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Bimber BN, Sunshine J, McElfresh GW, Reed JS, Pathak R, Bateman KB, Hughes CM, Gilbride RM, Ford JC, Morrow D, Lifson JD, Sacha JB, Hansen SG, Picker LJ. Viral escape mutations do not account for non-protection from SIVmac239 challenge in RhCMV/SIV vaccinated rhesus macaques. Front Immunol 2024; 15:1444621. [PMID: 39170621 PMCID: PMC11336698 DOI: 10.3389/fimmu.2024.1444621] [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: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024] Open
Abstract
Simian immunodeficiency virus (SIV) vaccines based upon 68-1 Rhesus Cytomegalovirus (RhCMV) vectors show remarkable protection against pathogenic SIVmac239 challenge. Across multiple independent rhesus macaque (RM) challenge studies, nearly 60% of vaccinated RM show early, complete arrest of SIVmac239 replication after effective challenge, whereas the remainder show progressive infection similar to controls. Here, we performed viral sequencing to determine whether the failure to control viral replication in non-protected RMs is associated with the acquisition of viral escape mutations. While low level viral mutations accumulated in all animals by 28 days-post-challenge, which is after the establishment of viral control in protected animals, the dominant circulating virus in virtually all unprotected RMs was nearly identical to the challenge stock, and there was no difference in mutation patterns between this cohort and unvaccinated controls. These data definitively demonstrate that viral mutation does not explain lack of viral control in RMs not protected by RhCMV/SIV vaccination. We further demonstrate that during chronic infection RhCMV/SIV vaccinated RMs do not acquire escape mutation in epitopes targeted by RhCMV/SIV, but instead display mutation in canonical MHC-Ia epitopes similar to unvaccinated RMs. This suggests that after the initial failure of viral control, unconventional T cell responses induced by 68-1 RhCMV/SIV vaccination do not exert strong selective pressure on systemically replicating SIV.
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Affiliation(s)
- Benjamin N. Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Justine Sunshine
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - G. W. McElfresh
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Jason S. Reed
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Reese Pathak
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Katherine B. Bateman
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Colette M. Hughes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Roxanne M. Gilbride
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Julia C. Ford
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - David Morrow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, United States
| | - Jonah B. Sacha
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Scott G. Hansen
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
| | - Louis J. Picker
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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Wieczorek L, Chang D, Sanders-Buell E, Zemil M, Martinez E, Schoen J, Chenine AL, Molnar S, Barrows B, Poltavee K, Charurat ME, Abimiku A, Blattner W, Iroezindu M, Kokogho A, Michael NL, Crowell TA, Ake JA, Tovanabutra S, Polonis VR. Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG. Virol J 2024; 21:148. [PMID: 38951814 PMCID: PMC11218331 DOI: 10.1186/s12985-024-02394-y] [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: 02/23/2024] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.
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Affiliation(s)
- Lindsay Wieczorek
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - David Chang
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Office of AIDS Research, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Martinez
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Jesse Schoen
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Integrated Biotherapeutics, Rockville, MD, 20850, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Brittani Barrows
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Lentigen Technology, Gaithersburg, MD, 20878, USA
| | - Kultida Poltavee
- SEARCH, Insititute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alash'le Abimiku
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Blattner
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Afoke Kokogho
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Trevor A Crowell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA.
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Zhou Z, Zhang X, Wang M, Jiang F, Tong J, Nie J, Zhao C, Zheng H, Zhang Z, Shi P, Fan W, Wang Y, Huang W. HIV-1 env gene mutations outside the targeting probe affects IPDA efficiency. iScience 2024; 27:109941. [PMID: 38812543 PMCID: PMC11133923 DOI: 10.1016/j.isci.2024.109941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/29/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
The intact proviral DNA assay (IPDA) based on droplet digital PCR was developed to identify intact proviral DNA and quantify HIV-1 latency reservoirs in patients infected with HIV-1. However, the genetic characteristics of different HIV-1 subtypes are non-consistent due to their high mutation and recombination rates. Here, we identified that the IPDA based on the sequences features of an HIV-1 subtype could not effectively detect different HIV-1 subtypes due to the high diversity of HIV-1. Furthermore, we demonstrated that mutations in env gene outside the probe binding site affect the detection efficiency of IPDA. Since mutations in env gene outside the probe binding site may also lead to the formation of stop codons, thereby preventing the formation of viruses and ultimately overestimating the number of HIV-1 latency reservoirs, it is important to address the effect of mutations on the IPDA.
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Affiliation(s)
- Zehua Zhou
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- Beijing Minhai Biotechnology Co., Ltd., Beijing, China
| | - Xinyu Zhang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Meiyu Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fei Jiang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jincheng Tong
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Jianhui Nie
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Chenyan Zhao
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Haifa Zheng
- Beijing Minhai Biotechnology Co., Ltd., Beijing, China
| | - Zhen Zhang
- Infection Division, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Penghui Shi
- Department of Clinical Laboratory Medicine, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Weiguang Fan
- Department of Clinical Laboratory Medicine, the People’s Hospital of Baoding, 608 Dongfeng East Road, Lianchi District, Baoding, Hebei 071000, China
| | - Youchun Wang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
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4
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Wolf T, Calisan KK, Stitz J, Barbe S. The effects of high shear rates on the average hydrodynamic diameter measured in biomimetic HIV Gag virus-like particle dispersions. Front Bioeng Biotechnol 2024; 12:1367405. [PMID: 38860137 PMCID: PMC11163053 DOI: 10.3389/fbioe.2024.1367405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
HIV Gag virus-like particles (HIV Gag VLPs) are promising HIV vaccine candidates. In the literature, they are often described as shear-sensitive particles, and authors usually recommend the operation of tangential flow filtration (TFF) gently at shear rates below 4,000 s-1 to 6,000 s-1. This in turn poses a severe limitation to the performance of TFF-mediated concentration of VLPs, which would be substantially enhanced by working at higher shear rates. To our knowledge, studies examining the shear sensitivity of HIV Gag VLPs and providing detailed information and evidence for the fragility of these particles have not been conducted yet. Thus, we investigated the effect of high shear rates on the colloidal stability of mosaic VLPs (Mos-VLPs) as relevant examples for HIV Gag VLPs. For this purpose, Mos-VLPs were exposed to different shear rates ranging from 3,395 s-1 to 22, 365 s-1 for 2 h. The average hydrodynamic diameter (AHD) and the polydispersity index (PDI) of the associated particle size distribution were used as stability indicators and measured after the treatment and during storage through dynamic light scattering. At high shear rates, we observed an increase in both AHD and PDI during the storage of HIV Mos1.Gag VLPs (bVLP-without envelope proteins) and Mos1.Gag + Mos2S.Env VLPs (eVLP-with envelope proteins). eVLPs exhibited higher colloidal stability than bVLPs, and we discuss the potential stabilizing role of envelope proteins. We finally demonstrated that the dispersion medium also has a considerable impact on the stability of Mos-VLPs.
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Affiliation(s)
- Tobias Wolf
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
- Institue of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Kerim Kadir Calisan
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
| | - Jörn Stitz
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
| | - Stéphan Barbe
- Research Group Medical Biotechnology and Bioengineering, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Leverkusen, Germany
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5
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Bai H, Lewitus E, Li Y, Thomas PV, Zemil M, Merbah M, Peterson CE, Thuraisamy T, Rees PA, Hajduczki A, Dussupt V, Slike B, Mendez-Rivera L, Schmid A, Kavusak E, Rao M, Smith G, Frey J, Sims A, Wieczorek L, Polonis V, Krebs SJ, Ake JA, Vasan S, Bolton DL, Joyce MG, Townsley S, Rolland M. Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding. Nat Commun 2024; 15:3924. [PMID: 38724518 PMCID: PMC11082178 DOI: 10.1038/s41467-024-48139-x] [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: 06/26/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
An effective HIV-1 vaccine must elicit broadly neutralizing antibodies (bnAbs) against highly diverse Envelope glycoproteins (Env). Since Env with the longest hypervariable (HV) loops is more resistant to the cognate bnAbs than Env with shorter HV loops, we redesigned hypervariable loops for updated Env consensus sequences of subtypes B and C and CRF01_AE. Using modeling with AlphaFold2, we reduced the length of V1, V2, and V5 HV loops while maintaining the integrity of the Env structure and glycan shield, and modified the V4 HV loop. Spacers are designed to limit strain-specific targeting. All updated Env are infectious as pseudoviruses. Preliminary structural characterization suggests that the modified HV loops have a limited impact on Env's conformation. Binding assays show improved binding to modified subtype B and CRF01_AE Env but not to subtype C Env. Neutralization assays show increases in sensitivity to bnAbs, although not always consistently across clades. Strikingly, the HV loop modification renders the resistant CRF01_AE Env sensitive to 10-1074 despite the absence of a glycan at N332.
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Affiliation(s)
- Hongjun Bai
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Paul V Thomas
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Mélanie Merbah
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Caroline E Peterson
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Thujitha Thuraisamy
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Phyllis A Rees
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Agnes Hajduczki
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Bonnie Slike
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Annika Schmid
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Erin Kavusak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Mekhala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Gabriel Smith
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Jessica Frey
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Alicea Sims
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Victoria Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Diane L Bolton
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - M Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Samantha Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
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6
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Lewitus E, Li Y, Bai H, Pham P, Rolland M. HIV-1 Gag, Pol, and Env diversified with limited adaptation since the 1980s. mBio 2024; 15:e0174923. [PMID: 38329340 PMCID: PMC10936417 DOI: 10.1128/mbio.01749-23] [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: 07/07/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Knowledge of HIV-1 global sequence diversity is critical for developing an effective prophylactic against HIV-1 infection. We developed the Hervé platform to analyze and visualize trends in HIV-1 diversification. Using Hervé, we analyzed 4,830 Env, 4,407 Gag, and 3,002 Pol publicly available independent sequences corresponding to subtypes A1, A6, B, C, D, F1, and G and circulating recombinant forms (CRFs) 01_AE, 02_AG, and 07_BC; sequences were sampled between 1980 and 2020 from 82 countries. HIV-1 diversified with a median of 1.82 amino acid substitutions per year in Env, 0.297 in Gag, and 0.779 in Pol. Yet, Env subtype B diversification plateaued post-2000. Pairwise diversity within subtypes and CRFs increased by 41.82% (range = 24.85%-54.41%) in Env, 56.93% (15.38%-89.16%) in Gag, and 46.12% (11.70%-70.57%) in Pol. Consensus sequences based on sequences sampled in each decade remained relatively stable over time. Similarly, at antibody epitope sites, only 0-8 residues that were minority variants became consensus over time in any subtype/CRF and only one known drug resistance mutation site differed from the reference (subtype G). The apparent contradiction between the fast diversification of HIV-1 and its limited adaptation illustrates that HIV-1 evolution is not directional and its consensus is at the intersection of millions of within-host selective processes occurring in a star-like manner. While a consensus sequence is a better representation of HIV-1 diversity than any individual sequence, consensus sequences have progressively become more distant from the circulating sequences they represent. IMPORTANCE Global surveillance of HIV-1 sequences is critical for designing relevant prophylactic and therapeutic interventions to infection. We designed an open-source platform, Hervé, for analyzing and visualizing the diversification dynamics of HIV-1 protein sequences. We characterized the evolution of over 12,000 HIV-1 Env, Gag, and Pol protein sequences from 1980-2020 and found that, despite a steady increase in intra-subtype and circulating recombinant form diversity, the most frequent residue at each site, i.e., the consensus, has varied only moderately.
