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首页> 外文期刊>Food microbiology >Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR
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Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR

机译：使用下一代测序和数字PCR分析涉及大型诺如病毒胃肠炎暴发的冷冻草莓

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Virus-contaminated frozen berries have been frequently identified as cause of foodborne disease outbreaks. To provide new tools for virus detection and characterization in berries, next generation sequencing (NGS) and reverse transcription-digital PCR (RT-dPCR) techniques were tested here with strawberries previously involved in a large-scale norovirus (NoV) gastroenteritis outbreak in Germany. By NGS, about 29 million sequence reads were generated, which mainly showed identities to sequences from the plant matrix and from the bacterial flora. Most abundant virus sequences originated from plant-specific viruses, whereas sequences with high identity to human viruses were rare. Only two sequence reads showed homologies to human NoV. They were identical to GII.P16/GII.13 NoV sequences from patients and a strawberry sample independently analyzed during the outbreak. Quantification of the GII NoV RNA of the berries using RT-dPCR confirmed a low mean virus amount of 185 copies/25 g, which is similar to independently assessed RT-qPCR results (257 copies/25 g). The study shows that identification of human-pathogenic viruses in naturally contaminated frozen berries is possible using NGS technologies. However, the method needs to be further optimized in order to enable convenient and reproducible detection of a low amount of human-pathogenic virus sequences in a background of highly abundant nucleic acids of other sources.
机译：经常被病毒污染的冷冻浆果被确定为食源性疾病暴发的原因。为了提供用于浆果中病毒检测和鉴定的新工具，此处对以前参与德国大规模诺如病毒（NoV）肠胃炎暴发的草莓进行了下一代测序（NGS）和逆转录数字PCR（RT-dPCR）技术的测试。 。通过NGS，产生了约2900万个序列读数，主要显示了与植物基质和细菌菌群中序列的同一性。大多数丰富的病毒序列起源于植物特异性病毒，而与人类病毒具有高度同一性的序列却很少。仅两个序列读数显示出与人类NoV的同源性。它们与爆发期间独立分析的患者和草莓样品的GII.P16 / GII.13 NoV序列相同。使用RT-dPCR对浆果的GII NoV RNA进行定量，确认平均病毒量较低，为185拷贝/ 25 g，这与独立评估的RT-qPCR结果（257拷贝/ 25 g）相似。研究表明，使用NGS技术可以鉴定自然污染的冷冻浆果中的人类致病病毒。但是，该方法需要进一步优化，以便在其他来源的高度丰富的核酸的背景下，方便，可重复地检测少量的人类致病病毒序列。

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