Full-length title: Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection.

Abstract

Strategies to cure HIV-infected patients by virus-targeting drugs have failed to date. We identified a HIV-1-seropositive woman who spontaneously suppressed HIV replication and had normal CD4-cell counts, no HIV-disease, no replication-competent virus and no cell HIV DNA detected with a routine assay. We suspected that dramatic HIV DNA degradation occurred post-infection. We performed multiple nested-PCRs followed by Sanger sequencing and applied a multiplex-PCR approach. Furthermore, we implemented a new technique based on two hybridization steps on beads prior to next-generation sequencing that removed human DNA then retrieved integrated HIV sequences with HIV-specific probes. We assembled ≈45% of the HIV genome and further analyzed the G-to-A mutations putatively generated by cellular APOBEC3 enzymes that can change tryptophan codons into stop codons. We found more G-to-A mutations in the HIV DNA from the woman than in that of her transmitting partner. Moreover, 74% of the tryptophan codons were changed to stop codons (25%) or were deleted as a possible consequence of gene inactivation. Finally, we found that this woman's cells remained HIV-susceptible in vitro. Our findings show that she does not exhibit innate HIV-resistance but may have been cured of it by extrinsic factors, a plausible candidate for which is the gut microbiota.

• Authors: Philippe Colson, Catherine Dhiver, Catherine Tamalet, Jeremy Delerce, Olga O Glazunova, Maxime Gaudin, Anthony Levasseur, Didier Raoult
• Journal: Scientific reports (Sci Rep) Vol. 10 Issue 1 Pg. 2548 (02 13 2020) ISSN: 2045-2322 [Electronic] England
• PMID: 32054885 (Publication Type: Case Reports, Journal Article, Research Support, Non-U.S. Gov't, Retracted Publication)

Chemical References

• Codon, Terminator
• DNA, Viral
• Tryptophan
• APOBEC Deaminases
• APOBEC3 proteins, human
• Cytidine Deaminase

Topics

• APOBEC Deaminases
• Codon, Terminator (genetics)
• Cytidine Deaminase (genetics)
• DNA, Viral (genetics, isolation & purification)
• Female
• Gastrointestinal Microbiome (genetics)
• Genome, Viral (genetics)
• HIV Infections (epidemiology, genetics, virology)
• HIV Seropositivity (genetics)
• HIV-1 (genetics, pathogenicity)
• Humans
• Mutation (genetics)
• Tryptophan (genetics)
• Virus Replication (genetics)