Changing pattern of prevalence, genetic diversity, and mixed infections of viruses associated with acute gastroenteritis in pediatric patients in New Delhi, India

Risk Factors and Hospitalizations Associated with Pediatric Adenovirus and Rotavirus Infections in Northern Lebanon

Background and Objectives: Acute gastroenteritis (AGE) is a major contributor to pediatric morbidity and mortality worldwide. There is a scarcity of data on AGE in North Lebanon, a region profoundly affected by the Syrian refugee crisis and water sanitation issues. This study examines the prevalence, risk factors, and seasonal variations in adenovirus and rotavirus infections in children with AGE in North Lebanon. Materials and Methods: A cross-sectional study was conducted from September 2022 to August 2023 on 400 children (1 month to 5 years old) with AGE that were admitted to pediatric departments of three private hospitals in North Lebanon. Stool samples were collected and tested using chromatographic immunoassays. Comprehensive demographic and clinical data were collected and analyzed. Results: Rotavirus was the most frequent viral agent (28%), followed by adenovirus (12.3%) and mixed infections (5.5%). Rotavirus vaccination demonstrated a significant protective effect, and lower infection rates were associated with breastfeeding and consumption of bottled water (p < 0.001). Higher infection rates correlated with lower levels of maternal education and household incomes (p < 0.001). Malnutrition significantly increased susceptibility to rotavirus infections (p < 0.001). Conclusions: This study emphasized the urgent need for targeted public health interventions in North Lebanon to mitigate the burden of rotavirus and adenovirus-induced acute gastroenteritis among children.

Norovirus outbreaks due to contaminated drinking water and probable person-to-person transmission, Kerala, India, 2021

BACKGROUND

In July 2021, the Alappuzha district in Kerala, India, reported an unexpected number of acute gastroenteritis (772) cases (Outbreak A). On October 10, 2021, a university in Wayanad, Kerala, reported 25 acute gastroenteritis cases (Outbreak B). We described both the outbreaks and determined the agent, source and risk factors.

METHODS

We defined a suspected case as the occurrence of vomiting or at least three episodes of loose stools within 24 h and a confirmed case as those with stool samples/rectal swabs positive for norovirus. We did a matched case-control study in Outbreak A and a retrospective cohort study in Outbreak B. We calculated the adjusted odds ratio (aOR) in outbreak A, relative risk (aRR) in outbreak B and population attributable fraction (PAF). We tested stool and water samples for bacteria and viruses.

RESULTS

We identified Group II norovirus in stool samples in both outbreaks and 4/5 water samples in Outbreak A. Suspected norovirus infection was associated with drinking inadequately boiled water from the municipal water supply in outbreak A [aOR: 4.5; 95 % C.I: 1.2-15.8; PAF: 0.23] and well water in hostels in outbreak B [aRR: 2.2; 95 % C.I: 1.2-3.9; PAF: 0.15]. In Outbreak A, groundwater from tube wells was mixed in the municipal water supply overhead tanks without chlorination.

CONCLUSION

The gastroenteritis outbreaks were caused by Group II norovirus due to the consumption of inadequately boiled contaminated groundwater (outbreak A) and well water (outbreak B). We recommended superchlorination of overhead tanks and wells and boiled water for drinking.

Comprehensive full genome analysis of norovirus strains from eastern India, 2017-2021

BACKGROUND

Worldwide, noroviruses are the leading cause of acute gastroenteritis (AGE) in people of all age groups. In India, norovirus rates between 1.4 to 44.4% have been reported. Only a very few complete norovirus genome sequences from India have been reported.

OBJECTIVE

To perform full genome sequencing of noroviruses circulating in India during 2017-2021, identify circulating genotypes, assess evolution including detection of recombination events.

METHODOLOGY

Forty-five archived norovirus-positive samples collected between October 2017 to July 2021 from patients with AGE from two hospitals in Kolkata, India were processed for full genome sequencing. Phylogenetic analysis, recombination breakpoint analysis and comprehensive mutation analysis were also performed.

RESULTS

Full genome analysis of norovirus sequences revealed that strains belonging to genogroup (G)I were genotyped as GI.3[P13]. Among the different norovirus capsid-polymerase combinations, GII.3[P16], GII.4 Sydney[P16], GII.4 Sydney[P31], GII.13[P16], GII.16[P16] and GII.17 were identified. Phylogenetic analysis confirmed phylogenetic relatedness with previously reported norovirus strains and all viruses were analyzed by Simplot. GII[P16] viruses with multiple residue mutations within the non-structural region were detected among circulating GII.4 and GII.3 strains. Comprehensive mutation analysis and selection pressure analysis of GII[P16] viruses showed positive as well as negative selection sites. A GII.17 strain (NICED-BCH-11889) had an untypeable polymerase type, closely related to GII[P38].

