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Bengu N, Cromhout G, Adland E, Govender K, Herbert N, Lim N, Fillis R, Sprenger K, Vieira V, Kannie S, van Lobenstein J, Chinniah K, Kapongo C, Bhoola R, Krishna M, Mchunu N, Pascucci GR, Cotugno N, Palma P, Tagarro A, Rojo P, Roider J, Garcia-Guerrero MC, Ochsenbauer C, Groll A, Reddy K, Giaquinto C, Rossi P, Hong S, Dong K, Ansari MA, Puertas MC, Ndung'u T, Capparelli E, Lichterfeld M, Martinez-Picado J, Kappes JC, Archary M, Goulder P. Sustained aviremia despite anti-retroviral therapy non-adherence in male children after in utero HIV transmission. Nat Med 2024:10.1038/s41591-024-03105-4. [PMID: 38843818 DOI: 10.1038/s41591-024-03105-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
After sporadic reports of post-treatment control of HIV in children who initiated combination anti-retroviral therapy (cART) early, we prospectively studied 284 very-early-cART-treated children from KwaZulu-Natal, South Africa, after vertical HIV transmission to assess control of viremia. Eighty-four percent of the children achieved aviremia on cART, but aviremia persisting to 36 or more months was observed in only 32%. We observed that male infants have lower baseline plasma viral loads (P = 0.01). Unexpectedly, a subset (n = 5) of males maintained aviremia despite unscheduled complete discontinuation of cART lasting 3-10 months (n = 4) or intermittent cART adherence during 17-month loss to follow-up (n = 1). We further observed, in vertically transmitted viruses, a negative correlation between type I interferon (IFN-I) resistance and viral replication capacity (VRC) (P < 0.0001) that was markedly stronger for males than for females (r = -0.51 versus r = -0.07 for IFN-α). Although viruses transmitted to male fetuses were more IFN-I sensitive and of higher VRC than those transmitted to females in the full cohort (P < 0.0001 and P = 0.0003, respectively), the viruses transmitted to the five males maintaining cART-free aviremia had significantly lower replication capacity (P < 0.0001). These data suggest that viremic control can occur in some infants with in utero-acquired HIV infection after early cART initiation and may be associated with innate immune sex differences.
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Affiliation(s)
- Nomonde Bengu
- Queen Nandi Regional Hospital, Empangeni, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Gabriela Cromhout
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Department of Paediatrics, University of KwaZulu-Natal, Durban, South Africa
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | | | - Nicholas Lim
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Rowena Fillis
- Harry Gwala Regional Hospital, Pietermaritzburg, South Africa
| | - Kenneth Sprenger
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Samantha Kannie
- General Justice Gizenga Mpanza Regional Hospital, Stanger, South Africa
| | | | | | | | - Roopesh Bhoola
- Harry Gwala Regional Hospital, Pietermaritzburg, South Africa
| | - Malini Krishna
- Harry Gwala Regional Hospital, Pietermaritzburg, South Africa
| | - Noxolo Mchunu
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Giuseppe Rubens Pascucci
- Clinical Immunology and Vaccinology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Probiomics S.r.l., Rome, Italy
| | - Nicola Cotugno
- Clinical Immunology and Vaccinology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- University of Rome Tor Vergata, Rome, Italy
| | - Paolo Palma
- Clinical Immunology and Vaccinology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- University of Rome Tor Vergata, Rome, Italy
| | - Alfredo Tagarro
- Fundación de Investigación Biomédica Hospital 12 de Octubre, Instituto de Investigación 12 de Octubre (imas12), Madrid, Spain
- Department of Pediatrics, Infanta Sofia University Hospital and Henares University Hospital Foundation for Biomedical Research and Innovation, Madrid, Spain
- Universidad Europea de Madrid, Madrid, Spain
| | - Pablo Rojo
- Fundación de Investigación Biomédica Hospital 12 de Octubre, Instituto de Investigación 12 de Octubre (imas12), Madrid, Spain
| | | | | | | | | | - Kavidha Reddy
- Africa Health Research Institute, Durban, South Africa
| | | | - Paolo Rossi
- Clinical Immunology and Vaccinology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- University of Rome Tor Vergata, Rome, Italy
| | - Seohyun Hong
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Krista Dong
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - M Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maria C Puertas
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Division of Infection and Immunity, University College London, London, UK
| | | | | | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - John C Kappes
- University of Alabama at Birmingham, Birmingham, AL, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, USA
| | - Moherndran Archary
- Department of Paediatrics, University of KwaZulu-Natal, Durban, South Africa
| | - Philip Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- Africa Health Research Institute, Durban, South Africa.
