FN Archimer Export Format
PT J
TI A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks
BT 
AF Desdouits, Marion
   Wacrenier, Candice
   Ollivier, Joanna
   Schaeffer, Julien
   LE GUYADER, Soizick
AS 1:1;2:1;3:1;4:1;5:1;
FF 1:PDG-RBE-SGMM-LSEM;2:PDG-RBE-SGMM-LSEM;3:PDG-RBE-SGMM-LSEM;4:PDG-RBE-SGMM-LSEM;5:PDG-RBE-SGMM-LSEM;
C1 Laboratoire de Microbiologie (LSEM), Ifremer, rue de l’Ile d’Yeu, B.P. 21105, CEDEX 03, 44311 Nantes, France
C2 IFREMER, FRANCE
SI NANTES
SE PDG-RBE-SGMM-LSEM
IN WOS Ifremer UPR
   DOAJ
IF 1
TC 14
UR https://archimer.ifremer.fr/doc/00646/75831/76818.pdf
   https://archimer.ifremer.fr/doc/00646/75831/76819.pdf
LA English
DT Article
DE ;norovirus;foodborne virus;metagenomics;amplicon deep sequencing;viral diversity
AB Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks. 
PY 2020
PD SEP
SO Viruses-basel
SN 1999-4915
PU MDPI AG
VL 12
IS 9
UT 000582008900001
DI 10.3390/v12090978
ID 75831
ER

EF