CONCLUSION

This study highlights the circulation of diverse norovirus strains in eastern India. These findings are important for understanding norovirus epidemiology in India and may have implications for future vaccine development.

Molecular Characterization of Gastroenteric Viruses in Wastewater from Cities in Uruguay

Group A Rotavirus, Human Astrovirus, and Norovirus (RVA, HAstV, and NoV) are recognized as the major causative agents of acute gastroenteritis in children and adults worldwide. The aim of this study was to determine the prevalence and molecular epidemiology of RVA, HAstV, and NoV in wastewater from three cities in Uruguay. Thirty-six samples from Bella Unión, Salto, and Fray Bentos cities were analyzed using quantitative and qualitative PCR. RVA was the most frequently detected virus (50%), followed by HAstV (39%), NoV GII (36%), and NoV GI (25%). RVA strains were characterized as P[8] and G3 based on the VP4 and VP7 genes, respectively. Among NoV-positive samples, genotypes GI.2, GI.3, GI.5, GI.6, GI.7, GII.2, GII.6, and GII.4 were detected, and only one HAstV genotype (MLB1) was found. Our wastewater-based epidemiological approach provides a snapshot of the overall genetic diversity of these viruses in three cities of the Uruguay River basin during 2017-2018. These findings reinforce the importance of this environmental surveillance tool for monitoring epidemiological trends of enteric viruses circulating in the population, which can be used to guide public health intervention.

A Review of Interactions between Plants and Whitefly-Transmitted Begomoviruses

The transmission of plant viruses from infected to healthy host plants is a process in which insects play a major role, using various transmission strategies. Environmental factors have an impact on the transmission of viruses and the subsequent development of infections or diseases. When viruses are successful, plant virus diseases can reach epidemic proportions. Many plants across different regions are vulnerable to viral infections transmitted by the whitefly vector. Begomoviruses, which are transmitted by whiteflies, represent a significant threat to agriculture worldwide. The review highlights the mechanisms of virus acquisition and transmission by whiteflies and explores the factors influencing these interactions. Understanding the impacts of these changes is crucial for managing the spread of pests and mitigating damage to crops. It underscores the need for continued research to elucidate the mechanisms driving plant-insect-virus interactions and to identify new approaches for sustainable pest management.

Norovirus gastroenteritis in children under-five years hospitalized for diarrhea in two cities of northeast India: A retrospective study

PURPOSE

Norovirus gastroenteritis, known to cause 'winter vomiting disease' is increasingly being identified as a major cause of viral gastroenteritis worldwide. The impact and prevalence of this viral disease are lacking in many parts of India including northeast India. This study aimed to determine the prevalence and association of norovirus gastroenteritis among under-five-year-old hospitalized children in two cities in northeast India (Dibrugarh in Assam & Dimapur in Nagaland).

MATERIALS AND METHODS

A retrospective analysis of 407 randomly selected diarrheal stool samples was conducted using a commercial multiplex probed-based real-time RT-PCR assay capable of detecting six-viral gastroenteritis pathogens including Norovirus GI, Norovirus GII, Rotavirus, Human Adenovirus, Human Astrovirus, and Sapovirus.

RESULTS

Results showed that norovirus was detected in 18.4% of the samples (75/407; 95% CI: 14.8%-22.5%), with norovirus genogroup II being the predominant group in 97.3% of norovirus cases. A significant association of norovirus diarrhea was found with seasonality, with higher prevalence in colder months compared to warmer months (22.4% vs 9.1%, p-value:0.002). Additionally, 66.7% (50/75) of cases of norovirus gastroenteritis had reported vomiting as the major symptom and had a shorter duration of diarrhea (p-value 0.03). Co-infections with other viral pathogens were seen in 45.9% (187/407) of the cases. The detection of rotavirus was 67.1% (273/407), human adenovirus (45.9%; 187/407), sapovirus and astrovirus (5.9%, 24/407 each), and norovirus GI (0.5%, 2/407) among the cases.

CONCLUSION

This study reports the prevalence of norovirus gastroenteritis in northeast India and further highlights that norovirus gastroenteritis is responsible for substantial cases of hospitalization of under-five years children in the region.

Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis

AIM

Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis.

METHODS

Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis.