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
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2
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Sonela N, Mann J, Godwe C, Goni OH, Tchakoute M, Nkoue N, de Oliveira T, Brockman MA, Brumme ZL, Ndung'u T, Tongo M. No detectable differences in Nef-mediated downregulation of HLA-I and CD4 molecules among HIV-1 group M lineages circulating in Cameroon, where the pandemic originated. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2024; 4:fviro.2024.1379217. [PMID: 38883214 PMCID: PMC7616105 DOI: 10.3389/fviro.2024.1379217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins. We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroon, where multiple variants have been circulating since the pandemic's origin. Single HIV-1 Nef clones from 234 HIV-1-ART naïve individuals living in remote villages and two cosmopolitan cities of Cameroon, sampled between 2000 and 2013, were isolated from plasma HIV RNA and analyzed for their capacity to downregulate HLA-I and CD4 molecules. We found that, despite a large degree of within- and inter- lineage variation, the ability of Nef to downregulate HLA-I was similar across these different viruses. Moreover, Nef-mediated CD4 downregulation activity was also well conserved across the different lineages found in Cameroon. In addition, we observed a trend towards higher HLA-I downregulation activity of viruses circulating in the cosmopolitan cities versus the remote villages, whereas the CD4 downregulation activities were similar across the two settings. Furthermore, we noted a significant decline of HLA-I downregulation activity from 2000 to 2013, providing additional evidence supporting the attenuation of the global HIV-1M population over time. Finally, we identified 18 amino acids associated with differential HLA-I downregulation and 13 amino acids associated with differential CD4 downregulation within the dominant CRF02_AG lineage. Our lack of observation of HIV lineage-related differences in Nef-mediated HLA-I and CD4 downregulation function suggests that these activities do not substantively influence the prevalence of different HIV-1M lineages in Cameroon.
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Affiliation(s)
- Nelson Sonela
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Jaclyn Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Celestin Godwe
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Biochemistry, University of Douala, Douala, Cameroon
| | - Oumarou H Goni
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Microbiology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Mérime Tchakoute
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Nathalie Nkoue
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mark A Brockman
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
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Zhang Z, Nishimura A, Trovão NS, Cherry JL, Holbrook AJ, Ji X, Lemey P, Suchard MA. Accelerating Bayesian inference of dependency between mixed-type biological traits. PLoS Comput Biol 2023; 19:e1011419. [PMID: 37639445 PMCID: PMC10491301 DOI: 10.1371/journal.pcbi.1011419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Inferring dependencies between mixed-type biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The state-of-the-art approach uses a phylogenetic multivariate probit model to accommodate binary and continuous traits via a latent variable framework, and utilizes an efficient bouncy particle sampler (BPS) to tackle the computational bottleneck-integrating many latent variables from a high-dimensional truncated normal distribution. This approach breaks down as the number of specimens grows and fails to reliably characterize conditional dependencies between traits. Here, we propose an inference pipeline for phylogenetic probit models that greatly outperforms BPS. The novelty lies in 1) a combination of the recent Zigzag Hamiltonian Monte Carlo (Zigzag-HMC) with linear-time gradient evaluations and 2) a joint sampling scheme for highly correlated latent variables and correlation matrix elements. In an application exploring HIV-1 evolution from 535 viruses, the inference requires joint sampling from an 11,235-dimensional truncated normal and a 24-dimensional covariance matrix. Our method yields a 5-fold speedup compared to BPS and makes it possible to learn partial correlations between candidate viral mutations and virulence. Computational speedup now enables us to tackle even larger problems: we study the evolution of influenza H1N1 glycosylations on around 900 viruses. For broader applicability, we extend the phylogenetic probit model to incorporate categorical traits, and demonstrate its use to study Aquilegia flower and pollinator co-evolution.
