Prevalence of rotavirus, adenovirus, norovirus, and astrovirus infections and coinfections among hospitalized children in northern France. J Clin Microbiol. 2010;48:1943-1946. [PMID: 20305010 DOI: 10.1128/jcm.02181-09]

Remarkable increase in the detection and molecular characterization of adenovirus F41 in children with acute gastroenteritis in Japan, 2017-2023

Human adenovirus (HAdV) is one of the causative viruses of acute gastroenteritis (AGE) in children worldwide. Species F is known to be enteric adenovirus (genotypes 40 and 41) detected in stool samples. In Japan, we conducted an epidemiological study and molecular characterization of HAdV before and after the COVID-19 pandemic from 2017 to 2023. Among 821 patients, HAdV was detected in 118 AGE cases (14.4%). During a period of 6 years, the HAdV detection rates for each year were relatively low at 3.7% and 0%, in 2017-2018, and 2020-2021, respectively. However, the detection rate increased to remarkably high rates, ranging from 13.3% to 27.3% in the other 4-year periods. Of these HAdV-positive strains, 83.1% were F41 genotypes and 16.9% were other genotypes (A31, B3, C1, C2/C6, and C5). Phylogenetic analyses of the nucleotide and deduced amino acid sequences of the full-length hexon gene demonstrated that HAdV-F41 strains were comprised of three clades, and each clade was distributed across the study period from 2017 to 2023. Analysis of deduced amino acid sequences of the hexon gene of the representative HAdV-F41 strains from each clade revealed numerous amino acid substitutions across hypervariable regions (HVRs) from HVR-1 to HVR-7, two insertions in HVR-1 and HVR-7, and two deletions in HVR-1 and HVR-2 of the hexon gene compared to those of the prototype strain, particularly, those of clade 3 HAdV-F41 strains. The findings suggested that the HAdV-F41 of each clade was stable, conserved, and co-circulated for over two decades in Japan.

Molecular analysis of adenovirus strains responsible for gastroenteritis in children, under five, in Tunisia

Purpose of work

Enteric Adenovirus (EAdV) is recognized as one of the most commonly identified agents responsible for severe acute gastroenteritis (AGEs) in the stools of infants.We sought to determine the rate of human adenovirus (HAdV) infections, and the genotypic characterization of circulating strains of HAdV in children under 5 years of age with AGEs in university and regional hospitals, located in the Center-East of Tunisia, from January 2014 to December 2016.

Methods

A classic PCR was performed on 582 stool samples taken within 5 days of the onset of symptoms. Chosen positive samples were sequenced, and some of the results were confirmed by the Next Generation Sequencing technique (NGS). Partial nucleotide sequences of the Hexon gene obtained in this study were compared with the NCBI GenBank database using BLAST. Multiple sequence alignment and phylogenetic analysis were conducted using MEGA6 software. The phylogenetic tree was generated using the maximum-likelihood method and bootstrap analysis was performed with 1000 replications.

Results

Out of 582 samples, 52 (8.93 %) cases were positive for HAdV, with a male predominance (57.4 %). Phylogenetic analyses showed that Tunisian HAdV strains clustered into five HAdV lineages corresponding to serotypes F41 (14/28), C2 (9/28), C5 (3/28), E4 (1/28), and A18 (1/28). HAdV was more frequent in children aged up to 12 months, as compared to the other age groups. The HAdV activity was noted in almost all the months of the year with a peak in autumn, in 2014 and 2015, and in winter in 2016.

Conclusion

This study showed that infections with HAdV species were frequent in children suffering from AGE with the predominance of HAdV F41 and C2. This result underlines the importance of regular monitoring of circulating genotypes, and it could be useful for future epidemiological research.

Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through computational lens

In the present study, we investigated the conformational dynamics of histo-blood group antigens (HBGAs) and their interactions with the VP8* domain of four rotavirus genotypes (P[4], P[6], P[19], and P[11]) utilizing all-atom molecular dynamics simulations in explicit water. Our study revealed distinct changes in the dynamic behavior of the same glycan due to linkage variations. We observed that LNFPI HBGA having a terminal β linkage shows two dominant conformations after complexation, whereas only one was obtained for LNFPI with a terminal α linkage. Interestingly, both variants displayed a single dominant structure in the free state. Similarly, LNT and LNnT show a shift in their dihedral linkage profile between their two terminal monosaccharides because of a change in the linkage from β(1-3) to β(1-4). The molecular mechanics generalized Born surface area (MM/GBSA) calculations yielded the highest binding affinity for LNFPI(β)/P[6] (-13.93 kcal/mol) due to the formation of numerous hydrogen bonds between VP8* and HBGAs. LNnT binds more strongly to P[11] (-12.88 kcal/mol) than LNT (-4.41 kcal/mol), suggesting a single change in the glycan linkage might impact its binding profile significantly. We have also identified critical amino acids and monosaccharides (Gal and GlcNAc) that contributed significantly to the protein-ligand binding through the per-residue decomposition of binding free energy. Moreover, we found that the interaction between the same glycan and different protein receptors within the same rotavirus genogroup influenced the micro-level dynamics of the glycan. Overall, our study helps a deeper understanding of the H-type HBGA and rotavirus spike protein interaction.Communicated by Ramaswamy H. Sarma.

Epidemiology of gastrointestinal infections: lessons learned from syndromic testing, Region Zealand, Denmark

The aim of this study was to investigate the value of syndromic diagnostic testing for a better understanding of the epidemiology of gastrointestinal infections in Denmark. Here we evaluated the QIAstat-Dx® Gastrointestinal (GI) Panel 1 assay on 18,610 fecal samples requested for analysis for enteric pathogens in Region Zealand, Denmark, in 1 year (October 1, 2021, to September 30, 2022). In total, 6905 (37%) samples were detected positive for one or more diarrhoeal bacteria, viruses, and protozoa. The most common bacterial, viral, and parasitic pathogens detected with the QIAstat-Dx® Gastrointestinal Panel 1 were EPEC (in patients ≥ 2 years of age) (n = 1420 (20.6%)), rotavirus (n = 948 (13.7%)), and Cryptosporidium spp. (n = 196 (2.84%)). We identified a large diversity in infections likely reflecting substantial differences in the epidemiology including origin of infections, mode of transmission, seasonality, age-dependent susceptibility to disease, severity, and travel history. All pathogens were detected as both single and coinfections. Viral infections peaked in March with a positive rate of 31.6%, and bacterial infections peaked in August with a positive rate of 35.3%. ETEC, Shigella/EIEC, EAEC, and P. shigelloides were most related to travel activity, and coinfections were frequent. The distribution of Ct values varied significantly between the pathogens, with the lowest Ct values (median 17-18) observed in astrovirus, adenovirus, and rotavirus. Our results highlight the value of providing extensive diagnostic testing on fecal samples for sufficient detection of relevant diarrhoeal pathogens for optimal clinical care.

