Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

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.

NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water

“…NoV GII.4 has been reported to be the most predominant genotype worldwide [95,96]. This is consistent with our findings, in which the presence of the GII.4 genotype was widely observed in different samples using ADS, including river water and treated wastewater samples, and also in a parsley sample.…”

“…The Llobregat river contained a wide diversity of HAstVs, including the species Mamastrovirus 1, 6, and 8. HAstVs are important agents causing acute gastroenteritis in children and have been involved in outbreaks affecting adults [95,98]. Although HAstV prevalence seems to be of lower importance compared to the number of outbreaks caused by NoV, its importance might be underestimated [5].…”

“…Although HAstV prevalence seems to be of lower importance compared to the number of outbreaks caused by NoV, its importance might be underestimated [5]. Recently, HAstVs have also been associated with other pathologies, such as meningitis and acute flaccid paralysis [95,[99][100][101]. HAstV-1, which was found in river water samples, is the most common type associated with infantile gastroenteritis [95,102].…”

“…Recently, HAstVs have also been associated with other pathologies, such as meningitis and acute flaccid paralysis [95,[99][100][101]. HAstV-1, which was found in river water samples, is the most common type associated with infantile gastroenteritis [95,102]. Picornaviridae sequences found in river water samples belonged to the genus Kobuvirus, specifically to Aichivirus A, a viral species that includes members recognized as human pathogens that cause gastroenteritis outbreaks [103][104][105].…”

Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses

“…Other viruses associated with gastroenteritis in humans include coronaviruses, toroviruses, picornaviruses, Viruses 2021, 13, 975 2 of 21 and picobirnaviruses [1]. With progressive advances in sequencing-based approaches to identify causative pathogens, we are increasingly adept at defining those viruses causing symptoms, characterizing their prevalence during asymptomatic infection, and identifying novel viral pathogens [9,10]. However, characterization of the effects of established or novel strains on the host requires the use of both in vitro and in vivo experimental model systems, many of which have, until recently, been lacking for these pathogens.…”