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Affiliation(s)
- Zhenyu Zhang
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Akihiko Nishimura
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew J. Holbrook
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, Louisiana, United States of America
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Biomathematics, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
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4
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Mokaleng B, Choga WT, Bareng OT, Maruapula D, Ditshwanelo D, Kelentse N, Mokgethi P, Moraka NO, Motswaledi MS, Tawe L, Koofhethile CK, Moyo S, Zachariah M, Gaseitsiwe S. No Difference in the Prevalence of HIV-1 gag Cytotoxic T-Lymphocyte-Associated Escape Mutations in Viral Sequences from Early and Late Parts of the HIV-1 Subtype C Pandemic in Botswana. Vaccines (Basel) 2023; 11:1000. [PMID: 37243104 PMCID: PMC10221913 DOI: 10.3390/vaccines11051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
HIV is known to accumulate escape mutations in the gag gene in response to the immune response from cytotoxic T lymphocytes (CTLs). These mutations can occur within an individual as well as at a population level. The population of Botswana exhibits a high prevalence of HLA*B57 and HLA*B58, which are associated with effective immune control of HIV. In this retrospective cross-sectional investigation, HIV-1 gag gene sequences were analyzed from recently infected participants across two time periods which were 10 years apart: the early time point (ETP) and late time point (LTP). The prevalence of CTL escape mutations was relatively similar between the two time points-ETP (10.6%) and LTP (9.7%). The P17 protein had the most mutations (9.4%) out of the 36 mutations that were identified. Three mutations (A83T, K18R, Y79H) in P17 and T190A in P24 were unique to the ETP sequences at a prevalence of 2.4%, 4.9%, 7.3%, and 5%, respectively. Mutations unique to the LTP sequences were all in the P24 protein, including T190V (3%), E177D (6%), R264K (3%), G248D (1%), and M228L (11%). Mutation K331R was statistically higher in the ETP (10%) compared to the LTP (1%) sequences (p < 0.01), while H219Q was higher in the LTP (21%) compared to the ETP (5%) (p < 0.01). Phylogenetically, the gag sequences clustered dependently on the time points. We observed a slower adaptation of HIV-1C to CTL immune pressure at a population level in Botswana. These insights into the genetic diversity and sequence clustering of HIV-1C can aid in the design of future vaccine strategies.
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Affiliation(s)
- Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Wonderful Tatenda Choga
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Ontlametse Thato Bareng
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Nametso Kelentse
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone 999106, Botswana
| | - Natasha Onalenna Moraka
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Modisa Sekhamo Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Leabaneng Tawe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Matshediso Zachariah
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone 999106, Botswana; (M.S.M.); (L.T.); (M.Z.)
