Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection.
The latent reservoir is a major barrier to HIV eradication. Reservoir size is emerging as an important biomarker to assess the likelihood of HIV remission in the absence of antiretroviral therapy (ART) and may be reduced by earlier initiation of ART that restricts HIV spread into CD4+ T cells. Reservoir size is traditionally measured with a quantitative viral outgrowth assay (QVOA) that induces replication-competent HIV production through in vitro stimulation of resting CD4+ T cells. However, the recent identification of replication-intact, non-induced proviral genomes (NIPG) suggests the QVOA significantly underestimates (by 62-fold) latent reservoir size in chronically-infected adults. Whether formation and persistence of Intact, NIPG is thwarted by early ART initiation and long-term virologic suppression in perinatal infection is unclear. Here, we show that the latent reservoir in 11 early treated, long-term suppressed perinatally infected children and adolescents was not inducible by QVOA and dominated by defective, NIPG. Single genome analysis of 164 NIPG from 232 million cultured resting CD4+ T cells revealed no replication-intact, near-full length sequences. Forty-three (26%) NIPG contained APOBEC3G-mediated hypermutation, 115 (70%) NIPG contained large internal deletions, one NIPG contained nonsense mutations and indels, and 5 (3%) NIPG were assigned as "Not Evaluable" due to multiple failed sequencing attempts that precluded further classification. The lack of replication competent inducible provirus and intact NIPG in this cohort indicate early, long-term ART of perinatal infection leads to marked diminution of replication-competent HIV-1 reservoirs, creating a favorable state towards interventions aimed at virologic remission.
Department of Pediatrics-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Kaitlin
http://orcid.org/0000-0002-8707-7339
K
Rainwater-Lovett
Department of Pediatrics-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Carrie
C
Ziemniak
Department of Pediatrics, University of Maryland, Baltimore, MD, United States of America.
Douglas
D
Watson
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America.
Katherine
K
Luzuriaga
Maternal and Pediatric Infectious Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Rockville, MD, United States of America.
George
G
Siberry
Department of Pediatric Infectious Diseases, Children's Hospital and Research Center Oakland, Oakland, CA, United States of America.
Ann
A
Petru
Department of Pediatrics-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
YaHui
Y
Chen
Department of Pediatrics-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Priyanka
P
Uprety
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America.
Margaret
http://orcid.org/0000-0002-9707-4991
M
McManus
Department of Medicine-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Ya-Chi
YC
Ho
Bioinfoexperts LLC, Thibodaux, LA, United States of America.
Susanna L
http://orcid.org/0000-0002-8163-5571
SL
Lamers
Department of Pediatrics-Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
Deborah
D
Persaud
D000293:Adolescent; D023241:Antiretroviral Therapy, Highly Active; D018791:CD4 Lymphocyte Count; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology / Q000821:virology; D002648:Child; D002675:Child, Preschool; D004279:DNA, Viral; D005260:Female; D015483:HIV Antibodies / Q000276:immunology; D015658:HIV Infections / Q000188:drug therapy / Q000276:immunology / Q000821:virology*; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D007223:Infant; D009154:Mutation; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious; D011533:Proviruses / Q000235:genetics; D019562:Viral Load; D017735:Virus Latency
D004279:DNA, Viral; D015483:HIV Antibodies