Abstract
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.
Highlights
Gastroenteritis is an important health problem around the globe affecting people at any age, but it is especially severe among children and the elderly
A summary of the MiSeq output obtained from each sequenced pool containing the raw read number, andand viralviral sequences detected, among other information, is presented as number,contigs, contigs, sequences detected, among other information, is Supplementary presented as material
In combination with or without a viral enrichment approach, has the potential to uncover any viral species that might be present in a given sample
Summary
Gastroenteritis is an important health problem around the globe affecting people at any age, but it is especially severe among children and the elderly. Among all gastroenteritis etiological agents, viruses account for approximately 70% of acute cases in children with rotavirus (RV), norovirus (NoV), and adenovirus (AdV), accounting for the majority of cases [3,4], with an increase in astrovirus (AstV) and sapovirus (SaV) in the same age groups [5,6]. Despite these important viral agents, it has been estimated that nearly 40% of gastroenteritis cases have an unknown etiological agent, suggesting that most could be caused by undiscovered viruses [7]. More than 10,261 validated, complete viral genomes are available in databases (e.g., the National Center for Biotechnology Information (NCBI)
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