An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Why is this work in the frame?
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
No Canadian affiliation. An affiliation-only frame — the usual design — would never have seen this work. It is one of the works that make the case for inverting the frame.
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Genome biology
- Topic
- Evolution and Genetic Dynamics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- Office of Research Infrastructure Programs, National Institutes of HealthUniversity of California, DavisNational Institutes of HealthNational Institute of Allergy and Infectious DiseasesMedical Research CouncilSurgical Reconstruction and Microbiology Research CentreCalifornia National Primate Research CenterHamilton Health Sciences FoundationNational Institute for Health and Care ResearchCenters for Disease Control and PreventionGeorgia Clinical and Translational Science AllianceNational Center for Advancing Translational SciencesFlorida Department of Health
- Keywords
- BiologyAmpliconGenetic diversityComputational biologyDeep sequencingVirusEvolutionary biologyGeneticsGenomeGenePolymerase chain reactionPopulation
- Has abstract in OpenAlex
- yes