Author | Grubaugh, Nathan D. | |
Author | Gangavarapu, Karthik | |
Author | Quick, Joshua | |
Author | Matteson, Nathaniel L. | |
Author | Jesus, Jaqueline Goes de | |
Author | Main, Bradley J. | |
Author | Tan, Amanda L. | |
Author | Paul, Lauren M. | |
Author | Brackney, Doug E. | |
Author | Grewal, Saran | |
Author | Gurfield, Nikos | |
Author | Van Rompay, Koen K. A. | |
Author | Isern, Sharon | |
Author | Michael, Scott F. | |
Author | Coffey, Lark L. | |
Author | Loman, Nicholas J. | |
Author | Andersen, Kristian G. | |
Access date | 2019-02-28T18:11:40Z | |
Available date | 2019-02-28T18:11:40Z | |
Document date | 2019 | |
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. | pt_BR |
ISSN | 1474-760X | pt_BR |
URI | https://www.arca.fiocruz.br/handle/icict/31947 | |
Sponsorship | NDG was supported by NIH training grant 5T32AI007244-33. JQ is supported
by a grant from the NIHR Surgical Reconstruction and Microbiology Research
Centre (SRMRC). KKAVR is supported by the Office of Research Infrastructure
Programs/OD (P51OD011107) to CNPRC and NIH R21AI129479. SI and SFM
are supported by NIH NIAID R01AI099210. LLC was supported by startup funds from the UC Davis Department of Pathology, Microbiology and
Immunology and the Pacific Southwest Regional Center of Excellence for
Vector-Borne Diseases funded by the U.S. Centers for Disease Control and
Prevention (Cooperative Agreement 1U01CK000516). BJM was supported by
Abt Associates and a consortium of vector control districts in California:
Coachella Valley, Orange County, Greater Los Angeles County, San Gabriel
Valley, West Valley, Kern, Butte County, Tulare, Sacramento-Yolo, Placer, and
Turlock. The rhesus macaque studies were supported by NIH 1R21AI129479–01
& Supplement, California National Primate Research Center pilot research grant
P51OD011107 and FDA HHS HHSF223201610542P. NJL is supported by a
Medical Research Council Bioinformatics Fellowship as part of the Cloud
Infrastructure for Microbial Bioinformatics (CLIMB) project. KGA is a Pew
Biomedical Scholar, and is supported by NIH NCATS CTSA UL1TR001114, NIAID
contract HHSN272201400048C, NIAID R21AI137690, NIAID U19AI135995, and
The Ray Thomas Foundation. | pt_BR |
Language | eng | pt_BR |
Publisher | BMC | pt_BR |
Rights | open access | pt_BR |
Subject in Portuguese | Sequenciamento viral | pt_BR |
Subject in Portuguese | Sequenciamento de amplificação | pt_BR |
Subject in Portuguese | Evolução do Intrahost | pt_BR |
Subject in Portuguese | Zika | pt_BR |
Subject in Portuguese | West Nile | pt_BR |
Subject in Portuguese | chamada de SNP | pt_BR |
Title | An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar | pt_BR |
Type | Article | pt_BR |
DOI | 10.1186/s13059-018-1618-7 | |
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. | pt_BR |
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. | pt_BR |
Affilliation | The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA. | pt_BR |
Affilliation | University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK. | pt_BR |
Affilliation | The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA. | pt_BR |
Affilliation | University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK / Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Laboratório de Patologia Experimental. Salvador, BA, Brasil. | pt_BR |
Affilliation | University of California. Department of Pathology, Microbiology and Immunology. Davis, CA, USA. | pt_BR |
Affilliation | Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA. | pt_BR |
Affilliation | Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA. | pt_BR |
Affilliation | The Connecticut Agricultural Experiment Station. Department of Environmental Sciences.New Haven, CT, USA. | pt_BR |
Affilliation | San Diego County Vector Control Program. Department of Environmental Health. San Diego, CA, USA. | pt_BR |
Affilliation | San Diego County Vector Control Program. Department of Environmental Health. San Diego, CA, USA. | pt_BR |
Affilliation | University of California. California National Primate Research Center. Department of Pathology, Microbiology and Immunology. Davis, CA, USA. | pt_BR |
Affilliation | Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA. | pt_BR |
Affilliation | Florida Gulf Coast University. College of Arts and Sciences. Department of Biological Sciences. Fort Myers, FL, USA. | pt_BR |
Affilliation | University of California. Department of Pathology, Microbiology and Immunology. Davis, CA, USA. | pt_BR |
Affilliation | University of Birmingham. Institute of Microbiology and Infection. Birmingham, UK. | pt_BR |
Affilliation | The Scripps Research Institute. Department of Immunology and Microbiology. La Jolla, CA, USA / Scripps Research Translational Institute. La Jolla, CA , USA. | pt_BR |
Subject | Viral sequencing | pt_BR |
Subject | Amplicon sequencing | pt_BR |
Subject | Intrahost evolution | pt_BR |
Subject | Zika | pt_BR |
Subject | West Nile | pt_BR |
Subject | SNP calling | pt_BR |