1
|
Lee GQ, Khadka P, Gowanlock SN, Copertino DC, Duncan MC, Omondi FH, Kinloch NN, Kasule J, Kityamuweesi T, Buule P, Jamiru S, Tomusange S, Anok A, Chen Z, Jones RB, Galiwango RM, Reynolds SJ, Quinn TC, Brumme ZL, Redd AD, Prodger JL. HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy. Nat Commun 2024; 15:5480. [PMID: 38956017 PMCID: PMC11219899 DOI: 10.1038/s41467-024-48985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/13/2024] [Indexed: 07/04/2024] Open
Abstract
The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.
Collapse
Affiliation(s)
- Guinevere Q Lee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA.
| | - Pragya Khadka
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Dennis C Copertino
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Zhengming Chen
- Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA
| | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
| |
Collapse
|
2
|
Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303990. [PMID: 38558994 PMCID: PMC10980117 DOI: 10.1101/2024.03.14.24303990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was estimated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Evolutionary dynamics were assessed among demographic and behavioral sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by more than four-fold. Inter-subtype HIV diversity has generally increased. While p24 intra-subtype genetic diversity and divergence leveled off after 2014, diversity and divergence of gp41 increased through 2017. Inter- and intra-subtype viral diversity increased across all population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics in declining African HIV epidemics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.
Collapse
Affiliation(s)
- Seungwon Kim
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Michael A. Martin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Redd
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Joshua T. Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven J. Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, England, United Kingdom
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Kalisizo, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - M. Kate Grabowski
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| |
Collapse
|
3
|
Kufera JT, Armstrong C, Wu F, Singhal A, Zhang H, Lai J, Wilkins HN, Simonetti FR, Siliciano JD, Siliciano RF. CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation. J Exp Med 2024; 221:e20231511. [PMID: 38270554 PMCID: PMC10818065 DOI: 10.1084/jem.20231511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/04/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
The latent reservoir for HIV-1 in resting CD4+ T cells persists despite antiretroviral therapy as a barrier to cure. The antigen-driven proliferation of infected cells is a major mechanism of reservoir persistence. However, activation through the T cell antigen receptor (TCR) can induce latent proviruses, leading to viral cytopathic effects and immune clearance. In single-cell studies, we show that, relative to uninfected cells or cells with a defective provirus, CD4+ T cells with an intact provirus have a profound proliferative defect in response to TCR stimulation. Virion production was observed in only 16.5% of cultures with an intact provirus, but proliferation was reduced even when no virion production was detected. Proliferation was inversely correlated with in vivo clone size. These results may reflect the effects of previous in vivo proliferation and do not support attempts to reduce the reservoir with antiproliferative agents, which may have greater effects on normal T cell responses.
Collapse
Affiliation(s)
- Joshua T. Kufera
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciara Armstrong
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fengting Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anushka Singhal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hannah N. Wilkins
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| |
Collapse
|
4
|
Kyser AJ, Fotouh B, Mahmoud MY, Frieboes HB. Rising role of 3D-printing in delivery of therapeutics for infectious disease. J Control Release 2024; 366:349-365. [PMID: 38182058 PMCID: PMC10923108 DOI: 10.1016/j.jconrel.2023.12.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Modern drug delivery to tackle infectious disease has drawn close to personalizing medicine for specific patient populations. Challenges include antibiotic-resistant infections, healthcare associated infections, and customizing treatments for local patient populations. Recently, 3D-printing has become a facilitator for the development of personalized pharmaceutic drug delivery systems. With a variety of manufacturing techniques, 3D-printing offers advantages in drug delivery development for controlled, fine-tuned release and platforms for different routes of administration. This review summarizes 3D-printing techniques in pharmaceutics and drug delivery focusing on treating infectious diseases, and discusses the influence of 3D-printing design considerations on drug delivery platforms targeting these diseases. Additionally, applications of 3D-printing in infectious diseases are summarized, with the goal to provide insight into how future delivery innovations may benefit from 3D-printing to address the global challenges in infectious disease.
