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An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
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 meas...
| Autores principales: | , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2019
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325816/ https://www.ncbi.nlm.nih.gov/pubmed/30621750 http://dx.doi.org/10.1186/s13059-018-1618-7 |
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| author | Grubaugh, Nathan D. Gangavarapu, Karthik Quick, Joshua Matteson, Nathaniel L. De Jesus, Jaqueline Goes Main, Bradley J. Tan, Amanda L. Paul, Lauren M. Brackney, Doug E. Grewal, Saran Gurfield, Nikos Van Rompay, Koen K. A. Isern, Sharon Michael, Scott F. Coffey, Lark L. Loman, Nicholas J. Andersen, Kristian G. |
| author_facet | Grubaugh, Nathan D. Gangavarapu, Karthik Quick, Joshua Matteson, Nathaniel L. De Jesus, Jaqueline Goes Main, Bradley J. Tan, Amanda L. Paul, Lauren M. Brackney, Doug E. Grewal, Saran Gurfield, Nikos Van Rompay, Koen K. A. Isern, Sharon Michael, Scott F. Coffey, Lark L. Loman, Nicholas J. Andersen, Kristian G. |
| author_sort | Grubaugh, Nathan D. |
| collection | PubMed |
| description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1618-7) contains supplementary material, which is available to authorized users. |
| format | Online Article Text |
| id | pubmed-6325816 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2019 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-63258162019-01-11 An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar Grubaugh, Nathan D. Gangavarapu, Karthik Quick, Joshua Matteson, Nathaniel L. De Jesus, Jaqueline Goes Main, Bradley J. Tan, Amanda L. Paul, Lauren M. Brackney, Doug E. Grewal, Saran Gurfield, Nikos Van Rompay, Koen K. A. Isern, Sharon Michael, Scott F. Coffey, Lark L. Loman, Nicholas J. Andersen, Kristian G. Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1618-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-08 /pmc/articles/PMC6325816/ /pubmed/30621750 http://dx.doi.org/10.1186/s13059-018-1618-7 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| spellingShingle | Method Grubaugh, Nathan D. Gangavarapu, Karthik Quick, Joshua Matteson, Nathaniel L. De Jesus, Jaqueline Goes Main, Bradley J. Tan, Amanda L. Paul, Lauren M. Brackney, Doug E. Grewal, Saran Gurfield, Nikos Van Rompay, Koen K. A. Isern, Sharon Michael, Scott F. Coffey, Lark L. Loman, Nicholas J. Andersen, Kristian G. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title_full | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title_fullStr | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title_full_unstemmed | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title_short | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar |
| title_sort | amplicon-based sequencing framework for accurately measuring intrahost virus diversity using primalseq and ivar |
| topic | Method |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325816/ https://www.ncbi.nlm.nih.gov/pubmed/30621750 http://dx.doi.org/10.1186/s13059-018-1618-7 |
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