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.

Intra- and Cross-Species Transmission of Astroviruses

“…The directionality of this transmission has been debated, indicating that transmission from humans to livestock could be occurring in addition to traditional zoonosis. It has been proposed that recombination events have also occurred between human and feline AstVs [52]. Together these data demonstrate how the close proximity of humans with other species harboring AstVs can facilitate recombination and cross-species transmission between them.…”

High Throughput Sequencing for the Detection and Characterization of RNA Viruses

“…In particular, with respect to RNA viruses, this further contributes to the associated challenge, requiring a Family specific priming PCR approach. Amplicon based sequencing approaches, (particularly tiling or “jackhammer”) have been widely applied for the detection of RNA viruses with varying levels of success (Marston et al, 2013 ; Cruz et al, 2016 ; Cuevas et al, 2016 ; Hanke et al, 2016 ; Imamura et al, 2016b ; Boonchan et al, 2017 ; Johnson et al, 2017 ; Parra et al, 2017 ; Quick et al, 2017 ; Hata et al, 2018 ; Lun et al, 2018 ; Suffredini et al, 2018 ; Wang et al, 2018 ; Cinek et al, 2019 ; Di et al, 2019 ; Fumian et al, 2019 ; Gradel et al, 2019 ; Eden et al, 2020 ; Fauver et al, 2020 ; Lu et al, 2020 ; Mancini et al, 2020 ). Tiling or “jackhammer” approaches involve designing a series of primers that generate short products across the whole target genome and can be Family or genus specific.…”

Daily Lifestyle and Inflammatory Skin Diseases

“…EPA suppresses the production of TNF-α and IL-1β, and inflammatory lipid mediators, such as PGE2 and LTB4 [ 57 ]. Patients with psoriasis exhibit a lower intake of ω-3 fatty acids compared with healthy controls [ 10 ], and the metabolites of ω-3 fatty acids, resolvin E1, resolvin D1, and Maresin 1, exert anti-inflammatory actions in imiquimod-induced psoriasis-like skin inflammation in mice [ 58 , 59 , 60 ]. Impaired skin inflammation was also observed in approximately 80% of patients with psoriasis using fish oil supplements [ 61 ].…”