Collapse
Affiliation(s)
- Anthony J Kyser
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA.
| | - Bassam Fotouh
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA.
| | - Mohamed Y Mahmoud
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA; Department of Toxicology and Forensic Medicine, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Hermann B Frieboes
- Department of Bioengineering, University of Louisville Speed School of Engineering, Louisville, KY 40202, USA; Center for Predictive Medicine, University of Louisville, Louisville, KY 40202, USA; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA; UofL Health - Brown Cancer Center, University of Louisville, KY 40202, USA.
| |
Collapse
|
5
|
Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
Collapse
Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
| |
Collapse
|
6
|
Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
Collapse
Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | | |
Collapse
|
7
|
Kapaata A, Balinda SN, Hare J, Leonova O, Kikaire B, Egesa M, Lubyayi L, Macharia GN, Kamali A, Gilmour J, Bagaya B, Salazar-Gonzalez JF, Kaleebu P. Infection with HIV-1 subtype D among acutely infected Ugandans is associated with higher median concentration of cytokines compared to subtype A. IJID REGIONS 2022; 3:89-95. [PMID: 35755471 PMCID: PMC9205166 DOI: 10.1016/j.ijregi.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
Abstract
HIV-1 subtype D exhibited significantly higher median concentrations of cytokines IL-12/23p40 and IL-1α were associated with faster CD4+T cell count decline bFGF was associated with maintenance of CD4+ counts above 350 cells/microliter
Objective The observation that HIV-1 subtype D progresses faster to disease than subtype A prompted us to examine cytokine levels early after infection within the predominant viral subtypes that circulate in Uganda and address the following research questions: (1) Do cytokine levels vary between subtypes A1 and D? (2) Do cytokine profiles correlate with disease outcomes? Methods To address these questions, HIV-1 subtypes were determined by population sequencing of the HIV-1 pol gene and 37 plasma cytokine concentrations were evaluated using V-Plex kits on Meso Scale Discovery platform in 65 recent sero-converters. Results HIV-1 subtype D (pol) infections exhibited significantly higher median plasma concentrations of IL-5, IL-16, IL-1α, IL-7, IL-17A, CCL11 (Eotaxin-1), CXCL10 (IP-10), CCL13 (MCP-4) and VEGF-D compared to subtype A1 (pol) infections. We also found that IL-12/23p40 and IL-1α were associated with faster CD4+T cell count decline, while bFGF was associated with maintenance of CD4+ counts above 350 cells/microliter. Conclusion Our results suggest that increased production of cytokines in early HIV infection may trigger a disruption of the immune environment and contribute to pathogenic mechanisms underlying the accelerated disease progression seen in individuals infected with HIV-1 subtype D in Uganda.
Collapse
Affiliation(s)
- Anne Kapaata
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- Corresponding author:
| | - Sheila N. Balinda
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Jonathan Hare
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Olga Leonova
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Bernard Kikaire
- Uganda Virus Research Institute
- Department of Paediatrics, College of Health sciences, Makerere university
| | - Moses Egesa
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Lawrence Lubyayi
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Gladys N. Macharia
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | | | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London, UK
| | - Bernard Bagaya
- Department of Microbiology, College of Health Sciences, Makerere university
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| |
Collapse
|
8
|
Ekpenyong ME, Adegoke AA, Edoho ME, Inyang UG, Udo IJ, Ekaidem IS, Osang F, Uto NP, Geoffery JI. Collaborative Mining of Whole Genome Sequences for Intelligent HIV-1 Sub-Strain(s) Discovery. Curr HIV Res 2022; 20:163-183. [PMID: 35142269 DOI: 10.2174/1570162x20666220210142209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Effective global antiretroviral vaccines and therapeutic strategies depend on the diversity, evolution, and epidemiology of their various strains as well as their transmission and pathogenesis. Most viral disease-causing particles are clustered into a taxonomy of subtypes to suggest pointers toward nucleotide-specific vaccines or therapeutic applications of clinical significance sufficient for sequence-specific diagnosis and homologous viral studies. These are very useful to formulate predictors to induce cross-resistance to some retroviral control drugs being used across study areas. OBJECTIVE This research proposed a collaborative framework of hybridized (Machine Learning and Natural Language Processing) techniques to discover hidden genome patterns and feature predictors, for HIV-1 genome sequences mining. METHOD 630 human HIV-1 genome sequences above 8500 bps were excavated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov) for 21 countries across different continents, Antarctica exempt. These sequences were transformed and learned using a self-organizing map (SOM). To discriminate emerging/new sub-strain(s), the HIV-1 reference genome was included as part of the input isolates/samples during the training. After training the SOM, component planes defining pattern clusters of the input datasets were generated, for cognitive knowledge mining and subsequent labelling of the datasets. Additional genome features including dinucleotide transmission recurrences, codon recurrences, and mutation recurrences, were finally extracted from the raw genomes to construct output classification targets for supervised learning. RESULTS SOM training explains the inherent pattern diversity of HIV-1 genomes as well as inter- and intra-country transmissions in which mobility might play an active role, as corroborated by literature. Nine sub-strains were discovered after disassembling the SOM correlation hunting matrix space attributed to disparate clusters. Cognitive knowledge mining separated similar pattern clusters bounded by a certain degree of correlation range, discovered by the SOM. A Kruskal-Wallis rank-sum test and Wilcoxon rank-sum test showed statistically significant variations in dinucleotide, codon, and mutation patterns. CONCLUSION Results of the discovered sub-strains and response clusters visualizations corroborate existing literature, with significant haplotype variations. The proposed framework would assist in the development of decision support systems for easy contact tracing, infectious disease surveillance, and studying the progressive evolution of the reference HIV-1 genome.
