Investigation into a school enterovirus outbreak using PCR detection and serotype identification based on the 5' non-coding region

Molecular characterization of a novel clade echovirus 3 isolated from patients with hand-foot-and-mouth disease in southwest China

Echovirus 3 (E3) belongs to the species Enterovirus B. Currently, three nearly whole-genome sequences of E3 are available in GenBank in China. In this study, we determined the whole genomic sequences of six E3 strains isolated from the stools of patients with hand-foot-and-mouth disease in Southwest China in 2022. Their nucleotide and amino acid sequences shared 82.1%-86.4% and 96.6%-97.2% identity with the prototype Morrisey strain, respectively, and showed 87.1% and 97.2% mutual identity. The six E3 strains are not clustered with other Chinese strains and formed a novel subgenotype (C6) with the recent American and British strains. Recombination analyses revealed that intertype recombination had occurred in the 2 C and 3D regions of the six E3 strains with coxsackieviruses B5 and B4, respectively. This study augments the nearly whole-genome sequences of E3 in the GenBank database and extends the molecular characterization of this virus in China.

Description of non-polio enteroviruses identified in two national surveillance programmes in South Africa

Background

Human enteroviruses (EV) consist of 106 serotypes and four species: EV-A, EV-B, EV-C and EV-D. Enteroviruses cause clinical symptoms varying from severe to mild. Knowledge of EV burden in South Africa is limited, and as non-polio EV are important causes of acute flaccid paralysis (AFP) and meningitis, information on the circulating serotypes is vital.

Methods

Between 2010 and 2012, a total of 832 stool and viral isolate specimens were obtained from two national surveillance programmes at the National Institute for Communicable Diseases: the Rotavirus Sentinel Surveillance Programme (RSSP) and the AFP surveillance programme. Real-time polymerase chain reaction and Sanger sequencing were performed to detect and serotype EV.

Results

Non-polio EV were detected in 446 specimens, of which 308 were sequenced. Stool specimens yielded a greater variety of serotypes than viral cultures. EV-B viruses were predominant (58.44%), whilst EV-C viruses were detected in 31% of the specimens tested. South African prevalence for these viruses was higher than other countries, such as France with less than 2%, and Spain and the United States with less than 10%. The most common serotype detected was Enterovirus 99 (EV-C, 8.63%), which has not been reported in other regions.

Conclusion

Direct sequencing from stool specimens yields a broader, more comprehensive description of EV infections compared to sequencing from viral cultures. Disease-associated serotypes were detected, but only in small numbers. This study provides a baseline for EV strain circulation; however, surveillance needs to be expanded to improve EV knowledge in South Africa.

A Review and Update on Waterborne Viral Diseases Associated with Swimming Pools

Infectious agents, including bacteria, viruses, protozoa, and molds, may threaten the health of swimming pool bathers. Viruses are a major cause of recreationally-associated waterborne diseases linked to pools, lakes, ponds, thermal pools/spas, rivers, and hot springs. They can make their way into waters through the accidental release of fecal matter, body fluids (saliva, mucus), or skin flakes by symptomatic or asymptomatic carriers. We present an updated overview of epidemiological data on viral outbreaks, a project motivated, among other things, by the availability of improved viral detection methodologies. Special attention is paid to outbreak investigations (source of the outbreak, pathways of transmission, chlorination/disinfection). Epidemiological studies on incidents of viral contamination of swimming pools under non-epidemic conditions are also reviewed.

Molecular characterization of an outbreak of enterovirus-associated meningitis in Mossel Bay, South Africa, December 2015-January 2016

BACKGROUND

Human enteroviruses (HEVs) are common causal agents of aseptic meningitis in young children. Laboratory and syndromic surveillance during December 2015 and January 2016 noted an unusually high number of paediatric aseptic meningitis cases at a hospital in Mossel Bay, Western Cape Province, South Africa. HEV was detected in clinical samples, prompting an outbreak investigation.

METHODS

Epidemiological investigations were conducted to ascertain possible linkage between cases. Amplification, sequencing and phylogenetic analysis of the 5'UTR and VP1 regions was undertaken to determine the HEV serotype associated with the outbreak as well as other cases of aseptic meningitis in the area in the preceding 6 weeks.

RESULTS

Over the 2-month period, 63 CSF samples were available for testing. A total of 43 outbreak cases (68.3%) were observed, and the 26 (60.5%) that could be typed were coxsackie virus A9 (CVA9). Children attending three crèche facilities were epidemiologically linked, accounting for 60.5% (26/43) of the CVA9 cases. The majority of patients were under 10 years of age (55/63, 87.3%) and there was a male predominance (66%). Nucleotide sequence analysis of the 5'UTR and VP1 regions identified 2 lineages of CVA9 co-circulating during the outbreak, although the VP1 capsid protein sequence was identical as all nucleotide differences were synonymous. There was a unique isoleucine at position 64 and all outbreak viruses had a valine to threonine change in the hypervariable BC loop of VP1. Other HEV types circulating in the preceding period were echovirus 30 (n = 4), echovirus 5 (n = 3) and 1 each of echovirus 6, echovirus 9 and echovirus 15.