Diverse genotypes of human enteric and non-enteric adenoviruses circulating in children hospitalized with acute gastroenteritis in Thailand, from 2018 to 2021

Human adenovirus (HAdV) is a common viral pathogen that causes diarrhea in children worldwide. The aim of this study was to investigate the prevalence and genotype diversity of HAdV strains circulating in children admitted to the hospitals with acute gastroenteritis (AGE) in Chiang Mai, Thailand, from 2018 to 2021. A total of 1,790 stool samples were screened for HAdV by PCR method, and 80 (4.5%) were positive for HAdV. Of these, children under 5 years of age accounted for 90.0% of HAdV-positive cases with the highest infection rate at the age group of 48-60 months old. The infection rate was not significantly different between boys and girls. The HAdV infection was detected sporadically throughout the year without a discrete seasonal pattern. Five species of both enteric and non-enteric HAdVs (A, B, C, E, and F) with 10 different genotypes, including HAdV-F41 (25.0%), HAdV-B3 (17.5%), HAdV-F40 (16.3%), HAdV-C1 (15.0%), HAdV-C5 (7.5%), HAdV-C2 (6.3%), HAdV-B7 (5.0%), HAdV-A12 (3.8%), HAdV-E4 (2.5%), and HAdV-B11 (1.3%), were detected in this study. In conclusion, our study reported the prevalence and seasonality of HAdV infection with a wide variety of HAdV genotypes circulating in children hospitalized with AGE during a period of 2018-2021 in Chiang Mai, Thailand. IMPORTANCE In the present study, the prevalence of human adenovirus (HAdV) infection in children with acute gastroenteritis (AGE) in Chiang Mai, Thailand, from 2018 to 2021 was detected at 4.5%. Diverse species and genotypes of HAdVs (HAdV-A12, HAdV-B3, HAdV-B7, HAdV-B11, HAdV-C1, HAdV-C2, HAdV-C5, HAdV-E4, HAdV-F40, and HAdV-F41) had been identified. The highest infection rate was found in children aged 48-60 months old. The HAdV infection was detected sporadically throughout the year. These findings imply that a wide variety of HAdV genotypes circulate in pediatric patients with AGE in Chiang Mai, Thailand.

Surveillance and epidemiological characterization of human adenovirus infections among outpatient children with acute gastroenteritis during the COVID-19 epidemic in Shanghai, China

BACKGROUND

Human adenovirus (HAdV) has been recognized as one of the common enteric viruses associated with acute gastroenteritis (AGE) in children. The aim of this study was carried out to illustrate the epidemiological characterization of HAdV Infections among children younger than 15 years in Shanghai during COVID-19.

METHODS

During May 2020 and April 2022, 1048 fecal samples were collected from children ≤ 15 years diagnosed with AGE in the Children's Hospital of Fudan University. HAdV was identified by PCR and sequenced with specific primers. All the obtained sequences were analyzed by MEGA (version 6.0). Demographic information and clinical features data were also collected and analyzed.

RESULTS

In total, 97 (9.3%, 97/1048) samples were detected to be HAdV during May 2020 and April 2022. We found an atypical upsurge in HAdV infection in the year 2021 after a major suppression in the year 2020. Approximately 84.5% (82/97) of HAdV-infected children were aged 0-60 months. Among the 97 HAdV-positive samples, only two species and five genotypes were detected. HAdV-F (88.7%, 86/97) was the most prevalent species and HAdV-F41 (87.6%, 85/97) was the most common genotype. Diarrhea, vomiting, and fever were the main clinical manifestations in children infected with HAdV. The children aged from 0 to 12 months showed simpler patterns of clinical presentation than those of children older than 13 months.

CONCLUSIONS

Our findings described the epidemiological changes of HAdV infection in children with AGE during the COVID-19, which further underscored the importance of continuous surveillance of HAdV at both local and global scales.

Enteric and non-enteric adenoviruses in children with acute gastroenteritis in Western India

Human adenoviruses (HAdVs) are the viral agents responsible for a wide spectrum of acute and chronic diseases. HAdVs are the most important etiological agents of acute gastroenteritis (AGE) and are identified as the major contributor to the deaths of diarrheal children globally. The significant rise in HAdV infections in rotavirus-vaccinated children documented in multiple studies demands continuous monitoring of HAdV strains. After the inclusion of rotavirus vaccines in the immunization schedule of India, public health research regarding prevalence, etiology, and risk factors is highly necessary for evidence-based policies and their implementation to sustain diarrhea prevention programs. In the present study, children admitted for AGE between 2013 and 2016 in seven different hospitals in Maharashtra and Gujrat states of Western India were subjected for investigation. HAdVs were found in 5.2% of the fecal specimens with the dominance of species-F (52.4%) strains, followed by the occurrence of non-enteric adenoviruses of species A (17.4%), C (11.4%), B (8.2%), and D (3.2%). The species-F strains were predominant in Ahmadabad (78.5%), Mumbai (61.5%), and Surat (57.1%) cities, followed by species-A strains. In Pune city, species B strains were detected in all HAdV patients, with none of the species A strains. Clinically, patients infected with enteric and non-enteric HAdV strains were indistinguishable. However, a high viral load was observed in species-F specimens as compared to non-species-F. The present study on fecal specimens collected in the pre-rotavirus vaccination era from hospitalized AGE patients will be important for future comparative analysis to know the exact impact of vaccination in children of Western India.

The role of viruses in human acute appendicitis: a systematic literature review

BACKGROUND

There have been debates about the human appendix function, and while previous research suggested it might be a vestigial organ with no functional significance, recent studies have pointed out that it might have an important role in the immune system. Acute appendicitis (AA) is a common cause of emergency abdominal surgery in the world. Some epidemiologic investigations have found an association between appendicitis and viral infections. In this study, we have reviewed systematically articles to discover viral infections that cause appendicitis and find any possible correlations between the two.

METHODS

This systematic review was performed by searching among electronic databases including Web of Science, PubMed, Scopus, and EMBASE on viruses and appendicitis topics.

RESULTS

Conducted search leads to 983 results in all databases after the duplicate removal and screening by title, abstract, and full-text based on inclusion criteria lead to 19 studies. There were several assays to detect the viruses, which are thought to be AA causative agents. RT-PCR and immunoassays were the mainstay methods to detect the probable cause.

CONCLUSION

Investigations suggested that some viruses including measles virus (MV), influenza virus, dengue fever virus (DFV), human immunodeficiency virus (HIV), human herpesviruses, rotavirus, and adenovirus are associated with acute appendicitis. Despite the available reports, the specific mechanisms behind the relationship between acute appendicitis and viral infections are yet to be understood. Therefore, further investigations are necessary to find out the pathogenesis and pathophysiology of viral complications in appendicitis.

Diagnosis of gastrointestinal infections: comparison between traditional microbiology and a commercial syndromic molecular-based panel

Traditional diagnosis of infectious gastroenteritis is based on culture, microscopy and antigen detection. The development of gastrointestinal syndromic panels based on molecular techniques have allowed rapid and simultaneous identification of multiple pathogens. The objective was to evaluate the implementation of Allplex™ Gastrointestinal Panel Assays (AGPA): Allplex™ GI-Virus, Allplex™ GI-Bacteria (I) and Allplex™ GI-Parasite by comparing with traditional diagnosis. A retrospective comparative study was conducted at Hospital Universitario La Paz, between the first year of implementation of the AGPA (April 1, 2018 to March 31, 2019) and the results obtained during the previous year with traditional methods (April 1, 2017 to March 31, 2018). With the implementation of AGPA we obtained an increase in the detection of rotavirus and adenovirus, being statistically significant for rotavirus ([CI95%:3.60-6.79]; P < 0.05) and an increase in the positivity rates of all the bacteria tested, with the exception of Salmonella spp. ([CI95%:3.60-6.79]; P < 0.05). Comparing the bacteria recovered by culture, we obtained an increase in the case of Shigella spp. cultivation during the AGPA period. Regarding protozoa, we achieved a significant increase in the positivity rates for Cryptosporidium spp. ([CI95%:1.98-3.01] P < 0.05), Giardia intestinalis ([CI95%:3.94-5.25]; P < 0.05) and Blastocystis spp. ([CI95%:9.44-11.36]; P < 0.05). There was an improvement in report turnaround time when comparing molecular diagnosis to bacterial culture and concentration plus microscopy for parasites; but not compared with antigen detection. The molecular diagnosis approach with AGPA were more sensitive and had a faster turnaround time for some targets, and in our setting, enabled an increased diagnostic capacity for viruses and protozoa.

