Brown PO. Integration. In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. p. 161–294.

Google Scholar 

Pearson R, Kim YK, Hokello J, Lassen K, Friedman J, Tyagi M, Karn J. Epigenetic silencing of human immunodeficiency virus (HIV) transcription by formation of restrictive chromatin structures at the viral long terminal repeat drives the progressive entry of HIV into latency. J Virol. 2008;82:12291–303.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Siliciano JD, Siliciano RF. Enhanced culture assay for detection and quantitation of latently infected, resting CD4+ T-cells carrying replication-competent virus in HIV-1 infected individuals. Method Mol Biol. 2005;304:3–15.

Google Scholar 

Ho YC, Shan L, Hosmane NN, Wang J, Sarah B, Laskey SB, Daniel IS, Rosenbloom DIS, Lai J, Blankson JN, Siliciano JD, Siliciano RF. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell. 2013;155(3):540–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bruner KM, Murray AJ, Pollack RA, Soliman MG, Laskey SB, Capoferri AA, Lai J, Strain MC, Lada SM, Hoh R, Ho YC, Richman DD, Deeks SG, Siliciano JD, Siliciano RF. Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat Med. 2016;22(9):1043–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bruner KM, Wang Z, Simonetti FR, Bender AM, Kwon KJ, Sengupta S, Fray EJ, Beg SA, Antar AAR, Jenike KM, Bertagnolli LN, Capoferri AA, Kufera JT, Timmons A, Nobles C, Gregg J, Wada N, Ho YC, Zhang H, Margolick JB, Blankson JN, Deeks SG, Bushman FD, Siliciano JD, Laird GM, Siliciano RF. A quantitative approach for measuring the reservoir of latent HIV-1 proviruses. Nature. 2019;566(7742):120–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanchez G, Xu X, Chermann JC, Hirsch I. Accumulation of defective viral genomes in peripheral blood mononuclear cells of human immunodeficiency virus type 1-infected individuals. J Virol. 1997;71(3):2233–40.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yu Q, König R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin JM, Landau NR. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol. 2004;11(5):435–42.

Article  CAS  PubMed  Google Scholar 

Bebenek K, Abbotts J, Roberts JD, Wilson SH, Kunkel TA. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J Biol Chem. 1989;264(28):16948–56.

Article  CAS  PubMed  Google Scholar 

Kauder SE, Bosque A, Lindqvist A, Planelles V, Verdin E. Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog. 2009;5(6):e1000495.2d.

Article  Google Scholar 

Imamichi H, Dewar RL, Adelsberger JW, Rehm CA, O’Doherty U, Paxinos EE, Fauci AS, Lane HC. Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy. Proc Natl Acad Sci USA. 2016;113(31):8783–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Imamichi H, Smith M, Adelsberger JW, Izumi T, Scrimieri F, Sherman BT, Rehm CA, Imamichi T, Pau A, Catalfamo M, Fauci AS, Lane HC. Defective HIV-1 proviruses produce viral proteins. Proc Natl Acad Sci USA. 2020;117(7):3704–10.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gurgo C, Guo HG, Franchini G, Aldovini A, Collalti E, Farrell K, Wong-Staal F, Gallo RC, Reitz MS Jr. Envelope sequences of two new United States HIV-1 isolates. Virology. 1988;164:531–6.

Article  CAS  PubMed  Google Scholar 

Schimmel P. The emerging complexity of the tRNA world: mammalian RNAs beyond protein synthesis. Nat Rev Mol Cell Biol. 2018;19:45–58.

Article  CAS  PubMed  Google Scholar 

Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem. 2023;299(10): 105246.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Konstantinova P, de Haan P, Das AT, Berkhout B. Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1. Nucl Acid Res. 2006;34(8):2206–18.

Article  CAS  Google Scholar 

Colicelli J, Goff SP. Structure of a cloned circular retroviral DNA containing a tRNA sequence between the terminal repeats. J Virol. 1986;57:674–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Butler SL, Hansen MS, Bushman FD. A quantitative assay for HIV DNA integration in vivo. Nat Med. 2001;7:631–4.

Article  CAS  PubMed  Google Scholar 

Richetta C, Subra F, Malet I, Leh H, Charpentier C, Corona A, Cullin G, Descampes D, Veprez E, Parissi V, Calvez V, Tramontano E, Marcelin A-G, Delelis O. Mutations in the 3’-PPT lead to HIV-1 replication without integration. J Virol. 2022;96(14):e00676-e722.

Article  PubMed  PubMed Central  Google Scholar 

Gurgo C, Fenizia C, McKinnon K, Hsia RC, Franchini G. Expression of HIV from a 1-LTR circular DNA in the absence of integration. Retrovirology. 2025;22(1):2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gioia L, Siddique A, Head SR, Salomon DR, Su AI. A genome-wide survey of mutations in the Jurkat cell line. BMC Genomics. 2018;19(1):334.

Article  PubMed  PubMed Central  Google Scholar 

Moore MD, Hu W-S. HIV-1 RNA dimerization: It takes two to tango. AIDS Rev. 2009;11:91–102.

PubMed  PubMed Central  Google Scholar 

Coffin J. Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol. 1979;42:1–26.

Article  CAS  PubMed  Google Scholar 

Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol. 2009;385(3):693–713.

Article  CAS  PubMed  Google Scholar 

Simon-Loriere E, Holmes E. Why do RNA viruses recombine? Nat Rev Microbiol. 2011;9:817–26.

Article  Google Scholar 

Kuzin AB, Lyubomirskaya NV, Khudaibergenova BM, Ilyin YV, Kim AI. Precise excision of the retrotransposon gypsy from the forked and cut loci in a genetically unstable D. melanogaster strain. Nucl Acid Res. 1994;22(22):4641–5.

Article  CAS  Google Scholar 

Nefedova LN, Liubomirskaia NV, Il’in IV, Kim AI. Precise excision of long terminal repeats of the gypsy(mdg4) retrotransposon of Drosophila melanogaster detected in Escherichia coli cells is explained by its integrase function. Genetika. 2006;42(12):1656–63.

CAS  PubMed  Google Scholar 

McCullers TJ, Steiniger M. Transposable elements in Drosophila. Mob Genet Elements. 2017;7(3):1–18.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Colicelli J, Goff SP. Isolation of a recombinant murine leukemia virus utilizing a new primer tRNA. J Virol. 1986;57:37–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Panet A, Berliner H. Binding of tRNA to reverse transcriptase of RNA tumor viruses. J Virol. 1978;26:214–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kleiman L. tRNA(Lys3): the primer tRNA for reverse transcription in HIV-1. IUBMB Life. 2002;53:107–14.

Article