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AN AMPLICON-BASED SEQUENCING FRAMEWORK FOR ACCURATELY MEASURING INTRAHOST VIRUS DIVERSITY USING PRIMALSEQ AND IVAR
Grubaugh, Nathan D. et al. | Date Issued: 2019
Author
Grubaugh, Nathan D.
Gangavarapu, Karthik
Quick, Joshua
Matteson, Nathaniel L.
Jesus, Jaqueline Goes de
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.
Affilliation
The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA / Yale School of Public Health. Department of Epidemiology of Microbial Diseases. New Haven, CT, USA.
The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA.
University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.
The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA.
University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil.
University of California. Department of Pathology, Microbiology and Immunology. Davis, CA, USA.
Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA.
Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA.
The Connecticut Agricultural Experiment Station. Department of Environmental Sciences.New Haven, CT, USA.
San Diego County Vector Control Program. Department of Environmental Health. San Diego, CA, USA.
San Diego County Vector Control Program. Department of Environmental Health. San Diego, CA, USA.
University of California. California National Primate Research Center. Department of Pathology, Microbiology and Immunology. Davis, CA, USA.
Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA.
Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA.
University of California. Department of Pathology, Microbiology and Immunology. Davis, CA, USA.
University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK.
The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA / Scripps Research Translational Institute. La Jolla, CA , USA.
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.
Keywords in Portuguese
Sequenciamento viral
Sequenciamento de amplificação
Evolução do Intrahost
Zika
West Nile
chamada de SNP
 
Keywords
Viral sequencing
Amplicon sequencing
Intrahost evolution
Zika
West Nile
SNP calling
 
Publisher
BMC
Citation
GRUBAUGH, Nathan D. et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology, v. 20, p. 1-19, 2019.
DOI
10.1186/s13059-018-1618-7
ISSN
1474-760X