An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Goes De Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman, Kristian G. Andersen

ABSTRACT

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. More... »

PAGES

8

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-018-1618-7

    DOI

    http://dx.doi.org/10.1186/s13059-018-1618-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1111266029

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30621750


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