Human stool contains a previously unrecognized diversity of novel astroviruses

Abstract

Human astroviruses are a leading cause of gastrointestinal disease. Since their discovery in 1975, 8 closely related serotypes have been described in humans, and more recently, two new astrovirus species, astrovirus MLB1 and astrovirus VA1, were identified in diarrhea patients. In this study, we used consensus astrovirus primers targeting the RNA polymerase to define the diversity of astroviruses present in pediatric patients with diarrhea on two continents. From 416 stool specimens comprising two different cohorts from Vellore, India, 35 samples were positive. These positive samples were analyzed further by either sequencing of the ~400 bp amplicon generated by the consensus PCR or by performing additional RT-PCR specific for individual astroviruses. 19 samples contained the classic human astrovirus serotypes 1-8 while 7 samples were positive for the recently described astrovirus MLB1. Strikingly, from samples that were positive in the consensus PCR screen but negative in the specific PCR assays, five samples contained sequences that were highly divergent from all previously described astroviruses. Sequence analysis suggested that three novel astroviruses, tentatively named astroviruses VA2, MLB2 and VA3, were present in these five patient specimens (AstV-VA2 in 2 patients, AstV-MLB2 in 2 patients and AstV-VA3 in one patient). Using the same RT-PCR screening strategy, 13 samples out of 466 tested stool specimens collected in St. Louis, USA were positive. Nine samples were positive for the classic human astroviruses. One sample was positive for AstV-VA2, and 3 samples were positive for AstV-MLB2 demonstrating that these two viruses are globally widespread. Collectively, these findings underscore the tremendous diversity of astroviruses present in fecal specimens from diarrhea patients. Given that a significant fraction of diarrhea etiologies is currently unknown, it is plausible that these or other yet unrecognized astroviruses may be responsible for at least part of the undiagnosed cases.

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

“…In contrast, VA-AstVs were less frequently detected in the influent samples, suggesting that VA-AstVs are not as prevalent as classic HAstVs or MLB-AstVs in humans. Similarly, clinical studies investigating infantile diarrheal samples in India, the United States, Egypt, and China reported the more frequent occurrence of MLB-AstVs than VA-AstVs (22,49,50). A previous clinical study reported the less frequent detection of MLB-AstV, but the study investigated samples from adults with diarrhea and children without diarrhea (20).…”

“…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.…”

“…A previous study suggested an association of VA-AstVs with gastroenteritis outbreaks, although the pathogenicity of the novel AstVs has not been well documented to date (23). Finkbeiner et al (22) pointed out that the novel AstVs could be the cause of gastroenteritis diseases whose etiologies are undetermined. Further studies are needed for characterization of the novel AstVs with respect to their pathogenicity, epidemiology, and fate in the water environment.…”

“…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). To date, MLB-AstVs have been divided into 3 genotypes (MLB-AstV genotype 1 [MLB-AstV-1] to MLB-AstV-3) and VAAstVs have been divided into 4 genotypes (VA-AstV genotype 1 [VA-AstV-1] to VA-AstV-4) (7,20,23,24).…”

Astrovirus Pathogenesis

“…HAstV-MLB1 was initially discovered in pediatric stool samples from Australia [39][40][41], whereas HAstV-MLB2 and HAstV-MLB3 were discovered in India [42,43]. The HAstV-VA1-VA3 viruses were first discovered in an outbreak of gastroenteritis in Virginia, USA [44,45]; HAstV-VA4 in a cohort of Indian children with diarrhea [43]; and HAstV-VA5 in a cohort in Gambia [46]. The prevalence of the non-canonical viruses varies greatly according to geographic location [6], and their association with clinical disease remains somewhat of a mystery in comparison to the canonical strains.…”