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

Autor: Grubaugh ND; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. nathan.grubaugh@yale.edu.; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA. nathan.grubaugh@yale.edu., Gangavarapu K; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA. gkarthik@scripps.edu., Quick J; Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK., Matteson NL; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA., De Jesus JG; Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.; Laboratory of Experimental Pathology, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil., Main BJ; Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA., Tan AL; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA., Paul LM; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA., Brackney DE; Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA., Grewal S; Department of Environmental Health, San Diego County Vector Control Program, San Diego, CA, 92123, USA., Gurfield N; Department of Environmental Health, San Diego County Vector Control Program, San Diego, CA, 92123, USA., Van Rompay KKA; California National Primate Research Center and Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA., Isern S; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA., Michael SF; Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA., Coffey LL; Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA., Loman NJ; Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK., Andersen KG; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.; Scripps Research Translational Institute, La Jolla, CA, 92037, USA.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2019 Jan 08; Vol. 20 (1), pp. 8. Date of Electronic Publication: 2019 Jan 08.
DOI: 10.1186/s13059-018-1618-7
Abstrakt: 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.
Databáze: MEDLINE