Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

Abstract

Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of “micro-mass sequencing” that entails minimal starting sample quantity (<100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank.

Wastewater Analysis Indicates that Genetically Diverse Astroviruses, Including Strains Belonging to Novel Clades MLB and VA, Are Circulating within Japanese Populations

“…The presence of these novel AstVs has been documented in several countries, including Australia, China, India, Nepal, the Netherlands, Nigeria, Pakistan, and the United States, but not in Japan (19,20,22,23,47,48). We identified MLB-AstVs in all influent samples collected between November 2007 and March 2008.…”

“…In spite of their importance as enteric pathogens, the occurrence and other characteristics of HAstVs in water compared to those of other enteric viruses, such as noroviruses, rotaviruses, and adenoviruses, have not been well documented (17, 18). Due to the scarcity of knowledge, the fate of HAstVs in water environments and wastewater treatment processes is not well understood.Recent studies based on viral metagenomic analysis have identified some novel AstVs, namely, clade MLB AstVs (MLB-AstVs) and clade VA (HMO) AstVs (VA-AstVs), in human feces (19,20). The novel AstV strains are genetically distinct from the classic HAstV strains (20)(21)(22); in fact, VA-AstVs are genetically more closely related to mink/ovine AstVs than to classic HAstVs (20,22).…”

“…Recent studies based on viral metagenomic analysis have identified some novel AstVs, namely, clade MLB AstVs (MLB-AstVs) and clade VA (HMO) AstVs (VA-AstVs), in human feces (19,20). The novel AstV strains are genetically distinct from the classic HAstV strains (20)(21)(22); in fact, VA-AstVs are genetically more closely related to mink/ovine AstVs than to classic HAstVs (20,22).…”

Detection of Newly Described Astrovirus MLB1 in Stool Samples from Children

“…This study was an extension of recently published reports of characterization of AstV-MLB1 from a fecal sample obtained in Australia in 1999 ( 2 , 3 ). These studies provide evidence of a divergent group of astroviruses and their etiologic association with human disease.…”

Detection and Molecular Characterization of Porcine Picobirnavirus in Feces of Domestic Pigs from Kolkata, India

“…Thereafter, PBVs were detected from different countries in feces of humans, a wide range of mammals, birds, reptiles and even from environmental samples [1-5, 7, 8, 12, 14, 16-18, 20-23, 25, 27-30, 34, 36]. PBVs were detected from immunocompromised patients [24] in which implied to be ''opportunistic pathogens'' and have also been detected from asymptomatic hosts [11]. The question whether PBV is an 'innocuous agent' of the intestine remains to be investigated [2,7,19,31,35].…”