Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing
Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing
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DOI：
10.1099/jgv.0.001003
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发表时间：
2018-02-01
影响因子：
3.8
通讯作者：
Karganova, Galina G.
中科院分区：
文献类型：
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作者：
Litov, Alexander G.;Deviatkin, Andrey A.;Karganova, Galina G.
我们研究了具有共同祖先的两个蜱传脑炎病毒（TBEV）群体中的微小变异：小鼠脑适应变异EK-328 c和蜱适应变异M。在Illumina MiSeq 2*250配对末端v2化学上用来自RT-PCR病毒RNA的定制扩增子进行高通量测序。使用LowFreq程序（默认设置）和Sanger测序的共有序列作为参考，鉴定了研究群体内丰度为1%及以上的变体。在我们先前研究的背景下使用所获得的数据，我们得出结论，TBEV变体，其不同于主要群体表型，并且可以在有利的环境条件下成为病毒群体的主要部分，可以以低于1%的丰度长期存在。我们的数据与文献的比较使我们能够得出结论，实验室变异EK-328 c和变异M与来自自然群体和一些快速进化的RNA病毒的TBEV变异具有相似的SNV计数。
We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.