Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

Bonny, Patrice; Schaeffer, Julien; Besnard, Alban; Desdouits, Marion; Ngang, Jean Justin Essia; Guyader, Françoise S. Le

doi:10.3389/fmicb.2021.770385

Cited by 10 publications

(13 citation statements)

References 44 publications

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“…This technique was found to efficiently obtain complete genomes of different human enteric viruses in sewage samples and related bioaccumulated oysters (Strubbia 2019). Such an approach was also applied to naturally contaminated clams collected in the Sanaga river (Cameroon) and allowed the detection of a large diversity of RNA viruses including human or animal norovirus sequences (Bonny et al 2021). Here, the method was promising on TSS samples but performed less well on naturally contaminated samples from the BLS and OB sets, presumably due to longer storage and loss of NoV genome integrity.…”

Section: Discussionmentioning

confidence: 99%

Application of Next Generation Sequencing on Norovirus‐contaminated oyster samples

Ollivier

Lowther

Desdouits

et al. 2022

EFSA Supporting Publications

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Bivalve molluscan shellfish (BMS) contamination with gastroenteritis viruses such as norovirus (NoV) is recognized as a significant public health risk worldwide. These foodborne epidemics are characterized by very low viral concentrations in the implicated foods, and by diverse viruses or multiple NoV strains originating from human sewage, resulting in different strains (co‐)infecting the consumers. Next‐generation sequencing (NGS) offers promising means to describe the diversity of strains present in BMS or to retrace transmission chains in outbreak settings, but their sensitivity and reproducibility remained to be assessed for this application. In this work, we evaluated the ability of three promising NGS methods to sequence diverse NoV in environmental or food BMS and human stool samples. Using laboratory‐prepared samples of known NoV composition, we evaluated the sensitivity, reproducibility, repeatability and selectivity of metabarcoding, capture‐based metagenomics and long amplicon sequencing, considering representative NoV strains from genogroup I and II, and the impact of the BMS matrix. The metabarcoding, with separate amplification of polymerase and capsid gene segments followed by Illumina sequencing, was the most sensitive method. It was applied to a selection of 212 BMS samples collected through the European Commission’s NoV baseline survey (BLS), demonstrating a high diversity of NoV sequences found in the BMS which reflect the diversity of NoV strains circulating in the European human population. Besides, a capture‐based metagenomics with enrichment of vertebrate viruses was applied on 20 of these BLS samples as well as 20 BMS linked to outbreaks and 10 related human stool samples. In BMS, it yielded NoV sequences compatible with the genomes identified in stool samples, but they were too short to allow definitive confirmation of the infection source. The present report describes NGS methods, including the bioinformatic pipelines, applicable to molecular epidemiology of NoV in BMS, their current limitations and expected outcomes.

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Section: Discussionmentioning

confidence: 99%

Application of Next Generation Sequencing on Norovirus‐contaminated oyster samples

Ollivier

Lowther

Desdouits

et al. 2022

EFSA Supporting Publications

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“…A novel bastrovirus called AtBastV/GCCDC11/2022 was found in the gut samples of Asiatic toads, with similar genomic characteristics to those previously described for BastVs. BastVs is a novel group of hepe-astrovirus-like viruses identified in human stools [ 29 ], raw sewage [ 30 ], pigs [ 31 ], bats [ 32 ], rats, as well as in clams [ 33 ] by metagenomics sequencing. The RNA genome of AtBastV/GCCDC11 consists of three ORFs: ORF1, ORF2, and ORF3.…”

Section: Discussionmentioning

confidence: 99%

First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing

Chen

Zhao

et al. 2023

Viruses

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Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.

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“…Bioinformatic analysis was performed using a Nextflow pipeline as previously described ( Bonny et al, 2021 ). For the first part of the analysis, reads from each library as well as reads merged from all four libraries per sample were considered (5 analysis for each sample; Figure 2 ).…”

Section: Methodsmentioning

confidence: 99%

“…However, most of the time only amplicon-based metagenomic approaches have solved the issue of sensitivity to describe the genetic diversity of one virus genus ( Suffredini et al, 2018 ; Fumian et al, 2019 ; Mabasa et al, 2022 ). In previous works, we found that sample pre-treatment and capture-based enrichment during the library preparation stage allowed the recovery of higher numbers of viral reads and thus the identification of longer viral contigs ( Strubbia et al, 2019 ; Bonny et al, 2021 ).…”

Section: Introductionmentioning

confidence: 98%

Looking into sewage: how far can metagenomics help to detect human enteric viruses?

et al. 2023

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The impact of human sewage on environmental and food contamination constitutes an important safety issue. Indeed, human sewage reflects the microbiome of the local population, and a variety of human viruses can be detected in wastewater samples. Being able to describe the diversity of viruses present in sewage will provide information on the health of the surrounding population health and will help to prevent further transmission. Metagenomic developments, allowing the description of all the different genomes present in a sample, are very promising tools for virome analysis. However, looking for human enteric viruses with short RNA genomes which are present at low concentrations is challenging. In this study we demonstrate the benefits of performing technical replicates to improve viral identification by increasing contig length, and the set-up of quality criteria to increase confidence in results. Our approach was able to effectively identify some virus sequences and successfully describe the viral diversity. The method yielded full genomes either for norovirus, enterovirus and rotavirus, even if, for these segmented genomes, combining genes remain a difficult issue. Developing reliable viromic methods is important as wastewater sample analysis provides an important tool to prevent further virus transmission by raising alerts in case of viral outbreaks or emergence.

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Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

Cited by 10 publications

References 44 publications

Application of Next Generation Sequencing on Norovirus‐contaminated oyster samples

Application of Next Generation Sequencing on Norovirus‐contaminated oyster samples

First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing

Looking into sewage: how far can metagenomics help to detect human enteric viruses?

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