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Affiliation(s)
- Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Hongjun Bai
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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7
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Li S, Qiu M, Li S, Li C, Lin H, Qiu Y, Qi W, Feng B, Cui M, Yang S, Zheng W, Shang S, Tian K, Zhu J, Lu Y, Chen N. A chimeric porcine reproductive and respiratory syndrome virus 1 strain containing synthetic ORF2-6 genes can trigger T follicular helper cell and heterologous neutralizing antibody responses and confer enhanced cross-protection. Vet Res 2024; 55:28. [PMID: 38449049 PMCID: PMC10918997 DOI: 10.1186/s13567-024-01280-3] [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: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
The prevalence of porcine reproductive and respiratory syndrome virus 1 (PRRSV1) isolates has continued to increase in Chinese swine herds in recent years. However, no effective control strategy is available for PRRSV1 infection in China. In this study, we generated the first infectious cDNA clone (rHLJB1) of a Chinese PRRSV1 isolate and subsequently used it as a backbone to construct an ORF2-6 chimeric virus (ORF2-6-CON). This virus contained a synthesized consensus sequence of the PRRSV1 ORF2-6 gene encoding all the envelope proteins. The ORF2-6 consensus sequence shared > 90% nucleotide similarity with four representative strains (Amervac, BJEU06-1, HKEU16 and NMEU09-1) of PRRSV1 in China. ORF2-6-CON had replication efficacy similar to that of the backbone rHLJB1 virus in primary alveolar macrophages (PAMs) and exhibited cell tropism in Marc-145 cells. Piglet inoculation and challenge studies indicated that ORF2-6-CON is not pathogenic to piglets and can induce enhanced cross-protection against a heterologous SD1291 isolate. Notably, ORF2-6-CON inoculation induced higher levels of heterologous neutralizing antibodies (nAbs) against SD1291 than rHLJB1 inoculation, which was concurrent with a higher percentage of T follicular helper (Tfh) cells in tracheobronchial lymph nodes (TBLNs), providing the first clue that porcine Tfh cells are correlated with heterologous PRRSV nAb responses. The number of SD1291-strain-specific IFNγ-secreting cells was similar in ORF2-6-CON-inoculated and rHLJB1-inoculated pigs. Overall, our findings support that the Marc-145-adapted ORF2-6-CON can trigger Tfh cell and heterologous nAb responses to confer improved cross-protection and may serve as a candidate strain for the development of a cross-protective PRRSV1 vaccine.
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Affiliation(s)
- Shubin Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Ming Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Shuai Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Chen Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Hong Lin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuejia Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Wenhao Qi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Binghui Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Meng Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Shuai Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Shaobin Shang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Kegong Tian
- National Research Center for Veterinary Medicine, Luoyang, 471000, China
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China.
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China.
| | - Yu Lu
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou, 225300, China.
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, 225009, China.
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fuzhou, 350002, China.
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8
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Hikichi Y, Grover JR, Schäfer A, Mothes W, Freed EO. Epistatic pathways can drive HIV-1 escape from integrase strand transfer inhibitors. SCIENCE ADVANCES 2024; 10:eadn0042. [PMID: 38427738 PMCID: PMC10906922 DOI: 10.1126/sciadv.adn0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
People living with human immunodeficiency virus (HIV) receiving integrase strand transfer inhibitors (INSTIs) have been reported to experience virological failure in the absence of resistance mutations in integrase. To elucidate INSTI resistance mechanisms, we propagated HIV-1 in the presence of escalating concentrations of the INSTI dolutegravir. HIV-1 became resistant to dolutegravir by sequentially acquiring mutations in the envelope glycoprotein (Env) and the nucleocapsid protein. The selected Env mutations enhance the ability of the virus to spread via cell-cell transfer, thereby increasing the multiplicity of infection (MOI). While the selected Env mutations confer broad resistance to multiple classes of antiretrovirals, the fold resistance is ~2 logs higher for INSTIs than for other classes of drugs. We demonstrate that INSTIs are more readily overwhelmed by high MOI than other classes of antiretrovirals. Our findings advance the understanding of how HIV-1 can evolve resistance to antiretrovirals, including the potent INSTIs, in the absence of drug-target gene mutations.
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Affiliation(s)
- Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Alicia Schäfer
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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9
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Nkolola JP, Barouch DH. Prophylactic HIV-1 vaccine trials: past, present, and future. Lancet HIV 2024; 11:e117-e124. [PMID: 38141639 DOI: 10.1016/s2352-3018(23)00264-3] [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: 07/05/2023] [Revised: 09/24/2023] [Accepted: 10/11/2023] [Indexed: 12/25/2023]
Abstract
An effective HIV-1 vaccine is a global health priority but has remained elusive for more than 40 years. Key scientific hurdles that have hampered vaccine development are the unprecedented genetic variability of the virus, the rapid establishment of persistent viral latency, and the challenges associated with induction of broadly neutralising antibodies. Clinical trials have been instrumental in evaluating scientific concepts and testing vaccine strategies. This Review discusses lessons learned from clinical trials of HIV-1 vaccines, current technologies that are being explored, and future considerations in the development of a safe and effective HIV-1 vaccine.
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Affiliation(s)
- Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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10
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Juyal A, Hosseini R, Novikov D, Grinshpon M, Zelikovsky A. Reconstruction of Viral Variants via Monte Carlo Clustering. J Comput Biol 2023; 30:1009-1018. [PMID: 37695837 PMCID: PMC10518690 DOI: 10.1089/cmb.2023.0154] [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] [Indexed: 09/13/2023] Open
Abstract
Identifying viral variants through clustering is essential for understanding the composition and structure of viral populations within and between hosts, which play a crucial role in disease progression and epidemic spread. This article proposes and validates novel Monte Carlo (MC) methods for clustering aligned viral sequences by minimizing either entropy or Hamming distance from consensuses. We validate these methods on four benchmarks: two SARS-CoV-2 interhost data sets and two HIV intrahost data sets. A parallelized version of our tool is scalable to very large data sets. We show that both entropy and Hamming distance-based MC clusterings discern the meaningful information from sequencing data. The proposed clustering methods consistently converge to similar clusterings across different runs. Finally, we show that MC clustering improves reconstruction of intrahost viral population from sequencing data.
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Affiliation(s)
- Akshay Juyal
- Department of Computer Science and Georgia State University, Atlanta, Georgia, USA
| | - Roya Hosseini
- Department of Computer Science and Georgia State University, Atlanta, Georgia, USA
| | - Daniel Novikov
- Department of Computer Science and Georgia State University, Atlanta, Georgia, USA
| | - Mark Grinshpon
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Alex Zelikovsky
- Department of Computer Science and Georgia State University, Atlanta, Georgia, USA
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11
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Yao X, Wang Q, Han C, Nie J, Chang Y, Xu L, Wu B, Yan J, Chen Z, Kong W, Shi Y, Shan Y. Combined Nano-Vector Mediated-Transfer to Suppress HIV-1 Infection with Targeted Antibodies in-vitro. Int J Nanomedicine 2023; 18:4635-4645. [PMID: 37605734 PMCID: PMC10440090 DOI: 10.2147/ijn.s412915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Introduction Broadly neutralizing antibodies (bNAbs) have the ability to neutralize a considerable breadth of genetically diverse human immunodeficiency virus (HIV) strains. Passive immunization can potentially provide protection against HIV infection in animal models. However, the direct antibody infusion effect is limited due to the short half-life and deficient immunogenicity of the antibody. As an alternative strategy, we propose the use of nano viral vectors, specifically the adeno-associated virus (AAV), to continuously and systematically produce bNAbs against HIV. Methods Plasmids expressing bNAbs PG9, PG16, 10E8, and NIH45-46 antibodies were constructed, targeting three different epitopes of HIV. Additionally, the bNAbs gene mediated by rAAV8 was administered to generate long-term expression with a single injection. We established both single and combined immunization groups. The neutralizing activity of antibodies expressed in mice sera was subsequently evaluated. Results The expression of bNAbs in BALB/c mice can last for >24 weeks after a single intramuscular injection of rAAV8. Further studies show that neutralization of the HIV pseudovirus by sera from co-immunized mice with rAAV8 expressing 10E8 and PG16 was enhanced compared with mice immunized with 10E8 or PG16 alone. Conclusion The prolonged expression of neutralizing antibodies can be maintained over long periods in BALB/c mice. This combined immunization is a promising candidate strategy for HIV treatment.
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Affiliation(s)
- Xin Yao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Qingyu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Changge Han
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Jiaojiao Nie
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Yaotian Chang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Lipeng Xu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Bingya Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Jingtian Yan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Zhiyuan Chen
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Yuhua Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, 130012, People’s Republic of China
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12
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Wan M, Yang X, Sun J, Giorgi EE, Ding X, Zhou Y, Zhang Y, Su W, Jiang C, Shan Y, Gao F. Enhancement of Neutralization Responses through Sequential Immunization of Stable Env Trimers Based on Consensus Sequences from Select Time Points by Mimicking Natural Infection. Int J Mol Sci 2023; 24:12642. [PMID: 37628824 PMCID: PMC10454455 DOI: 10.3390/ijms241612642] [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: 07/18/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
HIV-1 vaccines have been challenging to develop, partly due to the high level of genetic variation in its genome. Thus, a vaccine that can induce cross-reactive neutralization activities will be needed. Studies on the co-evolution of antibodies and viruses indicate that mimicking the natural infection is likely to induce broadly neutralizing antibodies (bnAbs). We generated the consensus Env sequence for each time point in subject CH505, who developed broad neutralization activities, and selected five critical time points before broad neutralization was detected. These consensus sequences were designed to express stable Env trimers. Priming with the transmitted/founder Env timer and sequential boosting with these consensus Env trimers from different time points induced broader and more potent neutralizing activities than the BG505 Env trimer in guinea pigs. Analysis of the neutralization profiles showed that sequential immunization of Env trimers favored nAbs with gp120/gp41 interface specificity while the BG505 Env trimer favored nAbs with V2 specificity. The unique features such as consensus sequences, stable Env trimers and the sequential immunization to mimic natural infection likely has allowed the induction of improved neutralization responses.
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Affiliation(s)
- Mingming Wan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
| | - Xiao Yang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
| | - Jie Sun
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
| | - Elena E. Giorgi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA;
| | - Xue Ding
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
| | - Yan Zhou
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yong Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Weiheng Su
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; (M.W.); (X.Y.); (J.S.); (X.D.); (Y.Z.); (Y.Z.); (W.S.); (C.J.)
