FN Archimer Export Format
PT J
TI Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters
BT 
AF Strubbia, Sofia
   Schaeffer, Julien
   Oude Munnink, Bas B.
   Besnard, Alban
   Phan, My V. T.
   Nieuwenhuijse, David F.
   de Graaf, Miranda
   Schapendonk, Claudia M. E.
   Wacrenier, Candice
   Cotten, Matthew
   Koopmans, Marion P. G.
   LE GUYADER, Soizick
AS 1:1;2:1;3:2;4:1;5:2;6:2;7:2;8:2;9:1;10:2;11:2;12:1;
FF 1:PDG-RBE-SGMM-LSEM;2:PDG-RBE-SGMM-LSEM;3:;4:PDG-RBE-SGMM-LSEM;5:;6:;7:;8:;9:PDG-RBE-SGMM-LSEM;10:;11:;12:PDG-RBE-SGMM-LSEM;
C1 Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
   Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
C2 IFREMER, FRANCE
   ERASMUS MC, NETHERLANDS
SI NANTES
SE PDG-RBE-SGMM-LSEM
IN WOS Ifremer UPR
   DOAJ
   copubli-europe
IF 4.235
TC 20
UR https://archimer.ifremer.fr/doc/00586/69765/67656.pdf
LA English
DT Article
DE ;norovirus;sewage;oysters;metagenomic sequencing;metavirome
AB Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations. 
PY 2019
PD OCT
SO Frontiers In Microbiology
SN 1664-302X
PU Frontiers Media SA
VL 10
IS 2394
UT 000491978100001
DI 10.3389/fmicb.2019.02394
ID 69765
ER

EF