several other countries, but its viral characteristics are underreported.

METHODS

Through Taiwan's National Virologic Surveillance, information regarding ~100,000 child respiratory samples (2002-2015) was linked to concurrent (0-6 days before the sampling date) outpatient records from the National Health Insurance databases, including ~15,000 HA-related and ~7000 HFMD-related samples. We assessed sample representation and NPEV positive rates, and estimated total numbers of EV-A71 and CV-A16.

RESULTS

There were more HA events (4.0 millions) than HFMD events (1.2 millions) in Taiwan. In every 1000 events with HFMD and HA, 6.0 and 4.1, respectively, respiratory samples were collected. The NPEV positive rate in HFMD-related samples was 48%, consistent across most sampling seasons, and predominantly EV-A71 or CV-A16 (74%). By comparison, the HA-related samples had a lower positive rate overall (43%), occasionally EV-A71 or CV-A16 (13%), and the positive rate depended strongly on HA incidence (P < 10). Compared with sampling HFMD alone, inclusion of HA-related information predicted an earlier onset of EV-A71 outbreak in 2011, and predicted 30% more EV-A71 cases.

CONCLUSIONS

This is the first representative report on viral characteristics of HA. Our findings confirm that HFMD monitoring is a reliable strategy, but there is a measurable additional benefit when HA is also monitored.

Incidence, aetiology, and serotype spectrum analysis of adult hand, foot, and mouth disease patients: A retrospective observational cohort study in northern Zhejiang, China

BACKGROUND

Hand, foot, and mouth disease (HFMD) in adults has rarely been reported in the literature, although its clinical significance is underestimated. This study was performed to systematically elucidate the epidemiological characteristics of adult HFMD.

METHODS

A total of 266 adult patients with HFMD were recruited. The control group comprised 40 healthy adults. Swabs and serum samples were collected. Enterovirus strains were tested by RT-PCR, and cytokine expression was examined using commercial kits. Socio-demographic data were collected through follow-up telephone calls. Daily meteorological data were obtained from the China Meteorological Data Sharing Service System. Socio-economic data were collected from the statistical bureau.

RESULTS

This study identified several unique spatiotemporal patterns in adult HFMD. Having a child recently diagnosed with HFMD was a risk factor for HFMD, whereas keeping pets was a protective factor against HFMD. The results of this study indicate the existence of subclinical carriers or misdiagnosed patients who might be the latent infectious source of HFMD. Further, this study also indicated that adults may act as the main infectious source of trans-regional spread of HFMD.

CONCLUSIONS

This study revealed the potential hazards of adult HFMD and is a reminder of the vital clinical significance of further research into adult HFMD.

Evolutionary histories of coxsackievirus B5 and swine vesicular disease virus reconstructed by phylodynamic and sequence variation analyses

Coxsackievirus (CV)-B5 is a common human enterovirus reported worldwide; swine vesicular disease virus (SVDV) is a porcine variant of CV-B5. To clarify the transmission dynamics and molecular basis of host switching between CV-B5 and SVDV, we analysed and compared the VP1 and partial 3D^pol gene regions of these two viruses. Spatiotemporal dynamics of viral transmission were estimated using a Bayesian statistical inference framework. The detected selection events were used to analyse the key molecules associated with host switching. Analyses of VP1 sequences revealed six CV-B5 genotypes (A1–A4 and B1–B2) and three SVDV genotypes (I–III). Analyses of partial 3D^pol revealed five clusters (A–E). The genotypes evolved sequentially over different periods, albeit with some overlap. The major hub of CV-B5 transmission was in China whereas the major hubs of SVDV transmission were in Italy. Network analysis based on deduced amino acid sequences showed a diverse extension of the VP1 structural protein, whereas most sequences were clustered into two haplotypes in the partial 3D^pol region. Residue 178 of VP1 showed four epistatic interactions with residues known to play essential roles in viral host tropism, cell entry, and viral decoating.