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
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13
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Niu J, Wang Q, Zhao W, Meng B, Xu Y, Zhang X, Feng Y, Qi Q, Hao Y, Zhang X, Liu Y, Xiang J, Shao Y, Yang B. Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs. Nat Commun 2023; 14:4676. [PMID: 37542068 PMCID: PMC10403546 DOI: 10.1038/s41467-023-40321-x] [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: 11/11/2022] [Accepted: 07/21/2023] [Indexed: 08/06/2023] Open
Abstract
Structure-guided immunofocusing HIV-1 vaccine design entails a comprehensive understanding of Envs from diverse HIV-1 subtypes, including circulating recombinant forms (CRFs). Here, we present the cryo-EM structures of Envs from two Asia prevalent CRFs (CRF01_AE and CRF07_BC) at 3.0 and 3.5 Å. We compare the structures and glycosylation patterns of Envs from different subtypes and perform cross-clade statistical analyses to reveal the unique features of CRF01_AE V1 region, which are associated with the resistance to certain bNAbs. We also solve a 4.1 Å cryo-EM structure of CRF01_AE Env in complex with F6, the first bNAb from CRF01_AE-infected individuals. F6 recognizes a gp120-gp41 spanning epitope to allosterically destabilize the Env trimer apex and weaken inter-protomer packing, which in turn hinders the receptor binding and induces Env trimer disassembly, demonstrating a dual mechanism of neutralization. These findings broaden our understanding of CRF Envs and shed lights on immunofocusing HIV-1 vaccine design.
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Affiliation(s)
- Jun Niu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wenwen Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Youwei Xu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xianfang Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qilian Qi
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yanling Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ying Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jiangchao Xiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Changping Laboratory, Beijing, 102206, China.
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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14
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Fili M, Hu G, Han C, Kort A, Trettin J, Haim H. A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients. Algorithms Mol Biol 2023; 18:4. [PMID: 37337202 DOI: 10.1186/s13015-023-00228-0] [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: 12/29/2022] [Accepted: 06/04/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Therapeutics against the envelope (Env) proteins of human immunodeficiency virus type 1 (HIV-1) effectively reduce viral loads in patients. However, due to mutations, new therapy-resistant Env variants frequently emerge. The sites of mutations on Env that appear in each patient are considered random and unpredictable. Here we developed an algorithm to estimate for each patient the mutational state of each position based on the mutational state of adjacent positions on the three-dimensional structure of the protein. METHODS We developed a dynamic ensemble selection algorithm designated k-best classifiers. It identifies the best classifiers within the neighborhood of a new observation and applies them to predict the variability state of each observation. To evaluate the algorithm, we applied amino acid sequences of Envs from 300 HIV-1-infected individuals (at least six sequences per patient). For each patient, amino acid variability values at all Env positions were mapped onto the three-dimensional structure of the protein. Then, the variability state of each position was estimated by the variability at adjacent positions of the protein. RESULTS The proposed algorithm showed higher performance than the base learner and a panel of classification algorithms. The mutational state of positions in the high-mannose patch and CD4-binding site of Env, which are targeted by multiple therapeutics, was predicted well. Importantly, the algorithm outperformed other classification techniques for predicting the variability state at multi-position footprints of therapeutics on Env. CONCLUSIONS The proposed algorithm applies a dynamic classifier-scoring approach that increases its performance relative to other classification methods. Better understanding of the spatiotemporal patterns of variability across Env may lead to new treatment strategies that are tailored to the unique mutational patterns of each patient. More generally, we propose the algorithm as a new high-performance dynamic ensemble selection technique.
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Affiliation(s)
- Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA.
| | - Changze Han
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA
| | - Alexa Kort
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA
| | - John Trettin
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, 3014 Black Engineering, 2529 Union Drive, Ames, IA, 50011, USA
| | - Hillel Haim
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Rd, 3-770 BSB, Iowa City, IA, 52242, USA.
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15
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Deubler M, Weißenborn L, Leukel S, Horn AHC, Eichler J, Sticht H. Computational Characterization of the Binding Properties of the HIV1-Neutralizing Antibody PG16 and Design of PG16-Derived CDRH3 Peptides. BIOLOGY 2023; 12:824. [PMID: 37372110 DOI: 10.3390/biology12060824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/28/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
PG16 is a broadly neutralizing antibody that binds to the gp120 subunit of the HIV-1 Env protein. The major interaction site is formed by the unusually long complementarity determining region (CDR) H3. The CDRH3 residue Tyr100H is known to represent a tyrosine sulfation site; however, this modification is not present in the experimental complex structure of PG16 with full-length HIV-1 Env. To investigate the role of sulfation for this complex, we modeled the sulfation of Tyr100H and compared the dynamics and energetics of the modified and unmodified complex by molecular dynamics simulations at the atomic level. Our results show that sulfation does not affect the overall conformation of CDRH3, but still enhances gp120 interactions both at the site of modification and for the neighboring residues. This stabilization affects not only protein-protein contacts, but also the interactions between PG16 and the gp120 glycan shield. Furthermore, we also investigated whether PG16-CDRH3 is a suitable template for the development of peptide mimetics. For a peptide spanning residues 93-105 of PG16, we obtained an experimental EC50 value of 3nm for the binding of gp120 to the peptide. This affinity can be enhanced by almost one order of magnitude by artificial disulfide bonding between residues 99 and 100F. In contrast, any truncation results in significantly lower affinity, suggesting that the entire peptide segment is involved in gp120 recognition. Given their high affinity, it should be possible to further optimize the PG16-derived peptides as potential inhibitors of HIV invasion.
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Affiliation(s)
- Manuel Deubler
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Lucas Weißenborn
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Simon Leukel
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Anselm H C Horn
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
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16
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Picker LJ, Lifson JD, Gale M, Hansen SG, Früh K. Programming cytomegalovirus as an HIV vaccine. Trends Immunol 2023; 44:287-304. [PMID: 36894436 PMCID: PMC10089689 DOI: 10.1016/j.it.2023.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/09/2023]
Abstract
The initial development of cytomegalovirus (CMV) as a vaccine vector for HIV/simian immunodeficiency virus (SIV) was predicated on its potential to pre-position high-frequency, effector-differentiated, CD8+ T cells in tissues for immediate immune interception of nascent primary infection. This goal was achieved and also led to the unexpected discoveries that non-human primate (NHP) CMVs can be programmed to differentially elicit CD8+ T cell responses that recognize viral peptides via classical MHC-Ia, and/or MHC-II, and/or MHC-E, and that MHC-E-restricted CD8+ T cell responses can uniquely mediate stringent arrest and subsequent clearance of highly pathogenic SIV, an unprecedented type of vaccine-mediated protection. These discoveries delineate CMV vector-elicited MHC-E-restricted CD8+ T cells as a functionally distinct T cell response with the potential for superior efficacy against HIV-1, and possibly other infectious agents or cancers.
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Affiliation(s)
- Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, MD, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
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17
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Novelty Search Promotes Antigenic Diversity in Microbial Pathogens. Pathogens 2023; 12:pathogens12030388. [PMID: 36986310 PMCID: PMC10053453 DOI: 10.3390/pathogens12030388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/12/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Driven by host–pathogen coevolution, cell surface antigens are often the fastest evolving parts of a microbial pathogen. The persistent evolutionary impetus for novel antigen variants suggests the utility of novelty-seeking algorithms in predicting antigen diversification in microbial pathogens. In contrast to traditional genetic algorithms maximizing variant fitness, novelty-seeking algorithms optimize variant novelty. Here, we designed and implemented three evolutionary algorithms (fitness-seeking, novelty-seeking, and hybrid) and evaluated their performances in 10 simulated and 2 empirically derived antigen fitness landscapes. The hybrid walks combining fitness- and novelty-seeking strategies overcame the limitations of each algorithm alone, and consistently reached global fitness peaks. Thus, hybrid walks provide a model for microbial pathogens escaping host immunity without compromising variant fitness. Biological processes facilitating novelty-seeking evolution in natural pathogen populations include hypermutability, recombination, wide dispersal, and immune-compromised hosts. The high efficiency of the hybrid algorithm improves the evolutionary predictability of novel antigen variants. We propose the design of escape-proof vaccines based on high-fitness variants covering a majority of the basins of attraction on the fitness landscape representing all potential variants of a microbial antigen.
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18
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Michelo CM, Fiore-Gartland A, Dalel JA, Hayes P, Tang J, McGowan E, Kilembe W, Fernandez N, Gilmour J, Hunter E. Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes. Vaccines (Basel) 2023; 11:472. [PMID: 36851349 PMCID: PMC9961105 DOI: 10.3390/vaccines11020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.
