Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

Benjamin N. Bimber; Dawn M. Dudley; Michael Lauck; Ericka A. Becker; Emily N. Chin; Simon M. Lank; Haiying L. Grunenwald; Nicholas C. Caruccio; Mark Maffitt; Nancy A. Wilson; Jason S. Reed; James M. Sosman; Leandro F. Tarosso; Sabri Sanabani; Esper G. Kallas; Austin L. Hughes; David H. O'Connor

doi:10.1128/JVI.01378-10

Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

Benjamin N. Bimber, Dawn M. Dudley, Michael Lauck, Ericka A. Becker, Emily N. Chin, Simon M. Lank, Haiying L. Grunenwald, Nicholas C. Caruccio, Mark Maffitt, Nancy A. Wilson, Jason S. Reed, James M. Sosman, Leandro F. Tarosso, Sabri Sanabani, Esper G. Kallas, Austin L. Hughes, David H. O'Connor

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57 Scopus citations

Abstract

Rapid evolution and high intrahost sequence diversity are hallmarks of human and simian immunodefi-ciency virus (HIV/SIV) infection. Minor viral variants have important implications for drug resistance, receptor tropism, and immune evasion. Here, we used ultradeep pyrosequencing to sequence complete HIV/SIV genomes, detecting variants present at a frequency as low as 1%. This approach provides a more complete characterization of the viral population than is possible with conventional methods, revealing low-level drug resistance and detecting previously hidden changes in the viral population. While this work applies pyrosequencing to immunodeficiency viruses, this approach could be applied to virtually any viral pathogen.

Original language	English (US)
Pages (from-to)	12087-12092
Number of pages	6
Journal	Journal of virology
Volume	84
Issue number	22
DOIs	https://doi.org/10.1128/JVI.01378-10
State	Published - Nov 2010
Externally published	Yes

ASJC Scopus subject areas

Microbiology
Immunology
Insect Science
Virology

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Bimber, B. N., Dudley, D. M., Lauck, M., Becker, E. A., Chin, E. N., Lank, S. M., Grunenwald, H. L., Caruccio, N. C., Maffitt, M., Wilson, N. A., Reed, J. S., Sosman, J. M., Tarosso, L. F., Sanabani, S., Kallas, E. G., Hughes, A. L., & O'Connor, D. H. (2010). Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. Journal of virology, 84(22), 12087-12092. https://doi.org/10.1128/JVI.01378-10

Bimber, BN, Dudley, DM, Lauck, M, Becker, EA, Chin, EN, Lank, SM, Grunenwald, HL, Caruccio, NC, Maffitt, M, Wilson, NA, Reed, JS, Sosman, JM, Tarosso, LF, Sanabani, S, Kallas, EG, Hughes, AL & O'Connor, DH 2010, 'Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing', Journal of virology, vol. 84, no. 22, pp. 12087-12092. https://doi.org/10.1128/JVI.01378-10

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abstract = "Rapid evolution and high intrahost sequence diversity are hallmarks of human and simian immunodefi-ciency virus (HIV/SIV) infection. Minor viral variants have important implications for drug resistance, receptor tropism, and immune evasion. Here, we used ultradeep pyrosequencing to sequence complete HIV/SIV genomes, detecting variants present at a frequency as low as 1%. This approach provides a more complete characterization of the viral population than is possible with conventional methods, revealing low-level drug resistance and detecting previously hidden changes in the viral population. While this work applies pyrosequencing to immunodeficiency viruses, this approach could be applied to virtually any viral pathogen.",

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AU - Chin, Emily N.

AU - Lank, Simon M.

AU - Grunenwald, Haiying L.

AU - Caruccio, Nicholas C.

AU - Maffitt, Mark

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AU - Reed, Jason S.

AU - Sosman, James M.

AU - Tarosso, Leandro F.

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Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

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