CONCLUSION

CVA9 was identified as the pathogen responsible for the large outbreak of aseptic meningitis, with 2 distinct co-circulating lineages.

Exotic Tourist Destinations and Transmission of Infections by Swimming Pools and Hot Springs-A Literature Review

A growing number of people undertake international travel, and yet faster growth of such travel is expected in the tropics. Information on the hazards presented by pool and hot spring waters in tropical countries is very limited. This review aims to collate available information on pool water quality, alongside data on cases and outbreaks associated with swimming in pools in tropical regions affecting both local populations and travellers. Bacteria species commonly causing cases and outbreaks in the tropics as well as elsewhere in the world were excluded, and the review focuses on studies related to pathogens that, with the exception of Cryptosporidium, are unusual in more temperate climates. Studies concerning subtropical countries were included in the light of climate change. Diseases transmitted by vectors breeding in poorly maintained, neglected or abandoned pools were also included. 83 studies dealing with Microsporidia, Leptospira spp., Schistosomas spp., Cryptosporidium spp., Acanthamoeba spp., Naegleria spp., Clostridium trachomatis, viruses, and vectors breeding in swimming pool and hot tub waters, and fulfilling predefined criteria, have been included in our survey of the literature. In conclusion, prevention strategies for pool safety in the tropics are imperative. Public health authorities need to provide guidance to westerners travelling to exotic destinations on how to protect their health in swimming pools.

Molecular characterisation of enteroviruses and clinical findings from a cluster of paediatric viral meningitis cases in Tshwane, South Africa 2010-2011

BACKGROUND

Human enteroviruses (HEVs) are the most common viral pathogen associated with paediatric aseptic meningitis. From October 2010 to February 2011 a cluster of HEV-associated meningitis cases was identified in paediatric patients who had presented at two large tertiary hospitals in Pretoria in the Tshwane Metropolitan Area, Gauteng, South Africa (SA).

OBJECTIVES

The aim of this study was to review the clinical features and to characterise the HEV strains associated with this cluster of meningitis cases.

STUDY DESIGN

In this retrospective study HEVs, detected by real time reverse transcription-polymerase chain reaction in acute phase cerebrospinal fluid specimens from 30 patients with aseptic meningitis, were characterised and the clinical presentations of these patients were described.

RESULTS

Fever (83%), headache (70%) and vomiting (67%) were the most prominent symptoms with signs of meningeal irritation recorded in 67% of the patients. There was a neutrophil predominance in the cerebrospinal fluid of 57% of the patients with pleocytosis. Based on partial nucleotide sequence analysis of the HEV viral protein 1 gene, echovirus (E) serotype 4 (E-4) was identified in 80% (24/30) of specimens with E-9 (3/30) and coxsackie virus B5 (1/30) detected less frequently.

CONCLUSION

In this cluster of aseptic meningitis cases E-4 was the predominant strain with E-9, and to a lesser extent other HEVs, identified less frequently.

Methods to detect infectious human enteric viruses in environmental water samples

Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples.

High degree of genetic diversity of non-polio enteroviruses identified in Georgia by environmental and clinical surveillance, 2002–2005

Enterovirus surveillance data are useful for establishing temporal and geographical patterns of circulation and for virus characterization to determine phylogenetic relationships between strains. Almost no information is available on circulating enteroviruses in Georgia and the surrounding region. To describe enterovirus circulation in Georgia, determine relationships with previously characterized strains and assess the role of environmental and clinical enterovirus surveillance, this study analysed a total of 112 non-polio enterovirus isolates identified during 2002–2005 from sewage and human stool samples. Viruses were isolated in cell culture using standard methods and typed by partial sequencing of the VP1 gene. A total of 20 different non-polio enterovirus serotypes were identified over the 4-year period. The most commonly detected enteroviruses included echovirus (E) 6 (21 isolates; 18.8 %), E20, E3 and E7 (11 isolates each; 9.8 %), E11, coxsackievirus (CV) B4 and CVB5 (seven isolates each; 6.3 %), and E13, E19 and E30 (six isolates each; 5.4 %). Phylogenetic analysis showed that many serotypes were represented by more than one genetic lineage. The present study showed a very high degree of enterovirus diversity in Georgia and demonstrated the added value of environmental enterovirus surveillance, particularly in settings with limited clinical surveillance. Several serotypes would not have been detected without having both clinical and environmental surveillance in place. Several serotypes detected in Georgia were among those rarely reported in the USA and Europe (e.g. E3, E20 and E19). As the emergence of new genetic lineages of enterovirus in a particular area is often associated with large-scale outbreaks, continued monitoring of enterovirus strains by both environmental and clinical surveillance and genetic characterization should be encouraged.

