Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar
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Elsevier B.V.
Abstract
Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail. © 2022 The Authors
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Gastroenteritis, Next-generation sequencing, Unknown etiology, Viral metagenomic, Viruses, Child, Child, preschool, Feces, Humans, Infant, Qatar, Rotavirus, Clostridium difficile toxin a, Acute gastroenteritis, Adenoviridae, Article, Campylobacter coli, Campylobacter jejuni, Campylobacter upsaliensis, Clostridioides difficile, Coxsackievirus a16, Cryptosporidium, Cyclospora cayetanensis, Dehydration, Developing country, Diarrhea, Disease burden, Disease severity, Entamoeba histolytica, Enteroaggregative escherichia coli, Enteropathogenic escherichia coli, Enterotoxigenic escherichia coli, Escherichia coli, Feces analysis, Female, Genotype, Genotyping, Giardia intestinalis, High throughput sequencing, Human, Human respiratory syncytial virus, Human respiratory syncytial virus a, Influenza, Influenza a virus, Influenza virus, Major clinical study, Male, Metagenomics, Molecular diagnosis, Morbidity, Mortality, Nonhuman, Norovirus, Plant virus, Plesiomonas shigelloides, Polymerase chain reaction, Rna extraction, Sequence analysis, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Viral metagenomics, Virus detection, Virus etiology, Virus genome, Vomiting, Yersinia enterocolitica, Genetics, Preschool child, Virus