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Affiliation(s)
- Clive M. Michelo
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jama A. Dalel
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - William Kilembe
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Eric Hunter
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
- Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Emory National Primate Research Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
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19
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Cohen KW, Fiore-Gartland A, Walsh SR, Yusim K, Frahm N, Elizaga ML, Maenza J, Scott H, Mayer KH, Goepfert PA, Edupuganti S, Pantaleo G, Hutter J, Morris DE, De Rosa SC, Geraghty DE, Robb ML, Michael NL, Fischer W, Giorgi EE, Malhi H, Pensiero MN, Ferrari G, Tomaras GD, Montefiori DC, Gilbert PB, McElrath MJ, Haynes BF, Korber BT, Baden LR. Trivalent mosaic or consensus HIV immunogens prime humoral and broader cellular immune responses in adults. J Clin Invest 2023; 133:e163338. [PMID: 36787249 PMCID: PMC9927951 DOI: 10.1172/jci163338] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/27/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUNDMosaic and consensus HIV-1 immunogens provide two distinct approaches to elicit greater breadth of coverage against globally circulating HIV-1 and have shown improved immunologic breadth in nonhuman primate models.METHODSThis double-blind randomized trial enrolled 105 healthy HIV-uninfected adults who received 3 doses of either a trivalent global mosaic, a group M consensus (CON-S), or a natural clade B (Nat-B) gp160 env DNA vaccine followed by 2 doses of a heterologous modified vaccinia Ankara-vectored HIV-1 vaccine or placebo. We performed prespecified blinded immunogenicity analyses at day 70 and day 238 after the first immunization. T cell responses to vaccine antigens and 5 heterologous Env variants were fully mapped.RESULTSEnv-specific CD4+ T cell responses were induced in 71% of the mosaic vaccine recipients versus 48% of the CON-S recipients and 48% of the natural Env recipients. The mean number of T cell epitopes recognized was 2.5 (95% CI, 1.2-4.2) for mosaic recipients, 1.6 (95% CI, 0.82-2.6) for CON-S recipients, and 1.1 (95% CI, 0.62-1.71) for Nat-B recipients. Mean breadth was significantly greater in the mosaic group than in the Nat-B group using overall (P = 0.014), prime-matched (P = 0.002), heterologous (P = 0.046), and boost-matched (P = 0.009) measures. Overall T cell breadth was largely due to Env-specific CD4+ T cell responses.CONCLUSIONPriming with a mosaic antigen significantly increased the number of epitopes recognized by Env-specific T cells and enabled more, albeit still limited, cross-recognition of heterologous variants. Mosaic and consensus immunogens are promising approaches to address global diversity of HIV-1.TRIAL REGISTRATIONClinicalTrials.gov NCT02296541.FUNDINGUS NIH grants UM1 AI068614, UM1 AI068635, UM1 AI068618, UM1 AI069412, UL1 RR025758, P30 AI064518, UM1 AI100645, and UM1 AI144371, and Bill & Melinda Gates Foundation grant OPP52282.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephen R. Walsh
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Karina Yusim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Marnie L. Elizaga
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hyman Scott
- San Francisco Department of Public Health, San Francisco, California, USA
| | - Kenneth H. Mayer
- Harvard Medical School, Boston, Massachusetts, USA
- The Fenway Institute, Fenway Health, Boston, Massachusetts, USA
| | | | | | | | - Julia Hutter
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Daryl E. Morris
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Daniel E. Geraghty
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Merlin L. Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Nelson L. Michael
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Will Fischer
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Elena E. Giorgi
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Harmandeep Malhi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael N. Pensiero
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute and
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | - Bette T. Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, and New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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20
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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21
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [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: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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22
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Safety and immunogenicity of a mosaic vaccine booster against Omicron and other SARS-CoV-2 variants: a randomized phase 2 trial. Signal Transduct Target Ther 2023; 8:20. [PMID: 36596779 PMCID: PMC9808735 DOI: 10.1038/s41392-022-01295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 01/04/2023] Open
Abstract
An ongoing randomized, double-blind, controlled phase 2 trial was conducted to evaluate the safety and immunogenicity of a mosaic-type recombinant vaccine candidate, named NVSI-06-09, as a booster dose in subjects aged 18 years and older from the United Arab Emirates (UAE), who had administered two or three doses of inactivated vaccine BBIBP-CorV at least 6 months prior to enrollment. The participants were randomly assigned with 1:1 to receive a booster dose of NVSI-06-09 or BBIBP-CorV. The primary outcomes were immunogenicity and safety against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, and the exploratory outcome was cross-immunogenicity against other circulating strains. Between May 25 and 30, 2022, 516 adults received booster vaccination with 260 in NVSI-06-09 group and 256 in BBIBP-CorV group. Interim results showed a similar safety profile between two booster groups, with low incidence of adverse reactions of grade 1 or 2. For immunogenicity, by day 14 post-booster, the fold rises in neutralizing antibody geometric mean titers (GMTs) from baseline elicited by NVSI-06-09 were remarkably higher than those by BBIBP-CorV against the prototype strain (19.67 vs 4.47-fold), Omicron BA.1.1 (42.35 vs 3.78-fold), BA.2 (25.09 vs 2.91-fold), BA.4 (22.42 vs 2.69-fold), and BA.5 variants (27.06 vs 4.73-fold). Similarly, the neutralizing GMTs boosted by NVSI-06-09 against Beta and Delta variants were also 6.60-fold and 7.17-fold higher than those by BBIBP-CorV. Our findings indicated that a booster dose of NVSI-06-09 was well-tolerated and elicited broad-spectrum neutralizing responses against divergent SARS-CoV-2 variants, including Omicron and its sub-lineages.
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23
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Li X, Liao D, Li Z, Li J, Diaz M, Verkoczy L, Gao F. Autoreactivity and broad neutralization of antibodies against HIV-1 are governed by distinct mutations: Implications for vaccine design strategies. Front Immunol 2022; 13:977630. [PMID: 36479128 PMCID: PMC9720396 DOI: 10.3389/fimmu.2022.977630] [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: 06/24/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Many of the best HIV-1 broadly neutralizing antibodies (bnAbs) known have poly-/autoreactive features that disfavor normal B cell development and maturation, posing a major hurdle in developing an effective HIV-1 vaccine. Key to resolving this problem is to understand if, and to what extent, neutralization breadth-conferring mutations acquired by bnAbs contribute to their autoreactivity. Here, we back-mutated all known changes made by a prototype CD4 binding site-directed bnAb lineage, CH103-106, during its later maturation steps. Strikingly, of 29 mutations examined, only four were crucial for increased autoreactivity, with minimal or no impact on neutralization. Furthermore, three of these residues were clustered in the heavy chain complementarity-determining region 2 (HCDR2). Our results demonstrate that broad neutralization activity and autoreactivity in the CH103-106 bnAb lineage can be governed by a few, distinct mutations during maturation. This provides strong rationale for developing immunogens that favor bnAb lineages bearing "neutralization-only" mutations into current HIV-1 vaccine designs.
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Affiliation(s)
- Xiaojun Li
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Dongmei Liao
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Zhengyang Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Jixi Li
- School of Life Sciences, Fudan University, Shanghai, China
| | - Marilyn Diaz
- Applied Biomedical Science Institute, San Diego, CA, United States
| | - Laurent Verkoczy
- Applied Biomedical Science Institute, San Diego, CA, United States
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
- Institute of Molecular and Medical Virology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdongg, China
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24
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Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens. PLoS Comput Biol 2022; 18:e1010624. [PMID: 36315492 PMCID: PMC9621458 DOI: 10.1371/journal.pcbi.1010624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The immense global diversity of HIV-1 is a significant obstacle to developing a safe and effective vaccine. We recently showed that infections established with multiple founder variants are associated with the development of neutralization breadth years later. We propose a novel vaccine design strategy that integrates the variability observed in acute HIV-1 infections with multiple founder variants. We developed a probabilistic model to simulate this variability, yielding a set of sequences that present the minimal diversity seen in an infection with multiple founders. We applied this model to a subtype C consensus sequence for the Envelope (Env) (used as input) and showed that the simulated Env sequences mimic the mutational landscape of an infection with multiple founder variants, including diversity at antibody epitopes. The derived set of multi-founder-variant-like, minimally distant antigens is designed to be used as a vaccine cocktail specific to a HIV-1 subtype or circulating recombinant form and is expected to promote the development of broadly neutralizing antibodies. Diverse HIV-1 populations are generally thought to promote neutralizing responses. Current leading HIV-1 vaccine design strategies maximize the distance between antigens to attempt to cover global HIV-1 diversity or serialize immunizations to recapitulate the temporal evolution of HIV-1 during infection. To date, no vaccine has elicited broadly neutralizing antibodies. As we recently demonstrated that infection with multiple HIV-1 founder variants is predictive of neutralization breadth, we propose a novel strategy that endeavors to promote the development of broadly neutralizing antibodies by replicating the diversity of multi-founder variant acute infections. By training an HIV-1 Env consensus sequence on the diversity from acute infections with multiple founders, we derived in silico a set of minimally distant antigens that is representative of the diversity seen in a multi-founder acute infection. As the model is particular to the input sequence, it can produce antigens specific to any HIV-1 subtype or circulating recombinant form (CRF). We applied this to HIV-1 subtype C and obtained a set of minimally distant antigens that can be used as a vaccine cocktail.
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25
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Tee KK, Thomson MM, Hemelaar J. Editorial: HIV-1 genetic diversity, volume II. Front Microbiol 2022; 13:1007037. [PMID: 36071960 PMCID: PMC9443081 DOI: 10.3389/fmicb.2022.1007037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Kok Keng Tee
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiolog, Instituto de Salud Carlos III, Madrid, Spain
- Michael M. Thomson
| | - Joris Hemelaar
- Infectious Disease Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Joris Hemelaar
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26
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Dhande JR, Bagul RD, Thakar MR. HIV-gp140-Specific Antibodies Generated From Indian Long-Term Non-Progressors Mediate Potent ADCC Activity and Effectively Lyse Reactivated HIV Reservoir. Front Immunol 2022; 13:844610. [PMID: 35309295 PMCID: PMC8924355 DOI: 10.3389/fimmu.2022.844610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Strategies to reduce the human immunodeficiency virus (HIV) reservoir are urgently required. The antibody-dependent cellular cytotoxicity (ADCC)-mediating anti-HIV antibodies have shown an association with HIV control. We assessed if such antibodies can be generated in vitro and whether the generated antibodies can facilitate the reduction of reactivated HIV reservoir. We isolated HIV-1-gp140-specific memory B cells from HIV-1-infected long-term non-progressors (LTNPs) with or without plasma ADCC and cultured them to generate anti-HIV antibodies. The ability of the generated antibodies to mediate ADCC and facilitate NK cell-mediated lysis of reactivated HIV reservoir was assessed by the rapid fluorometric antibody-dependent cellular cytotoxicity assay and a flow-based novel latency reduction assay, respectively. All LTNPs showed the presence of gp140-specific memory B cells [median: 0.79% (0.54%–1.225%)], which were successfully differentiated into plasma cells [median 72.0% (68.7–82.2%)] in an in-vitro culture and secreted antibodies [median OD: 0.253 (0.205–0.274)]. The HIV-gp140-specific antibodies were generated from 11/13 LTNPs irrespective of their plasma ADCC status. The generated antibodies from LTNPs with plasma ADCC showed higher ADCC potency (median: 37.6%, IQR: 32.95%–51%) and higher reduction in reactivated HIV reservoir (median: 62.5%, IQR: 58.71%–64.92%) as compared with the antibodies generated from LTNPs without plasma ADCC (ADCC: median: 8.85%, IQR: 8%–9.7%; and % p24 reduction median: 13.84, IQR: 9.863%–17.81%). The potency of these antibodies to reduce latent reservoir was two-fold higher than the respective plasma ADCC. The study showed that the potent ADCC-mediating antibodies could be generated from memory B cells of the LTNPs with plasma ADCC activity. These antibodies also showed potent ability to facilitate NK cell-mediated lysis of reactivated HIV reservoirs. It also indicated that memory B cells from individuals with plasma ADCC activity should be preferentially used for such antibody generation. The important role of these antibodies in the reduction of latent reservoirs needs to be further evaluated as a useful strategy to obtain a functional cure for HIV infection.
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27
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Cook JD, Khondker A, Lee JE. Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies. Commun Biol 2022; 5:291. [PMID: 35361878 PMCID: PMC8971491 DOI: 10.1038/s42003-022-03235-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/08/2022] [Indexed: 12/17/2022] Open
Abstract
The early humoral immune response to acute HIV-1 infection is largely non-neutralizing. The principal target of these antibodies is the primary immunodominant region (PID) on the gp41 fusion protein. The PID is a highly conserved 15-residue region displayed on the surface of HIV-1 virions. In this study, we analyzed the humoral determinants of HIV-1 gp41 PID binding using biophysical, structural, and computational methods. In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation. Molecular dynamics simulations showed that the PID is structurally plastic suggesting that the PID can form an ensemble of structural states recognized by various non-neutralizing antibodies, facilitating HIV-1 immunodominance observed in acute and chronic HIV-1 infections. An improved understanding of how the HIV-1 gp41 PID misdirects the early humoral response should guide the development of an effective HIV-1 vaccine. The 15-amino-acid primary immunodominant (PID) region on HIV-1 gp41 adopts an ensemble of conformational states. This conformational plasticity is suggested to misdirect the early humoral immune response.