Viruses in recreational water-borne disease outbreaks: a review

Viruses are believed to be a significant cause of recreationally associated water-borne disease. However, they have been difficult to document because of the wide variety of illnesses that they cause and the limitations in previous detection methods. Noroviruses are believed to be the single largest cause of outbreaks, which have been documented in the published literature 45% (n = 25), followed by adenovirus (24%), echovirus (18%), hepatitis A virus (7%) and coxsackieviruses (5%). Just under half of the outbreaks occurred in swimming pools (49%), while the second largest outbreak occurred in lakes or ponds (40%). The number of reported outbreaks associated with noroviruses has increased significantly in recent years probably because of better methods for virus detection. Inadequate disinfection was related to 69% (n = 18) of swimming pool outbreaks. A lack of required reporting and nonuniform water quality and chlorination/disinfection standards continues to contribute to water-borne recreational disease outbreaks.

Chapter 9 The Detection of Waterborne Viruses

Viruses in water are usually present in concentrations too low for detection by direct analysis. Virological investigation of water samples is always a multi-stage process involving concentration of viruses present followed by an appropriate detection procedure. There are several approaches to detection of viruses. Part or all of the concentrate may be inoculated into cell cultures to detect infectious cytopathogenic virus, and if this is done in a quantitative fashion the virus can be enumerated, the count being reported as plaque-forming units, the tissue culture infectious dose, or most probable number units. The virus may be isolated and identified from the cell cultures. Viruses that multiply without producing an identifiable cytopathic effect in culture may sometimes be detected by immunoperoxidase or immunofluorescence staining. The concentrate may also be analyzed by molecular biological procedures (usually polymerase chain reaction (PCR) or real-time-PCR). The problem then is that such techniques do not usually detect the infectious virus, and novel approaches have been made recently to meet this challenge.

Aseptic meningitis

PURPOSE OF REVIEW

To highlight some of the recent key epidemiologic and clinical diagnostic dilemmas of aseptic meningitis and to evaluate some tests that may help distinguish aseptic compared with bacterial meningitis.

RECENT FINDINGS

Enteroviruses remain the most common cause of aseptic meningitis. Certain enteroviruses (e.g. coxsackie B5, echovirus 6, 9 and 30) are more likely to cause meningitis outbreaks, while others (coxsackie A9, B3 and B4) are mostly endemic. Nucleic acid tests are more sensitive than cultures in diagnosing enteroviral infections. In centers where the turnaround time for these tests is less than 24 h, there can be substantial cost savings and avoidance of unnecessary treatment of aseptic meningitis with antibiotics. Serum and stool specimens are important adjunct samples for diagnosing enteroviral infections in children. Cerebrospinal fluid protein (> or = 0.5 g/l) and serum procalcitonin (> or = 0.5 ng/ml) appear to be useful laboratory markers for distinguishing between bacterial and aseptic meningitis in children aged 28 days to 16 years, but they have relatively low sensitivity and specificity.

SUMMARY

Enteroviruses are the major causes of aseptic meningitis. The major focus of diagnosis remains ruling out bacterial infection or confirming enteroviral etiology of infection. Properly implemented nucleic acid tests have the potential to reduce cost and unnecessary treatment.

Detection of noroviruses in foods: a study on virus extraction procedures in foods implicated in outbreaks of human gastroenteritis

Disease outbreaks in which foods are epidemiologically implicated as the common source are frequently reported. Noroviruses and enteric hepatitis A viruses are among the most prevalent causative agents of foodborne diseases. However, the detection of these viruses in foods other than shellfish is often time-consuming and unsuccessful. In this study, three virus concentration methods were compared: polyethylene glycol (PEG) plus NaCl, ultracentrifugation, and ultrafiltration. Two RNA extraction methods, TRIzol and RNeasy Mini Kit (Qiagen), were compared for detection of viruses in whipped cream and lettuce (as representatives of the dairy and vegetable-fruit food groups, respectively). A seeding experiment with canine calicivirus was conducted to determine the efficiency of each virus extraction procedure. The PEG-NaCl-TRIzol method was most efficient for the detection of viruses in whipped cream and the ultracentrifugation-RNeasy-Mini Kit procedure was best for detection on lettuce. Based on the seeding experiments, food items implicated in norovirus-associated gastroenteritis outbreaks were subjected to the optimal procedure for a specific composition and matrix. No noroviruses were detected in the implicated food items, possibly because the concentration of virus on the food item was too low or because of the presence of inhibitory factors. For each food group, a specific procedure is optimal. Inhibitory factors should be controlled in these procedures because they influence virus detection in food.