scholarly journals Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain)

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 184
Author(s):  
Sibele de Oliveira-Tozetto ◽  
Cristina Santiso-Bellón ◽  
Josep M. Ferrer-Chirivella ◽  
Noemi Navarro-Lleó ◽  
Susana Vila-Vicent ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Age Groups ◽  
Enteric Virus ◽  
Diagnostic Procedures ◽  
University Hospital ◽  
Molecular Diagnostic ◽  
Positive Rate ◽  
Enteric Infections ◽  
Stool Samples

Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.

scholarly journals Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses

2016 ◽  
Vol 10 (1) ◽  
pp. 78-89 ◽  
Author(s):  
Haifeng Chen ◽  
Yuan Hu
Keyword(s):  
Acute Gastroenteritis ◽  
Disease Burden ◽  
Age Groups ◽  
Etiologic Agent ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Human Noroviruses ◽  
Viral Illness ◽  
Sporadic Acute Gastroenteritis

Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.

Investigation of Children with Acute Gastroenteritis by Multiplex PCR Method in Central Part of Turkey

2022 ◽  
Author(s):  
Fatih Yılmaz ◽  
Havva Kaya ◽  
Mehmet Özdemir
Keyword(s):  
Multiplex Pcr ◽  
Acute Gastroenteritis ◽  
Hospital Admissions ◽  
Age Groups ◽  
Viral Gastroenteritis ◽  
Viral Agent ◽  
Mortality And Morbidity ◽  
Stool Samples ◽  
Pcr Method ◽  
Norovirus Gii

Abstract Objective Gastroenteritis is a disease that affects all age groups, especially children, and causes high mortality and morbidity in all countries. The most common agents of acute gastroenteritis are viral agents. As a result, millions of diarrhea attacks and hospital admissions occur worldwide every year due to viral gastroenteritis. This study uses the multiplex polymerase chain reaction (PCR) method to investigate the viruses that are the causative agents of viral gastroenteritis in the pediatric patient group in Konya, Turkey. Methods Stool samples of 94 patients aged 0 to 18 years sent from Emergency clinics and Pediatric outpatient clinics, Meram Medical Faculty Hospital Pediatric clinics, Konya Necmettin Erbakan University to Medical Microbiology Laboratory with a diagnosis of gastroenteritis between February and December 2018 were included in the study. Stool samples were stored at –80°C until the time of the analysis. Deoxyribonucleic acid/ribonucleic acid isolation from stool samples was performed with EZ1 Virus Mini Kit v2.0 (Qiagen, Hilden, Germany) using an automatic extraction system (BioRobot EZ1 system, Qiagen). The presence of astrovirus, rotavirus, adenovirus, norovirus (GI, GII), and sapovirus agents was investigated by the multiplex PCR method (Fast Track Diagnostics, Luxembourg) viral gastroenteritis kit. Results Viral gastroenteritis agents were detected in 56.3% of the patients. One viral agent was detected in 47 (50%) of these patients and at least two viral agents in 6 (6.3%) of them. Norovirus GII was detected in 20 (21.2%) of the children included in the study, adenovirus in 13 (13.8%), rotavirus in 11 (12.8%), astrovirus in 11 (11.7%), sapovirus in 4 (4.2%), and norovirus GI in 1 (1.06%). When the distribution of viral agents was examined by months, the most number of agents were observed (21; 35%) in May, followed by April and June (12; 20%). Considering the distribution of the prevalence of the agents by age, it was seen to be mainly between 0 and 12 months (42%). Conclusion Considering that the most common viral agent in our region is norovirus GII, it will be useful to investigate the norovirus that is not routinely examined in children who are admitted to clinics with the complaint of gastroenteritis. It will be appropriate to examine routinely adenovirus, rotavirus, and norovirus in the laboratory, especially in children with diarrhea and vomiting in the winter and spring months.