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Affiliation(s)
- Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Adree Khondker
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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Thomas AS, Coote C, Moreau Y, Isaac JE, Ewing AC, Kourtis AP, Sagar M. Antibody-dependent cellular cytotoxicity (ADCC) responses along with ADCC susceptibility influence HIV-1 mother to child transmission. JCI Insight 2022; 7:159435. [PMID: 35324477 PMCID: PMC9090239 DOI: 10.1172/jci.insight.159435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND HIV-1 vaccine efforts are primarily directed towards eliciting neutralizing antibodies (nAbs). However, vaccine trials and mother to child natural history cohort investigations indicate that antibody-dependent cellular cytotoxicity (ADCC), not nAbs, correlate with prevention. The ADCC characteristics associated with lack of HIV-1 acquisition remain unclear. METHODS Here we examine ADCC and nAb properties in pre-transmission plasma from HIV-1 exposed infants and from the corresponding transmitting and non-transmitting mothers' breast milk and plasma. Breadth and potency (BP) is assessed against a panel of heterologous, non-maternal, variants. ADCC and neutralization sensitivity is estimated for the strains present in the infected mothers. RESULTS Infants that eventually acquire HIV-1 and those that remain uninfected have similar pre-transmission ADCC BP. The viruses circulating in the transmitting and the non-transmitting mothers also have similar ADCC susceptibility. Infants with a combination of higher pre-transmission ADCC BP and exposure to more ADCC susceptible strains are less likely to acquire HIV-1. In contrast, higher pre-existing infant neutralization BP and greater maternal virus neutralization sensitivity does not associate with transmission. Infants have higher ADCC BP closer to birth and in the presence of high plasma IgG relative to IgA levels. Mothers with potent humoral responses against their autologous viruses harbor more ADCC sensitive strains. CONCLUSION ADCC sensitivity of the exposure variants along with preexisting ADCC BP influence mother to child HIV-1 transmission during breastfeeding. Vaccination strategies that enhance ADCC responses are likely not sufficient to prevent HIV-1 transmission because strains present in chronically infected individuals can have low ADCC susceptibility. TRIAL REGISTRATION NCT00164736 for BAN study.
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Affiliation(s)
- Allison S Thomas
- Department of Microbiology, Boston University School of Medicine, Boston, United States of America
| | - Carolyn Coote
- Department of Medicine, Boston Medical Center, Boston, United States of America
| | - Yvetane Moreau
- Department of Medicine, Boston Medical Center, Boston, United States of America
| | - John E Isaac
- Department of Medicine, Boston Medical Center, Boston, United States of America
| | - Alexander C Ewing
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Athena P Kourtis
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Manish Sagar
- Department of Medicine, Boston Medical Center, Boston, United States of America
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Timofeeva A, Sedykh S, Nevinsky G. Post-Immune Antibodies in HIV-1 Infection in the Context of Vaccine Development: A Variety of Biological Functions and Catalytic Activities. Vaccines (Basel) 2022; 10:384. [PMID: 35335016 PMCID: PMC8955465 DOI: 10.3390/vaccines10030384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Unlike many other viruses, HIV-1 is highly variable. The structure of the viral envelope changes as the infection progresses and is one of the biggest obstacles in developing an HIV-1 vaccine. HIV-1 infection can cause the production of various natural autoantibodies, including catalytic antibodies hydrolyzing DNA, myelin basic protein, histones, HIV-integrase, HIV-reverse transcriptase, β-casein, serum albumin, and some other natural substrates. Currently, there are various directions for the development of HIV-1 vaccines: stimulation of the immune response on the mucous membranes; induction of cytotoxic T cells, which lyse infected cells and hold back HIV-infection; immunization with recombinant Env proteins or vectors encoding Env; mRNA-based vaccines and some others. However, despite many attempts to develop an HIV-1 vaccine, none have been successful. Here we review the entire spectrum of antibodies found in HIV-infected patients, including neutralizing antibodies specific to various viral epitopes, as well as antibodies formed against various autoantigens, catalytic antibodies against autoantigens, and some viral proteins. We consider various promising targets for developing a vaccine that will not produce unwanted antibodies in vaccinated patients. In addition, we review common problems in the development of a vaccine against HIV-1.
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Affiliation(s)
- Anna Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
| | - Sergey Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Georgy Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (S.S.); (G.N.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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30
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High thermostability improves neutralizing antibody responses induced by native-like HIV-1 envelope trimers. NPJ Vaccines 2022; 7:27. [PMID: 35228534 PMCID: PMC8885667 DOI: 10.1038/s41541-022-00446-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/20/2022] [Indexed: 12/01/2022] Open
Abstract
Soluble HIV-1 envelope glycoprotein (Env) immunogens are a prime constituent of candidate vaccines designed to induce broadly neutralizing antibodies. Several lines of evidence suggest that enhancing Env immunogen thermostability can improve neutralizing antibody (NAb) responses. Here, we generated BG505 SOSIP.v9 trimers, which displayed virtually no reactivity with non-neutralizing antibodies and showed increased global and epitope thermostability, compared to previous BG505 SOSIP versions. Chemical crosslinking of BG505 SOSIP.v9 further increased the melting temperature to 91.3 °C, which is almost 25 °C higher than that of the prototype SOSIP.664 trimer. Next, we compared the immunogenicity of a palette of BG505-based SOSIP trimers with a gradient of thermostabilities in rabbits. We also included SOSIP.v9 proteins in which a strain-specific immunodominant epitope was masked by glycans to redirect the NAb response to other subdominant epitopes. We found that increased trimer thermostability correlated with increased potency and consistency of the autologous NAb response. Furthermore, glycan masking steered the NAb response to subdominant epitopes without decreasing the potency of the autologous NAb response. In summary, SOSIP.v9 trimers and their glycan masked versions represent an improved platform for HIV-1 Env based vaccination strategies.
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31
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Fused deposition modeling three-dimensional printing of flexible polyurethane intravaginal rings with controlled tunable release profiles for multiple active drugs. Drug Deliv Transl Res 2022; 12:906-924. [PMID: 35211869 PMCID: PMC8870081 DOI: 10.1007/s13346-022-01133-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2022] [Indexed: 11/23/2022]
Abstract
We designed and engineered novel intravaginal ring (IVR) medical devices via fused deposition modeling (FDM) three-dimensional (3D) printing for controlled delivery of hydroxychloroquine, IgG, gp120 fragment (encompassing the CD4 binding site), and coumarin 6 PLGA-PEG nanoparticles (C6NP). The hydrophilic polyurethanes were utilized to 3D-print reservoir-type IVRs containing a tunable release controlling membrane (RCM) with varying thickness and adaptable micro porous structures (by altering the printing patterns and interior fill densities) for controlled sustained drug delivery over 14 days. FDM 3D printing of IVRs were optimized and implemented using a lab-developed Cartesian 3D printer. The structures were investigated by scanning electron microscopy (SEM) imaging and in vitro release was performed using 5 mL of daily-replenished vaginal fluid simulant (pH 4.2). The release kinetics of the IVR segments were tunable with various RCM (outer diameter to inner diameter ratio ranging from 1.12 to 2.61) produced from FDM 3D printing by controlling the printing perimeter to provide daily zero-order release of HCQ ranging from 23.54 ± 3.54 to 261.09 ± 32.49 µg/mL/day. IgG, gp120 fragment, and C6NP release rates demonstrated pattern and in-fill density-dependent characteristics. The current study demonstrated the utility of FDM 3D printing to rapidly fabricate complex micro-structures for tunable and sustained delivery of a variety of compounds including HCQ, IgG, gp120 fragment, and C6NP from IVRs in a controlled manner.
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32
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Dhar S, Zhang C, Măndoiu II, Bansal MS. TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:230-242. [PMID: 34255632 PMCID: PMC8956368 DOI: 10.1109/tcbb.2021.3096455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 07/03/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The inference of disease transmission networks is an important problem in epidemiology. One popular approach for building transmission networks is to reconstruct a phylogenetic tree using sequences from disease strains sampled from infected hosts and infer transmissions based on this tree. However, most existing phylogenetic approaches for transmission network inference are highly computationally intensive and cannot take within-host strain diversity into account. Here, we introduce a new phylogenetic approach for inferring transmission networks, TNet, that addresses these limitations. TNet uses multiple strain sequences from each sampled host to infer transmissions and is simpler and more accurate than existing approaches. Furthermore, TNet is highly scalable and able to distinguish between ambiguous and unambiguous transmission inferences. We evaluated TNet on a large collection of 560 simulated transmission networks of various sizes and diverse host, sequence, and transmission characteristics, as well as on 10 real transmission datasets with known transmission histories. Our results show that TNet outperforms two other recently developed methods, phyloscanner and SharpTNI, that also consider within-host strain diversity. We also applied TNet to a large collection of SARS-CoV-2 genomes sampled from infected individuals in many countries around the world, demonstrating how our inference framework can be adapted to accurately infer geographical transmission networks. TNet is freely available from https://compbio.engr.uconn.edu/software/TNet/.
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Affiliation(s)
- Saurav Dhar
- Department of Computer Science & EngineeringUniversity of ConnecticutStorrsCT06269USA
| | - Chengchen Zhang
- Department of Computer Science & EngineeringUniversity of ConnecticutStorrsCT06269USA
| | - Ion I. Măndoiu
- Department of Computer Science & EngineeringUniversity of ConnecticutStorrsCT06269USA
| | - Mukul S. Bansal
- Department of Computer Science & EngineeringUniversity of ConnecticutStorrsCT06269USA
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33
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Rosengarten JF, Schatz S, Wolf T, Barbe S, Stitz J. Components of a HIV-1 vaccine mediate virus-like particle (VLP)-formation and display of envelope proteins exposing broadly neutralizing epitopes. Virology 2022; 568:41-48. [DOI: 10.1016/j.virol.2022.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022]
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Shepherd BO, Chang D, Vasan S, Ake J, Modjarrad K. HIV and SARS-CoV-2: Tracing a Path of Vaccine Research and Development. Curr HIV/AIDS Rep 2022; 19:86-93. [PMID: 35089535 PMCID: PMC8795326 DOI: 10.1007/s11904-021-00597-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/02/2022]
Abstract
PURPOSE OF REVIEW This review examines the major advances and obstacles in the field of HIV vaccine research as they pertain to informing the development of vaccines against SARS-CoV-2. RECENT FINDINGS Although the field of HIV research has yet to deliver a licensed vaccine, the technologies developed and knowledge gained in basic scientific disciplines, translational research, and community engagement have positively impacted the development of vaccines for other viruses, most notably and recently for SARS-CoV-2. These advances include the advent of viral vectors and mRNA as vaccine delivery platforms; the use of structural biology for immunogen design; an emergence of novel adjuvant formulations; a more sophisticated understanding of viral phylogenetics; improvements in the development and harmonization of accurate assays for vaccine immunogenicity; and maturation of the fields of bioethics and community engagement for clinical trials conducted in diverse populations. Decades of foundational research and investments into HIV biology, though yet to yield an authorized or approved vaccine for HIV/AIDS, have now paid dividends in the rapid development of safe and effective SARS-CoV-2 vaccines. This latter success presents an opportunity for feedback on improved pathways for development of safe and efficacious vaccines against HIV and other pathogens.
