An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
By N. Grubaugh, K. Gangavarapu, Joshua Quick, N. Matteson, Jaqueline Goes de Jesus, Bradley J. Main, A. L. Tan, Lauren M. Paul, D. Brackney, Saran Grewal and 7 more. Genome Biology, 2018
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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.
Subfields: Genetics, Molecular Biology, Public Health, Environmental and Occupational Health
View Paper: https://www.semanticscholar.org/paper/e3e8d94f05fda796f6b728f4c471777c15a201b6
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Citations in the corpus
- Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater (2020, methodology): “Limitations of Study Nanopore sequencing has an error rate of 10%–15%, which precludes the reliable detection of rare genotypes.(33,42) Therefore, the protocol used here is limited to the detection of genotypes with >10%–15% representation.”