Collapse
Affiliation(s)
- Moses E Ekpenyong
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
- Centre for Research and Development, University of Uyo, Uyo, Nigeria
| | - Anthony A Adegoke
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Mercy E Edoho
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Udoinyang G Inyang
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Ifiok J Udo
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| | - Itemobong S Ekaidem
- Department of Chemical Pathology, College of Health Sciences, University of Uyo, Uyo, Nigeria
| | - Francis Osang
- Department of Computer Science, Faculty of Science, National Open University, Abuja, Nigeria
| | - Nseobong P Uto
- School of Mathematics and Statistics, University of St Andrews, Scotland, United Kingdom
| | - Joseph I Geoffery
- Department of Computer Science, Faculty of Science, University of Uyo, Uyo, Nigeria
| |
Collapse
|
9
|
Balinda SN, Kapaata A, Xu R, Salazar MG, Mezzell AT, Qin Q, Herard K, Dilernia D, Kamali A, Ruzagira E, Kibengo FM, Song H, Ochsenbauer C, Salazar-Gonzalez JF, Gilmour J, Hunter E, Yue L, Kaleebu P. Characterization of Near Full-Length Transmitted/Founder HIV-1 Subtype D and A/D Recombinant Genomes in a Heterosexual Ugandan Population (2006–2011). Viruses 2022; 14:v14020334. [PMID: 35215928 PMCID: PMC8874453 DOI: 10.3390/v14020334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Detailed characterization of transmitted HIV-1 variants in Uganda is fundamentally important to inform vaccine design, yet studies on the transmitted full-length strains of subtype D viruses are limited. Here, we amplified single genomes and characterized viruses, some of which were previously classified as subtype D by sub-genomic pol sequencing that were transmitted in Uganda between December 2006 to June 2011. Analysis of 5′ and 3′ half genome sequences showed 73% (19/26) of infections involved single virus transmissions, whereas 27% (7/26) of infections involved multiple variant transmissions based on predictions of a model of random virus evolution. Subtype analysis of inferred transmitted/founder viruses showed a high transmission rate of inter-subtype recombinants (69%, 20/29) involving mainly A1/D, while pure subtype D variants accounted for one-third of infections (31%, 9/29). Recombination patterns included a predominance of subtype D in the gag/pol region and a highly recombinogenic envelope gene. The signal peptide-C1 region and gp41 transmembrane domain (Tat2/Rev2 flanking region) were hotspots for A1/D recombination events. Analysis of a panel of 14 transmitted/founder molecular clones showed no difference in replication capacity between subtype D viruses (n = 3) and inter-subtype mosaic recombinants (n = 11). However, individuals infected with high replication capacity viruses had a faster CD4 T cell loss. The high transmission rate of unique inter-subtype recombinants is striking and emphasizes the extraordinary challenge for vaccine design and, in particular, for the highly variable and recombinogenic envelope gene, which is targeted by rational designs aimed to elicit broadly neutralizing antibodies.
