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

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

doi:10.3389/fmicb.2021.770385

Abstract

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.

Highlights

In the last few years, Generation Sequencing (NGS) has been increasingly used to study microbial populations in environmental samples
The same number of samples was collected from each site, and no difference in terms of prevalence or genomic concentrations was detected for norovirus contamination
Regarding hepatitis A virus contamination, only six samples were detected positive on site Bol compared to 10 samples on site Mou, with low concentrations very close to the limit of quantification

Summary

Introduction

In the last few years, Generation Sequencing (NGS) has been increasingly used to study microbial populations in environmental samples. As a catch-all agnostic approach, it holds great promise for monitoring and determining viral diversity in food and environmental samples such as sewage and shellfish (Desdouits et al, 2020; Nieuwenhuijse et al, 2020). Sewage sampling is clearly a good approach, but when the animal or wildlife excreta has to be considered, other approaches are necessary (Nieuwenhuijse et al, 2020; Osterhauss et al, 2020)

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