Prevalence and molecular characterization of human rhinovirus in stool samples of individuals with and without acute gastroenteritis

2016 ◽  
Vol 89 (5) ◽  
pp. 801-808 ◽  
Author(s):  
Prapaporn Khoonta ◽  
Piyada Linsuwanon ◽  
Nawarat Posuwan ◽  
Sompong Vongpunsawad ◽  
Sunchai Payungporn ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Acute Gastroenteritis ◽  
Human Rhinovirus ◽  
Stool Samples

scholarly journals Identifying Enteropathogens in Children with Acute Gastroenteritis Presenting with Isolated Vomiting–Appetite Study

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S360-S361
Author(s):  
Bonita Lee ◽  
Xiao-Li Pang ◽  
Ran Zhuo ◽  
Brendon Parsons ◽  
Linda Chui ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Enteric Virus ◽  
Enteric Bacteria ◽  
Pediatric Emergency ◽  
Health Clinic ◽  
E Coli ◽  
Rectal Swabs ◽  
Stool Samples ◽  
D 12

Abstract Background As diarrheal stool samples are the recommended specimen for testing in acute gastroenteritis (AGE), etiological investigations are rarely performed in children presenting with isolated vomiting. This study identifies enteropathogens in children with AGE presenting with isolated vomiting. Methods Children <18 years old with ≥3 episodes of vomiting/diarrhea in 24 hours and <7 days of symptoms were recruited in 2 pediatric emergency departments, a public health clinic and via Health Link, a provincial nurse advice phone line. Rectal swabs and stool samples were collected and tested using the Luminex xTAG GPP, an in-house 5-virus RT-qPCR panel and enteric bacterial culture. Vomiting and diarrhea data were collected at enrollment (day 0) and at day 14. Results Between Dec 9, 2014 and Apr 14, 2016, 2,184 children were enrolled and tested: 784 (36%) presented with isolated vomiting, 250 (11%) with isolated diarrhea (ID), 1,138 (52%) with both vomiting and diarrhea (V&D), 12 had missing data. The detection of enteropathogens was 56% when presenting with isolated vomiting, 55% with ID and 83% with V&D. Of the 784 children with isolated vomiting, 54% (n = 424) had one or more viruses: the most common was norovirus (NoV) (n = 244, 50%), followed by adenovirus (Adv) (91, 19%), rotavirus (Rota) (57, 12%), sapovirus (84, 17%) and astrovirus (10, 2%). Fifty-eight cases had >1 virus; co-infection with NoV and Adv was the most common (n = 23). Ten of these 424 patients also had enteric bacteria (2 Aeromonas, 2 ETEC, 2 Salmonella, 2 Yersinia, 1 Campylobacter, 1 E coli O157) and 8/9 (89%) of these patients reported development of diarrhea at day 14. In comparison, 212/383 (55%) of patients with virus only reported diarrhea at follow up. Enteric bacteria with no virus was detected in 11 patients (3 Aeromonas, 3 Salmonella, 3 STEC, 1 Campylobacter, 1 E coli O157) and 3/10 of these patients reported diarrhea. Conclusion Over 50% of AGE presented with isolated vomiting had enteric virus identified in stool or rectal swabs, representing a significant pathogen-based disease burden not previously included in healthcare planning (e.g., Rota vaccine). NoV was the predominant agent followed by Adv and Rota. Finding enteric bacteria in these cases is novel and requires further study. Disclosures All authors: No reported disclosures.

scholarly journals Genomic Characterization of Three Melon Necrotic Spot Viruses Detected in Human Stool Specimens

2017 ◽  
Vol 5 (11) ◽  
Author(s):  
Rachel Marine ◽  
Christina Castro ◽  
Laura Magaña ◽  
Terry Fei Fan Ng ◽  
Kshama Aswath ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Viral Metagenomics ◽  
Necrotic Spot ◽  
Coding Sequences ◽  
Genomic Characterization ◽  
Stool Samples ◽  
Stool Specimens ◽  
Human Stool

ABSTRACT The complete coding sequences of three melon necrotic spot viruses (MNSVs) were obtained from viral metagenomics of stool samples from patients with acute gastroenteritis. These genomes were most similar to Spanish strains sequenced in 2003 and a novel MNSV watermelon strain in 2014.

scholarly journals Etiological and Epidemiological of Viral Diarrhea Among Children Under the Age of Five in Shenyang From 2018 to 2020

2021 ◽  
Author(s):  
Xinxin Dong ◽  
Ying Qi ◽  
Ruiyu Chai ◽  
Han Xu ◽  
Jin Wang ◽  
...  
Keyword(s):  
Causes Of Death ◽  
Viral Infections ◽  
Age Groups ◽  
Viral Diarrhea ◽  
Predominant Type ◽  
Positive Rate ◽  
Stool Samples ◽  
Stool Specimens ◽  
The Government ◽  
Epidemiological Characteristics