Collapse
Affiliation(s)
- Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
- Correspondence: ; Tel.: +25-675-466-0098
| | - Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Allison T. Mezzell
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 3230, Eden Ave, Cincinnati, OH 45267, USA;
| | - Qianhong Qin
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Kimberly Herard
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Anatoli Kamali
- International AIDS Vaccine Initiative (IAVI), Nairobi 00202, Kenya;
| | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Freddie M. Kibengo
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Heeyah Song
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London SW10 9NH, UK;
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Ling Yue
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| |
Collapse
|
10
|
Malatinkova E, Thomas J, De Spiegelaere W, Rutsaert S, Geretti AM, Pollakis G, Paxton WA, Vandekerckhove L, Ruggiero A. Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences. Life (Basel) 2021; 11:life11121410. [PMID: 34947941 PMCID: PMC8706387 DOI: 10.3390/life11121410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/28/2022] Open
Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2–5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. Alu-5LTR assay sensitivity was also determined using an “integrated standard”; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
Collapse
Affiliation(s)
- Eva Malatinkova
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Ward De Spiegelaere
- Laboratory of Veterinary Morphology, Faculty of Veterinary Sciences, Ghent University, B-9820 Ghent, Belgium;
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Anna Maria Geretti
- Fondazione PTV and Faculty of Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - William A. Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium; (E.M.); (S.R.); (L.V.)
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK; (J.T.); (G.P.); (W.A.P.)
- Department Neurosciences, Biomedicine and Movement Sciences, School of Medicine-University of Verona, 37129 Verona, Italy
- Correspondence: ; Tel.: +39-045-802-7190
| |
Collapse
|
11
|
Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
Collapse
Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| |
Collapse
|
12
|
Simonetti FR, Zhang H, Soroosh GP, Duan J, Rhodehouse K, Hill AL, Beg SA, McCormick K, Raymond HE, Nobles CL, Everett JK, Kwon KJ, White JA, Lai J, Margolick JB, Hoh R, Deeks SG, Bushman FD, Siliciano JD, Siliciano RF. Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo. J Clin Invest 2021; 131:145254. [PMID: 33301425 DOI: 10.1172/jci145254] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
Collapse
Affiliation(s)
- Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Garshasb P Soroosh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hayley E Raymond
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
| |
Collapse
|
13
|
Cole B, Lambrechts L, Gantner P, Noppe Y, Bonine N, Witkowski W, Chen L, Palmer S, Mullins JI, Chomont N, Pardons M, Vandekerckhove L. In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia. Nat Commun 2021; 12:3727. [PMID: 34140517 PMCID: PMC8211655 DOI: 10.1038/s41467-021-24080-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/22/2021] [Indexed: 02/07/2023] Open
Abstract
Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution from cell clones that harbor inducible proviruses to plasma viremia is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5'-end of the genome, often involving the major splice donor site. TCR and integration site sequencing reveal that cell clones with predicted pathogen-specificity can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we find several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, suggesting that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.
Collapse
Affiliation(s)
- Basiel Cole
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Laurens Lambrechts
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Pierre Gantner
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Ytse Noppe
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Noah Bonine
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
- BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Lennie Chen
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicolas Chomont
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium.
| |
Collapse
|
14
|
Ssemwanga D, Bbosa N, Nsubuga RN, Ssekagiri A, Kapaata A, Nannyonjo M, Nassolo F, Karabarinde A, Mugisha J, Seeley J, Yebra G, Leigh Brown A, Kaleebu P. The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda. Viruses 2020; 12:v12111283. [PMID: 33182587 PMCID: PMC7697205 DOI: 10.3390/v12111283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 pol sequences (GPC: n = 1418, non-GPC sites: n = 1223, Central Uganda: n = 1010 and Eastern Uganda: n = 145) generated between 2003–2015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (≥5 individuals, n = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06–1.54), being >25 years (aOR = 1.52; 95% CI, 1.16–2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22–9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.
