Exploring the Astrovirome of Shellfish Matrices Using Nanopore Sequencing

Astroviruses are important human enteric pathogens transmissible with contaminated food and water. Astroviruses have also been identified in mammals, birds, lower vertebrates and invertebrates. The genetic diversity of human and animal astroviruses poses a challenge for diagnostics and taxonomy. As...

Full description

Saved in:
Bibliographic Details
Published in:Veterinary sciences 2023-02, Vol.10 (3), p.175
Main Authors: Beikpour, Farzad, Pellegrini, Francesco, Lanave, Gianvito, Camero, Michele, Catella, Cristiana, Di Martino, Barbara, Di Profio, Federica, Masotti, Chiara, Battistini, Roberta, Serracca, Laura, La Rosa, Giuseppina, Martella, Vito, Suffredini, Elisabetta
Format: Article
Language:English
Subjects:
Astroviridae
astrovirus
Birds
Children
Diseases
DNA sequencing
DNA-directed RNA polymerase
Encephalitis
enteric
Food contamination
Gastrointestinal diseases
Genetic diversity
Genomes
Immunocompromised hosts
Invertebrates
Mollusks
Nucleotide sequencing
Oysters
Pathogens
Phylogenetics
Polymerase chain reaction
Process controls
Proteins
Protocol
Reptiles & amphibians
RNA
RNA polymerase
RNA-directed RNA polymerase
Shellfish
Surface water
virome
Viruses
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Astroviruses are important human enteric pathogens transmissible with contaminated food and water. Astroviruses have also been identified in mammals, birds, lower vertebrates and invertebrates. The genetic diversity of human and animal astroviruses poses a challenge for diagnostics and taxonomy. As a proof of concept, we used a panastrovirus consensus primer set, able to amplify in a nested RT-PCR protocol a 400-nt-long fragment of the RNA-dependent RNA polymerase of most members of the family, in conjunction with a nanopore sequencing platform, to generate information on the astrovirome in filter-feeding mollusks. Amplicons generated from bivalve samples were used to generate libraries for deep sequencing. In three samples, only one unique RdRp sequence type was obtained. However, in seven samples and in three barcodes with eleven pooled samples, we identified a variety of known and unknown RdRp sequence types, in most cases distantly related to astrovirus sequences available in the databases. In total, 37 different sequence contigs were generated. Avian-origin astrovirus sequences were predominant, likely due to contamination of shellfish harvesting waters by marine birds. Astroviruses of the aquatic eco-system were also identified, whereas human astroviruses were not detected.
ISSN:2306-7381
2306-7381
DOI:10.3390/vetsci10030175