RESULTS

Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I² = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%).

CONCLUSION

The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.

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.

Epidemiological investigations of diarrhea in children in Praia city, Cape Verde

Introduction

Diarrheal disease is a major cause of infant mortality and morbidity in Africa and results primarily from contaminated food and water sources, but its prevalence predictors in Cape Verde are not completely known. For this reason, this study aimed to identify the etiological agents of diarrhea in Cape Verdean children and assess its associated risk factors.

Methods

A survey questionnaire was used, and a total of 105 stool samples from children with diarrhea aged 0-12 years at the Central Hospital of Praia (Santiago, Cape Verde) were analyzed. The analyses were carried out using Biofire FilmArray Gastrointestinal Panels. Possible risk factors for these pathogens were analyzed using logistic regression, chi-square tests, or Fisher's exact test.

Results

Among the bacteria, enteroaggregative Escherichia coli (45.71%; 95% CI: 36.71-56.70), enteropathogenic E. coli (40%; 95% CI: 30.56-50.02), Shigella/enteroinvasive E. coli (29.52%; 95% CI: 21.02-39.22), E. coli enterotoxigenic (12.38%; 95% CI: 6.76-20.24), Campylobacter sp. (10.48%; 95% CI: 5.35-1.97), Vibrio sp. (4.76%; 95% CI: 1.56-10.76), Clostridioides difficile (3.81%; 95% CI: 1.05-9.47), Vibrio cholerae (2.86%; 0.59-8.12), Shiga-like toxin-producing E. coli (2.86%; 0.59-8.12) and Salmonella sp. (0.95%; 0.02-5.19) were identified; four viruses, Rotavirus A (28.57%; 95% CI: 20.18-38.21), Sapovirus I. II. IV and V (11.43%; 95% CI: 6.05-19.11), Norovirus GI.GII (6.67%; 95% CI: 2.72-13.25) and Adenovirus F 40.41 (6.67%; 95% CI: 2.72-13.25) were also observed. All the pathogens detected in this study were found in coinfections. Significant associations with risk factors were found; specifically, having a bathroom at home reduced the risk of Campylobacter sp., having animals at home increased the risk of Shigella/EIEC infection, and drinking bottled water reduced the risk of Sapovirus infection.

Discussion

From the findings of this study, it can be concluded that, in Cape Verde, there is a high prevalence and diversity of pathogens among children. Our results could help to establish an adequate diagnosis and effective treatments for diarrheal disease.

Prevalence and genotypes distribution of group A rotavirus among outpatient children under 5 years with acute diarrhea in Shanghai, China, 2012-2018

Background

Group A rotavirus (RVA) remains the main causative agent of acute diarrhea among children under five years in countries that have not yet introduced the RVA vaccine worldwide. Long-term and continuous monitoring data on RVA infection in outpatient children were lacking in Shanghai. We investigated the prevalence and distribution of RVA genotypes in outpatient children with acute diarrhea in Shanghai from 2012 to 2018.

Methods

Stool specimens of outpatient children under five years were collected from the Children’s Hospital of Fudan University in Shanghai, China. All the samples enrolled in this study were detected and characterized for the P and G genotypes of RVA were determined using the semi-multiplex RT-PCR technique.

Results

Of 1814 children enrolled with acute diarrhea and having specimens collected, 246 (13.6%) were infected with RVA. The highest frequency of RVA was observed in children younger than two years old (87.0%, 214/246). Year-round RVA transmission was observed and the RVA detection rate peaked every winter and troughed in summer. In this study, 12 different RVA strains were identified in children. G9P[8] (49.2%, 121/246) was detected as the most prevalent genotype, followed by G–P[8] (22.8%, 56/246), G3P[8] (11.4%, 28/246), and G9P- (4.9%, 12/246). Although RVA strains detected in this study varied with the time, G9P[8] has been the most predominant circulating genotype since 2012. Furthermore, 12.2% (30/246) RVA positive samples were co-infected with other diarrhea viruses.

Conclusion

The present analysis showed that RVA was still a major cause of children with acute diarrhea in Shanghai from 2012 to 2018. A great diversity of RVA strains circulated in children with acute diarrhea with G9P[8] being the predominant genotype since 2012. Long-term and continuous monitoring of RVA genotypes is therefore indispensable to refine future vaccine strategy in Shanghai.

