HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3′-PPT Mutations, Circular DNA Transcription and Recombination
Abstract
:1. Introduction
2. Materials and Methods
2.1. Virus Cultures Under Cabotegravir Treatment
2.2. HIV Genome Amplification
2.3. Sequencing of HIV Integrase Gene and LTRs
2.4. Strategies to Detect Integrated HIV
2.5. In Vitro Culture Fitness Competition in the Absence of CAB
3. Results
3.1. Assessment of In Vitro Int Resistance with RAL and CAB Treatment
3.2. Appearance of 3′-PPT Mutations In Vitro Under Steady-State Therapeutic Levels of CAB
3.2.1. HIV RNA
3.2.2. HIV DNA
3.3. Evidence of the Origin of 3′-PPT Mutations
3.4. Recombination of 2-LTR Circles with Human DNA
3.5. Fitness of the CAB-Selected 3′-PPT Mutant Virus
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
References
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(RT)-PCR Primer Pair | Genomic Region | Oligonucleotide Sequence 5′-3′ | Nt Positions in HIV-1IIIB Genomic DNA |
---|---|---|---|
1 | int | F: TCTAGCTTTGCAGGATTCGG R: CAGTCTCTTTCTCCTGTATG | 4034–4053 5293–5312 |
2 | Nef-3′LTR R | F: CTAACGCTGATTGTGCCTGGC R: TGTACAGCCAAAAAGCAGCTGC | 8981–9001 9550–9570 |
3a | 2-LTR cross junction (short) | F: ATCTGAGCCTGGGAGCTCTC R: GTACTAGCTTGTAGCACCATC | 9593–9612 130–150 |
3b | 2-LTR cross junction (long) | F:TCAAGTAGTGTGTGCCCGTCTGT R: GCAGCTGCTTATATGTAGGATCTGAG | 9667–9689 414–439 |
4 | 1 and 2 LTR circle | F:CTAACGCTGATTGTGCCTGGC R:TAATAYTGACGCTCTCGCACCCAT | 8981–9001 790–813 |
5 | HuAluF HuAluR To gag | CTCCCAAAGTGCTGGGATTACA TGTAATCCCAGCACTTTGGGAG TAATAYTGACGCTCTCGCACCCAT | N/A N/A 790–813 |
6 | HuAluF HuAluR To nef | CTCCCAAAGTGCTGGGATTACA TGTAATCCCAGCACTTTGGGAG CTAACGCTGATTGTGCCTGGC | N/A N/A 8981–9001 |
7 | Nef-2-LTR junction | F:CTAACGCTGATTGTGCCTGGC R:GAGTGAATTAGCACTTCCAGTAC | 8981–9001 Junction (−2)–19 |
8 | Viral load | F:TGCTTAAGCCTCAATAAAGCTTGCCTTGA R:TCTGAGGGATCTCTAGTTACCAG | 515–543 581–603 |
(A) AGCAGT variant | ||||||
Culture 1 | Culture 2 | |||||
Day | Nef-U3 (#2) | Nef-gag (#3a) | Nef-junct * (#7) | Nef-U3 (#2) | Nef-gag (#3a) | Nef-junct * (#7) |
14 | NS | NS | NS | 8 | <2% | NS |
30 | NS | NS | NS | 26.6 | <2% | NS |
98 | 10.1 | 34.2 | 13.9 | 62.3 | 75.6 | 52.9 |
112 | 5.9 | 13.3 | 1.7 | 78 | 66 | 55.7 |
120 | 3.1 | 11.2 | 3.3 | 53.1 | 50.9 | 35.6 |
127 | 3.5 | 9.3 | 1.7 | 42.7 | 51.4 | 24.2 |
(B) GGAGCA variant | ||||||
Culture 1 | ||||||
Day | Nef-U3 (#2) | Nef-gag (#3a) | Nef-junct * (#7) | |||
98 | 78.2 | 51.9 | 13 | |||
112 | 90 | 81.6 | 17 | |||
120 | 93.7 | 84.9 | 27 | |||
127 | 93.8 | 82.6 | 16.5 |
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Wei, X.; Lipscomb, J.T.; Tino, A.S.; Cong, M.-e.; Ruone, S.; Bentz, M.L.; Sheth, M.; Garcia-Lerma, G.; Johnson, J.A. HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3′-PPT Mutations, Circular DNA Transcription and Recombination. Viruses 2024, 16, 1874. https://doi.org/10.3390/v16121874
Wei X, Lipscomb JT, Tino AS, Cong M-e, Ruone S, Bentz ML, Sheth M, Garcia-Lerma G, Johnson JA. HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3′-PPT Mutations, Circular DNA Transcription and Recombination. Viruses. 2024; 16(12):1874. https://doi.org/10.3390/v16121874
Chicago/Turabian StyleWei, Xierong, Jonathan T. Lipscomb, Ariana Santos Tino, Mian-er Cong, Susan Ruone, Meghan L. Bentz, Mili Sheth, Gerardo Garcia-Lerma, and Jeffrey A. Johnson. 2024. "HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3′-PPT Mutations, Circular DNA Transcription and Recombination" Viruses 16, no. 12: 1874. https://doi.org/10.3390/v16121874
APA StyleWei, X., Lipscomb, J. T., Tino, A. S., Cong, M.-e., Ruone, S., Bentz, M. L., Sheth, M., Garcia-Lerma, G., & Johnson, J. A. (2024). HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3′-PPT Mutations, Circular DNA Transcription and Recombination. Viruses, 16(12), 1874. https://doi.org/10.3390/v16121874