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership for HIV Research and Education, Gaborone 999106, Botswana; (B.M.); (W.T.C.); (O.T.B.); (D.M.); (D.D.); (N.K.); (P.M.); (N.O.M.); (C.K.K.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
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Koterov AN, Ushenkova LN, Biryukov AP. Hill’s Temporality Criterion: Reverse Causation and Its Radiation Aspect. BIOL BULL+ 2021. [DOI: 10.1134/s1062359020120031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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6
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Katoh J, Kawana-Tachikawa A, Shimizu A, Zhu D, Han C, Nakamura H, Koga M, Kikuchi T, Adachi E, Koibuchi T, Gao GF, Brumme ZL, Iwamoto A. Rapid HIV-1 Disease Progression in Individuals Infected with a Virus Adapted to Its Host Population. PLoS One 2016; 11:e0150397. [PMID: 26953793 PMCID: PMC4783116 DOI: 10.1371/journal.pone.0150397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
HIV-1 escape from CTL is predictable based on the Human Leukocyte Antigen (HLA) class I alleles expressed by the host. As such, HIV-1 sequences circulating in a population of hosts will harbor escape mutations specific to the HLA alleles of that population. In theory, this should increase the frequency of escape mutation transmission to persons expressing the restricting HLA allele, thereby compromising host immunity to the incoming HIV-1 strain. However, the clinical impact of infection with HIV-1 containing immune escape mutations has not conclusively been demonstrated. Japan’s population features limited HLA diversity which is driving population-level HIV adaptation: for example, >60% of Japanese express HLA-A*24:02 and its associated Nef-Y135F escape mutation represents the population consensus. As such, Japan is an ideal population in which to examine this phenomenon. Here, we combine genetic and immunological analyses to identify A*24:02-positive individuals likely to have been infected with Y135F-containing HIV-1. Over a ~5 year follow-up, these individuals exhibited significantly lower CD4 counts compared to individuals inferred to have been infected with wild-type HIV-1. Our results support a significant negative clinical impact of pathogen adaptation to host pressures at the population level.
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Affiliation(s)
- Jiro Katoh
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
| | - Ai Kawana-Tachikawa
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Akihisa Shimizu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Dayong Zhu
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Chungyong Han
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Hitomi Nakamura
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tadashi Kikuchi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Tomohiko Koibuchi
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - George F. Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Aikichi Iwamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo. Kashiwa-shi, Chiba, Japan
- Department of Infectious Disease Control, the International Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases and Applied Immunology, Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Asian Research Center for Infectious Diseases, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- * E-mail:
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7
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Kinloch NN, MacMillan DR, Le AQ, Cotton LA, Bangsberg DR, Buchbinder S, Carrington M, Fuchs J, Harrigan PR, Koblin B, Kushel M, Markowitz M, Mayer K, Milloy MJ, Schechter MT, Wagner T, Walker BD, Carlson JM, Poon AFY, Brumme ZL. Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic. J Virol 2016; 90:1244-58. [PMID: 26559841 PMCID: PMC4719594 DOI: 10.1128/jvi.02353-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era. IMPORTANCE HLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many-though not all-HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel R MacMillan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Laura A Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - David R Bangsberg
- Massachusetts General Hospital, Boston, Massachusetts, USA Harvard Medical School, Cambridge, Massachusetts, USA
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, USA University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Jonathan Fuchs
- San Francisco Department of Public Health, San Francisco, California, USA University of California, San Francisco, San Francisco, California, USA
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Margot Kushel
- University of California, San Francisco, San Francisco, California, USA
| | | | - Kenneth Mayer
- Harvard Medical School, Cambridge, Massachusetts, USA Fenway Community Health, Boston, Massachusetts, USA
| | - M J Milloy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin T Schechter
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Theresa Wagner
- San Francisco Department of Public Health, San Francisco, California, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | | | - Art F Y Poon
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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8
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Kløverpris HN, Leslie A, Goulder P. Role of HLA Adaptation in HIV Evolution. Front Immunol 2016; 6:665. [PMID: 26834742 PMCID: PMC4716577 DOI: 10.3389/fimmu.2015.00665] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/27/2015] [Indexed: 01/22/2023] Open
Abstract
Killing of HIV-infected cells by CD8+ T-cells imposes strong selection pressure on the virus toward escape. The HLA class I molecules that are successful in mediating some degree of control over the virus are those that tend to present epitopes in conserved regions of the proteome, such as in p24 Gag, in which escape also comes at a significant cost to viral replicative capacity (VRC). In some instances, compensatory mutations can fully correct for the fitness cost of such an escape variant; in others, correction is only partial. The consequences of these events within the HIV-infected host, and at the population level following transmission of escape variants, are discussed. The accumulation of escape mutants in populations over the course of the epidemic already shows instances of protective HLA molecules losing their impact, and in certain cases, a modest decline in HIV virulence in association with population-level increase in mutants that reduce VRC.