Use of multiplex PCR in diagnosis of childhood acute viral diarrhoea caused by rotavirus, norovirus, astrovirus and adenovirus in Upper Egypt

Background

Diarrhoea is still a major public health issue in developing countries, and it is one of the leading causes of morbidity and mortality in children. We aimed to assess the use of a multiplex reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of five viruses, including rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, responsible for gastroenteritis in children under 5 years old in primary care centres in Upper Egypt.

Subjects and methods

A total of 500 stool samples were collected. Fifty samples were randomly selected for viral examination using multiplex RT-PCR for the detection of rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, causing diarrhoea.

Results

Viruses were detected in 45 (90%) of the 50 stool samples. The most frequently identified virus was norovirus G2, followed by Group A rotavirus, astrovirus and adenovirus. Mixed infection by two and three viruses was observed in 7/50 cases (14%) and 2/50 cases (4%), respectively. Norovirus G1 was not detected in the samples examined.

Conclusion

Our study reveals that multiplex PCR allows for the detection of multiple viral targets in only one reaction, rendering the assay easier to perform compared to existing testing methodologies (RT-PCR and electron microscopy). Additionally, most of the viruses were detected in summer, and the highest prevalence was in the age group less than 1 year. Norovirus G2 and rotavirus were the most frequent agents and the most common coinfections responsible for gastroenteritis in children.

Molecular Epidemiology of Human Adenovirus, Astrovirus, and Sapovirus Among Outpatient Children With Acute Diarrhea in Chongqing, China, 2017-2019

OBJECTIVE

To investigate the epidemiology of human adenovirus (HAdV), human astrovirus (HAstV), and sapovirus (SaV), children with acute diarrhea in Chongqing, China from 2017 to 2019 were enrolled. Improved surveillance could provide better guidance for diarrhea prevention.

METHODS

Between 2017 and 2019, fecal specimens were collected from children <14 years of age presenting with acute diarrhea for treatment at the outpatient department of the Children's Hospital, Chongqing Medical University. Human HAdV in the fecal specimens was detected by PCR, while RT-PCR was adopted for the detection of HAstV and SaV.

RESULTS

A total of 1,352 fecal specimens were screened in this study. The detection rate of HAdV was 4.44% (60/1352), HAstV was 2.81% (38/1352), and SaV was 1.04% (14/1352). The prevalence of enteric viruses in males was not significantly different to females (p > 0.05). We found 96.67% (58/60) of the HAdV-positive cases, 92.11% (35/38) of the HAstV-positive cases, and 100% (14/14) of the SaV-positive cases among the children under 4 years old. HAdV cases were identified throughout the year, while the infection of HAstV peaked from March to May every year. By contrast, SaV was detected in May, July, and from September to December. In total, 41 strains of HAdV-F were identified, including F41 (39/60) and F40 (2/60). Furthermore, A31, B3, B7, C1, C2, C5, and C6 were also detected in the study. In addition, we detected two genotypes of HAstV, HAstV-1 (34/38) and HAstV-5 (4/38), and two genotypes of SaV, GI0.1 (13/14), GI0.2 (1/14).

CONCLUSION

The enteric viruses HAdV, HAstV, and SaV contribute to the overall burden of diarrhea in Chongqing, especially in children <4 years of age. Two genotypes were identified for HAstV (HAstV-1 and HAstV-5) and SaV (GI.1 and GI.2) with an additional nine genotypes detected in HAdV cases. While the F41 HAdV strain was predominant, HAdV-A31 was also detected in 10% of cases. The study results along with continuous surveillance of enteric viruses will aid in the design and implementation of future enteric vaccines and diarrhea mitigation strategies.

Detection and characterization of human astrovirus and sapovirus in outpatients with acute gastroenteritis in Guangzhou, China

Background

Human astrovirus (HAstV) and sapovirus (SaV) are common pathogens that can cause acute gastroenteritis (AGE). However, very few studies have reported the molecular epidemiology and clinical information on HAstV and SaV in China. This study aims to determine the molecular epidemiology and clinical features of HAstV and SaV in patients with AGE in Guangzhou, China.

Methods

For this study, 656 patients with AGE were enrolled. Their stool samples were screened for 15 enteropathogens using Luminex xTAG^® Gastrointestinal Pathogen Panel. HAstV and SaV were detected through an in-house multiplex reverse transcriptase polymerase chain reaction followed by phylogenetic analysis. We described and compared clinical features of AGE in patients with HAstV and SaV.