Collapse
Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
- Correspondence: ; Tel.: +256-(0)-417-704000
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Rebecca N. Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alfred Ssekagiri
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
| | - Anne Kapaata
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Maria Nannyonjo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Faridah Nassolo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alex Karabarinde
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Joseph Mugisha
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Janet Seeley
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London WC1H 9SH, UK
| | - Gonzalo Yebra
- The Roslin Institute, Royal (Dick) School of Veterinary Medicine, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK;
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
| |
Collapse
|
15
|
Howison M, Coetzer M, Kantor R. Measurement error and variant-calling in deep Illumina sequencing of HIV. Bioinformatics 2020; 35:2029-2035. [PMID: 30407489 DOI: 10.1093/bioinformatics/bty919] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 09/21/2018] [Accepted: 11/06/2018] [Indexed: 01/23/2023] Open
Abstract
MOTIVATION Next-generation deep sequencing of viral genomes, particularly on the Illumina platform, is increasingly applied in HIV research. Yet, there is no standard protocol or method used by the research community to account for measurement errors that arise during sample preparation and sequencing. Correctly calling high and low-frequency variants while controlling for erroneous variants is an important precursor to downstream interpretation, such as studying the emergence of HIV drug-resistance mutations, which in turn has clinical applications and can improve patient care. RESULTS We developed a new variant-calling pipeline, hivmmer, for Illumina sequences from HIV viral genomes. First, we validated hivmmer by comparing it to other variant-calling pipelines on real HIV plasmid datasets. We found that hivmmer achieves a lower rate of erroneous variants, and that all methods agree on the frequency of correctly called variants. Next, we compared the methods on an HIV plasmid dataset that was sequenced using Primer ID, an amplicon-tagging protocol, which is designed to reduce errors and amplification bias during library preparation. We show that the Primer ID consensus exhibits fewer erroneous variants compared to the variant-calling pipelines, and that hivmmer more closely approaches this low error rate compared to the other pipelines. The frequency estimates from the Primer ID consensus do not differ significantly from those of the variant-calling pipelines. AVAILABILITY AND IMPLEMENTATION hivmmer is freely available for non-commercial use from https://github.com/kantorlab/hivmmer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mark Howison
- Watson Institute for International and Public Affairs
| | - Mia Coetzer
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, USA
| | - Rami Kantor
- Division of Infectious Diseases, The Alpert Medical School, Brown University, Providence, RI, USA
| |
Collapse
|
16
|
Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O, Abeler-Dörner L, Ayles H, Bonsall D, Bowden R, Calvez V, Cohen M, Denis A, Frampton D, de Oliveira T, Essex M, Fidler S, Fraser C, Golubchik T, Hayes R, Herbeck JT, Hoppe A, Kaleebu P, Kellam P, Kityo C, Leigh-Brown A, Lingappa JR, Novitsky V, Paton N, Pillay D, Rambaut A, Ratmann O, Seeley J, Ssemwanga D, Tanser F. Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda. AIDS Res Hum Retroviruses 2020; 36:467-474. [PMID: 31914792 DOI: 10.1089/aid.2019.0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.
Collapse
Affiliation(s)
- Adam A. Capoferri
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mary Kate Grabowski
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | | | - Maria J. Wawer
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Entebbe, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Ronald H. Gray
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Rakai Health Sciences Program, Entebbe, Uganda
| | - Thomas C. Quinn
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | - Oliver Laeyendecker
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 84:104365. [PMID: 32417307 DOI: 10.1016/j.meegid.2020.104365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffling of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.
Collapse
|
18
|
Abstract
Development of improved approaches for HIV-1 prevention will likely be required for a durable end to the global AIDS pandemic. Recent advances in preclinical studies and early phase clinical trials offer renewed promise for immunologic strategies for blocking acquisition of HIV-1 infection. Clinical trials are currently underway to evaluate the efficacy of two vaccine candidates and a broadly neutralizing antibody (bNAb) to prevent HIV-1 infection in humans. However, the vast diversity of HIV-1 is a major challenge for both active and passive immunization. Here we review current immunologic strategies for HIV-1 prevention, with a focus on current and next-generation vaccines and bNAbs.
Collapse
Affiliation(s)
- Kathryn E Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- New Mexico Consortium, Los Alamos, New Mexico 87545, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA;
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, Massachusetts 02114, USA
| |
Collapse
|
19
|
Abstract
PURPOSE OF REVIEW To provide a summary of the current data on the global HIV subtype diversity and distribution by region. HIV is one of the most genetically diverse pathogens due to its high-mutation and recombination rates, large population size and rapid replication rate. This rapid evolutionary process has resulted in several HIV subtypes that are heterogeneously globally distributed. RECENT FINDINGS Subtype A remains the most prevalent strain in parts of East Africa, Russia and former Soviet Union countries; subtype B in Europe, Americas and Oceania; subtype C in Southern Africa and India; CRF01_AE in Asia and CRF02_AG in Western Africa. Recent studies based on near full-length genome sequencing highlighted the growing importance of recombinant variants and subtype C viruses. SUMMARY The dynamic change in HIV subtype distribution presents future challenges for diagnosis, treatment and vaccine design and development. An increase in recombinant viruses suggests that coinfection and superinfection by divergent HIV strains has become more common necessitating continuous surveillance to keep track of the viral diversity. Cheaper near full-length genome sequencing approaches are critical in improving HIV subtype estimations. However, missing subtype data and low sequence sampling levels are still a challenge in some geographical regions. VIDEO ABSTRACT: http://links.lww.com/COHA/A14.