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Affiliation(s)
- Henrik N Kløverpris
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa; Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban , South Africa
| | - Philip Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Department of Paediatrics, University of Oxford, Oxford, UK
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9
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Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Gatanag H, Oka S, Takiguchi M. Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Retrovirology 2015; 12:98. [PMID: 26585907 PMCID: PMC4653850 DOI: 10.1186/s12977-015-0223-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/08/2015] [Indexed: 01/29/2023] Open
Abstract
Background HLA class I-associated escape mutations in HIV-1 Gag can reduce viral replication, suggesting that associated fitness costs could impact HIV-1 disease progression. Previous studies in North American and African cohorts have reported reduced Gag-Protease mediated viral replication capacity (Gag-Pro RC) in individuals expressing protective HLA class I alleles including HLA-B*57:01, B*27:05, and B*81:01. These studies also reported significant positive associations between Gag-Pro RCs and plasma viral load (pVL). However, these HLA alleles are virtually absent in Japan, and the importance of Gag as an immune target is not clearly defined in this population. Results We generated chimeric NL4-3 viruses carrying patient-derived Gag-Protease from 306 treatment-naive Japanese individuals chronically infected with HIV-1 subtype B. We analyzed associations between Gag-Pro RC and clinical markers of HIV-1 infection and host HLA expression. We observed no significant correlation between Gag-Pro RC and pVL in Japan in the overall cohort. However, upon exclusion of individuals expressing Japanese protective alleles HLA-B*52:01 and B*67:01, Gag-Pro RC correlated positively with pVL and negatively with CD4 T-cell count. Our results thus contrast with studies from other global cohorts reporting significantly lower Gag-Pro RC among persons expressing protective HLA alleles, and positive relationships between Gag-Pro RC and pVL in the overall study populations. We also identified five amino acids in Gag-Protease significantly associated with Gag-Pro RC, whose effects on RC were confirmed by site-directed mutagenesis. However, of the four mutations that decreased Gag-Pro RC, none were associated with reductions in pVL in Japan though two were associated with lower pVL in North America. Conclusions These data indicate that Gag fitness does not affect clinical outcomes in subjects with protective HLA class I alleles as well as the whole Japanese population. Moreover, the impact of Gag fitness costs on HIV-1 clinical parameters in chronic infection is likely low in Japan compared to other global populations. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | | | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan. .,Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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10
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Adland E, Paioni P, Thobakgale C, Laker L, Mori L, Muenchhoff M, Csala A, Clapson M, Flynn J, Novelli V, Hurst J, Naidoo V, Shapiro R, Huang KHG, Frater J, Prendergast A, Prado JG, Ndung’u T, Walker BD, Carrington M, Jooste P, Goulder PJR. Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection. PLoS Pathog 2015; 11:e1004954. [PMID: 26076345 PMCID: PMC4468173 DOI: 10.1371/journal.ppat.1004954] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
HLA class I polymorphism has a major influence on adult HIV disease progression. An important mechanism mediating this effect is the impact on viral replicative capacity (VRC) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses. Factors that contribute to slow progression in pediatric HIV infection are less well understood. We here investigate the relationship between VRC and disease progression in pediatric infection, and the effect of HLA on VRC and on disease outcome in adult and pediatric infection. Studying a South African cohort of >350 ART-naïve, HIV-infected children and their mothers, we first observed that pediatric disease progression is significantly correlated with VRC. As expected, VRCs in mother-child pairs were strongly correlated (p = 0.004). The impact of the protective HLA alleles, HLA-B*57, HLA-B*58:01 and HLA-B*81:01, resulted in significantly lower VRCs in adults (p<0.0001), but not in children. Similarly, in adults, but not in children, VRCs were significantly higher in subjects expressing the disease-susceptible alleles HLA-B*18:01/45:01/58:02 (p = 0.007). Irrespective of the subject, VRCs were strongly correlated with the number of Gag CD8+ T-cell escape mutants driven by HLA-B*57/58:01/81:01 present in each virus (p = 0.0002). In contrast to the impact of VRC common to progression in adults and children, the HLA effects on disease outcome, that are substantial in adults, are small and statistically insignificant in infected children. These data further highlight the important role that VRC plays both in adult and pediatric progression, and demonstrate that HLA-independent factors, yet to be fully defined, are predominantly responsible for pediatric non-progression.
