FN Archimer Export Format
PT J
TI Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
BT 
AF BONNY, Patrice
   SCHAEFFER, Julien
   BESNARD, Alban
   DESDOUITS, Marion
   Essia Ngang, Jean Justin
   LE GUYADER, Soizick
AS 1:1,2,3;2:1;3:1;4:1;5:2,3;6:1;
FF 1:;2:PDG-RBE-SGMM-LSEM;3:PDG-RBE-SGMM-LSEM;4:PDG-RBE-SGMM-LSEM;5:;6:PDG-RBE-SGMM-LSEM;
C1 Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
   Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon
   Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
C2 IFREMER, FRANCE
   UNIV YAOUNDE, CAMEROON
   IMPM, CAMEROON
SI NANTES
SE PDG-RBE-SGMM-LSEM
IN WOS Ifremer UPR
   DOAJ
   copubli-int-hors-europe
   copubli-sud
IF 6.064
TC 6
UR https://archimer.ifremer.fr/doc/00737/84861/89887.pdf
LA English
DT Article
DE ;shellfish;metagenomics;human enteric viruses;mammal viruses;zoonosis
AB Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence. 
PY 2021
PD NOV
SO Frontiers In Microbiology
SN 1664-302X
PU Frontiers Media
VL 12
UT 000729925300001
DI 10.3389/fmicb.2021.770385
ID 84861
ER

EF