Abstract Diarrhea is one of the leading causes of death among children, especially in the age under five, but little data are available on the etiology of viral diarrhea in Shenyang. To understand the infection status and the relevant epidemiological characteristics of viral diarrhea and to fill gaps of how the distribution of viruses change across Shenyang in children under the age of five with diarrhea, stool specimens of children with diarrhea aged 0-59 months and surveillance data was collected from Sentinel Hospital of Shenyang. Rotavirus, calicivirus, adenovirus, and astrovirus 4 viruses were then analyzed, and the proportion of children who tested positive for each pathogen was calculated and seasonal and spatial patterns for major organisms were determined. Viruses were identified in 47.9% of the 897 samples from children with diarrhea. The main viruses of stool samples were rotavirus (16.9%, predominant type G9P[8]), calicivirus (14.7%, norovirus, predominant type GII ), adenovirus (11.8%), and astrovirus (4.5%). Viral infections were mainly detected in the age of 0-12 months. In the area of Shenyang, Huanggu has the most cases (198, 22.1%), followed by Dadong (137, 15.3%) and Hunnan (135, 15.1%). The positive rate of viruses in patients of different ages, seasons, and regions was not same. Public health entities and the government should develop corresponding measures for different age groups, seasons, and regions.

scholarly journals A Community Based Epidemiological Study on Intestinal Amoebiasis in Rural West Bengal, India

2012 ◽  
Vol 2 (3) ◽  
pp. 164-168
Author(s):  
Sintu Samanta ◽  
Soumyendu Mehra ◽  
Tapas K. Maiti ◽  
Pramit Ghosh ◽  
Sudip K. Ghosh
Keyword(s):  
Epidemiological Study ◽  
West Bengal ◽  
Age Groups ◽  
Diagnostic Procedures ◽  
Parasitic Infestation ◽  
Self Medication ◽  
Entamoeba Dispar ◽  
Cross Sectional ◽  
Demographic Correlates ◽  
Stool Samples

Objective: To assess the magnitude of Entamoeba histolytica/ Entamoeba dispar infestation and to study some socio-demographic correlates in relation to parasitic infestation in the study subjects. Material & Methods: A cross sectional epidemiological study was carried out in West Bengal, India among rural population of two districts. Stool samples from selected study subjects of all age groups were tested for presence of parasitic infestation by standard diagnostic procedures and data were collected to get information on socio demographic correlates of E. histolytica /E. dispar infestation. Results: Total 402 stool samples were tested. 23.4% of stool samples were positive for parasitic infestation. Major types were E. histolytica/E. dispar (17.7%), G. lambia (3.23%), B. hominis (2.23%), A. lumbricoidis (0.99%) and Hookworm (0.76%). Six samples were positive for mixed infection (1.49%). Among those infected with E. histolytica/E. dispar, majority were female (63.4%), middle aged 21-60yrs (53.5%). Magnitude was highest among geriatric people (26.7%) and children aged 6-10yrs (22.7%) and least among <5yrs age (9.1%). Majority of the infested persons were asymptomatic (52.1%). Participant’s self perception, self medication & water used for washing utensils were found to be significantly associated with parasitic infestation. Conclusion: Result reiterates the need for organized efforts for improvement of basic sanitation needs in the area to curb the parasitic morbidities. DOI: http://dx.doi.org/10.3126/ajms.v2i3.4375 Asian Journal of Medical Sciences 2 (2011) 164-168

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

Healthcare ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 9 ◽  
Author(s):  
Sarmila Tandukar ◽  
Jeevan Sherchand ◽  
Surendra Karki ◽  
Bikash Malla ◽  
Rajani Ghaju Shrestha ◽  
...  
Keyword(s):  
Drinking Water ◽  
Water Samples ◽  
Acute Gastroenteritis ◽  
Enteric Viruses ◽  
Enteric Virus ◽  
Viral Agent ◽  
Virus Species ◽  
Group A Rotaviruses ◽  
Group A ◽  
Stool Samples

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.

scholarly journals Genetic recombination and diversity of sapovirus in pediatric patients with acute gastroenteritis in Thailand, 2010–2018

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8520 ◽  
Author(s):  
Kattareeya Kumthip ◽  
Pattara Khamrin ◽  
Hiroshi Ushijima ◽  
Limin Chen ◽  
Shilin Li ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Genetic Recombination ◽  
Age Groups ◽  
Etiologic Agent ◽  
Rt Pcr ◽  
Chiang Mai ◽  
Predominant Genotype ◽  
Recombinant Strains ◽  
Stool Samples ◽  
First Time

