Next-generation amplicon sequencing identifies genetically diverse human astroviruses, including recombinant strains, in environmental waters

Akihiko Hata, Masaaki Kitajima, Eiji Haramoto, Suntae Lee, Masaru Ihara, Charles P Gerba, Hiroaki Tanaka

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3 Scopus citations


Human astroviruses are associated with gastroenteritis and known to contaminate water environments. Three different genetic clades of astroviruses are known to infect humans and each clade consists of diverse strains. This study aimed to determine the occurrence and genetic diversity of astrovirus strains in water samples in different geographical locations, i.e., influent and effluent wastewater samples (n = 24 each) in Arizona, U.S., and groundwater (n = 37) and river water (n = 14) samples collected in the Kathmandu Valley, Nepal, using next-generation amplicon sequencing. Astrovirus strains including rare types (types 6 and 7 classical human astroviruses), emerging type (type 5 VA-astroviruses), and putative recombinants were identified. Feline astrovirus strains were collaterally identified and recombination between human and feline astroviruses was suggested. Classical- and VA-astroviruses seemed to be prevalent during cooler months, while MLB-astroviruses were identified only during warmer months. This study demonstrated the effectiveness of next-generation amplicon sequencing for identification and characterization of genetically diverse astrovirus strains in environmental water.

Original languageEnglish (US)
Article number11837
JournalScientific Reports
Issue number1
Publication statusPublished - Dec 1 2018


ASJC Scopus subject areas

  • General

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