Results

Of the 656 stool samples, 63.72% (418/656) were found to be positive, with 550 enteropathogens (296 bacteria and 254 viruses). HAstV and SaV were detected in 20 (3.0%) and 12 (1.8%) samples, respectively. Four genotypes (genotypes 1, 2, 3, and 8) of HAstV and three genotypes (GI.1, GI.2 and GIV) of SaV were identified. Coinfection was observed in ten HAstV-positive and two SaV-positive samples. HAstV was more likely to occur in winter, while SaV in early spring. The median age of the patients with single HAstV infection was higher than that of the patients with other viruses (rotavirus, norovirus, and enteric adenovirus; P = 0.0476) and unknown etiology (P = 0.006). Coinfection with HAstV or SaV were not associated with disease severity (P > 0.05).

Conclusion

HAstV and SaV are the common causes of AGE in Guangzhou, China.

Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis

Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.

Genetic characterization and evolutionary analysis of norovirus genotypes circulating among children in eastern India during 2018-2019

Noroviruses are significant etiological agents of acute gastroenteritis (AGE) across all age groups, especially in children under 5 years of age. Although the prevalence of norovirus infection is known to have increased in various countries, in India there are few reports pertaining to the norovirus disease burden. We investigated the epidemiology and molecular characteristics of noroviruses in children seeking health care at two hospitals in Kolkata, Eastern India. Faecal specimens were collected between January 2018 and December 2019 from 2812 children under 5 years of age with acute gastroenteritis. Noroviruses were detected in 6.04% (170/2812) of the samples, and 12.9% (22/170) of these were cases of coinfection with rotavirus. Among children (≤5 years), a higher infection rate (8.2%, n = 94/1152) was observed in the 6 to 12 month age group. GII.4 Sydney 2012 was the dominant norovirus capsid genotype (n = 75/90, 83.3%), followed by GII.3 (n = 10/90, 11.1%). Other capsid types GII.13 (n = 4/90, 4.4%) and GII.17 (n = 1/90; 1.1%) were also detected at low frequency. Phylogenetic analysis showed that the GII.P16 polymerase of strains in this region clustered with those of the phylogenetically distinct monophyletic clade of GII.P16 strains, whose members have been circulating worldwide since 2014. Inter-genotypic norovirus recombinants such as GII.P16-GII.3 (n = 10) and GII.P16-GII.13 (n = 4) were also observed among the circulating strains. In comparison to previous studies from eastern India, the present study shows a higher detection rate of norovirus infection in the paediatric population suffering from acute gastroenteritis. Continuous surveillance is required for predicting the emergence of novel genotypes and recombinant strains and for future vaccine development.

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013-2016

G12 strains are now considered to be the sixth most prevalent human rotaviruses globally. India has introduced rotavirus vaccine Rotavac® into the national immunization program in 2016 and Himachal Pradesh (HP) is the first state to launch it. During epidemiological rotavirus surveillance in HP, predominance of G12 rotaviruses was observed. This study investigated the genetic variability and evolution of HP G12 strains (n = 15) associated with P-genotypes P[6], P[4], and P[8] identified between 2013 and 2016. Phylogenetic analysis of VP7 gene revealed that all characterized G12 strains clustered in lineage-III and diversified into three subclusters indicating that these strains may have originated from three different ancestral G12 strains. The comparative sequence analysis of HP strains with Rotavac® and Rotarix® vaccine strains revealed various amino acid substitutions in epitope regions of VP7 and VP4 proteins especially at the antibody neutralization sites. Only 12/29 VP7 epitope residues and 2/25 VP4 epitope residues were found to be conserved between HP rotavirus strains and vaccine strains. Both long and short electropherotypes were observed in G12P[4] strains, while a single long electropherotype was observed in G12P[6] strains. Children of ≤11 months were significantly infected with G12 rotaviruses. The frequency of vomiting episodes (≥5/day) was significantly higher in children infected with G12 rotavirus strains as compared to non-G12 rotaviruses (p = 0.0405). Our study provides the comprehensive data on clinical characteristics and evolutionary pattern of the G12 rotavirus, the most prevalent strain in HP and emphasizes the need to monitor these strains for inclusion in future vaccine.

