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

ABSTRACT: 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.

SUBMITTER: Hata A

PROVIDER: S-EPMC6081416 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

Hata Akihiko A Kitajima Masaaki M Haramoto Eiji E Lee Suntae S Ihara Masaru M Gerba Charles P CP Tanaka Hiroaki H

Scientific reports 20180807 1

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 co ...[more]

PMID: 30087387

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

Publications

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

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