The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Open accessAbstract
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.
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Cites
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The Sequence Alignment/Map format and SAMtools
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Nanopore sequencing and assembly of a human genome with ultra-long reads
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Self-citationRapid Evolution of RNA Genomes
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Self-citationGenotype and SNP calling from next-generation sequencing data
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Self-citationThomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K.-A., Eden, J.-S., Chang, S., Gall, M., Draper, J., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1000-7 · Cited by 325
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Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Lucas, C., Vogels, C. B. F., Yildirim, I., Rothman, J. E., Lu, P., Monteiro, V., Gehlhausen, J. R., Campbell, M., Silva, J., Tabachnikova, A., et al. (2021) · Nature · doi:10.1038/s41586-021-04085-y · Cited by 226
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Metadata
- Authors
- Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., Gurfield, N., Van Rompay, K. K. A., Isern, S., Michael, S. F., Coffey, L. L., Loman, N. J., & Andersen, K. G.
- Venue
- Genome Biology
- Published
- 2019-01-08
- Volume
- 20
- Issue
- 1
- Pages
- 8-8
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2952946229
- Cited by
- 1,014
- References
- 70
- FWCI
- 30.72
- Type
- journal article
- Language
- en
- Open access
- gold
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- Grubaugh, N. D., Gangavarapu, K., Quick, J., Matteson, N. L., De Jesus, J. G., Main, B. J., Tan, A. L., Paul, L. M., Brackney, D. E., Grewal, S., Gurfield, N., Van Rompay, K. K. A., Isern, S., Michael, S. F., Coffey, L. L., Loman, N. J., & Andersen, K. G. (2019). An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biology. https://doi.org/10.1186/s13059-018-1618-7
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