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Affiliation(s)
- Emily Adland
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Paolo Paioni
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Christina Thobakgale
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Leana Laker
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Luisa Mori
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Maximilian Muenchhoff
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Anna Csala
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Margaret Clapson
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Jacquie Flynn
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Vas Novelli
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
| | - Jacob Hurst
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, United Kingdom
| | - Vanessa Naidoo
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kuan-Hsiang Gary Huang
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - John Frater
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Oxford National Institute of Health Research, Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew Prendergast
- Centre for Paediatrics, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Julia G. Prado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
| | - Mary Carrington
- The Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard University, Boston, Massachusetts, United States of America
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape, South Africa
| | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Paediatric Infectious Diseases, Great Ormond St Hospital for Children, London, United Kingdom
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11
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Manocheewa S, Lanxon-Cookson EC, Liu Y, Swain JV, McClure J, Rao U, Maust B, Deng W, Sunshine JE, Kim M, Rolland M, Mullins JI. Pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses. J Vis Exp 2015:e52610. [PMID: 25993602 PMCID: PMC4542137 DOI: 10.3791/52610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro fitness assays are essential tools for determining viral replication fitness for viruses such as HIV-1. Various measurements have been used to extrapolate viral replication fitness, ranging from the number of viral particles per infectious unit, growth rate in cell culture, and relative fitness derived from multiple-cycle growth competition assays. Growth competition assays provide a particularly sensitive measurement of fitness since the viruses are competing for cellular targets under identical growth conditions. There are several experimental factors to consider when conducting growth competition assays, including the multiplicity of infection (MOI), sampling times, and viral detection and fitness calculation methods. Each factor can affect the end result and hence must be considered carefully during the experimental design. The protocol presented here includes steps from constructing a new recombinant HIV-1 clone to performing growth competition assays and analyzing the experimental results. This protocol utilizes experimental parameter values previously shown to yield consistent and robust results. Alternatives are discussed, as some parameters need to be adjusted according to the cell type and viruses being studied. The protocol contains two alternative viral detection methods to provide flexibility as the availability of instruments, reagents and expertise varies between laboratories.
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Affiliation(s)
| | | | - Yi Liu
- Department of Microbiology, University of Washington
| | | | - Jan McClure
- Department of Microbiology, University of Washington
| | - Ushnal Rao
- Department of Microbiology, University of Washington
| | - Brandon Maust
- Department of Microbiology, University of Washington
| | - Wenjie Deng
- Department of Microbiology, University of Washington
| | | | - Moon Kim
- Department of Microbiology, University of Washington
| | - Morgane Rolland
- U.S Military HIV Research Program, Walter Reed Army Institute of Research; Henry M. Jackson Foundation
| | - James I Mullins
- Department of Microbiology, University of Washington; Departments of Medicine and Laboratory Medicine, University of Washington;
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12
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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13
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Payne R, Muenchhoff M, Mann J, Roberts HE, Matthews P, Adland E, Hempenstall A, Huang KH, Brockman M, Brumme Z, Sinclair M, Miura T, Frater J, Essex M, Shapiro R, Walker BD, Ndung'u T, McLean AR, Carlson JM, Goulder PJR. Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Proc Natl Acad Sci U S A 2014; 111:E5393-400. [PMID: 25453107 PMCID: PMC4273423 DOI: 10.1073/pnas.1413339111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is widely believed that epidemics in new hosts diminish in virulence over time, with natural selection favoring pathogens that cause minimal disease. However, a tradeoff frequently exists between high virulence shortening host survival on the one hand but allowing faster transmission on the other. This is the case in HIV infection, where high viral loads increase transmission risk per coital act but reduce host longevity. We here investigate the impact on HIV virulence of HIV adaptation to HLA molecules that protect against disease progression, such as HLA-B*57 and HLA-B*58:01. We analyzed cohorts in Botswana and South Africa, two countries severely affected by the HIV epidemic. In Botswana, where the epidemic started earlier and adult seroprevalence has been higher, HIV adaptation to HLA including HLA-B*57/58:01 is greater compared with South Africa (P = 7 × 10(-82)), the protective effect of HLA-B*57/58:01 is absent (P = 0.0002), and population viral replicative capacity is lower (P = 0.03). These data suggest that viral evolution is occurring relatively rapidly, and that adaptation of HIV to the most protective HLA alleles may contribute to a lowering of viral replication capacity at the population level, and a consequent reduction in HIV virulence over time. The potential role in this process played by increasing antiretroviral therapy (ART) access is also explored. Models developed here suggest distinct benefits of ART, in addition to reducing HIV disease and transmission, in driving declines in HIV virulence over the course of the epidemic, thereby accelerating the effects of HLA-mediated viral adaptation.