Seroepidemiology of echovirus 30 in Korean children

BACKGROUND

Although aseptic meningitis associated with echovirus type 30 has emerged as a global public health concern, no data have been reported on Children's immune status against echovirus type 30. The current study aimed to investigate the seropositivity among Korean children for antibodies against echovirus 30.

METHODS

Two hundred and fifty residual serum samples were collected at St. Paul's Hospital. Individuals were categorized by age into four groups: group 1 (3 months-2 years), group 2 (3-6 years), group 3 (7-10 years) and group 4 (11-15 years). Neutralizing antibodies against echovirus 30 were measured.

RESULTS

Seroprotective neutralizing antibodies against echovirus 30 were detected in 129 (49%) individuals. Seropositivity rates were 23%, 48%, 55% and 73% in groups 1-4, respectively. For antibody titers, 1:256-1:512 was the highest neutralizing antibody titer range in group 2, while 1:1024-1:2048 in group 3 and 4. Among the seropositive individuals in group 3 and 4, 6% and 12% had neutralizing antibody titers of 1:2048, respectively.

CONCLUSIONS

The seropositivity rate increased significantly with age. The distribution of neutralizing antibody titers varied by age group, and higher ranges of neutralizing antibody titers were observed in higher age groups. These findings suggest high susceptibility to echovirus 30 infection in children younger than 2 years old. Echovirus 30 infection in childhood may have contributed to increased neutralizing antibody titers with age.

Seroepidemiology of coxsackievirus B5 in infants and children in Jiangsu province, China

Coxsackievirus B5 (CV-B5) is associated with various human diseases such as viral encephalitis, aseptic meningitis, paralysis, herpangina, and hand, foot and mouth disease (HFMD). However, there is currently no effective vaccine against CV-B5.The seroepidemiologic characteristics of CV-B5 remained unknown. A cohort study was carried out in 176 participants aged 6-35 months from January 2012 to January 2014. The serum samples were collected and tested for CV-B5 neutralizing antibodies (NtAbs) four times during these two years. The confirmed enterovirus cases were recorded through the surveillance system, and their throat or rectal swabs were collected for pathogen detection. According to the changes of CV-B5 NtAbs, two CV-B5 epidemics were detected among these participants during the two-year follow-up. Sixty-seven cases out of all participants had seroconversion in CV-B5 NtAbs. During the first epidemic from March 2012 to September 2012, CV-B5 seropositivity rate increased significantly (6.8%, 12/176 vs. 21.6%, 38/176, P = 0.000). The seroconversion rate and geometric mean fold-increase (GMFI) were 18.2% (32/176) and 55.7, respectively; During the second epidemic from September 2012 to January 2014, CV-B5 seropositivity rate also increased (21.6%, 38/176 vs. 38.6%, 68/176, P = 0.000), and the seroconversion rate and GMFI were 19.9% (35/176) and 46.5, respectively. Only one case had CV-B5 associated HFMD during the two-year follow-up, and CV-B5 from the throat swab isolate was GI.D3 subtype, which belonged to the major pandemic strain in mainland China. CV-B5 infection was common in infants and children in Jiangsu province, China. Therefore, it's necessary to strengthen the surveillance on CV-B5 and to understand the epidemic characteristics of CV-B5 infection.

Emerging Foodborne and Agriculture-Related Viruses

Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.

Sequence analysis of the first C2 subgenogroup strain of enterovirus 71 isolated in Korea

BACKGROUND

Enterovirus 71 (EV71) is an important causative agent of hand-foot-and-mouth disease with severe neurological complications, which may lead to death in children. Large outbreaks caused by EV71 have frequently occurred in Asia-Pacific region.

OBJECTIVES

In Korea, the outbreaks have been caused by EV71 subgenogroups C3, and C4. Only genogroup C, especially subgenogroup C1, C3, C4, and C5, has been detected by the national enterovirus surveillance system in Korea. This study reports the first isolation of EV71 A1451 strain, which belongs to subgenogroup C2.

