An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
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DOI：
10.1186/s13059-018-1618-7
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发表时间：
2019-01-08
期刊：
影响因子：
12.3
通讯作者：
Andersen, Kristian G.
中科院分区：
文献类型：
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作者：
Grubaugh, Nathan D.;Gangavarapu, Karthik;Andersen, Kristian G.
病毒如何在宿主体内进化可以决定感染的结果;然而，重建这一过程是具有挑战性的。我们评估了我们的多重扩增子方法PrimalSeq，以证明病毒浓度，测序覆盖率，引物错配和重复如何影响测量宿主内病毒多样性的准确性。我们开发了一种实验方案和计算工具iVar，用于使用PrimalSeq使用Illumina测量病毒多样性，并将结果与Oxford Nanopore测序进行比较。我们通过测量来自不同样本类型的寨卡和西尼罗河病毒多样性来证明PrimalSeq的实用性，并表明遗传多样性的积累受到实验和生物系统的影响。
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.