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Affiliation(s)
- Rebecca Payne
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | | | - Jaclyn Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Hannah E Roberts
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Philippa Matthews
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Allison Hempenstall
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Kuan-Hsiang Huang
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Mark Brockman
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Zabrina Brumme
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC V5A 1S6, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z 1Y6, Canada
| | - Marc Sinclair
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | | | - John Frater
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom; Oxford National Institute of Health Research, Biomedical Research Centre, Oxford OX1 3SY, United Kingdom
| | - Myron Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone BO 320, Botswana; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02215
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone BO 320, Botswana; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02215
| | - Bruce D Walker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02139
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02139
| | - Angela R McLean
- The Institute for Emerging Infections, The Oxford Martin School, University of Oxford, Oxford OX1 3BD, United Kingdom; Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; and
| | | | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa;
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14
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Abstract
Previous studies have demonstrated that effective cytotoxic T lymphocyte (CTL) responses drive the selection of escape mutations that reduce viral replication capacity (VRC). Escape mutations, including those with reduced VRC, can be transmitted and accumulate in a population. Here we compared two antiretroviral therapy (ART)-naive HIV clade B-infected cohorts, in Mexico and Barbados, in which the most protective HLA alleles (HLA-B*27/57/58:01/81:01) are differentially expressed, at 8% and 34%, respectively. Viral loads were significantly higher in Mexico than in Barbados (median, 40,774 versus 14,200; P < 0.0001), and absolute CD4+ T-cell counts were somewhat lower (median, 380/mm3 versus 403/mm3; P = 0.007). We tested the hypothesis that the disparate frequencies of these protective HLA alleles would be associated with a higher VRC at the population level in Mexico. Analysis of VRC in subjects in each cohort, matched for CD4+ T-cell count, revealed that the VRC was indeed higher in the Mexican cohort (mean, 1.13 versus 1.03; P = 0.0025). Although CD4 counts were matched, viral loads remained significantly higher in the Mexican subjects (P = 0.04). This VRC difference was reflected by a significantly higher frequency in the Barbados cohort of HLA-B*27/57/58:01/81:01-associated Gag escape mutations previously shown to incur a fitness cost on the virus (P = 0.004), a difference between the two cohorts that remained statistically significant even in subjects not expressing these protective alleles (P = 0.01). These data suggest that viral set points and disease progression rates at the population level may be significantly influenced by the prevalence of protective HLA alleles such as HLA-B*27/57/58:01/81:01 and that CD4 count-based guidelines to initiate antiretroviral therapy may need to be modified accordingly, to optimize the effectiveness of treatment-for-prevention strategies and reduce HIV transmission rates to the absolute minimum. IMPORTANCE Immune control of HIV at an individual level is strongly influenced by the HLA class I genotype. HLA class I molecules mediating effective immune control, such as HLA-B*27 and HLA-B*57, are associated with the selection of escape mutants that reduce viral replicative capacity. The escape mutants selected in infected patients can be transmitted and affect the viral load and CD4 count in the recipient. These findings prompt the hypothesis that the frequency of protective alleles in a population may affect viral set points and rates of disease progression in that population. These studies in Mexico and Barbados, where the prevalence rates of protective HLA alleles are 8% and 34%, respectively, support this hypothesis. These data suggest that antiretroviral therapy (ART) treatment-for-prevention strategies will be less successful in populations such as those in Mexico, where viral loads are higher for a given CD4 count. Consideration may therefore usefully be given to ART initiation at higher absolute CD4 counts in such populations to optimize the impact of ART for prevention.