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Affiliation(s)
- Brittany Ober Shepherd
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Suite 2A14, Silver Spring, MD 20910 USA ,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817 USA
| | - David Chang
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910 USA
| | - Sandhya Vasan
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Suite 2A14, Silver Spring, MD 20910 USA ,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817 USA ,US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910 USA
| | - Julie Ake
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817 USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Suite 2A14, Silver Spring, MD, 20910, USA.
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Abstract
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.
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Affiliation(s)
- Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), Vigo, Spain.
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36
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Campion SL, Brenna E, Thomson E, Fischer W, Ladell K, McLaren JE, Price DA, Frahm N, McElrath JM, Cohen KW, Maenza JR, Walsh SR, Baden LR, Haynes BF, Korber B, Borrow P, McMichael AJ. Preexisting memory CD4+ T cells contribute to the primary response in an HIV-1 vaccine trial. J Clin Invest 2021; 131:e150823. [PMID: 34850742 PMCID: PMC8631594 DOI: 10.1172/jci150823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Naive and memory CD4+ T cells reactive with human immunodeficiency virus type 1 (HIV-1) are detectable in unexposed, unimmunized individuals. The contribution of preexisting CD4+ T cells to a primary immune response was investigated in 20 HIV-1-seronegative volunteers vaccinated with an HIV-1 envelope (Env) plasmid DNA prime and recombinant modified vaccinia virus Ankara (MVA) boost in the HVTN 106 vaccine trial (clinicaltrials.gov NCT02296541). Prevaccination naive or memory CD4+ T cell responses directed against peptide epitopes in Env were identified in 14 individuals. After priming with DNA, 40% (8/20) of the elicited responses matched epitopes detected in the corresponding preimmunization memory repertoires, and clonotypes were shared before and after vaccination in 2 representative volunteers. In contrast, there were no shared epitope specificities between the preimmunization memory compartment and responses detected after boosting with recombinant MVA expressing a heterologous Env. Preexisting memory CD4+ T cells therefore shape the early immune response to vaccination with a previously unencountered HIV-1 antigen.
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Affiliation(s)
- Suzanne L. Campion
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Elena Brenna
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Elaine Thomson
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Will Fischer
- Los Alamos National Laboratory, Santa Fe, New Mexico, USA
| | | | | | - David A. Price
- Division of Infection and Immunity and
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Nicole Frahm
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Juliana M. McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Janine R. Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen R. Walsh
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Lindsey R. Baden
- Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Barton F. Haynes
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Bette Korber
- Los Alamos National Laboratory, Santa Fe, New Mexico, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J. McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Sequence and vector shapes vaccine induced antibody effector functions in HIV vaccine trials. PLoS Pathog 2021; 17:e1010016. [PMID: 34843602 PMCID: PMC8659322 DOI: 10.1371/journal.ppat.1010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/09/2021] [Accepted: 10/07/2021] [Indexed: 01/07/2023] Open
Abstract
Despite the advent of long-acting anti-retroviral therapy able to control and prevent infection, a preventative vaccine remains a global priority for the elimination of HIV. The moderately protective RV144 vaccine trial suggested functional IgG1 and IgG3 antibodies were a potential correlate of protection, but the RV144-inspired HVTN702 validation trial failed to demonstrate efficacy despite inducing targeted levels of IgG1/IgG3. Alterations in inserts, and antigens, adjuvant, and regimen also resulted in vaccine induced target quantitative levels of the immune correlates, but drove qualitative changes to the humoral immune response, pointing to the urgent need to define the influence of vaccine strategies on shaping antibody quality, not just quantity. Thus, defining how distinct prime/boost approaches tune long-lived functional antibodies represents an important goal in vaccine development. Here, we compared vaccine responses in Phase I and II studies in humans utilizing various combinations of DNA/vector, vector/vector and DNA/protein HIV vaccines. We found that adenoviral vector immunization, compared to pox-viral vectors, resulted in the most potent IgG1 and IgG3 responses, linked to highly functional antibody activity, including assisting NK cell related functions. Minimal differences were observed in the durability of the functional humoral immune response across vaccine regimens, except for antibody dependent phagocytic function, which persisted for longer periods in the DNA/rAd5 and rAd35/rAd5 regimen, likely driven by higher IgG1 levels. Collectively, these findings suggest adenoviral vectors drive superior antibody quality and durability that could inform future clinical vaccine studies. Trial registration: ClinicalTrials.gov NCT00801697, NCT00961883, NCT02207920, NCT00125970, NCT02852005).
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Fuentes-Trillo A, Monzó C, Manzano I, Santiso-Bellón C, Andrade JDSRD, Gozalbo-Rovira R, García-García AB, Rodríguez-Díaz J, Chaves FJ. Benchmarking different approaches for Norovirus genome assembly in metagenome samples. BMC Genomics 2021; 22:849. [PMID: 34819031 PMCID: PMC8611953 DOI: 10.1186/s12864-021-08067-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/10/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genome assembly of viruses with high mutation rates, such as Norovirus and other RNA viruses, or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies and strains. Furthermore, there is no standard method for obtaining whole-genome sequences in non-related patients. After polyA RNA isolation and sequencing in eight patients with acute gastroenteritis, we evaluated two de Bruijn graph assemblers (SPAdes and MEGAHIT), combined with four different and common pre-assembly strategies, and compared those yielding whole genome Norovirus contigs. RESULTS Reference-genome guided strategies with both host and target virus did not present any advantages compared to the assembly of non-filtered data in the case of SPAdes, and in the case of MEGAHIT, only host genome filtering presented improvements. MEGAHIT performed better than SPAdes in most samples, reaching complete genome sequences in most of them for all the strategies employed. Read binning with CD-HIT improved assembly when paired with different analysis strategies, and more notably in the case of SPAdes. CONCLUSIONS Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to analysis. We may need different approaches even for samples treated equally due to the presence of high intra host variability. We tested and compared different workflows for the accurate assembly of Norovirus genomes and established their assembly capacities for this purpose.
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Affiliation(s)
- Azahara Fuentes-Trillo
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | - Carolina Monzó
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | - Iris Manzano
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
| | | | | | | | - Ana-Bárbara García-García
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain.
- Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Felipe Javier Chaves
- Unit of Genomics and Diabetes. Research Foundation of Valencia University Clinical Hospital- INCLIVA, Valencia, Spain
- Spanish Biomedical Research Network in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Sequencing Multiplex S.L., Valencia, Spain
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Hayes P, Fernandez N, Ochsenbauer C, Dalel J, Hare J, King D, Black L, Streatfield C, Kakarla V, Macharia G, Makinde J, Price M, Hunter E, Gilmour J. Breadth of CD8 T-cell mediated inhibition of replication of diverse HIV-1 transmitted-founder isolates correlates with the breadth of recognition within a comprehensive HIV-1 Gag, Nef, Env and Pol potential T-cell epitope (PTE) peptide set. PLoS One 2021; 16:e0260118. [PMID: 34788349 PMCID: PMC8598018 DOI: 10.1371/journal.pone.0260118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Full characterisation of functional HIV-1-specific T-cell responses, including identification of recognised epitopes linked with functional antiviral responses, would aid development of effective vaccines but is hampered by HIV-1 sequence diversity. Typical approaches to identify T-cell epitopes utilising extensive peptide sets require subjects' cell numbers that exceed feasible sample volumes. To address this, CD8 T-cells were polyclonally expanded from PBMC from 13 anti-retroviral naïve subjects living with HIV using CD3/CD4 bi-specific antibody. Assessment of recognition of individual peptides within a set of 1408 HIV-1 Gag, Nef, Pol and Env potential T-cell epitope peptides was achieved by sequential IFNγ ELISpot assays using peptides pooled in 3-D matrices followed by confirmation with single peptides. A Renilla reniformis luciferase viral inhibition assay assessed CD8 T-cell-mediated inhibition of replication of a cross-clade panel of 10 HIV-1 isolates, including 9 transmitted-founder isolates. Polyclonal expansion from one frozen PBMC vial provided sufficient CD8 T-cells for both ELISpot steps in 12 of 13 subjects. A median of 33 peptides in 16 epitope regions were recognised including peptides located in previously characterised HIV-1 epitope-rich regions. There was no significant difference between ELISpot magnitudes for in vitro expanded CD8 T-cells and CD8 T-cells directly isolated from PBMCs. CD8 T-cells from all subjects inhibited a median of 7 HIV-1 isolates (range 4 to 10). The breadth of CD8 T-cell mediated HIV-1 inhibition was significantly positively correlated with CD8 T-cell breadth of peptide recognition. Polyclonal CD8 T-cell expansion allowed identification of HIV-1 isolates inhibited and peptides recognised within a large peptide set spanning the major HIV-1 proteins. This approach overcomes limitations associated with obtaining sufficient cell numbers to fully characterise HIV-1-specific CD8 T-cell responses by different functional readouts within the context of extreme HIV-1 diversity. Such an approach will have useful applications in clinical development for HIV-1 and other diseases.
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Affiliation(s)
- Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Lucas Black
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Claire Streatfield
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Vanaja Kakarla
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Matt Price
- IAVI, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Atlanta, Georgia, United States of America
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
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Kim J, Vasan S, Kim JH, Ake JA. Current approaches to HIV vaccine development: a narrative review. J Int AIDS Soc 2021; 24 Suppl 7:e25793. [PMID: 34806296 PMCID: PMC8606871 DOI: 10.1002/jia2.25793] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION The development of an effective vaccine to protect against HIV is a longstanding global health need complicated by challenges inherent to HIV biology and to the execution of vaccine efficacy testing in the context of evolving biomedical prevention interventions. This review describes lessons learnt from previous efficacy trials, highlights unanswered questions, and surveys new approaches in vaccine development addressing these gaps. METHODS We conducted a targeted peer-reviewed literature search of articles and conference abstracts from 1989 through 2021 for HIV vaccine studies and clinical trials. The US National Library of Medicine's Clinical Trials database was accessed to further identify clinical trials involving HIV vaccines. The content of the review was also informed by the authors' own experience and engagement with collaborators in HIV vaccine research. DISCUSSION The HIV vaccine field has successfully developed multiple vaccine platforms through advanced clinical studies; however, the modest efficacy signal of the RV144 Thai trial remains the only demonstration of HIV vaccine protection in humans. Current vaccine strategies include prime-boost strategies to improve elicitation of immune correlates derived from RV144, combination mosaic antigens, novel viral vectors, antigens designed to elicit broadly neutralizing antibody, new nucleic acid platforms and potent adjuvants to enhance immunogenicity across multiple classes of emerging vaccine candidates. CONCLUSIONS HIV vaccine developers have applied lessons learnt from previous successes and failures to innovative vaccine design approaches. These strategies have yielded novel mosaic antigen constructs now in efficacy testing, produced a diverse pipeline of early-stage immunogens and novel adjuvants, and advanced the field towards a globally effective HIV vaccine.