Clinical and Epidemiologic Features of Viral Gastroenteritis in Hospitalized Children: An 11-Year Surveillance in Palermo (Sicily)

In order to acquire information regarding viral agents and epidemiologic features of severe paediatric Viral Acute Gastroenteritis (VAGE) across multiple seasons in the pre-rotavirus-vaccine era, the epidemiologic characteristics of VAGE were investigated among paediatric patients hospitalized in a major Sicilian paediatric hospital from 2003 to 2013. Overall, 4725 children were observed and 2355 (49.8%) were diagnosed with a viral infection: 1448 (30.6%) were found positive to rotavirus, 645 (13.7%) to norovirus, 216 (4.6%) to adenovirus, and 46 (0.97%) to astrovirus. Viral infections showed different patterns of hospitalization in terms of age at risk (younger for rotavirus and adenovirus infections), seasonality (increased risk in winter for rotavirus and norovirus), trend over time (reduced risk in 2011-2013 for norovirus and rotavirus) and major diagnostic categories (digestive diseases more frequent in adenovirus and astrovirus but not in norovirus). This study increases general knowledge of VAGE epidemiology and contributes to suggest some a priori diagnostic criteria that could help clinicians to identify and treat viral agents responsible for gastroenteritis in hospital settings.

Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region

Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.

Epidemiology of Human Adenovirus in Pakistani Children Hospitalized with Community-Acquired Gastroenteritis under the Age of Five Years

Acute gastroenteritis is the major cause of morbidity and mortality among infants and children around the globe. Along with other enteropathogens, human adenovirus (HadV) is a major etiological agent associated with diarrhea in young children. However, information about the epidemiology of Adenoviruses in Pakistan is limited or has not been reported. A total of 1082 stool samples were collected from patients with acute gastroenteritis under the age of five years with symptoms of diarrhea, vomiting, nausea, and abdominal cramps who visited Benazir Bhutto Hospital Rawalpindi and Children's hospital in Lahore of Punjab Province in Pakistan. Of this, 384 cases with no blood in their stool, negative for Rotavirus, and under the age of five years were recruited in this study. Human Adenoviruses were isolated in the human epithelial HEp-2 cell line. Furthermore, adenovirus antigen detection was carried out by an enzyme-linked immunosorbent assay (ELISA), and then all positive and negative samples were confirmed by nested PCR. After inoculating a clear stool supernatant on HEp-2 cell lines, we observed a positive cytopathic effect in 65 (16%) cases. Using an enzyme-linked immunosorbent assay, HAdV antigens were detected in 54 (14.06%) of the clear supernatant from gastroenteritis cases. However, HAdV hexon coding regions were amplified in 57 (14.80%) fecal samples, mainly from patients ≤24 months of age. The findings of this study suggest that adenovirus circulates significantly in the children population under the age of five years and may be the potential etiological factor of acute gastroenteritis in the mentioned cities. This study provides baseline data about the possible role of adenovirus in causing viral diarrhea in children. Further large-scale epidemiological surveys are recommended to better understand disease burden, etiological agents, and its clinical impact across the country.

Human enteric adenovirus F40/41 as a major cause of acute gastroenteritis in children in Brazil, 2018 to 2020

Human adenovirus (HAdV) types F40/41 have long been recognized as major viral agents of acute gastroenteritis (AGE) in children. Despite this, studies on HAdV molecular epidemiology are sparse, and their real impact is likely under-estimated. Thus, our goal was to investigate HAdV incidence, enteric and non-enteric types circulation, co-detections with rotavirus and norovirus and DNA shedding in stool samples from inpatients and outpatients from eleven Brazilian states. During the three-year study, 1012 AGE stool samples were analysed by TaqMan-based qPCR, to detect and quantify HAdV. Positive samples were genotyped by partial sequencing of the hexon gene followed by phylogenetic analysis. Co-detections were accessed by screening for rotavirus and norovirus. Overall, we detected HAdV in 24.5% of single-detected samples (n = 248), with a prevalence of type F41 (35.8%). We observed a higher incidence in children between 6 to 24 months, without marked seasonality. Additionally, we observed a statistically higher median viral load among single-detections between enteric and non-enteric types and a significantly lower HAdV viral load compared to rotavirus and norovirus in co-detections (p < 0.0001). Our study contributes to the knowledge of HAdV epidemiology and reinforces the need for the inclusion of enteric types F40/41 in molecular surveillance programs.

Viral pathogens of acute gastroenteritis in Egyptian children: role of the parechovirus

BACKGROUND AND AIM

Human parechovirus (HPeV) has emerged as a pathogen associated with acute gastroenteritis (AGE).

AIM

To detect the presence of HPeV in the stool samples from Egyptian children with AGE seeking care and the possibility of its co-infection with other enteric viruses.

METHODOLOGY

One hundred stool samples were collected from children attending Mansoura University Children's Hospital with AGE. HPeV and astrovirus were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). At the same time, detection of rotavirus antigen and norovirus was achieved by enzyme-linked immunosorbent assay and rapid immunochromatographic method, respectively.

RESULTS

The most frequently detected virus was rotavirus (39%), followed by norovirus (27%), HPeV (19%), and astrovirus (12%). Interestingly, the single infection with HPeV was 5%. Among the 19 HPeV positive samples, the co-infection of HPeV with other enteric viruses was detected in 9(43.9%) for rotavirus, 7(36.8%) for norovirus, 2(10.5%) for astrovirus, in 3(15.8%) for rotavirus and norovirus and 1(5.3%) for norovirus and astrovirus. Regarding the clinical presentation, there was no significant difference between children infected with HPeV alone and those infected with viruses other than HPeV alone; fever (p = 0.3), vomiting (p = 0.12), abdominal pain (p = 0.12), and grades of severity (P = 0.82). HPeV alone infected children were of mild severity (60%), and their main presenting symptom was fever (60%).

CONCLUSIONS

Detection of HPeV as a single viral pathogen in the stool of some children with AGE showed that this virus could be a causative agent of AGE in Egyptian children. Therefore, HPeV could be included as one of the viruses screened for AGE diagnosis in children in Egypt.

Mutations in AR or SRD5A2 Genes: Clinical Findings, Endocrine Pitfalls, and Genetic Features of Children with 46,XY DSD

OBJECTIVE

Androgen insensivity syndrome (AIS) and 5α-reductase deficiency (5α-RD) present with indistinguishable phenotypes among the 46,XY disorders of sexual development (DSD) that usually necessitate molecular analyses for the definitive diagnosis in the prepubertal period. The aim was to evaluate the clinical, hormonal and genetic findings of 46,XY DSD patients who were diagnosed as AIS or 5α-RD.

METHODS

Patients diagnosed as AIS or 5α-RD according to clinical and hormonal evaluations were investigated. Sequence variants of steroid 5-α-reductase type 2 were analyzed in cases with testosterone/dihydrotestosterone (T/DHT) ratio of ≥20, whereas the androgen receptor (AR) gene was screened when the ratio was <20. Stepwise analysis of other associated genes were screened in cases with no causative variant found in initial analysis. For statistical comparisons, the group was divided into three main groups and subgroups according to their genetic diagnosis and T/DHT ratios.

RESULTS

A total of 128 DSD patients from 125 non-related families were enrolled. Birth weight SDS and gestational weeks were significantly higher in 5α-RD group than in AIS and undiagnosed groups. Completely female phenotype was higher in all subgroups of both AIS and 5α-RD patients than in the undiagnosed subgroups. In those patients with stimulated T/DHT <20 in the prepubertal period, stimulated T/DHT ratio was significantly lower in AIS than in the undiagnosed group, and higher in 5α-RD. Phenotype associated variants were detected in 24% (n=18 AIS, n=14 5α-RD) of the patients, revealing four novel AR variants (c.94G>T, p.Glu32*, c.330G>C, p.Leu110=; c.2084C>T, p.Pro695Leu, c.2585_2592delAGCTCCTG, p.(Lys862Argfs*16), of these c.330G>C with silent status remained undefined in terms of its causative effects.

CONCLUSION

T/DHT ratio is an important hormonal criterion, but in some cases, T/DHT ratio may lead to diagnostic confusion. Molecular diagnosis is important for the robust diagnosis of 46,XY DSD patients. Four novel AR variants were identified in our study.