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Cotton LA, Kuang XT, Le AQ, Carlson JM, Chan B, Chopera DR, Brumme CJ, Markle TJ, Martin E, Shahid A, Anmole G, Mwimanzi P, Nassab P, Penney KA, Rahman MA, Milloy MJ, Schechter MT, Markowitz M, Carrington M, Walker BD, Wagner T, Buchbinder S, Fuchs J, Koblin B, Mayer KH, Harrigan PR, Brockman MA, Poon AFY, Brumme ZL. Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet 2014; 10:e1004295. [PMID: 24762668 PMCID: PMC3998893 DOI: 10.1371/journal.pgen.1004295] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/21/2014] [Indexed: 11/20/2022] Open
Abstract
HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the extent and phenotypic impact of this phenomenon in an immunogenetically diverse population, we genotypically and functionally compared linked HLA and HIV (Gag/Nef) sequences from 358 historic (1979-1989) and 382 modern (2000-2011) specimens from four key cities in the North American epidemic (New York, Boston, San Francisco, Vancouver). Inferred HIV phylogenies were star-like, with approximately two-fold greater mean pairwise distances in modern versus historic sequences. The reconstructed epidemic ancestral (founder) HIV sequence was essentially identical to the North American subtype B consensus. Consistent with gradual diversification of a "consensus-like" founder virus, the median "background" frequencies of individual HLA-associated polymorphisms in HIV (in individuals lacking the restricting HLA[s]) were ∼ 2-fold higher in modern versus historic HIV sequences, though these remained notably low overall (e.g. in Gag, medians were 3.7% in the 2000s versus 2.0% in the 1980s). HIV polymorphisms exhibiting the greatest relative spread were those restricted by protective HLAs. Despite these increases, when HIV sequences were analyzed as a whole, their total average burden of polymorphisms that were "pre-adapted" to the average host HLA profile was only ∼ 2% greater in modern versus historic eras. Furthermore, HLA-associated polymorphisms identified in historic HIV sequences were consistent with those detectable today, with none identified that could explain the few HIV codons where the inferred epidemic ancestor differed from the modern consensus. Results are therefore consistent with slow HIV adaptation to HLA, but at a rate unlikely to yield imminent negative implications for cellular immunity, at least in North America. Intriguingly, temporal changes in protein activity of patient-derived Nef (though not Gag) sequences were observed, suggesting functional implications of population-level HIV evolution on certain viral proteins.
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Affiliation(s)
- Laura A. Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Xiaomei T. Kuang
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anh Q. Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Benjamin Chan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Denis R. Chopera
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Tristan J. Markle
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Martin
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Philip Mwimanzi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pauline Nassab
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kali A. Penney
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Manal A. Rahman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - M.-J. Milloy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin T. Schechter
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Theresa Wagner
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Jonathan Fuchs
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Beryl Koblin
- New York Blood Center, New York, New York, United States of America
| | - Kenneth H. Mayer
- Fenway Community Health, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F. Y. Poon
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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Capel E, Parera M, Clotet B, Martínez MA. Significant changes in integrase-associated HIV-1 replication capacity between early and late isolates. Virology 2013; 444:274-81. [DOI: 10.1016/j.virol.2013.06.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/18/2013] [Accepted: 06/24/2013] [Indexed: 11/29/2022]
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