Background Human sapovirus (SaV) is an etiologic agent of acute gastroenteritis (AGE) in all age groups worldwide. Genetic recombination of SaV has been reported from many countries. So far, none of SaV recombinant strain has been reported from Thailand. This study examined the genetic recombination and genotype diversity of SaV in children hospitalized with AGE in Chiang Mai, Thailand. Methods Stool samples were collected from children suffering from diarrhea who admitted to the hospitals in Chiang Mai, Thailand between 2010 and 2018. SaV was detected by RT-PCR and the polymerase and capsid gene sequences were analysed. Results From a total of 3,057 samples tested, 50 (1.6%) were positive for SaV. Among positive samples, SaV genotype GI.1 was the most predominant genotype (40%; 20/50), followed by GII.1 and GII.5 (each of 16%; 8/50), GI.2 (14%; 7/50), GIV.1 (4%; 2/50), and GI.5 (2%; 1/50). In addition, 4 SaV recombinant strains of GII.1/GII.4 were identified in this study (8%; 4/50). Conclusions The data revealed the genetic diversity of SaV circulating in children with AGE in Chiang Mai, Thailand during 2010 to 2018 and the intragenogroup SaV recombinant strains were reported for the first time in Thailand.

scholarly journals Molecular epidemiology and genetic diversity of norovirus among hospitalized children with acute gastroenteritis in Tianjin, China, 2018–2020

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yulian Fang ◽  
Zhaoying Dong ◽  
Yan Liu ◽  
Wei Wang ◽  
Mengzhu Hou ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Acute Gastroenteritis ◽  
Age Groups ◽  
Molecular Characteristics ◽  
Rt Pcr ◽  
Predominant Genotype ◽  
Epidemiological Analysis ◽  
Version 2.0 ◽  
Stool Samples ◽  
Polymerase Chain

Abstract Background Norovirus (NoV) is a major cause of viral acute gastroenteritis (AGE) in children worldwide. Epidemiological analysis with respect to the virus strains is limited in China. This study aimed to investigate the prevalence, patterns, and molecular characteristics of NoV infection among children with AGE in China. Methods A total 4848 stool samples were collected from children who were admitted with AGE in Tianjin Children’s Hospital from August 2018 to July 2020. NoV was preliminarily detected using real-time reverse transcription polymerase chain reaction (RT-PCR). Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid genes of positive samples were amplified by conventional RT-PCR and then sequenced. The NoV genotype was determined by online Norovirus Typing Tool Version 2.0, and phylogenetic analysis was conducted using MEGA 6.0. Results The prevalence of NoV was 26.4% (1280/4848). NoV was detected in all age groups, with the 7–12 months group having the highest detection rate (655/2014, 32.5%). NoV was detected during most part of the year with higher frequency in winter than other seasons. Based on the genetic analysis of RdRp, GII. Pe was the most predominant genotype detected at 70.7% (381/539) followed by GII.P12 at 25.4% (137/539). GII.4 was the most predominant capsid genotype detected at 65.3% (338/518) followed by GII.3 at 26.8% (139/518). Based on the genetic analysis of RdRp and capsid sequences, the strains were clustered into 10 RdRp–capsid genotypes: GII.Pe-GII.4 Sydney 2012 (65.5%), GII.P12-GII.3 (27.2%), GII.P16-GII.2 (1.8%), GII.P12-GII.2 (0.2%), GII.P17-GII.17 (1.1%), GII.Pe-GII.3 (1.8%), GII.Pe-GII.2 (1.1%), GII.Pe-GII.1 (0.4%), GII.16-GII.4 Sydney 2012 (0.7%), and GII.P7-GII.6 (0.2%). The predominant NoV genotypes changed from GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 between August 2018 and July 2019 to GII.Pe-GII.4 Sydney 2012 and GII.P16-GII.2 between August 2019 and July 2020. The patients with GII.Pe-GII.4 Sydney 2012 genotype were more likely to suffer from vomiting symptom than those with GII.P12-GII.3. Conclusions NoV is an important pathogen responsible for viral AGE among children in China. GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 were major recombinant genotypes. Knowledge of circulating genotypes and seasonal trends is of great importance for disease prevention and surveillance.

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