Polymerase Chain Reaction Study of Human Bocavirus in Children with Acute Gastroenteritis

Aim:

The present study aimed to detect Human bocavirus (HBoV) in stool samples from young children below 5 years complaining of acute gastroenteritis (GE) in addition to detection of rotavirus, norovirus, and astrovirus.

Methods:

The study included 90 children below 5 years with acute GE with excluded bacterial pathogens. The determination of the presence of HBoV was performed by nested polymerase chain reaction (PCR) beside determination of astrovirus and norovirus by multiplex PCR and rotavirus antigen by enzyme-linked immunosorbent assay (ELISA).

Results:

The most prevalent virus among the studied viruses was rotavirus (33.3%) detected by ELISA for antigen in the stool. The other three viruses detected by molecular methods were bocavirus (14.4%), astrovirus (13.3%), and norovirus (10%). Mixed viral infection with two or more viruses was detected in 16 children (17.8%). The most common was bocavirus and rotavirus in 6 patients (37.5%). In the study of demographic and clinical presentations of the children with HBoV, the affected children were mainly females, i.e., 10 (76.9%), from rural residence i.e., 11 (84.6%) with the mild classification of GE in 7 children (53.8%) and moderate GE in 6 children (46.2%) and none of them had severe GE. Fever was the most common presenting sign in those children (53.8%) followed by vomiting (46.2%).

Conclusion:

The study highlights the existence of HBoV in children with acute GE under the age of five. The infection associated with this virus was either mild or moderate in severity. The combined viral infection was common especially associated with rotavirus. There is a need for further additional study to identify the type of the circulated strain of bocavirus and the confections with other pathogens.

Prevalence and seasonal pattern of enteric viruses among hospitalized children with acute gastroenteritis in Samawah, Iraq

Almost all of the deaths happening under the age of 5 occur in the developed countries of Africa and Asia. This study included children admitted to the surgical care, aged 6 months to 5 years, who suffered from acute gastroenteritis and received treatment at Samawah, Iraq, from December 2018 to December 2019. Test results detected different types of rotaviruses, adenoviruses, astroviruses using ELISA. 56.6% of the infections were attributed to a viral pathogen. The main cause was attributed to rotavirus and adenovirus. The causative agents of diarrheal diseases in 28.1% of cases are rotaviruses, in 17.05% – adenoviruses, in 11.43% – astroviruses. Viral mono-infections are detected more often than mixed infections. Viral intestinal infections are characterized by seasonality and rise in the cold season, with a peak incidence of rotavirus infection in April, adenovirus infection in November, and astrovirus infection in December.

Low Frequency of Adenovirus, Rotavirus, and Norovirus in Pediatric Diarrheal Samples from Central Iran

Background: Acute viral gastroenteritis is a disorder that affects children globally but mostly in developing countries. Adenoviruses, rotaviruses, and noroviruses are the leading viral causes of childhood gastroenteritis. Objectives: This study is the first to investigate the frequency of these viruses in diarrheal samples from pediatric patients living in central Iran. Methods: A total of 173 samples of pediatric diarrhea, from May 2015 to May 2016, were included in this descriptive cross-sectional study. The samples were analyzed using in-house developed PCR and reverse transcription (RT)-PCR methods to investigate the frequency of adenoviruses, rotaviruses, and noroviruses. Results: Out of 173 samples of pediatric diarrhea, eight were shown to contain enteric viruses (4.6%): (1) four with adenoviruses (2.3%); (2) three with rotaviruses (1.7%); and (3) one with a genogroup II norovirus (0.6%). Most of the positive samples were obtained from children under the age of seven. The most common additional clinical symptoms in pediatric patients with viral agents were fever, vomiting, and abdominal pain. Conclusions: In central Iran, adenoviruses and rotaviruses were rarely found as agents responsible for gastroenteritis. Although viral gastroenteritis in this area had less frequency than bacterial gastroenteritis, we need to monitor all enteropathogenic agents for longer periods to understand better real endemicity and the possibility of unexpected viral enteritis outbreaks.

Nosocomial acute gastroenteritis outbreak caused by an equine-like G3P[8] DS-1-like rotavirus and GII.4 Sydney[P16] norovirus at a pediatric hospital in Rio de Janeiro, Brazil, 2019

Worldwide, rotavirus (RVA) and norovirus are considered major etiological agents of acute gastroenteritis (AGE) in pediatric population admitted to hospitals. This study describes the investigation of nosocomial infections caused by emergent RVA and norovirus strains reported at a pediatric hospital in southern Brazil in May 2019. This outbreak affected 30 people among children and adults. Nine stool samples (eight children and one nurse) were obtained and analyzed by RT-qPCR to detect and quantify RVA and norovirus. Positive samples were genotyped by sequencing and subjected to phylogenetic analysis. We detected RVA in 44.4% (4/9) and norovirus in 55.5% (5/9) at high viral loads, ranging from 3.5 × 10⁷ to 6.1 × 10⁷ and 3.2 × 10² to 3.2 × 10⁹ genome copies/g of stool, respectively. Co-infections were not observed. RVA VP4 and VP7 gene sequencing in combination with polyacrylamide gel electrophoresis identified the circulation of equine-like G3P[8] DS-1-like, and the partial sequencing of the other nine genes revealed that strains possessed I2-R2-C2-M2-A2-N1-T2-E2-H2 genotype background. The emergent recombinant norovirus variant, GII.4 Sydney[P16], was identified by ORF1-2 sequencing. Active surveillance and effective prevention measures should be constantly reinforced to avoid the spread of nosocomial viral infections into hospitals, which could severely affect pediatric patients admitted with underlying health conditions.

Human Astrovirus Outbreak in a Daycare Center and Propagation among Household Contacts

We investigated an outbreak of acute gastroenteritis due to human astrovirus in a daycare center, describing the transmission mechanism, the most affected age groups, conditioning factors and the extent of the outbreak among household contacts of the daycare center attenders. Data were collected from persons exposed at the daycare center and their home contacts. Fecal samples from affected and non-affected daycare center attenders were analyzed for viruses causing acute gastroenteritis by RT-PCR. The percentage of households affected and the attack rates (AR) were calculated. The attack rates were compared using the rate ratio (RR) with 95% confidence intervals. Information was obtained from 245 people (76 attenders and 169 contacts) of whom 49 were clinical cases. Five HAstV-4, two HAstV-8 and three non-typable HAstV cases were identified (six from clinical cases and four from asymptomatic infected people). The global AR was 20% (41.2% in children aged < 2 years). Data were obtained from 67 households: 20 households of affected attenders and 47 of non-affected attendees. Household contacts of affected attenders had a higher AR (74.3%) than that of non-affected attendees (2.4%). We found asymptomatic infections amongst daycare attendees. The transmission of HAstV during the outbreak was not limited to the daycare center but extended to household contacts of both affected and non-affected attenders.

Prevalence and Distribution of Rotavirus Genotypes Among Children With Acute Gastroenteritis in Areas Other Than Java Island, Indonesia, 2016-2018

Group A rotaviruses (RVAs) are the leading cause of acute gastroenteritis, which is often associated with severe symptoms in children under 5 years old. Genetic reassortments and interspecies transmission commonly occur, resulting in a great diversity of RVA circulating in the world. The aim of this study is to determine the prevalence and distribution of RVA genotypes among children in Indonesia over the years 2016–2018 across representative areas of the country. Stool samples were collected from 202 pediatric patients with acute gastroenteritis in three regions of Indonesia (West Nusa Tenggara, South Sumatra, and West Papua) in 2016–2018. Rotavirus G and P genotypes were determined by reverse transcription PCR (RT-PCR) and direct sequencing analysis. The prevalences of RVA in South Sumatra (55.4%) and West Papua (54.0%) were significantly higher than that in East Java (31.7%) as determined in our previous study. The prevalence in West Nusa Tenggara (42.6%) was the lowest among three regions, but higher than that in East Java. Interestingly, equine-like G3 rotavirus strains were found as predominant strains in South Sumatra in 2016 and in West Papua in 2017–2018. Moreover, the equine-like G3 strains in South Sumatra detected in 2016 were completely replaced by human G1 and G2 in 2018. In conclusion, RVA infection in South Sumatra and West Papua was highly endemic. Equine-like G3 strains were also spread to South Sumatra (West Indonesia) and West Papua (East Indonesia), as well as Java Island. Dynamic change in rotavirus genotypes from equine-like G3 to human genotypes was also observed. Continuous monitoring may be warranted in isolated areas in Indonesia.