Prevalence and genetic diversity of gastroenteritis viruses in hospitalized children < 5 years of age in Maharashtra state, Western India, 2017-2019

Four gastroenteritis viruses were responsible for 54% of the acute gastroenteritis (AGE) cases in children hospitalized between May 2017 and December 2019 in Pune city of Maharashtra state, Western India. The majority (79%) of the children were <2 years of age. The prevalence of Rotavirus A (RVA) was 30.5% followed by 14.3% for norovirus, 8.4% for adenovirus, and 5.5% for astrovirus. The severity of the disease was highest in patients with coinfections compared with the patients with a single infection or negative for all (p = 0.024). Genotyping analysis showed that the majority of the RVA-positive samples (66%) could be typed as G3P[8], 63.6% of the norovirus as GII.4 Sydney [P16], 44% of the adenovirus as type 41%, and 56.2% of the astrovirus as astrovirus type 1. The almost equivalent prevalence of rotavirus and nonrotaviruses and acute gastroenteritis (AGE) cases without known etiology in around 46% of the cases was noted in the present study. Our data highlight that after the recent inclusion of rotavirus vaccines as a part of the National Immunization schedule in India, conducting extensive AGE surveillance in children should include nonrotaviruses such as norovirus.

Global prevalence and genotype distribution of norovirus infection in children with gastroenteritis: A meta-analysis on 6 years of research from 2015 to 2020

In the post rotavirus vaccine era, norovirus (NoV) plays an increasingly important role in epidemic and sporadic gastroenteritis among children. This study was designed to provide an updated meta-analytic review of the prevalence of NoV among paediatric patients with gastroenteritis and to clarify the relationship between NoV infection and gastroenteritis. Systematic searches of the literature for potentially relevant studies were carried out from 1 January 2015 to 29 May 2020. The inverse variance method was chosen for weighting of the studies, and the random-effects model was used to analyse data. To determine the association between NoV infection and gastroenteritis in children, pooled odds ratio (OR) and its 95% confidence interval (CI) were computed for case-control studies. The pooled prevalence of NoV infection among 12,0531 children with gastroenteritis from 45 countries across the world was 17.7% (95% CI: 16.3%-19.2%). There were 28 studies with a case-control design, and the pooled prevalence of NoV infection among 11,954 control subjects was 6.7% (95% CI: 5.1%-8.8%). The pooled OR of the association of NoV infection and gastroenteritis was 2.7 (95% CI: 2.2-3.4). The most common NoV genotypes were GII.4 (59.3%) and GII.3 (14.9%). The highest frequency of NoV was found in the age group below 1 year. Our findings indicated a substantial burden of gastroenteritis caused by NoV globally, with GII.4 and GII.3 the major genotypes responsible for the majority of NoV-associated gastroenteritis cases among children. Younger age and male sex can be considered risk factors for NoV-associated gastroenteritis among children.

Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil

From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.

Etiological Spectrum of Infective Diarrhea in Renal Transplant Patient by Stool PCR: An Indian Perspective

Introduction:

Diarrhea is a common cause of morbidity and mortality among renal transplant patients. The etiological spectrum of pathogens varies with regional diversity, socioeconomic conditions, sanitation, and eating habits. We aimed to delineate the etiological profile of gastrointestinal pathogens in renal transplant patients using the stool Polymerase chain reaction.

Methods:

In this single-center, retrospective analysis of patients from January 2016 to January 2018, all renal transplant patients who were admitted with severe diarrhea and underwent the stool Polymerase chain reaction (PCR) were included. In the control group, we included patients from the general population who were admitted with similar complaints in the general medicine ward and underwent stool PCR over the same duration.

Results:

One hundred ten admissions occurred over 2 years in the transplant group. 86% of samples were positive for infection. More than one organism was seen in 68% of the patient. Norovirus was the most common organism isolated. Giardia lamblia with Norovirus was the most common coinfection among the transplant population. In the control group, 87% of samples tested positive, with 53% of patients having more than one organism. Enteroaggregative E. coli was the common organism, Enteroaggregative E. coli with Enteropathogenic E. coli and Enterotoxigenic E. coli were the most common organism in combination. Both the groups had similar incidence of infection with multiple organisms.

Conclusion:

The etiological profile of gastrointestinal pathogens differs significantly between the transplant and general population. Coinfections are common in both populations. Norovirus is the most common pathogen in the transplant population, presenting as isolated as well as in coinfections.