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Affiliation(s)
- Jiae Kim
- US Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMarylandUSA
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMarylandUSA
| | - Sandhya Vasan
- US Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMarylandUSA
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaMarylandUSA
| | | | - Julie A. Ake
- US Military HIV Research ProgramWalter Reed Army Institute of ResearchSilver SpringMarylandUSA
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Derking R, Sanders RW. Structure-guided envelope trimer design in HIV-1 vaccine development: a narrative review. J Int AIDS Soc 2021; 24 Suppl 7:e25797. [PMID: 34806305 PMCID: PMC8606863 DOI: 10.1002/jia2.25797] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The development of a human immunodeficiency virus 1 (HIV-1) vaccine remains a formidable challenge. An effective vaccine likely requires the induction of broadly neutralizing antibodies (bNAbs), which likely involves the use of native-like HIV-1 envelope (Env) trimers at some or all stages of vaccination. Development of such trimers has been very difficult, but much progress has been made in the past decade, starting with the BG505 SOSIP trimer, elucidation of its atomic structure and implementing subsequent design iterations. This progress facilitated understanding the weaknesses of the Env trimer, fuelled structure-guided HIV-1 vaccine design and assisted in the development of new vaccine designs. This review summarizes the relevant literature focusing on studies using structural biology to reveal and define HIV-1 Env sites of vulnerability; to improve Env trimers, by creating more stable versions; understanding antibody responses in preclinical vaccination studies at the atomic level; understanding the glycan shield; and to improve "on-target" antibody responses versus "off-target" responses. METHODS The authors conducted a narrative review of recently published articles that made a major contribution to HIV-1 structural biology and vaccine design efforts between the years 2000 and 2021. DISCUSSION The field of structural biology is evolving at an unprecedented pace, where cryo-electron microscopy (cryo-EM) and X-ray crystallography provide complementary information. Resolving protein structures is necessary for defining which Env surfaces are accessible for the immune system and can be targeted by neutralizing antibodies. Recently developed techniques, such as electron microscopy-based polyclonal epitope mapping (EMPEM) are revolutionizing the way we are analysing immune responses and shed light on the immunodominant targets on new vaccine immunogens. Such information accelerates iterative vaccine design; for example, by reducing undesirable off-target responses, while improving immunogens to drive the more desirable on-target responses. CONCLUSIONS Resolving high-resolution structures of the HIV-1 Env trimer was instrumental in understanding and improving recombinant HIV-1 Env trimers that mimic the structure of viral HIV-1 Env spikes. Newly emerging techniques in structural biology are aiding vaccine design efforts and improving immunogens. The role of structural biology in HIV-1 vaccine design has indeed become very prominent and is unlikely to diminish any time soon.
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Affiliation(s)
- Ronald Derking
- Department of Medical MicrobiologyAmsterdam Infection & Immunity InstituteAmsterdam UMC, AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rogier W. Sanders
- Department of Medical MicrobiologyAmsterdam Infection & Immunity InstituteAmsterdam UMC, AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Microbiology and ImmunologyWeill Medical College of Cornell UniversityNew YorkNew YorkUSA
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Potent Induction of Envelope-Specific Antibody Responses by Virus-Like Particle (VLP) Immunogens Based on HIV-1 Envelopes from Patients with Early Broadly Neutralizing Responses. J Virol 2021; 96:e0134321. [PMID: 34668778 PMCID: PMC8754226 DOI: 10.1128/jvi.01343-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Longitudinal studies in HIV-1-infected individuals have indicated that 2 to 3 years of infection are required to develop broadly neutralizing antibodies. However, we have previously identified individuals with broadly neutralizing activity (bNA) in early HIV-1 infection, indicating that a vaccine may be capable of bNA induction after short periods of antigen exposure. Here, we describe 5 HIV-1 envelope sequences from individuals who have developed bNA within the first 100 days of infection (early neutralizers) and selected two of them to design immunogens based on HIV-1-Gag virus-like particles (VLPs). These VLPs were homogeneous and incorporated the corresponding envelopes (7 to 9 μg of gp120 in 1010 VLPs). Both envelopes (Envs) bound to well-characterized broadly neutralizing antibodies (bNAbs), including trimer-specific antibodies (PGT145, VRC01, and 35022). For immunogenicity testing, we immunized rabbits with the Env-VLPs or with the corresponding stabilized soluble envelope trimers. A short immunization protocol (105 days) was used to recapitulate the early nAb induction observed after HIV-1 infection in these two individuals. All VLP and trimeric envelope immunogens induced a comparably strong anti-gp120 response despite having immunized rabbits with 30 times less gp120 in the case of the Env-VLPs. In addition, animals immunized with VLP-formulated Envs induced antibodies that cross-recognized the corresponding soluble stabilized trimer and vice versa, even though no neutralizing activity was observed. Nevertheless, our data may provide a new platform of immunogens, based on HIV-1 envelopes from patients with early broadly neutralizing responses, with the potential to generate protective immune responses using vaccination protocols similar to those used in classical preventive vaccines. IMPORTANCE It is generally accepted that an effective HIV-1 vaccine should be able to induce broad-spectrum neutralizing antibodies. Since most of these antibodies require long periods of somatic maturation in vivo, several groups are developing immunogens, based on the HIV envelope protein, that require complex and lengthy immunization protocols that would be difficult to implement in the general population. Here, we show that rabbits immunized with new envelopes (VLP formulated) from two individuals who demonstrated broadly neutralizing activity very early after infection induced specific HIV-1 antibodies after a short immunization protocol. This evidence provides the basis for generating protective immune responses with classic vaccination protocols with vaccine prototypes based on HIV envelope sequences from individuals who have developed early broadly neutralizing responses.
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Parker Miller E, Finkelstein MT, Erdman MC, Seth PC, Fera D. A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses 2021; 13:v13091774. [PMID: 34578355 PMCID: PMC8472920 DOI: 10.3390/v13091774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Antibodies that can neutralize diverse HIV-1 strains develop in ~10–20% of HIV-1 infected individuals, and their elicitation is a goal of vaccine design. Such antibodies can also serve as therapeutics for those who have already been infected with the virus. Structural characterizations of broadly reactive antibodies in complex with the HIV-1 spike indicate that there are a limited number of sites of vulnerability on the spike. Analysis of their structures can help reveal commonalities that would be useful in vaccine design and provide insights on combinations of antibodies that can be used to minimize the incidence of viral resistance mutations. In this review, we give an update on recent structures determined of the spike in complex with broadly neutralizing antibodies in the context of all epitopes on the HIV-1 spike identified to date.
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Yi K, Kim SY, Bleazard T, Kim T, Youk J, Ju YS. Mutational spectrum of SARS-CoV-2 during the global pandemic. Exp Mol Med 2021; 53:1229-1237. [PMID: 34453107 PMCID: PMC8393781 DOI: 10.1038/s12276-021-00658-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
Viruses accumulate mutations under the influence of natural selection and host-virus interactions. Through a systematic comparison of 351,525 full viral genome sequences collected during the recent COVID-19 pandemic, we reveal the spectrum of SARS-CoV-2 mutations. Unlike those of other viruses, the mutational spectrum of SARS-CoV-2 exhibits extreme asymmetry, with a much higher rate of C>U than U>C substitutions, as well as a higher rate of G>U than U>G substitutions. This suggests directional genome sequence evolution during transmission. The substantial asymmetry and directionality of the mutational spectrum enable pseudotemporal tracing of SARS-CoV-2 without prior information about the root sequence, collection time, and sampling region. This shows that the viral genome sequences collected in Asia are similar to the original genome sequence. Adjusted estimation of the dN/dS ratio accounting for the asymmetrical mutational spectrum also shows evidence of negative selection on viral genes, consistent with previous reports. Our findings provide deep insights into the mutational processes in SARS-CoV-2 viral infection and advance the understanding of the history and future evolution of the virus.
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Affiliation(s)
- Kijong Yi
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Su Yeon Kim
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Thomas Bleazard
- grid.70909.370000 0001 2199 6511National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG UK
| | - Taewoo Kim
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea
| | - Jeonghwan Youk
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea ,grid.511166.4GENOME INSIGHT Inc, Daejeon, 34051 Korea
| | - Young Seok Ju
- grid.37172.300000 0001 2292 0500Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 Korea ,grid.511166.4GENOME INSIGHT Inc, Daejeon, 34051 Korea
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Sliepen K, Schermer E, Bontjer I, Burger JA, Lévai RF, Mundsperger P, Brouwer PJM, Tolazzi M, Farsang A, Katinger D, Moore JP, Scarlatti G, Shattock RJ, Sattentau QJ, Sanders RW. Interplay of diverse adjuvants and nanoparticle presentation of native-like HIV-1 envelope trimers. NPJ Vaccines 2021; 6:103. [PMID: 34404812 PMCID: PMC8371121 DOI: 10.1038/s41541-021-00364-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
The immunogenicity of HIV-1 envelope (Env) trimers is generally poor. We used the clinically relevant ConM SOSIP trimer to compare the ability of different adjuvants (squalene emulsion, ISCOMATRIX, GLA-LSQ, and MPLA liposomes) to support neutralizing antibody (NAb) responses in rabbits. The trimers were administered as free proteins or on nanoparticles. The rank order for the adjuvants was ISCOMATRIX > SE > GLA-LSQ ~ MPLA liposomes > no adjuvant. Stronger NAb responses were elicited when the ConM SOSIP trimers were presented on ferritin nanoparticles. We also found that the GLA-LSQ adjuvant induced an unexpectedly strong antibody response to the ferritin core of the nanoparticles. This "off-target" effect may have compromised its ability to induce the more desired antitrimer antibodies. In summary, both adjuvants and nanoparticle display can improve the magnitude of the antibody response to SOSIP trimers but the best combination of trimer presentation and adjuvant can only be identified experimentally.
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Affiliation(s)
- Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Edith Schermer
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Réka Felfödiné Lévai
- Control Laboratory of Veterinary Medicinal Products and Animal Facility, Directorate of Veterinary Medicinal Products, National Food Chain Safety Office, Budapest, Hungary
| | | | - Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Monica Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Attila Farsang
- Control Laboratory of Veterinary Medicinal Products and Animal Facility, Directorate of Veterinary Medicinal Products, National Food Chain Safety Office, Budapest, Hungary
| | - Dietmar Katinger
- Polymun Scientific Immunbiologische Forschung GmbH, Klosterneuburg, Austria
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Robin J Shattock
- Imperial College London, Department of Medicine, Division of Infectious Diseases, Section of Virology, Norfolk Place, London, W21PG, UK
| | - Quentin J Sattentau
- The Sir William Dunn School of Pathology, The University of Oxford, Oxford, OX13RE, UK
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
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Gräf T, Bello G, Andrade P, Arantes I, Pereira JM, da Silva ABP, Veiga RV, Mariani D, Boullosa LT, Arruda MB, Fernandez JCC, Dennis AM, Rasmussen DA, Tanuri A. HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network. Sci Rep 2021; 11:15842. [PMID: 34349153 PMCID: PMC8338987 DOI: 10.1038/s41598-021-94542-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 12/04/2022] Open
Abstract
HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.
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Affiliation(s)
- Tiago Gräf
- Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Rua Waldemar Falcão, 121, Salvador, 40296-710, Brazil.
