Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 63,093 bioRxiv papers from 279,869 authors.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Nathan D Grubaugh,
Nathaniel L Matteson,
Jaqueline Goes De Jesus,
Bradley J Main,
Amanda L Tan,
Lauren M Paul,
Doug E Brackney,
Koen KA Van Rompay,
Scott F Michael,
Lark L Coffey,
Nicholas J Loman,
Kristian G Andersen
Posted 05 Aug 2018
bioRxiv DOI: 10.1101/383513 (published DOI: 10.1186/s13059-018-1618-7)
Posted 05 Aug 2018
How viruses evolves within hosts can dictate infection outcomes; however, accurately reconstructing this process is challenging from samples with low virus concentrations. We evaluated our highly multiplexed amplicon approach - PrimalSeq - to enrich for viral RNA and demonstrate how virus concentration, sequencing coverage depth, primer mismatches, and technical replicates influence the accuracy of measuring intrahost virus diversity. Using this data, we developed an open source experimental protocol and computational tool (iVar; github.com/andersen-lab/ivar) for using PrimalSeq to measure intrahost virus diversity using Illumina and compared the results to Oxford Nanopore sequencing. Furthermore, we demonstrate the utility of our approach by measuring Zika and West Nile virus diversity from varied sample types, and show that the accumulation of genetic diversity is heavily influenced by experimental and biological systems.
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