HIV-1 APOBEC-context mutations detected by next-generation sequencing in plasma: implications for drug resistance interpretation
Clicks: 1
ID: 316075
2026
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This
article has not been analysed, so there is no overall score —
reader engagement is measured and shown alongside.
Reader Engagement
0.0
/100
1 views
0 readers
AI Quality Assessment
Not analyzed
Readership in this journal
Ranked #318 of 431 articles by views in The Journal of infectious diseases
Most read
Least read
Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 431 in total.
Mint this article as an NFT
Not yet mintedCreate a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.
5
SUSD
one-off · no wallet required
Abstract
BACKGROUND & AIMS: APOBEC3-mediated cytidine deamination produces characteristic G→A substitutions in HIV genomes, classically described in proviral DNA but also detectable in plasma HIV-1 RNA using next-generation sequencing (NGS). APOBEC-signature mutations reflect enrichment of G→A substitutions in APOBEC target motifs, whereas APOBEC-context mutations correspond to substitutions at drug resistance-associated positions compatible with APOBEC editing. We evaluated their prevalence and implications for resistance interpretation in plasma NGS sequences. METHODS: We performed a retrospective multicentre analysis of plasma HIV-1 NGS-sequences from antiretroviral-naïve individuals in the period 2022-2023. Sequencing was performed in participating laboratories, and FASTQ files were centrally reanalysed using DeepChek. APOBEC-signature mutations, APOBEC-context drug resistance mutations (DRMs), and stop codons were evaluated across protease, reverse transcriptase, and integrase. Variant frequencies were analysed using thresholds of 1%, 3%, and 5%. RESULTS: Among 290 individuals, 268 had complete NGS data. At a 1% threshold, APOBEC-signature mutations were detected in 159 individuals and APOBEC-context DRMs in 64 (22%). The coexistence of both patterns was observed in 52 individuals (18%), decreasing to 17 (6%) and 8 (3%) at 3% and 5% thresholds, respectively. Certain mutations, including M184I, G190E, G140S, and R263K, remained detectable at higher thresholds. Integrase mutation R263K frequently co-occurred with multiple APOBEC-signature mutations and stop codons, consistent with extensive APOBEC-mediated editing. CONCLUSIONS: APOBEC-associated mutational patterns can be detected in plasma HIV-1 RNA by NGS and may affect interpretation of resistance results. Conservative frequency thresholds (5%) and evaluation of APOBEC signatures may help reduce misclassification of APOBEC-induced variants as clinically relevant resistance.
| Reference Key |
openalex_W7163636295
Use this key to autocite in the manuscript while using
SciMatic Manuscript Manager or Thesis Manager
|
|---|---|
| Authors | Marta Illescas-López, Paloma Muñoz, Adolfo de Salazar, Rafael Delgado, Asunción Iborra, Juan Carlos Galán, Raquel Carracedo, Mayra Sigcha, Carla López-Causapé, Ana Fuentes, Antonio Aguilera, Cristina Marco‐Sánchez, Féderico García |
| Journal | The Journal of infectious diseases |
| Year | 2026 |
| DOI |
10.1093/infdis/jiag277
|
| URL | |
| Keywords | Keywords not found |
Citations
No citations found. To add a citation, contact the admin at info@scimatic.org
Comments
No comments yet. Be the first to comment on this article.