Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set used for cDNA synthesis. A set of In-house designed (I-HD) hexamers, selected to lower mollusk amplification, gave promising results in terms of viral reads abundancy. However, the best correlation between CT values, thus concentrations, and number of reads was observed using random hexamers. Random hexamers also provided the highest numbers of reads and allowed the identification of sequence of different human enteric viruses. Regarding human norovirus, different genogroups and genotypes were identified among contigs longer than 500 bp. Two full genomes and six sequences longer than 3600 bases were obtained allowing a precise strain identification. The use of technical triplicates was found valuable to increase the chances to sequence viral strains present at low concentrations. Analyzing viral contamination in shellfish samples is quite challenging, however this work demonstrates that the recovery of full genome or long contigs, allowing clear identification of viral strains is possible.

中文翻译：

---

评估牡蛎中诺如病毒基因组多样性的元基因组：对六聚体选择和靶向捕获的富集的影响。

多年来，人们已经确定了通过食用食物传播人类病毒的情况，国际贸易增加了传播病毒病原体的风险。宏基因组学方法的发展对于监视食物和水中的病毒具有许多希望。这项工作旨在通过使用宏基因组学方法分析诺如病毒的多样性并评估三种牡蛎类型中依赖菌株的积累模式。在基于捕获的方法评估深度测序过程中增强病毒读取恢复之前，先评估了不同的六聚体对初免cDNA的作用。这项研究包括使用人工污染的牡蛎的技术复制品，以及对多种阴性对照进行分析。结果表明，用于合成cDNA的六聚体具有明显的影响。一组内部设计的（I-HD）六聚体，选择以降低软体动物的扩增，在病毒读取丰度方面给出了可喜的结果。但是，使用随机六聚体观察到了CT值，浓度和读取次数之间的最佳相关性。随机六聚体还提供了最高的读取次数，并允许鉴定不同人类肠道病毒的序列。关于人类诺如病毒，在长于500 bp的重叠群中发现了不同的基因组和基因型。获得了两个完整的基因组和六个比3600个碱基长的序列，从而可以进行精确的菌株鉴定。发现使用三份技术对增加对低浓度存在的病毒株进行测序的机会很有价值。分析贝类样品中的病毒污染非常具有挑战性，