| Title: |
Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors |
| Authors: |
Patro, Sean C; Brandt, Leah D; Bale, Michael J; Halvas, Elias K; Joseph, Kevin W; Shao, Wei; Wu, Xiaolin; Guo, Shuang; Murrell, Ben; Wiegand, Ann; Spindler, Jonathan; Raley, Castle; Hautman, Christopher; Sobolewski, Michele; Fennessey, Christine M; Hu, Wei-Shau; Luke, Brian; Hasson, Jenna M; Niyongabo, Aurelie; Capoferri, Adam A; Keele, Brandon F; Milush, Jeff; Hoh, Rebecca; Deeks, Steven G; Maldarelli, Frank; Hughes, Stephen H; Coffin, John M; Rausch, Jason W; Mellors, John W; Kearney, Mary F |
| Source: |
Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 51 |
| Publisher Information: |
eScholarship, University of California |
| Publication Year: |
2019 |
| Collection: |
University of California: eScholarship |
| Subject Terms: |
31 Biological Sciences (for-2020); 32 Biomedical and Clinical Sciences (for-2020); 3105 Genetics (for-2020); 3204 Immunology (for-2020); 3207 Medical Microbiology (for-2020); Infectious Diseases (rcdc); Health Disparities and Racial or Ethnic Minority Health Research (rcdc); Cancer (rcdc); Cancer Genomics (rcdc); Human Genome (rcdc); HIV/AIDS (rcdc); Women's Health (rcdc); Health Disparities (rcdc); Genetics (rcdc); 2.2 Factors relating to the physical environment (hrcs-rac); Infection (hrcs-hc); Anti-Retroviral Agents (mesh); Base Sequence (mesh); Cell Line (mesh); DNA; Viral (mesh); Drug Resistance; HIV Infections (mesh); HIV-1 (mesh); Humans (mesh); Leukocytes; Mononuclear (mesh); Lymph Nodes (mesh); Mutation (mesh); Proviruses (mesh) |
| Subject Geographic: |
25891 - 25899 |
| Description: |
Understanding HIV-1 persistence despite antiretroviral therapy (ART) is of paramount importance. Both single-genome sequencing (SGS) and integration site analysis (ISA) provide useful information regarding the structure of persistent HIV DNA populations; however, until recently, there was no way to link integration sites to their cognate proviral sequences. Here, we used multiple-displacement amplification (MDA) of cellular DNA diluted to a proviral endpoint to obtain full-length proviral sequences and their corresponding sites of integration. We applied this method to lymph node and peripheral blood mononuclear cells from 5 ART-treated donors to determine whether groups of identical subgenomic sequences in the 2 compartments are the result of clonal expansion of infected cells or a viral genetic bottleneck. We found that identical proviral sequences can result from both cellular expansion and viral genetic bottlenecks occurring prior to ART initiation and following ART failure. We identified an expanded T cell clone carrying an intact provirus that matched a variant previously detected by viral outgrowth assays and expanded clones with wild-type and drug-resistant defective proviruses. We also found 2 clones from 1 donor that carried identical proviruses except for nonoverlapping deletions, from which we could infer the sequence of the intact parental virus. Thus, MDA-SGS can be used for "viral reconstruction" to better understand intrapatient HIV-1 evolution and to determine the clonality and structure of proviruses within expanded clones, including those with drug-resistant mutations. Importantly, we demonstrate that identical sequences observed by standard SGS are not always sufficient to establish proviral clonality. |
| Document Type: |
article in journal/newspaper |
| File Description: |
application/pdf |
| Language: |
unknown |
| Relation: |
qt4zk5v6hv; https://escholarship.org/uc/item/4zk5v6hv; https://escholarship.org/content/qt4zk5v6hv/qt4zk5v6hv.pdf |
| DOI: |
10.1073/pnas.1910334116 |
| Availability: |
https://escholarship.org/uc/item/4zk5v6hv; https://escholarship.org/content/qt4zk5v6hv/qt4zk5v6hv.pdf; https://doi.org/10.1073/pnas.1910334116 |
| Rights: |
public |
| Accession Number: |
edsbas.1A6B2FAA |
| Database: |
BASE |