STUDY DESIGN

EV71 was isolated from a Korean patient with meningoencephalitis. Complete genome analysis and phylogenetic analysis was performed to identify the characteristics of the strain.

RESULTS

Comparative genome analysis of the A1451 strain indicated that this novel C2 strain is associated with the Taiwan strains, which are recombinant virus combined with subgenogroup C2 and B3.

CONCLUSIONS

Because the subgenogroup B3 was not previously detected in Korea, the A1451 strain is regarded as an imported recombinant virus. Periodic surveillance of EV71 is required to control the spread of this disease and its introduction from overseas.

Epidemiology and virologic investigation of human enterovirus 71 infection in the Republic of Korea from 2007 to 2012: a nationwide cross-sectional study

BACKGROUND

Enterovirus (EV) 71 is the main pathogen associated with hand, foot and mouth disease (HFMD) or herpangina. Outbreaks of HFMD caused by EV71 infection are associated severe neurological disease and high mortality rates in children. Several sporadic cases of EV71 infection occurred in the Republic of Korea (ROK) in 2000, and EV71 infections were not reported thereafter until 2006. In this prospective study, we report the epidemic and virologic characteristics of the EV71 endemic from 2007 to 2012 in the Republic of Korea.

METHODS

We analyzed characteristics of the EV71 infection-associated epidemic from collected specimens and clinical information from 9987 patients with suspected EV infection from the National EV Surveillance System in ROK. To identify the EV71 subgenotype, the homology of viral protein 1 sequences obtained using reverse transcription polymerase chain reaction was compared with the sequences on other countries available from GenBank database.

RESULTS

EV71 was detected in 585 (16.7 %) specimens (cerebrospinal fluid, stool or rectal swabs, throat swabs and blood) during study period and was most frequently observed during epidemic seasons in 2009-2012. Major manifestations due to EV71 infection were HFMD (62.2 %) and HFMD with severe neurological complications (28.4 %). Five deaths (0.9 %) due to EV71 infection occurred, with an increased mortality rate during the period after 2009. Most patients (476; 81.4 %) were less than 5 years of age. Analysis of the monthly distribution showed that there was an obvious seasonal pattern to the epidemics, with infections appearing from June to August. The major subgenotype of EV71 isolates circulating in ROK was the C4a strain, which has also appeared in China, Japan and Vietnam.

CONCLUSIONS

This surveillance provided valuable data on the epidemic characteristics of EV71 infections in ROK during a 6-year period. Our findings provide data to assist during future outbreaks of EV71 and associated acute neurologic disease.

Diagnostic uncertainty of herpangina and hand-foot-and-mouth disease and its impact on national enterovirus syndromic monitoring

The community burden of enterovirus is often monitored through syndromic monitoring systems based on reported cases of enterovirus-related infection (EVI) diagnoses. The extent to which this is affected by under- and over-diagnosis has not been reported. In Taiwan, children often make more than one healthcare visit during an episode of infection. We used change of diagnosis within an episode of infection as a guide of diagnostic uncertainty in a nationally representative cohort of Taiwanese children (n = 13 284) followed from birth to the 9th birthday through electronic health records. We conducted a nested case-control analysis and estimated cross-diagnosis ratios (CDRs) as the observed proportion of acute respiratory infection (ARI) diagnoses following an EVI diagnosis in excess of background ARI burdens. With 19 357 EVI diagnoses in this cohort, the CDR within 7 days was 1·51 (95% confidence interval 1·45–1·57), confirming a significant excess of ARI diagnoses within the week following an EVI diagnosis. We used age-specific CDRs to calibrate the weekly EVI burden in children aged 3–5 years in 2008, and the difference between observed and calibrated weekly EVI burdens was small. Therefore, there was evidence suggesting a small uncertainty in EVI diagnosis, but the observed EVI burdens through syndromic monitoring were not substantially affected by the small uncertainty.

