In vivo validation of the viral barcoding of simian immunodeficiency virus SIVmac239 and the development of new barcoded SIV and subtype B and C simian-human immunodeficiency viruses

Sirish Khanal, Christine M. Fennessey, Sean P. O'Brien, Abigail Thorpe, Carolyn Reid, Taina T. Immonen, Rodman Smith, Julian W. Bess, Adrienne E. Swanstrom, Gregory Q. Del Prete, Miles P. Davenport, Afam A. Okoye, Louis J. Picker, Jeffrey D. Lifson, Brandon F. Keele

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

Genetically barcoded viral populations are powerful tools for evaluating the overall viral population structure as well as assessing the dynamics and evolution of individual lineages in vivo over time. Barcoded viruses are generated by inserting a small, genetically unique tag into the viral genome, which is retained in progeny virus. We recently reported barcoding the well-characterized molecular clone simian immunodeficiency virus (SIV) SIVmac239, resulting in a synthetic swarm (SIVmac239M) containing approximately 10,000 distinct viral clonotypes for which all genetic differences were within a 34-base barcode that could be tracked using nextgeneration deep sequencing. Here, we assessed the population size, distribution, and authenticity of individual viral clonotypes within this synthetic swarm using samples from 120 rhesus macaques infected intravenously. The number of replicating barcodes in plasma correlated with the infectious inoculum dose, and the primary viral growth rate was similar in all infected animals regardless of the inoculum size. Overall, 97% of detectable clonotypes in the viral stock were identified in the plasma of at least one infected animal. Additionally, we prepared a secondgeneration barcoded SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and an additional barcoded stock with suboptimal nucleotides corrected (SIVmac239Opt5M). We also generated four barcoded stocks from subtype B and C simian-human immunodeficiency virus (SHIV) clones. These new SHIV clones may be particularly valuable models to evaluate Envtargeting approaches to study viral transmission or viral reservoir clearance. Overall, this work further establishes the reliability of the barcoded virus approach and highlights the feasibility of adapting this technique to other viral clones. IMPORTANCE We recently developed and published a description of a barcoded simian immunodeficiency virus that has a short random sequence inserted directly into the viral genome. This allows for the tracking of individual viral lineages with high fidelity and ultradeep sensitivity. This virus was used to infect 120 rhesus macaques, and we report here the analysis of the barcodes of these animals during primary infection. We found that the vast majority of barcodes were functional in vivo. We then expanded the barcoding approach in a second-generation SIVmac239 stock (SIVmac239M2) with over 16 times the number of barcoded variants of the original stock and a barcoded stock of SIVmac239Opt5M whose sequence had 5 changes from the wild-type SIVmac239 sequence. We also generated 4 barcoded stocks from subtype B and C SHIV clones each containing a human immunodeficiency virus (HIV) type 1 envelope. These virus models are functional and can be useful for studying viral transmission and HIV cure/reservoir research.

Original languageEnglish (US)
Article numbere01420-19
JournalJournal of virology
Volume94
Issue number1
DOIs
StatePublished - Jan 1 2020

Keywords

  • Barcoded virus
  • Nonhuman primates
  • Simian immunodeficiency virus
  • Viral models

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

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    Khanal, S., Fennessey, C. M., O'Brien, S. P., Thorpe, A., Reid, C., Immonen, T. T., Smith, R., Bess, J. W., Swanstrom, A. E., Del Prete, G. Q., Davenport, M. P., Okoye, A. A., Picker, L. J., Lifson, J. D., & Keele, B. F. (2020). In vivo validation of the viral barcoding of simian immunodeficiency virus SIVmac239 and the development of new barcoded SIV and subtype B and C simian-human immunodeficiency viruses. Journal of virology, 94(1), [e01420-19]. https://doi.org/10.1128/JVI.01420-19