Molecular epidemiology and genetic diversity of norovirus infection in children hospitalized with acute gastroenteritis in East Java, Indonesia in 2015-2019

Noroviruses are recognized as a leading cause of outbreaks and sporadic cases of acute gastroenteritis (AGE) among individuals of all ages worldwide, especially in children <5 years old. We investigated the epidemiology of noroviruses among hospitalized children at two hospitals in East Java, Indonesia. Stool samples were collected from 966 children with AGE during September 2015-July 2019. All samples were analyzed by reverse transcription-polymerase chain reaction (RT-PCR) for the amplification of both the RNA-dependent RNA polymerase (RdRp) and the capsid genes of noroviruses. The genotypes were determined by phylogenetic analyses. In 2015-2019, noroviruses were detected in 12.3% (119/966) of the samples. Children <2 years old showed a significantly higher prevalence than those ≥2 years old (P = 0.01). NoV infections were observed throughout the year, with the highest prevalence in December. Based on our genetic analyses of RdRp, GII.[P31] (43.7%, 31/71) was the most prevalent RdRp genotype, followed by GII.[P16] (36.6%, 26/71). GII.[P31] was a dominant genotype in 2016 and 2018, whereas GII.[P16] was a dominant genotype in 2015 and 2017. Among the capsid genotypes, the most predominant norovirus genotype from 2015 to 2018 was GII.4 Sydney_2012 (33.6%, 40/119). The most prevalent genotype in each year was GII.13 in 2015, GII.4 Sydney_2012 in 2016 and 2018, and GII.3 in 2017. Based on the genetic analyses of RdRp and capsid sequences, the strains were clustered into 13 RdRp/capsid genotypes; 12 of them were discordant, e.g., GII.4 Sydney[P31], GII.3[P16], and GII.13[P16]. The predominant genotype in each year was GII.13[P16] in 2015, GII.4 Sydney[P31] in 2016, GII.3[P16] in 2017, and GII.4 Sydney[P31] in 2018. Our results demonstrate high detection rates and genetic diversity of norovirus GII genotypes in pediatric AGE samples from Indonesia. These findings strengthen the importance of the continuous molecular surveillance of emerging norovirus strains.

Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa

Background

Human norovirus (NoV) is an etiological agent associated with acute gastroenteritis (AGE) in both children and adults worldwide. However, very few studies have been reported on the prevalence and genetic diversity of NoV strains in children older than 5 years of age and adults with little or inadequate water and sanitation conditions.

Objectives

The aim of this study was assessing the prevalence of the human norovirus in older children and adults suffering with diarrhoea from rural communities in the Vhembe district, Limpopo province.

Methods

Between August 2017 and October 2018, stool samples were collected from outpatients suffering from AGE and screened for NoV strains using the RIDA©GENE norovirus I and II real-time one-step RT-PCR. RNA extracts of NoV-positive samples were subjected to RT-PCR amplification and nucleotide sequencing to genotype the positive NoV strains.

Results

Out of 80 collected stool samples, 13 (16%) were tested positive for norovirus. Genogroup GII was identified in 6/13 (46%) samples and genogroup GI in 7/13 (54%) samples. The sequence analyses showed multiple genotypes including GII.Pg, GII.1, GII.2, GII.4, and GI.3. Phylogenetic analysis revealed the relatedness of NoV genotypes identified with other strains reported globally.

Conclusion

Continued systematic surveillance to evaluate norovirus association with diarrhoea is needed to assist with epidemiological surveillance and disease burden in people of all the age groups.

Epidemiology and clinical features of rotavirus, adenovirus, and astrovirus infections and coinfections in children with acute gastroenteritis prior to rotavirus vaccine introduction in Meerut, North India

There are limited reports on the etiology of multiple enteric viruses causing acute gastroenteritis (AGE) in North India. In the present study we have determined the prevalence of three enteric viruses, namely rotavirus, astrovirus (AstV) and adenovirus (AdV) in a total of 312 diarrheic children (<5 years) hospitalized at Lala Lajpat Rai Memorial Medical College, Meerut, Uttar Pradesh from August 2014 to July 2016; and results were compared with data from Delhi. The fecal samples were individually screened for group A rotavirus (RVA), AdV, and AstV using enzyme immunoassay kits. At least one viral agent was detected in 29.2% of 312 fecal specimens. RNA of rotavirus antigen-positive samples was extracted by TRIzol method. Rotavirus G/P genotyping was performed using seminested multiplex reverse transcriptase-polymerase chain reaction. RVA was the most predominant virus (18.3%) followed by AstV (12.5%), and AdV (9.9%). Coinfections were detected in 10.6% cases and the most common coinfection in diarrheic children was RVA combined with AstV (36.4%). Overall, the enteric viruses were found most prevalent in the 6 to 11 months age group (P = .01). Increased duration of vomiting (≥3 days) was significantly (P = .04) associated with AdV infection (61.3%) as compared with AstV (30.76%) and rotavirus (26.31%). G1P[8] was detected throughout as the most prevalent rotavirus strain (10.5%). Unusual RV strains like G2P[6] and G2P[8] were also detected. Of note G3, G4, and G12 rotavirus were detected for the first time in Meerut. This is the first report that demonstrated the important contribution of multiple enteric viruses causing AGE in young children in this part of Uttar Pradesh (Meerut).