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

Effect of rotavirus vaccine implementation on the prevalence of coinfections with enteric viruses in Norway

Acute gastroenteritis (AGE) is a common illness in both adults and children worldwide and is caused by several microorganisms including viruses, bacteria, and parasites. Rotavirus (RV), which is the main cause of AGE, can occur as a mixed infection with other viruses. The aim of this study is to assess the molecular epidemiology of viral enteric viruses and assess RV coinfections with other enteric viruses and their influence on disease severity before and after RV vaccine introduction in children under 5 years of age. A total of 600 samples collected from children hospitalized for AGE in five large hospitals in Norway, and were analyzed for viral gastroenteritis agents by enzyme immunoassay and quantitative real-time polymerase chain reaction (qRT-PCR). Positive results confirmed either by Sanger sequencing or genotyped by multiplex semi-nested RT-PCR. In total, 243 of the 300 (81%) samples, collected from the prevaccine cohort, were positive for at least one of the four viruses tested in this study. RV was most frequently identified in 82.6% of the samples. In the postvaccine cohort, 114 of the 300 (38%) samples were positive for at least one of the viruses tested. RV found in 36.5% of the samples. Coinfections found less frequently in the postvaccine cohort. Among circulating enteric viruses in Norway, RV is the most important cause of viral gastrointestinal infection. As expected, there were fewer RV positive and fewer coinfections after RV vaccine implementation. The results provide valuable data that can aid in further evaluation of the vaccine impact.

Hospital-acquired rotavirus acute gastroenteritis in 10 consecutive seasons in Umbria (Italy)

Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young (aged <5 years) children. Several studies showed that RVA is one of the main cause of nosocomial gastroenteritis in hospitalized pediatric population worldwide, with an incidence ranging from 8 to 33 cases per 100 hospitalized children. Nosocomial infections, in which AGE symptoms develop at least 2 days after admission, may severely affect children already admitted to hospital for other causes. This study aimed to define the trends of the RVA genotypes through statistical analysis of the data obtained by the rotavirus surveillance in Umbria in 10 consecutive seasons, from 2007-2008 to 2016-2017, with update information on hospital-acquired RVA AGE. During RVA gastroenteritis surveillance in Umbria (Italy) in 2007 to 2017, a total of 741 RVA positive faecal samples were collected from children hospitalized with AGE, and RVA strains were genotyped following standard EuroRotaNet protocols. Of the 741 analyzed samples, 75 (10%) were reported to be hospital-acquired. Comparing the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections, we observed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community except in 2010 to 2011, 2011 to 2012, and 2012 to 2013 when G1P[8], G4P[8] and the novel strain G12P[8] caused a large community- and hospital-acquired outbreak. Of the 741 analyzed samples, 75 (10%) were reported to be hospital-acquired. Comparing the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections, we observed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community except in 2010 to 2011, 2011 to 2012, and 2012 to 2013 when G1P[8], G4P[8], and the novel strain G12P[8] caused a large community- and hospital-acquired outbreak. The information from this study will be useful to implement guidelines for preventing nosocomial RVA AGE, which should include an improved management of the hospitalized patients and an increase in vaccination coverage.

Viral gastroenteritis in Tocantins, Brazil: characterizing the diversity of human adenovirus F through next-generation sequencing and bioinformatics

Human enteric adenovirus species F (HAdV-F) is one of the most common pathogens responsible for acute gastroenteritis worldwide. Brazil is a country with continental dimensions where continuous multiregional surveillance is vital to establish a more complete picture of the epidemiology of HAdV-F. The aim of the current study was to investigate the molecular epidemiology of HAdV-F using full-genome data in rural and low-income urban areas in northern Brazil. This will allow a genetic comparison between Brazilian and global HAdV-F strains. The frequency of HAdV-F infections in patients with gastroenteritis and molecular typing of positive samples within this period was also analysed. A total of 251 stool samples collected between 2010 and 2016 from patients with acute gastroenteritis were screened for HAdV-F using next-generation sequencing techniques. HAdV-F infection was detected in 57.8 % (145/251) of samples. A total of 137 positive samples belonged to HAdV-F41 and 7 to HAdV-F40. HAdV-F40/41 dual infection was found in one sample. Detection rates did not vary significantly according to the year. Single HAdV-F infections were detected in 21.9 % (55/251) of samples and mixed infections in 37.4 % (94/251), with RVA/HAdV-F being the most frequent association (21.5 %; 54/251). Genetic analysis indicated that the HAdV-F strains circulating in Brazil were closely related to worldwide strains, and the existence of some temporal order was not observed. This is the first large-scale HAdV-F study in Brazil in which whole-genome data and DNA sequence analyses were used to characterize HAdV-F strains. Expanding the viral genome database could improve overall genotyping success and assist the National Center for Biotechnology Information (NCBI)/GenBank in standardizing the HAdV genome records by providing a large set of annotated HAdV-F genomes.

Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis

Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.

Strain-Specific Probiotic Properties of Bifidobacteria and Lactobacilli for the Prevention of Diarrhea Caused by Rotavirus in a Preclinical Model

Probiotic supplementation with different lactobacilli and bifidobacterial strains has demonstrated beneficial effects in infectious diarrhea caused by rotavirus (RV) in young children. Preclinical models of RV infection might be a good strategy to screen for the efficacy of new probiotic strains or to test their comparative efficacy. Neonatal Lewis rats were supplemented with Bifidobacterium breve M-16V, Lactobacillus acidophilus NCFM, Lactobacillus helveticus R0052, or Lactobacillus salivarius PS2 from days 2–14 of life. On day five, animals received RV SA-11 orally. Fecal samples were collected daily, weighed, and scored for the calculation of severity and incidence of diarrhea. In addition, fecal pH and fecal viral shedding were measured. Animals were sacrificed at the end of the study and their blood was obtained for the quantification of RV-specific immunoglobulins. RV infection was induced in ~90% of the animals. All probiotics caused a reduction of several clinical variables of severity and incidence of diarrhea, except L. salivarius PS2. L. acidophilus NCFM, B. breve M-16V, and L. helveticus R0052 seemed to be very effective probiotic strains. In addition, all Lactobacillus strains reduced the viral elimination one day post-inoculation. No differences were detected in the specific anti-RV humoral response. The present study highlights the strain-specific effects of probiotics and identifies promising probiotics for use in ameliorating and preventing RV-induced diarrhea in children, for example by including them in infant formulas.

An Effective Platform for Exploring Rotavirus Receptors by Bacterial Surface Display System

Rotavirus (RV) is a major foodborne pathogen. For RV prevention and control, it is a key to uncover the interaction mechanism between virus and its receptors. However, it is hard to specially purify the viral receptors, including histo-blood group antigens (HBGAs). Previously, the protruding domain protein (P protein) of human norovirus (genotype II.4) was displayed on the surface of Escherichia coli, and it specifically recognized and captured the viral ligands. In order to further verify the feasibility of the system, P protein was replaced by VP8* of RV (G9P[8]) in this study. In the system, VP8* could be correctly released by thrombin treatment with antigenicity retaining, which was confirmed by Western blot and Enzyme-Linked Immunosorbent Assays. Type A HBGAs from porcine gastric mucin (PGM) were recognized and captured by this system. From saliva mixture, the captured viral receptor bound with displayed VP8* was confirmed positive with monoclonal antibody against type A HBGAs. It indicated that the target ligands could be easily separated from the complex matrix. These results demonstrate that the bacterial surface display system will be an effective platform to explore viral receptors/ligands from cell lines or food matrix.

Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens

CONTEXT.—

Infectious gastroenteritis is caused by various pathogens, including bacteria, viruses, and parasites.

OBJECTIVE.—

To compare the performance of Seegene Allplex Gastrointestinal (24 targets: 13 bacteria, 5 viruses, and 6 parasites in 4 panels), Luminex xTAG Gastrointestinal Pathogen Panel (15 targets: 9 bacteria, 3 viruses, and 3 parasites), and BD MAX Enteric panel (5 bacteria and 3 parasites). We estimated the agreement among 3 molecular assays.

DESIGN.—

A total of 858 stool samples (554 bacterial/parasite and 304 viral pathogens) were included. A consensus positive/negative was defined as concordant results from at least 2 tests. To evaluate the agreement among the assays, κ value was calculated.

RESULTS.—

The overall positive percentage agreements of Seegene, Luminex, and BD MAX were 94% (258 of 275), 92% (254 of 275), and 78% (46 of 59), respectfully. For Salmonella, Luminex showed low negative percentage agreement because of frequent false positives (n = 31) showing low median fluorescent intensity. For viruses, positive/negative percentage agreements of Seegene and Luminex were 99%/96% and 93%/99%, respectively. Compared with routine microbiology testing, Seegene, Luminex, and BD MAX additionally identified 39, 40, and 12 pathogens, respectively. Sixty-one cases (16 cases with Seegene, 51 cases with Luminex, and 1 case with BD MAX) showed positive results for multiple pathogens, but only 3 were consensus positive.

CONCLUSIONS.—

These multiplex molecular assays appear to be promising tools for the detection and identification of multiple gastrointestinal pathogens simultaneously. However, careful interpretation of positive results for multiple pathogens is required.

Co-Infection by Waterborne Enteric Viruses in Children with Gastroenteritis in Nepal

Enteric viruses are highly contagious and a major cause of waterborne gastroenteritis in children younger than five years of age in developing world. This study examined the prevalence of enteric virus infection in children with gastroenteritis to identify risk factors for co-infections. In total, 107 stool samples were collected from patients with acute gastroenteritis along with samples of their household drinking water and other possible contamination sources, such as food and hand. The presence of major gastroenteritis-causing enteric virus species (group A rotaviruses, enteroviruses, adenoviruses, and noroviruses of genogroup I) in stool and water samples was examined using quantitative polymerase chain reaction. Among the 107 stool samples tested, 103 (96%) samples contained at least one of the four tested enteric viruses, and the combination of group A rotaviruses and enteroviruses was the most common co-infection (52%, n = 54/103). At least one viral agent was detected in 16 (16%) of 103 drinking water samples. Identical enteric viruses were detected in both the stool and water samples taken from the same patients in 13% of cases (n = 13/103). Group A rotaviruses were most frequently found in children suffering from acute diarrhea. No socio-demographic and clinical factors were associated with the risk of co-infection compared with mono-infection. These less commonly diagnosed viral etiological agents in hospitals are highly prevalent in patients with acute gastroenteritis.

Viral gastroenteritis among children of 0-5 years in Nigeria: Characterization of the first Nigerian aichivirus, recombinant noroviruses and detection of a zoonotic astrovirus

BACKGROUND

Viruses are the leading cause of acute gastroenteritis in children worldwide. Understanding of the occurrence and genetic diversity of these viruses can help to prevent infections.

OBJECTIVES

The present study describes the presence, genetic diversity and possible recombination of five enteric viruses in children with gastroenteritis in Southwestern Nigeria.

STUDY DESIGN

From August 2012 to December 2013, stool samples and sociodemographic data of 103 diarrheic children <5 years were collected to detect and characterize rotavirus A, norovirus, human astrovirus, aichivirus and sapovirus using PCR techniques followed by sequencing and phylogenetic analyses.

RESULTS

At least one virus was identified in 58.3% (60/103) of the stool samples. Rotavirus, norovirus and astrovirus were detected in 39.8% (41/103), 10.7% (11/103), and 6.8% (7/103) respectively. Notably, aichivirus was detected for the first time in Nigeria (1/103; 0.97%). Sapovirus was not detected in the study. Co-infections with rotavirus were observed in eight samples either with norovirus or astrovirus or aichivirus. Phylogenetic analyses of different genome regions of norovirus positive samples provided indication for recombinant norovirus strains. A novel astrovirus strain closely related to canine astrovirus was identified and further characterized for the first time.

CONCLUSIONS

Viruses are the common cause of acute gastroenteritis in Nigerian infants with rotavirus as most frequently detected pathogen. New norovirus recombinants and a not yet detected zoonotic astrovirus were circulating in Southwestern Nigeria, providing new information about emerging and unusual strains of viruses causing diarrhea.

Clinical relevance of enteropathogen co-infections in preschool children-a population-based repeated cross-sectional study

OBJECTIVES

This study aimed to (i) determine risk factors for enteropathogen co-infections, (ii) determine whether enteropathogen co-infections influence gastroenteritis risk, and (iii) determine whether enteropathogen co-infection occurred randomly in preschool children.

METHODS

A monthly-repeated cross-sectional survey in Dutch children aged 0-48 months was conducted during October 2012 to October 2014. A total of 981 stool samples were collected along with questionnaires collecting data on gastrointestinal symptoms and potential risk factors; 822 samples were successfully tested for 19 enteropathogens using real-time multiplex PCRs. Logistic regression analysis assessed co-infections in relation to gastroenteritis and potential risk factors.

RESULTS

In all, 598/822 (72.7%) stool samples tested positive for at least one enteropathogen, of which 290 (48.5%) were positive for two or more enteropathogens. Risk factors for two or more enteropathogen co-infections were young age (<12 months, OR 1.9, 95% CI 1.1-3.3; 13-36 months, OR 1.7, 95% CI 1.1-2.5, versus 37-48 months), day-care attendance (OR 1.8, 95% CI 1.3-2.5), households with three or more children versus those with one child (OR 1.7, 95% CI 1.1-2.8). Stool samples collected in spring less often had two or more enteropathogens versus summer (OR 0.4, 95% CI 0.2-0.7). Food allergy was a risk factor for three or more enteropathogen co-infections (OR 3.2, 95% CI 1.1-8.9). The frequency of co-infection was higher than expected for norovirus GI/norovirus GII, Clostridium difficile/norovirus GI, C. difficile/rotavirus, astrovirus/Dientamoeba fragilis, atypical enteropathogenic Escherichia coli/adenovirus, typical enteropathogenic E. coli/adenovirus, and enteroaggregative E. coli/astrovirus. No co-infection was associated with increased gastroenteritis risk.

CONCLUSIONS

Risk factors for enteropathogen co-infections were identified and specific enteropathogens co-occurred significantly more often than expected by chance. Enteropathogen co-infections were not associated with increased gastroenteritis risk, calling into question their clinical relevance in preschool children.

A Multiplex PCR/LDR Assay for Viral Agents of Diarrhea with the Capacity to Genotype Rotavirus

Rotavirus and noroviruses are major causes of diarrhea. Variable rotavirus vaccination efficacy in Africa and Asia is multifactorial, including the diversity of circulating strains and viral co-infection. We describe a multiplexed assay that detects and genotypes viruses from stool specimens. It includes a one-step reverse transcriptase PCR reaction, a ligase detection reaction (LDR), then hybridization of fluorescent products to micro-beads. In clinical samples it detects rotavirus, caliciviruses (sapovirus and norovirus), mixed infections, and genotypes or genogroups of rotaviruses and noroviruses, respectively. The assay also has the capacity to detect hepatitis A. The assay was validated on reference isolates and 296 stool specimens from the US and Ghana. The assay was 97% sensitive and 100% specific. The genogroup was concordant in 100% of norovirus, and the genotype in 91% and 89% of rotavirus G- and P-types, respectively. Two rare rotavirus strains, G6P[6] and G6P[8], were detected in stool specimens from Ghana. The high-throughput assay is sensitive, specific, and may be of utility in the epidemiological surveillance for rare and emerging viral strains post-rotavirus vaccine implementation.

