Abstract Title
Capture-based metaviromics to describe caliviridae diversity in contaminated shellfish
Presenter
Soizick F. Le Guyader, IFREMER Institute
Co-Author(s)
Sylvain Parnaudeau, Julien Schaeffer, Cécile Le Mennec, Joanna Ollivier, Marion Desdouits, Soizick F. Le Guyader
Abstract Category
Food & Environmental Virology-I (Food)
Abstract
Precise identification of norovirus or sapovirus in food samples such as oysters, is still challenging considering their large genomic diversity and the low concentration. However, to provide data for risk analysis, it seems important to accurately identify strain diversity.
First, using five shellfish samples analyzed in triplicates, three commercial kits allowing enrichment in viral sequences during library preparation were compared (9 libraries per sample). Of the tested kits, one displayed lower variation between replicates and allowed to sequence a higher diversity of calicivirus strains.
Second, this kit was applied to prepare the libraries from 160 oyster samples collected in four sites. 38 calicivirus contigs were obtained, from four contigs in one site to 15 in the most contaminated site. Contigs identification showed one site contaminated mainly by animal sapovirus (7 GIII sequences), two sites with a mixture of human and animal norovirus and sapovirus, while only human norovirus sequences (9) were identified in the fourth site.
Finally, 15 shellfish samples implicated in outbreaks were analyzed. For norovirus, five complete genomes (GI and GII) were recovered from three samples, and many other long fragments allowing the identification of GI, GII but also GIII, GIV and GVII strains. For sapovirus, one complete genome and 14 contigs characterized as GI and GII, one complete genome close to a GIII porcine and 12 other contigs related to animal origin were obtained.
To conclude, optimized sample preparation followed by capture-based metaviromics now allows the sequencing and identification of calicivirirus strains, in food such as shellfish.
First, using five shellfish samples analyzed in triplicates, three commercial kits allowing enrichment in viral sequences during library preparation were compared (9 libraries per sample). Of the tested kits, one displayed lower variation between replicates and allowed to sequence a higher diversity of calicivirus strains.
Second, this kit was applied to prepare the libraries from 160 oyster samples collected in four sites. 38 calicivirus contigs were obtained, from four contigs in one site to 15 in the most contaminated site. Contigs identification showed one site contaminated mainly by animal sapovirus (7 GIII sequences), two sites with a mixture of human and animal norovirus and sapovirus, while only human norovirus sequences (9) were identified in the fourth site.
Finally, 15 shellfish samples implicated in outbreaks were analyzed. For norovirus, five complete genomes (GI and GII) were recovered from three samples, and many other long fragments allowing the identification of GI, GII but also GIII, GIV and GVII strains. For sapovirus, one complete genome and 14 contigs characterized as GI and GII, one complete genome close to a GIII porcine and 12 other contigs related to animal origin were obtained.
To conclude, optimized sample preparation followed by capture-based metaviromics now allows the sequencing and identification of calicivirirus strains, in food such as shellfish.