Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing.
Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing.
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DOI：
10.3390/ijms221810069
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发表时间：
2021-09-17
影响因子：
5.6
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Cao Y;Liu H;Yan Y;Liu W;Liu D;Li J
流感病毒仍然对人类构成严重威胁，我们尚未能够有效预测未来的大流行毒株并提前准备疫苗。其中一个主要原因是流感病毒的高度遗传多样性。我们不知道一个病毒种群的单个克隆型，因为有些是大多数，而另一些只占种群的一小部分。第一代（FGS）和下一代测序（NGS）技术具有固有的局限性，无法解析病毒群体中的少数克隆型信息。具有超长reads的第三代测序（TGS）技术有望解决这一问题，但其错误率较高。在此，我们利用MinION平台评估了新兴的直接RNA测序和cDNA测序，并建立了一种结合了Illumina测序技术的高精度和纳米孔测序技术的长读数的新方法来解决流感病毒的变异和克隆型。此外，还编写了一个新的程序来消除纳米孔测序误差对分析结果的影响。通过这个管道，我们在实验中鉴定了47个克隆型。我们的结论是，这种方法可以快速区分病毒基因的克隆型，使研究人员能够在群体水平上了解病毒的适应和进化。
Influenza viruses still pose a serious threat to humans, and we have not yet been able to effectively predict future pandemic strains and prepare vaccines in advance. One of the main reasons is the high genetic diversity of influenza viruses. We do not know the individual clonotypes of a virus population because some are the majority and others make up only a small fraction of the population. First-generation (FGS) and next-generation sequencing (NGS) technologies have inherent limitations that are unable to resolve a minority clonotype’s information in the virus population. Third-generation sequencing (TGS) technologies with ultra-long reads have the potential to solve this problem but have a high error rate. Here, we evaluated emerging direct RNA sequencing and cDNA sequencing with the MinION platform and established a novel approach that combines the high accuracy of Illumina sequencing technology and long reads of nanopore sequencing technology to resolve both variants and clonotypes of influenza virus. Furthermore, a new program was written to eliminate the effect of nanopore sequencing errors for the analysis of the results. By using this pipeline, we identified 47 clonotypes in our experiment. We conclude that this approach can quickly discriminate the clonotypes of virus genes, allowing researchers to understand virus adaptation and evolution at the population level.
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影响因子：
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影响因子：
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作者：
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