Molecular Detection of Human Astrovirus in Children With Gastroenteritis, Northern Italy

BACKGROUND

Human astroviruses have increasingly been identified and are important agents of diarrheal disease, especially in infants and young children. This article presents the real-time polymerase chain reaction TaqMan assay for the detection and quantification of human astrovirus for clinical fecal samples collected from hospitalized children with acute gastroenteritis in Piedmont (northern Italy) from December 2014 to November 2015.

METHODS

A total of 159 fecal specimens from hospitalized children with acute gastroenteritis, previously screened for rotavirus, adenovirus, norovirus, human parechovirus, salivirus and sapovirus, were tested for human astrovirus.

RESULTS

The most commonly detected virus was norovirus GII (33.8%), followed by rotavirus (21.3%), sapovirus (10.9%), human parechovirus (8%), norovirus GI (6.7%), adenovirus (1%) and salivirus (0.52%). A total of 30 of 159 (18.87%) episodes of acute gastroenteritis were associated with human astrovirus genomic detection.

CONCLUSIONS

Our data showed that the detection rate of astrovirus in diarrheal children (18.87%) was higher than observed in other countries, where they were reported in diarrheal children in 10.3%-0.8% of patients and a mean incidence worldwide of 11%. Our data showed that the detection rate of astrovirus in pediatric gastroenteritis was greater than previously reported in Italy.

Clinical and Epidemiologic Profiles for Identifying Norovirus in Acute Gastroenteritis Outbreak Investigations

BACKGROUND

Noroviruses are the leading cause of acute gastroenteritis (AGE) outbreaks in the United States. However, outbreaks attributed to norovirus often lack confirmation by diagnostic testing. Clinical and epidemiologic profiles, such as the Kaplan criteria (vomiting in >50% cases, mean incubation period of 24-48 hours, mean duration of illness for 12-60 hours, and negative bacterial stool culture), have been used to distinguish norovirus outbreaks from those caused by bacteria.

METHODS

Kaplan criteria were evaluated among 10 023 outbreaks reported to the National Outbreak Reporting System (NORS) during 2009-2012. An alternate profile for distinguishing norovirus outbreaks from outbreaks caused by nonviral etiologies was identified using classification and regression tree (CART) modeling. Performance of the Kaplan criteria and alternate profile were compared among laboratory-confirmed outbreaks.

RESULTS

The Kaplan criteria were 63.9% sensitive and 100% specific in discriminating norovirus from nonviral outbreaks, but only 3.3% of norovirus and 1.2% of nonviral outbreaks reported all criteria. Clinical and epidemiologic characteristics identified with CART modeling (ratio of proportion of cases with fever to the proportion of cases with vomiting <1, proportion of cases with bloody stool <0.1, proportion of cases with vomiting ≥0.26) were 85.7% sensitive and 92.4% specific for distinguishing norovirus from nonviral outbreaks and were applicable to more than 8 times as many outbreaks compared with the Kaplan criteria.

CONCLUSIONS

Compared with the Kaplan criteria, the CART-derived profile had higher sensitivity and broader application in reported AGE outbreaks. Thus, this alternate profile may provide a more useful tool for identifying norovirus during outbreak investigations.

Co-circulation of classic and novel astrovirus strains in patients with acute gastroenteritis in Germany

OBJECTIVES

In order to analyze the molecular epidemiology of human astroviruses (HAstV) in Germany, a retrospective long-term study was performed to characterize circulating human astrovirus in patients with acute gastroenteritis in Germany.

METHODS

A total of 2877 stool samples, collected between January 2010 and December 2015 from sporadic cases and outbreaks of acute gastroenteritis were retrospectively analyzed for astrovirus. A two-step PCR algorithm was developed and used to identify and characterize human astrovirus infections.

RESULTS

Overall, 143 samples were astrovirus-positive (5.0%). Astrovirus infection was most frequently detectable in samples from children of 3-4 years (15%) followed by children of 1-2 years (8.6%), detection rates in adults were lower (1%-3.6%). A high number (71.3%) of co-infections, mainly with noro- or rotaviruses, were identified. Genotyping revealed that at least ten genotypes from all four human MAstV species were circulating in the study population. HAstV-1 was predominant in different age groups. Novel HAstV (MLB and VA genotypes) were also circulating in Germany.

CONCLUSION

Our findings give new insights into the circulation and genetic diversity of human astroviruses in patients with acute gastroenteritis. The novel HAstV-MLB and -VA genotypes could be characterized firstly in Germany while the analysis showed that these viruses have been dispersed in Germany since 2011 as a causative agent of acute gastroenteritis.

Detection of enteric- and non-enteric adenoviruses in gastroenteritis patients, Bangladesh, 2012-2015

Human adenoviruses (HAdVs) are common cause of nonbacterial acute gastroenteritis worldwide. Limited data exist on HAdVs molecular epidemiology associated with acute gastroenteritis in Bangladesh. We describe the genetic diversity and epidemiology of HAdVs among hospitalized diarrhea patients, including HAdV genotypes, clinical symptoms, and co-infecting enteric pathogens. Stool samples were collected from ongoing diarrhea surveillance during 2012-2015. HAdV was detected using PCR and genotyped by sequencing and phylogenetic analysis. Detailed socio-demographic and clinical information regarding each individual was recorded such as duration of diarrhea, dehydration status, vomiting, abdominal pain, fever, and severity. Of 871 fecal specimens, HAdV DNA was detected in 93 (10.7%). Among them 56% were co-infected with other known enteric viral and bacterial pathogens and 31.6% had severe gastroenteritis. The majority (55%) of HAdV positives were children <5 years of age. Two main clinical symptoms in HAdV infected patients were diarrhea and vomiting. HAdVs were detected throughout the year with low prevalence in winter (November-January). Five HAdV species (A, B, C, D, and F) including 17 different genotypes were identified during the study period, with enteric HAdV species F (HAdV-40/41) being the most dominant. However, non-enteric HAdV were also detected in substantial proportion of specimens (15% species C, 15% species D, 10.8% species A, and 4.3% species B). Our study demonstrates high genetic diversity of HAdVs including enteric and non-enteric HAdVs among diarrhea patients and provides a foundation for further clarification of the role of non-enteric HAdVs in diarrheal diseases.

Real-time RT-PCR, a necessary tool to support the diagnosis and surveillance of rotavirus in Mexico

Rotavirus produces diarrhea in children under 5 years old. Most of those conventional methods such as polyacrylamide gel electrophoresis (PAGE) and reverse transcription-polymerase chain reaction (RT-PCR) have been used for rotavirus detection. However, these techniques need a multi-step process to get the results. In comparison with conventional methods, the real-time RT-PCR is a highly sensitive method, which allows getting the results in only one day. In this study a real-time RT-PCR assay was tested using a panel of 440 samples from patients with acute gastroenteritis, and characterized by PAGE and RT-PCR. The results show that the real-time RT-PCR detected rotavirus from 73% of rotavirus-negative samples analyzed by PAGE and RT-PCR; thus, the percentage of rotavirus-positive samples increased to 81%. The results indicate that this real-time RT-PCR should be part of a routine analysis, and as a support of the diagnosis of rotavirus in Mexico.

Detection of 23 Gastrointestinal Pathogens Among Children Who Present With Diarrhea

BACKGROUND

Diarrheal diseases are a major cause of ambulatory care visits and hospitalizations among children. Because of overlapping signs and symptoms and expensive and inefficient testing methods, the etiology of pediatric diarrhea is rarely established.

METHODS

We identified children <18 years of age who were evaluated for diarrhea at Primary Children's Hospital in Salt Lake City, Utah, between October 2010 and September 2012. Stool specimens submitted for testing were evaluated by using the FilmArray gastrointestinal diagnostic system, which is a rapid multiplex polymerase chain reaction platform that can simultaneously detect 23 bacterial, viral, and protozoal agents.