Collapse
|
20
|
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
Collapse
Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | |
Collapse
|
21
|
Abeler-Dörner L, Grabowski MK, Rambaut A, Pillay D, Fraser C. PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa. Curr Opin HIV AIDS 2019; 14:173-180. [PMID: 30946141 PMCID: PMC6629166 DOI: 10.1097/coh.0000000000000542] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW The HIV epidemic in sub-Saharan Africa is far from being under control and the ambitious UNAIDS targets are unlikely to be met by 2020 as declines in per-capita incidence being largely offset by demographic trends. There is an increasing number of proven and specific HIV prevention tools, but little consensus on how best to deploy them. RECENT FINDINGS Traditionally, phylogenetics has been used in HIV research to reconstruct the history of the epidemic and date zoonotic infections, whereas more recent publications focus on HIV diversity and drug resistance. However, it is also the most powerful method of source attribution available for the study of HIV transmission. The PANGEA (Phylogenetics And Networks for Generalized Epidemics in Africa) consortium has generated over 18 000 NGS HIV sequences from five countries in sub-Saharan Africa. Using phylogenetic methods, we will identify characteristics of individuals or groups, which are most likely to be at risk of infection or at risk of infecting others. SUMMARY Combining phylogenetics, phylodynamics and epidemiology will allow PANGEA to highlight where prevention efforts should be focussed to reduce the HIV epidemic most effectively. To maximise the public health benefit of the data, PANGEA offers accreditation to external researchers, allowing them to access the data and join the consortium. We also welcome submissions of other HIV sequences from sub-Saharan Africa to the database.
Collapse
Affiliation(s)
- Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mary K. Grabowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Rakai Health Sciences Program, Baltimore, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK
| | - Deenan Pillay
- Africa Health Research Institute, KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
22
|
Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
Collapse
Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| |
Collapse
|
23
|
Einkauf KB, Lee GQ, Gao C, Sharaf R, Sun X, Hua S, Chen SM, Jiang C, Lian X, Chowdhury FZ, Rosenberg ES, Chun TW, Li JZ, Yu XG, Lichterfeld M. Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. J Clin Invest 2019; 129:988-998. [PMID: 30688658 DOI: 10.1172/jci124291] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Chromosomal integration of genome-intact HIV-1 sequences into the host genome creates a reservoir of virally infected cells that persists throughout life, necessitating indefinite antiretroviral suppression therapy. During effective antiviral treatment, the majority of these proviruses remain transcriptionally silent, but mechanisms responsible for viral latency are insufficiently clear. Here, we used matched integration site and proviral sequencing (MIP-Seq), an experimental approach involving multiple displacement amplification of individual proviral species, followed by near-full-length HIV-1 next-generation sequencing and corresponding chromosomal integration site analysis to selectively map the chromosomal positions of intact and defective proviruses in 3 HIV-1-infected individuals undergoing long-term antiretroviral therapy. Simultaneously, chromatin accessibility and gene expression in autologous CD4+ T cells were analyzed by assays for transposase-accessible chromatin using sequencing (ATAC-Seq) and RNA-Seq. We observed that in comparison to proviruses with defective sequences, intact HIV-1 proviruses were enriched for non-genic chromosomal positions and more frequently showed an opposite orientation relative to host genes. In addition, intact HIV-1 proviruses were preferentially integrated in either relative proximity to or increased distance from active transcriptional start sites and to accessible chromatin regions. These studies strongly suggest selection of intact proviruses with features of deeper viral latency during prolonged antiretroviral therapy, and may be informative for targeting the genome-intact viral reservoir.
Collapse
Affiliation(s)
- Kevin B Einkauf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Guinevere Q Lee
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Radwa Sharaf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samantha My Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chenyang Jiang
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xiaodong Lian
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, Maryland, USA
| | - Jonathan Z Li
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|