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paula Andrade
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ighor Arantes
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - João Marcos Pereira
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratório de Bioinformática and Evolução Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Bonfim Pinheiro da Silva
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratório de Bioinformática and Evolução Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael V Veiga
- Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz, Instituto Gonçalo Moniz, Salvador, Brazil.,Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lídia Theodoro Boullosa
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica B Arruda
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Carlos Couto Fernandez
- Laboratório de AIDS e Imunologia Molecular, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ann M Dennis
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, USA
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética-IB, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Huang Y, Seaton KE, Casapia M, Polakowski L, De Rosa SC, Cohen K, Yu C, Elizaga M, Paez C, Miner MD, Kelley CF, Maenza J, Keefer M, Lama JR, Sobieszczyk M, Buchbinder S, Baden LR, Lee C, Gulati V, Sinangil F, Montefiori D, McElrath MJ, Tomaras GD, Robinson HL, Goepfert P. AIDSVAX protein boost improves breadth and magnitude of vaccine-induced HIV-1 envelope-specific responses after a 7-year rest period. Vaccine 2021; 39:4641-4650. [PMID: 34229888 PMCID: PMC8853668 DOI: 10.1016/j.vaccine.2021.06.066] [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: 01/11/2021] [Revised: 05/03/2021] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Eliciting durable humoral immunity with sufficient breadth and magnitude is important for HIV-1 vaccine design. The HVTN 114 vaccine trial evaluated different boost regimens administered after a 7-year rest period in participants previously enrolled in HVTN 205, who received either three MVA/HIV62B (MMM) or two DNA and two MVA/HIV62B (DDMM) injections; both vaccines expressed multiple HIV-1 antigens in non-infectious virus-like-particles. The primary objective of HVTN 114 was to assess the impact of a heterologous gp120 protein AIDSVAX B/E boost on the magnitude, breadth and durability of vaccine-induced immune responses. METHODS We enrolled 27 participants from HVTN 205 into five groups. Eight participants who previously received MMM were randomized and boosted with either MVA/HIV62B alone (T1; n = 4) or MVA/HIV62B and AIDSVAX B/E (T2; n = 4). Nineteen participants who received DDMM were randomized and boosted with MVA/HIV62B alone (T3; n = 6), MVA/HIV62B and AIDSVAX B/E (T4; n = 6), or AIDSVAX B/E alone (T5; n = 7). Boosts were at months 0 and 4. Participants were followed for safety and immunogenicity for 10 months and were pooled for analysis based on the regimen: MVA-only (T1 + T3), MVA + AIDSVAX (T2 + T4), and AIDSVAX-only (T5). RESULTS All regimens were safe and well-tolerated. Prior to the boost vaccination, binding antibody and CD4+T-cell responses were observed 7 years after HVTN 205 vaccinations. Late boosting with AIDSVAX, with or without MVA, resulted in high binding antibody responses to gp120 and V1V2 epitopes, with increased magnitude and breadth compared to those observed in HVTN 205. Late boosting with MVA, with or without AIDSVAX, resulted in increased gp140 and gp41 antibody responses and higher CD4+T-cell responses to Env and Gag. CONCLUSIONS Late boosting with AIDSVAX, alone or in combination with MVA, can broaden binding antibody responses and increase T-cell responses even years following the original MVA/HIV62B with or without DNA-priming vaccine.
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Affiliation(s)
- Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Kelly E Seaton
- Duke Center for Human Systems Immunology, Duke University Departments of Surgery, Immunology, Pathology, Molecular Genetics and Microbiology, Durham, NC, USA
| | - Martin Casapia
- Asociacion Civil Selva Amazonica, Universidad Nacional de la Amazonia, Iquitos, Peru. Urbanizacion Jardin 27, Iquitos, Peru.
| | | | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kristen Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chenchen Yu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marnie Elizaga
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carmen Paez
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maurine D Miner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Keefer
- Infectious Diseases Division, Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Javier R Lama
- Asociacion Civil Impacta Salud y Educacion, Lima, Peru
| | - Magdalena Sobieszczyk
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center, NYC, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Lindsey R Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carter Lee
- Global Solutions for Infectious Diseases, Lafayette, CA, USA
| | - Vineeta Gulati
- Global Solutions for Infectious Diseases, Lafayette, CA, USA
| | - Faruk Sinangil
- Global Solutions for Infectious Diseases, Lafayette, CA, USA
| | - David Montefiori
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Georgia D Tomaras
- Duke Center for Human Systems Immunology, Duke University Departments of Surgery, Immunology, Pathology, Molecular Genetics and Microbiology, Durham, NC, USA
| | | | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Elangovan R, Jenks M, Yun J, Dickson-Tetteh L, Kirtley S, Hemelaar J. Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study. Front Microbiol 2021; 12:690647. [PMID: 34335516 PMCID: PMC8320730 DOI: 10.3389/fmicb.2021.690647] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
Global HIV-1 genetic diversity forms a major obstacle to the development of an HIV vaccine. It may be necessary to employ subtype-specific HIV-1 vaccines in individual countries according to their HIV-1 subtype distribution. We estimated the global and regional need for subtype-specific HIV-1 vaccines. We took into account the proportions of different HIV-1 variants circulating in each country, the genetic composition of HIV-1 recombinants, and the different genome segments (gag, pol, env) that may be incorporated into vaccines. We modeled different scenarios according to whether countries would employ subtype-specific HIV-1 vaccines against (1) the most common subtype; (2) subtypes contributing more than 5% of HIV infections; or (3) all circulating subtypes. For therapeutic vaccines targeting the most common HIV-1 subtype in each country, 16.5 million doses of subtype C vaccine were estimated globally, followed by subtypes A (14.3 million) and B (4.2 million). A vaccine based on env required 2.6 million subtype E doses, and a vaccine based on pol required 4.8 million subtype G doses. For prophylactic vaccines targeting the most common HIV-1 subtype in each country, 1.9 billion doses of subtype A vaccine were estimated globally, followed by subtype C (1.1 billion) and subtype B (1.0 billion). A vaccine based on env required 1.2 billion subtype E doses, and a vaccine based on pol required 0.3 billion subtype G doses. If subtype-specific HIV-1 vaccines are also directed against less common subtypes in each country, vaccines targeting subtypes D, F, H, and K are also needed and would require up to five times more vaccine doses in total. We conclude that to provide global coverage, subtype-specific HIV-1 vaccines need to be directed against subtypes A, B, and C. Vaccines targeting env also need to include subtype E and those targeting pol need to include subtype G.
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Affiliation(s)
| | - Michael Jenks
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Jason Yun
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Leslie Dickson-Tetteh
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Shona Kirtley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Centre for Statistics in Medicine, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Joris Hemelaar
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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49
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Fries CN, Chen JL, Dennis ML, Votaw NL, Eudailey J, Watts BE, Hainline KM, Cain DW, Barfield R, Chan C, Moody MA, Haynes BF, Saunders KO, Permar SR, Fouda GG, Collier JH. HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth. Sci Rep 2021; 11:14494. [PMID: 34262096 PMCID: PMC8280189 DOI: 10.1038/s41598-021-93702-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023] Open
Abstract
A major challenge in developing an effective vaccine against HIV-1 is the genetic diversity of its viral envelope. Because of the broad range of sequences exhibited by HIV-1 strains, protective antibodies must be able to bind and neutralize a widely mutated viral envelope protein. No vaccine has yet been designed which induces broadly neutralizing or protective immune responses against HIV in humans. Nanomaterial-based vaccines have shown the ability to generate antibody and cellular immune responses of increased breadth and neutralization potency. Thus, we have developed supramolecular nanofiber-based immunogens bearing the HIV gp120 envelope glycoprotein. These immunogens generated antibody responses that had increased magnitude and binding breadth compared to soluble gp120. By varying gp120 density on nanofibers, we determined that increased antigen valency was associated with increased antibody magnitude and germinal center responses. This study presents a proof-of-concept for a nanofiber vaccine platform generating broad, high binding antibody responses against the HIV-1 envelope glycoprotein.
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Affiliation(s)
- Chelsea N Fries
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Jui-Lin Chen
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Maria L Dennis
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Nicole L Votaw
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Joshua Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Brian E Watts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kelly M Hainline
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Richard Barfield
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O Saunders
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sallie R Permar
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pediatrics, New York-Presbyterian/Weill Cornell Medicine, New York, NY, 10065, USA
| | - Genevieve G Fouda
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Box 103020, Durham, NC, 27710, USA.
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, 101 Science Dr., Campus, Box 90281, Durham, NC, 27708, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA.
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50
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Hauser A, Carnell G, Held K, Sulbaran G, Tischbierek N, Rogers L, Pollakis G, Tonks P, Hoelscher M, Ding S, Sanders RW, Geldmacher C, Sattentau Q, Weissenhorn W, Heeney JL, Peterhoff D, Wagner R. Stepwise Conformational Stabilization of a HIV-1 Clade C Consensus Envelope Trimer Immunogen Impacts the Profile of Vaccine-Induced Antibody Responses. Vaccines (Basel) 2021; 9:750. [PMID: 34358165 PMCID: PMC8310183 DOI: 10.3390/vaccines9070750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/16/2023] Open
Abstract
Stabilization of the HIV-1 Envelope glycoprotein trimer (Env) in its native pre-fusion closed conformation is regarded as one of several requirements for the induction of neutralizing antibody (nAb) responses, which, in turn, will most likely be a prerequisite for the development of an efficacious preventive vaccine. Here, we systematically analyzed how the stepwise stabilization of a clade C consensus (ConC) Env immunogen impacts biochemical and biophysical protein traits such as antigenicity, thermal stability, structural integrity, and particle size distribution. The increasing degree of conformational rigidification positively correlates with favorable protein characteristics, leading to optimized homogeneity of the protein preparations, increased thermal stability, and an overall favorable binding profile of structure-dependent broadly neutralizing antibodies (bnAbs) and non-neutralizing antibodies (non-nAbs). We confirmed that increasing the structural integrity and stability of the Env trimers positively correlates with the quality of induced antibody responses by the immunogens. These and other data contribute to the selection of ConCv5 KIKO as novel Env immunogens for use within the European Union's H2020 Research Consortium EHVA (European HIV Alliance) for further preclinical analysis and phase 1 clinical development.
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Affiliation(s)
- Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Guidenn Sulbaran
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Nadine Tischbierek
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
| | - Lisa Rogers
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology, and Immunology (CIMI), University of Liverpool, Liverpool L69 7BE, UK;
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU EZI), Liverpool L69 7BE, UK
| | - Paul Tonks
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Song Ding
- EuroVacc Foundation, 1105 BP Amsterdam, The Netherlands;
| | - Rogier W. Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany; (K.H.); (L.R.); (M.H.); (C.G.)
- German Center for Infection Research (DZIF), Partner site Munich, 80802 Munich, Germany
| | - Quentin Sattentau
- The Sir Willian Dunn School of Pathology, The University of Oxford, Oxford OX1 3RE, UK;
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France; (G.S.); (W.W.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (P.T.); (J.L.H.)
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, 93053 Regensburg, Germany; (A.H.); (N.T.); (D.P.)
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, 93053 Regensburg, Germany
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