Schaeffer Julien, Desdouits Marion, Besnard Alban, Le Guyader Françoise S
Ifremer, Laboratoire de Microbiologie, U. Microbiologie Aliment Santé et Environnement, Nantes, France.
Front Microbiol. 2023 Apr 25;14:1161674. doi: 10.3389/fmicb.2023.1161674. eCollection 2023.
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.
人类污水对环境和食物污染的影响构成了一个重要的安全问题。实际上，人类污水反映了当地人群的微生物群，并且在废水样本中可以检测到多种人类病毒。能够描述污水中存在的病毒多样性将提供有关周围人群健康状况的信息，并有助于防止病毒的进一步传播。宏基因组学的发展使得能够描述样本中存在的所有不同基因组，是病毒组分析非常有前景的工具。然而，寻找低浓度存在的具有短RNA基因组的人类肠道病毒具有挑战性。在本研究中，我们证明了通过增加重叠群长度进行技术重复以改善病毒鉴定的益处，以及建立质量标准以提高对结果的信心。我们的方法能够有效地鉴定一些病毒序列并成功描述病毒多样性。该方法即使对于诺如病毒、肠道病毒和轮状病毒等分段基因组，也能产生完整的基因组，不过对于这些基因组，组合基因仍然是一个难题。开发可靠的病毒组学方法很重要，因为废水样本分析提供了一个重要工具，可通过在病毒爆发或出现时发出警报来防止病毒进一步传播。