Epidemiology and genetic diversity of group A rotavirus in acute diarrhea patients in pre-vaccination era in Himachal Pradesh, India

Acute gastroenteritis due to Group A rotaviruses remains the leading cause of mortality and morbidity in children in developing countries. India introduced its indigenous rotavirus vaccine Rotavac® in 2016 and Himachal Pradesh (HP) the first state to launch it. The present study aimed to evaluate rotavirus strain diversity associated with AGE prior to vaccine introduction in HP. A total of 331 fecal specimens collected from diarrheic children hospitalized at RPGMC Tanda, HP between July-2014 and June-2016 were screened for RVA by EIA. Rotavirus RNA was extracted by TRIZOL method and analyzed by RNA-PAGE. G/P typing was performed using semi-nested multiplex reverse transcriptase PCR. Rotavirus was detected in 45% (n = 149/331) of diarrheic children, with highest rate observed in the 6-11 months age group (47%). Vomiting was found more frequently associated with RV-infection. Among G-types, G12 was found most prevalent (33.1%) followed by G1 (28.4%), G9 (12.2%), G2 (9.5%), G3 (3.4%) and G10 (2.7%). G4 (0.7%) strains were rarely detected. Among P-types, P[6] was the most prevalent (40.5%) followed by P[8] (29.1%) and P[4] (14.2%). Of note, genotypes G3 and P[11] were detected for the first time in HP. Among G/P combinations, G12P[6] was most prevalent (30.4%) followed by G1P[8] (20.3%), G2P[4] (4.7%), G1P[6] (3.4%) and G3P[8] (2.7%). Interestingly, our study observed high percentage of unusual strains (14.2%) namely G9P[4], G2P[6], G2P[8], G12P[4] and G1P[11]. The regionally common strains G3P[6], G4P[6], G9P[6], G9P[8], G10P[6], G10P[8] and G12P[8] strains were very rarely detected. Of interest, RNA migration pattern of G1P[8] was DS-1 like and genomic heterogeneity was observed within G12P[4] strains with both long and short electropherotypes. Our study highlights rich genetic diversity with emergence of rare rotavirus strains circulating in HP and provides baseline data prior to Rotavac® introduction that will help to gauge the impact of the Rotavac® vaccine in HP.

Novel Human Astroviruses: Prevalence and Association with Common Enteric Viruses in Undiagnosed Gastroenteritis Cases in Spain

A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.

Molecular Epidemiology and Clinical Features of Rotavirus Infection Among Pediatric Patients in East Java, Indonesia During 2015-2018: Dynamic Changes in Rotavirus Genotypes From Equine-Like G3 to Typical Human G1/G3

Group A rotavirus (RVA) is the most important cause of severe gastroenteritis among children worldwide, and effective RVA vaccines have been introduced in many countries. Here we performed a molecular epidemiological analysis of RVA infection among pediatric patients in East Java, Indonesia, during 2015-2018. A total of 432 stool samples were collected from hospitalized pediatric patients with acute gastroenteritis. None of the patients in this cohort had been immunized with an RVA vaccine. The overall prevalence of RVA infection was 31.7% (137/432), and RVA infection was significantly more prevalent in the 6- to 11-month age group than in the other age groups (P < 0.05). Multiplex reverse transcription-PCR (RT-PCR) revealed that the most common G-P combination was equine-like G3P[8] (70.8%), followed by equine-like G3P[6] (12.4%), human G1P[8] (8.8%), G3P[6] (1.5%), and G1P[6] (0.7%). Interestingly, the equine-like strains were exclusively detected until May 2017, but in July 2017 they were completely replaced by a typical human genotype (G1 and G3), suggesting that the dynamic changes in RVA genotypes from equine-like G3 to typical human G1/G3 in Indonesia can occur even in the country with low RVA vaccine coverage rate. The mechanism of the dynamic changes in RVA genotypes needs to be explored. Infants and children with RVA-associated gastroenteritis presented more frequently with some dehydration, vomiting, and watery diarrhea, indicating a greater severity of RVA infection compared to those with non-RVA gastroenteritis. In conclusion, a dynamic change was found in the RVA genotype from equine-like G3 to a typical human genotype. Since severe cases of RVA infection were prevalent, especially in children aged 6 to 11 months or more generally in those less than 2 years old, RVA vaccination should be included in Indonesia's national immunization program.

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.