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. 2024 Jun 13;98(6):e0033524.
doi: 10.1128/jvi.00335-24. Epub 2024 May 24.

Reverse transcription of HIV-1 2-LTR circle transcripts does frequently cause 3'-polypurine tract mutations implicated in dolutegravir resistance

José G Dekker  1   2 , Bep Klaver  1   2 , Ben Berkhout  1   2 , Atze T Das  1   2
Affiliations

Reverse transcription of HIV-1 2-LTR circle transcripts does frequently cause 3'-polypurine tract mutations implicated in dolutegravir resistance

José G Dekker et al. J Virol. .
No abstract available

Keywords: HIV-1; dolutegravir; drug resistance mechanisms; drug-resistance evolution.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
3'PPT mutations observed upon long-term culturing of HIV-1 with integrase inhibitors. Schematic of the HIV genome with the nucleotide sequence of the 3’PPT region and the 3' end of the proviral DNA shown. Mutations in the 3'PPT region observed upon culturing wild-type HIV in MT-4 cells in the presence of up to 500 nM DTG (Malet et al.) (3) and in CEMx174 cells with 300 nM CAB (Wei et al.) (7) are shown (variant 1 and variant 2). The same 3'PPT mutations were identified upon culturing HIV variants in which either the T5-motif or the attachment (att) sequence had been randomized (att-S and att-L) in C8166 cells with 500 nM DTG. Nucleotides that differ from the wild-type HIV sequence are indicated in red (Δ, nucleotide deletion). Nucleotides randomized in the HIV libraries are underlined with dotted lines. The sequence similarity between the mutated 3'PPT sequences and the U5 sequence is underlined.
Fig 2
Fig 2
Regular HIV transcription and reverse transcription. Transcription of the HIV proviral DNA initiating at the 5'LTR and subsequent polyadenylation at the 3'LTR will result in full-length transcripts that are packaged into virus particles (step 1). Upon infection, the viral RT copies this RNA genome into double-stranded (ds)DNA (steps 2–10). The cellular tRNALys3 binding to the primer-binding site (PBS) functions as a primer for minus-strand DNA synthesis (step 2). After being reverse transcribed, the viral RNA template is degraded by the RNase H activity of RT. The 3'PPT and cPPT motifs resist cleavage and function as primer for plus-strand DNA synthesis before also being degraded by RNase H (steps 5–7). Complementarity of the sequences at the termini of the partially double-stranded linear HIV DNA induces circularization to 1-LTR circles (step 8). Subsequent continuation of second-strand DNA synthesis and linearization, which involves strand displacement of the LTR sequences, results in a linear dsDNA molecule with complete LTR motifs at both termini (step 9–10). This full-length 2-LTR dsDNA is integrated into the cellular DNA by the viral integrase protein (step 11a; no DTG). When integration is blocked, for example in the presence of DTG, 2-LTR DNA circles with a U5–U3 junction will accumulate (step 11b). The sequence of the U5–U3 junction is shown, with the U5 sequence similar to the mutated 3'PPT sequence (variant 1; Fig. 1) underlined. Adapted from Dekker et al. (6).
Fig 3
Fig 3
3'PPT mutations may result from 2-LTR circle transcripts when integration is blocked. (A) Transcription of 2-LTR DNA circles initiating at the 3'LTR can result in 5'-extended transcripts. During reverse transcription, the extended leader RNA sequence is copied into the cDNA (step 2). Transfer of a full-length cDNA formed upon reverse transcription of the complete R-U5-U3-R-U5 sequence leads to the formation of an RNA-DNA duplex with substantial mismatches between the R-U5 sequence at the 3' end of the cDNA and the nef-3'PPT sequence in the viral RNA template (step 3a), which will impede the continuation of minus-strand synthesis. Transfer of incomplete minus-strand cDNAs with only a few U5 nucleotides upstream of the U3 sequence can result in the formation of RNA-cDNA duplexes with a short mismatched U5 sequence at the 3' end of the cDNA, which does not obstruct the continuation of minus-strand DNA synthesis (step 3b). The viral RNA, including the 3'PPT sequence, is subsequently degraded by the RNase H activity of RT, except for the cPPT fragment (steps 4–5) that is used as primer for plus-strand DNA synthesis, which results in the formation of double-stranded 1-LTR DNA circles with a mutated 3'PPT sequence in both DNA strands (steps 6–9). Adapted from Dekker et al. (6). (B) Transfer of minus-strand cDNAs with six or three U5 nucleotides upstream of the U3 sequence will result in variant 1 (upper panel) and variant 2 (lower panel), respectively.
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References

    1. Brenner BG, Wainberg MA. 2017. Clinical benefit of dolutegravir in HIV-1 management related to the high genetic barrier to drug resistance. Virus Res 239:1–9. doi:10.1016/j.virusres.2016.07.006 - DOI - PubMed
    1. Dekker JG, Klaver B, Berkhout B, Das AT. 2022. Mutations in the HIV-1 3’-polypurine tract can confer dolutegravir resistance. Antimicrob Agents Chemother 66:e0102721. doi:10.1128/AAC.01027-21 - DOI - PMC - PubMed
    1. Malet I, Subra F, Charpentier C, Collin G, Descamps D, Calvez V, Marcelin AG, Delelis O. 2017. Mutations located outside the integrase gene can confer resistance to HIV-1 integrase strand transfer inhibitors. mBio 8:e00922-17. doi:10.1128/mBio.00922-17 - DOI - PMC - PubMed
    1. Hachiya A, Kubota M, Shigemi U, Ode H, Yokomaku Y, Kirby KA, Sarafianos SG, Iwatani Y. 2022. Specific mutations in the HIV-1 G-tract of the 3'-polypurine tract cause resistance to integrase strand transfer inhibitors. J Antimicrob Chemother 77:574–577. doi:10.1093/jac/dkab448 - DOI - PMC - PubMed
    1. Richetta C, Subra F, Malet I, Leh H, Charpentier C, Corona A, Collin G, Descamps D, Deprez E, Parissi V, Calvez V, Tramontano E, Marcelin AG, Delelis O. 2022. Mutations in the 3'-PPT lead to HIV-1 replication without integration. J Virol 96:e0067622. doi:10.1128/jvi.00676-22 - DOI - PMC - PubMed

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