RESULTS

A pathogen was detected in 561 (52%) of 1089 diarrheal episodes. The most commonly detected pathogens included toxigenic Clostridium difficile (16%), diarrheagenic Escherichia coli (15%), norovirus GI/GII (11%), and adenovirus F 40/41 (7%). Shiga toxin-producing E coli were detected in 43 (4%) specimens. Multiple pathogens were identified in 160 (15%) specimens. Viral pathogens (norovirus, adenovirus, rotavirus, and sapovirus) were more common among children <5 years old than among those 5 to 17 years old (38% vs 16%, respectively; P < .001). Bacterial pathogens were identified most commonly in children 2 to 4 years of age. Children with 1 or more underlying chronic medical conditions were less likely to have a pathogen identified than those without a chronic medical condition (45% vs 60%, respectively; P < .01). Viral pathogens were detected more commonly in the winter, whereas bacterial pathogens were detected more commonly in the summer.

CONCLUSIONS

Toxigenic C difficile, diarrheagenic E coli, and norovirus were the leading organisms detected among these children with diarrhea. Viral pathogens are identified frequently among young children with acute gastroenteritis.

High prevalence of GII norovirus in hospitalized children with acute diarrhea, in Beijing

This study was addressed to the relationship between norovirus and acute diarrhea in hospitalized children, including hospital-acquired infection (HAI) and community-acquired infection (CAI) in a children's hospital in Beijing. RT-PCR was used to detect norovirus in stool specimen, followed by sequence analysis for PCR products. From 2010 to 2013, a total of 1248 specimens, including 661 from the HAI group and 587 from the CAI group were tested for norovirus. Norovirus were detected in 380 of 1248 (30.4%) diarrheal specimens. The positive rate for norovirus detection was higher in children within HAI group than CAI group (35.3%, 232/661 vs. 25.6%, 148/587), and the difference was significant (X² = 14.35, P<0.05). For age distribution, the highest positivity rates of norovirus were in age of 0–5 months for HAI group and 12–23 months for CAI group. In the study, 262 amplicons of the VP1 region from norovirus-positive specimens were sequenced, which showed GII.3 and GII.4 norovirus were the most common genotypes detected in 50.0% (n = 131) and 48.9% (n = 128) of the positive specimens, respectively. Regarding the wards distribution, GII.3 norovirus was mainly detected in ward for neonatal diseases (36/85 in HAI group; 19/46 in CAI group), GII.4 norovirus was mainly detected in ward for respiratory and digestive diseases (21/85 in HAI group; 15/33 in CAI group). Conclusion: The data elaborated the importance of norovirus in hospital associated infectious diarrhea. The prevalence of norovirus is higher from HAI group than CAI group, and the norovirus from the patients in CAI group could be the source of infection in HAI group.

FilmArray™ GI panel performance for the diagnosis of acute gastroenteritis or hemorragic diarrhea

Background

Acute gastroenteritis is a common cause of morbidity and mortality in humans worldwide. The rapid and specific identification of infectious agents is crucial for correct patient management. However, diagnosis of acute gastroenteritis is usually performed with diagnostic panels that include only a few pathogens. In the present bicentric study, the diagnostic value of FilmArray™ GI panels was assessed in unformed stool samples of patients with acute gastroenteritis and in a series of samples collected from pediatric patients with heamorragic diarrhea. The clinical performance of the FilmArray™ gastrointestinal (GI) panel was assessed in 168 stool samples collected from patients with either acute gastroenteritis or hemorragic diarrhea. Samples showing discordant results between FilmArray and routine methods were further analyzed with an additional assay.

Results

Overall, the FilmArray™ GI panel detected at least one potential pathogen in 92/168 (54.8%) specimens. In 66/92 (71.8%) samples, only one pathogen was detected, while in 26/92 (28.2%) multiple pathogens were detected.

The most frequent pathogens were rotavirus 13.9% (22/168), Campylobacter 10.7% (18/168), Clostridium difficile 9.5% (16/168), and norovirus 8.9% (15/168). Clostridium difficile was identified only in patients with acute gastroenteritis (p < 0.01), while STEC was detected exclusively in patients with hemorragic diarrhea (p < 0.01). In addition, Campylobacter spp., Salmonella spp., EPEC and E. coli producing Shiga-like toxin were more frequently detected in patients with hemorragic diarrhea (p < 0.05). The overall percent agreement calculated in samples was 73.8% and 65.5%, while 34.5% were discordant. After additional confirmatory analyses, the proportion of discordant samples decreased to 7.7%. Rotavirus and astrovirus were the most frequently unconfirmed pathogens.

Conclusion

In conclusion, the FilmArray™ GI panel has proved to be a valuable new diagnostic tool for improving the diagnostic efficiency of GI pathogens.

Hydrologic, land cover, and seasonal patterns of waterborne pathogens in Great Lakes tributaries

Great Lakes tributaries are known to deliver waterborne pathogens from a host of sources. To examine the hydrologic, land cover, and seasonal patterns of waterborne pathogens (i.e. protozoa (2), pathogenic bacteria (4) human viruses, (8) and bovine viruses (8)) eight rivers were monitored in the Great Lakes Basin over 29 months from February 2011 to June 2013. Sampling locations represented a wide variety of land cover classes from urban to agriculture to forest. A custom automated pathogen sampler was deployed at eight sampling locations which provided unattended, flow-weighted, large-volume (120-1630 L) sampling. Human and bovine viruses and pathogenic bacteria were detected by real-time qPCR in 16%, 14%, and 1.4% of 290 samples collected while protozoa were never detected. The most frequently detected pathogens were: bovine polyomavirus (11%), and human adenovirus C, D, F (9%). Human and bovine viruses were present in 16.9% and 14.8% of runoff-event samples (n = 189) resulting from precipitation and snowmelt, and 13.9% and 12.9% of low-flow samples (n = 101), respectively, indicating multiple delivery mechanisms could be influential. Data indicated human and bovine virus prevalence was different depending on land cover within the watershed. Occurrence, concentration, and flux of human viruses were greatest in samples from the three sampling locations with greater than 25% urban influence than those with less than 25% urban influence. Similarly, occurrence, concentration, and flux of bovine viruses were greatest in samples from the two sampling locations with greater than 50 cattle/km² than those with less than 50 cattle/km². In seasonal analysis, human and bovine viruses occurred more frequently in spring and winter seasons than during the fall and summer. Concentration, occurrence, and flux in the context of hydrologic condition, seasonality, and land use must be considered for each watershed individually to develop effective watershed management strategies for pathogen reduction.

Group A rotavirus genotypes in hospital-acquired gastroenteritis in Italy, 2012-14

BACKGROUND

Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young (aged <5 years) children, causing ∼250,000 deaths worldwide, mostly in developing countries. Differences on nucleotide sequences of VP7 (G-type) and VP4 (P-type) genes are the basis for the binary RVA nomenclature. Although at least 32 G-types and 47 P-types of rotavirus are presently known, most RVA infections in humans worldwide are related to five major G/P combinations: G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8].

AIM

To provide the hospitals of the Italian surveillance network with update information on RVA AGE.

METHODS

During RVA gastroenteritis surveillance in Italy in 2012-14, a total of 2341 RVA-positive faecal samples were collected from children hospitalized with AGE, and RVA strains were genotyped following standard EuroRotaNet protocols.

FINDINGS

Most strains analysed belonged to the five major human genotypes and 118 out of 2341 (5.0%) were reported to be hospital-acquired. Comparison of the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections showed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community. G1P[8] and G9P[8] RVA strains were detected frequently, whereas G12P[8] caused a single large nosocomial outbreak.

CONCLUSION

The information from this study will be useful to implement guidelines for preventing RVA AGE and optimizing the management of patients in hospital wards.