Abstract Title
Norovirus genetic diversity on watershed scale: interest of passive sampling
Presenter
Soizick F. Le Guyader, IFREMER Institute
Co-Author(s)
Françoise Vincent-Hubert1, Antoine VERON1, Cyril Noel2, Julien Schaeffer1, Marion Desdouits1, Joanna Ollivier1, Pascal Garry1, Soizick F. Le Guyader1
1 IFREMER, Laboratoire Santé, Environnement et Microbiologie, Nantes, France
2 IFREMER, IRSI, SeBiMER Service de Bioinformatique, Plouzané, France
Abstract Category
Food & Environmental Virology-II (Wastewater & others)
Abstract
Norovirus contamination of watershed upstream of oyster-farming sites is a risk for microbial quality of oysters. Passive sampling demonstrated its usefulness for surveillance of viruses sporadically discharged in sewage and seawater. The aims of this study were (i) to identify the geographical origin of norovirus input on a watershed scale and (ii) to compare the genetic diversity of norovirus GI and GII in oyster samples and in water collected with passive sampler.
During 18 months, passive samplers were immersed for 48 hours at 12 sites, including 2 in oyster farming areas, where oysters were also positioned. Noroviruses GI and GII were detected by RT-qPCR in both matrices, and target metagenomic was performed in the VP1 region of GI and GII using Illumina MiSeq. A standardized automated metagenomics analysis workflow was optimized to reconstruct and identify norovirus sequences. Noroviruses GI and GII were identified in 15% of samplers (50/334) and 41% of oysters (23/56). Sequencing revealed a high genetic diversity, with six genotypes for GI-VP1 (GI.1, GI.2, GI.3, GI.4, GI.5 and GI.6), and nine for GII-VP1 (GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17). Genotyping carried out on oysters and samplers shows the complementarity of the two matrices, a higher genetic diversity during the winter period and inter-site variability for both matrices. This study demonstrated the value of passive sampling for both norovirus detection and metagenomic on a watershed scale.
During 18 months, passive samplers were immersed for 48 hours at 12 sites, including 2 in oyster farming areas, where oysters were also positioned. Noroviruses GI and GII were detected by RT-qPCR in both matrices, and target metagenomic was performed in the VP1 region of GI and GII using Illumina MiSeq. A standardized automated metagenomics analysis workflow was optimized to reconstruct and identify norovirus sequences. Noroviruses GI and GII were identified in 15% of samplers (50/334) and 41% of oysters (23/56). Sequencing revealed a high genetic diversity, with six genotypes for GI-VP1 (GI.1, GI.2, GI.3, GI.4, GI.5 and GI.6), and nine for GII-VP1 (GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17). Genotyping carried out on oysters and samplers shows the complementarity of the two matrices, a higher genetic diversity during the winter period and inter-site variability for both matrices. This study demonstrated the value of passive sampling for both norovirus detection and metagenomic on a watershed scale.