Genetic diversity of human adenovirus and human astrovirus in children with acute gastroenteritis in Northwest Ethiopia

Gelaw, Aschalew; Pietsch, Corinna; Liebert, Uwe G.

doi:10.1007/s00705-019-04421-8

Cited by 43 publications

(44 citation statements)

References 40 publications

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“…In the present study, the overall stool positivity rate for HAdV infection in this study was 3.47%, which is similar to what was reported in Brazil (3.9%), Bangladesh (4.82%), our previous studies (5.2%), but is much lower than in Northwest Ethiopia (32.0%) and Albania (23.2%) [18,24,[32][33][34]. According to our continuous monitoring data, the detection rate of HAdV in children with acute diarrheas was relatively stable in Shanghai from 2010 to 2018 [14].…”

Section: Discussionsupporting

confidence: 90%

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Molecular and Epidemiological of Human Adenovirus and Classic Human Astrovirus in Children With Acute Diarrhea in Shanghai, 2017-2018

Zhong

et al. 2020

Preprint

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Background: In addition to rotavirus and norovirus, human adenovirus (HAdV) and classic human astrovirus (classic HAstV) have been identified as important pathogens of acute diarrhea in infants and young children. Here, we presented the molecular epidemiology of HAdV and classic HAstV in children with acute diarrhea in Shanghai. Methods: Fecal specimens were collected from 804 outpatient infants and young children diagnosed as acute diarrhea in Shanghai from January 2017 to December 2018. All the samples were screened for the presence of HAdV and classic HAstV. HAdV and Classic HAstV were detected using traditional PCR and reverse-transcription PCR, respectively. All the HAdV and classic HAstV positive samples were genotyped by phylogenetic analysis. Results: Among these 804 fecal samples, 8.58% (69/804) samples were infected with at least one of HAdV or classic HAstV, and one of them was co-infected with these two viruses. The overall detection rates of HAdV and classic HAstV were 3.47% (28/804) and 5.22% (42/804), respectively. Four subgroups (A, B, C and F) of HAdV were detected and seven different genotypes (HAdV-C1, -C2, -B3, -C5, -A31, -F40 and -F41) were identified. Subgroup F had the highest constituent ratio at 64.29% (18/28) followed by non-enteric HAdV of subgroup C (21.43%, 6/28) and subgroup B 10.71% (3/28). HAdV-F41 (60.71%, 17/28) was the dominant genotype, followed by HAdV-C2 (14.29%, 4/28) and HAdV-B3 (10.71%, 3/28). Two diﬀerent genotypes of classic HAstV (HAstV-1 and HAstV-5) were identified in 42 samples during the study period. HAstV-1 (95.24%, 40/42) was the predominant genotype and the other two strains were genotyped as HAstV-5. Conclusions: Those findings indicate that HAdV and classic HAstV play an important role in the pathogenesis of acute diarrhea in children in Shanghai. Systematic and long-term surveillance of HAdV and classic HAstV are needed to monitor their prevalence in children and prevent major outbreak.

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Section: Discussionsupporting

confidence: 90%

“…Classic HAstV is responsible for 2 to 18.8% of acute diarrhea cases in children globally. HAstV-1 is the most prevalent genotype detected in children, whereas HAstV-2 ~ HAstV-8 are less prevalent [14,20,[24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Molecular and Epidemiological of Human Adenovirus and Classic Human Astrovirus in Children With Acute Diarrhea in Shanghai, 2017-2018

Zhong

et al. 2020

Preprint

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“…By a study in southern Brazil to investigate viruses causing gastroenteritis in hospitalised pediatric patients, the results showed that out of 225 fecal samples tested, human adenovirus was the predominant virus (16%), while 8% of the samples were positive for norovirus, and 6% were positive for rotavirus [24]. Additionally, many studies have shown that human enteric adenovirus types 40 and 41 (HAdV-40, AHdV-41) are an important cause of gastroenteritis [25][26][27][28]. In contrary to our study, updated estimates on diarrhoea-related childhood revealed that rotavirus is the leading cause of diarrhoea among children worldwide [29][30][31][32].…”

Section: Discussionmentioning

confidence: 99%

Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach

Mohammad

Madi

Al‐Nakib

2020

Virol J

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Background: Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods: We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results: Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion: Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.

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“…HAdV-F40/41 are distributed globally, with a frequency of detection ranging from 1.1-14 % in children, depending on the geographical area [11,[19][20][21]. In low-income countries, the prevalence of HAdV-F40/41 ranges from 4.3-32 % [22][23][24][25]. Other HAdV species, such as HAdV-A (types 12, 18 and 31), HAdV-C (types 1, 2 and 5) and HAdV-D (types 28, 29, 30, 32, 37 and 43-46), have also been associated, although less frequently, with diarrhoea [26][27][28][29].…”

Section: Introductionmentioning

confidence: 99%

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

Tahmasebi

Luchs

Tardy

et al. 2020

Journal of General Virology

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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.

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Genetic diversity of human adenovirus and human astrovirus in children with acute gastroenteritis in Northwest Ethiopia

Cited by 43 publications

References 40 publications

Molecular and Epidemiological of Human Adenovirus and Classic Human Astrovirus in Children With Acute Diarrhea in Shanghai, 2017-2018

Molecular and Epidemiological of Human Adenovirus and Classic Human Astrovirus in Children With Acute Diarrhea in Shanghai, 2017-2018

Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach

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

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