Epidemiologic and etiologic characteristics of hand, foot, and mouth disease in Chongqing, China between 2010 and 2013

Hand, foot, and mouth disease (HFMD) has become very common in children, with widespread occurrence across China. The aim of this study was to investigate the epidemiologic and etiologic characteristics of HFMD, including etiologic variations in Chongqing, China. An epidemiologic investigation was based on 3,472 patients who presented with HFMD manifestations and were admitted at the Children's Hospital of Chongqing Medical University between 2010 and 2013. Fecal specimens from 830 patients were analyzed by nested RT-PCR to identify the enterovirus pathogens, and the molecular characterization of HFMD was illustrated by phylogenetic tree analysis. The results of this study indicate that the peak of the HFMD epidemic in Chongqing between 2010 and 2013 occurred between April and July each year. The median age of onset was 2.24 years old, and children under the age of five accounted for 96.4% of all the HFMD cases; the male-to-female ratio was 1.89:1. Enterovirus 71 accounted for a major proportion of the isolated strains every year, including the majority (74%) of severe cases. However, the proportion of Coxsackie A (CV-A) 6 infections increased from 2.11% in 2010 to 16.36% in 2013, while the proportion of CV-A16 infections decreased from 31.23% in 2010 to 4.67% in 2013. Molecular epidemiologic study showed that all enterovirus 71 strains belonged to subgenotype C4a, whereas all CV-A16 strains belonged to genotype B1, including subgenotype B1a and subgenotype B1b.

Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2

BACKGROUND

Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013.

RESULTS

Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region.

CONCLUSIONS

Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.

Epidemiology and seroepidemiology of human enterovirus 71 among Thai populations

Background

Human enterovirus 71 (EV71) is an important pathogen caused large outbreaks in Asian-Pacific region with severe neurological complications and may lead to death in young children. Understanding of the etiological spectrum and epidemic changes of enterovirus and population’s immunity against EV71 are crucial for the implementation of future therapeutic and prophylactic intervention.

Results

A total of 1,182 patients who presented with the symptoms of hand foot and mouth disease (67.3%) or herpangina (HA) (16.7%) and admitted to the hospitals during 2008-2013 were tested for enterovirus using pan-enterovirus PCR targeting 5′-untranslated region and specific PCR for viral capsid protein 1 gene. Overall, 59.7% were pan-enterovirus positive comprising 9.1% EV71 and 31.2% coxsackievirus species A (CV-A) including 70.5% CV-A6, 27.6% CV-A16, 1.1% CV-A10, and 0.8% CV-A5. HFMD and HA occurred endemically during 2008-2011. The number of cases increased dramatically in June 2012 with the percentage of the recently emerged CV-A6 significantly rose to 28.4%. Co-circulation between different EV71 genotypes was observed during the outbreak. Total of 161 sera obtained from healthy individuals were tested for neutralizing antibodies (NAb) against EV71 subgenotype B5 (EV71-B5) using microneutralization assay. The seropositive rate of EV71-B5 was 65.8%. The age-adjusted seroprevalence for individuals was found to be lowest in children aged >6 months to 2 years (42.5%). The seropositive rate remained relatively low in preschool children aged > 2 years to 6 years (48.3%) and thereafter increased sharply to more than 80% in individuals aged > 6 years.

Conclusions

This study describes longitudinal data reflecting changing patterns of enterovirus prevalence over 6 years and demonstrates high seroprevalences of EV71-B5 NAb among Thai individuals. The rate of EV71 seropositive increased with age but without gender-specific significant difference. We identified that relative lower EV71 seropositive rate in early 2012 may demonstrate widely presented of EV71-B5 in the population before account for a large outbreak scale epidemic occurred in 2012 with due to a relatively high susceptibility of the younger population.