1
|
Li D, Liu L, Ye X, Chen Y, Ren Q, Xu S, Ren Y, Cao H, Wang T. Intermediate open state of CD4-bound HIV-1 env heterotrimers in asia CRFs. Biochem Biophys Res Commun 2024; 725:150249. [PMID: 38880081 DOI: 10.1016/j.bbrc.2024.150249] [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: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024]
Abstract
The HIV-1 envelope glycoprotein (Env) plays crucial role in viral infection by facilitating viral attachment to host cells and inducing fusion of the virus with the host cell membrane. This fusion allows the HIV-1 viral genome to enter the target cell then triggering various stages of the viral life cycle. The native Env directly interacts with the main receptor CD4 and the co-receptor (CCR5 or CXCR4) in human cell membrane then induces membrane fusion. The elucidation of the structure of Env with CD4 and co-receptors in different HIV-1 subtypes is essential for the understanding of the mechanism of virus entry. Here we report the Cryo-EM structure of the CD4-bound HIV-1 heterotrimeric Env from Asia prevalent CRF07_BC CH119 strain. In this structure, the binding of three CD4 molecules with Env induced extensively conformational changes in gp120, resulting in the transformation of the Env from close state to intermediate open state. Additionally, the conformational shift of V1/V2 loops of the heterotrimeric Env allosterically expose the V3 loop and promoting the further interactions with co-receptor CCR5 or CXCR4. These findings not only illustrate the structural complexity and plasticity of HIV-1 Env but also give new insights how the biological trimeric Env initialize the immune recognition and membrane fusion.
Collapse
Affiliation(s)
- Dan Li
- School of basic medical Sciences, Capital Medical University, 10 Xitoutiao You'anMen Street, Beijing, 100069, China; Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Li Liu
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China; Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - Xuejun Ye
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Yuyang Chen
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - Qiaoju Ren
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China
| | - ShaoJian Xu
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - Yan Ren
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China
| | - He Cao
- Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China.
| | - Tao Wang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China; Joint Laboratory for Infectious Disease Prevention and Control, Hygienic Section of Longhua Center for Disease Control and Prevention, Longhua District, Shenzhen, 518109, China; Key Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Nanshan District, Shenzhen, 518055, China.
| |
Collapse
|
2
|
Yuan D, Zhao F, Liu S, Liu Y, Yan H, Liu L, Su B, Wang B. Dual Infection of Different Clusters of HIV in People Living with HIV Worldwide: A Meta-Analysis Based on Next-Generation Sequencing Studies. AIDS Patient Care STDS 2024. [PMID: 38957963 DOI: 10.1089/apc.2024.0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024] Open
Abstract
To understand the global dual HIV infection (DI) profiles comprehensively, the databases Cochrane Library, Embase, PubMed, and Web of Science were the data sources up to March 31, 2024 (PROSPERO: CRD42023388328). Stata and R-language software were used to analyze the extracted data. Publication bias was assessed using Egger's test. Sensitivity analysis was conducted to evaluate the stability of the combined effect values. Data from 17 eligible studies across four continents (Africa, Asia, Europe, and North America) with 1,475 subjects were used. The combined dual infection rate (DIR) was 10.47% (95% CI: 7.11%-14.38%) without a time trend (p = 0.105). The DIRs of target population groups differed significantly, with FSWs having the highest DIR (15.14%), followed by general population (12.08%), MSM (11.84%), and DUs (9.76%). The subtype profiles of 122 patients with dual infection were extracted, and the results showed that intrasubtype infections were predominant in coinfection (16/22, 72.73%) and superinfection (68/100, 68.00%) groups, with the subtype pattern B and B accounts for the largest proportion. The global dual infection rate may be underestimated, even though the data fluctuated around 10% and showed no time trend. The occurrence of DI indicated that individuals still do not acquire sufficient resistance to HIV even after primary infection, which could potentially compromise the patient's treatment effect and lead to the emergence of new subtypes, posing a significant challenge to HIV prevention, control, and treatment, suggesting that behavioral counseling and health education for all HIV-infected individuals are still crucial during the antiviral therapy.
Collapse
Affiliation(s)
- Defu Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Southeast University, Nanjing, China
| | - Fei Zhao
- Beijing Key Laboratory for HIV/AIDS Research, Central Laboratory, Sino-French Joint Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Southeast University, Nanjing, China
| | - Yangyang Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Southeast University, Nanjing, China
| | - Hongxia Yan
- Beijing Key Laboratory for HIV/AIDS Research, Central Laboratory, Sino-French Joint Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lifeng Liu
- Beijing Key Laboratory for HIV/AIDS Research, Central Laboratory, Sino-French Joint Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Central Laboratory, Sino-French Joint Laboratory for HIV/AIDS Research, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bei Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Southeast University, Nanjing, China
| |
Collapse
|
3
|
Gonçalves P, Barreto J, Santos M, Leal S, Marcelino J, Abecasis A, Palladino C, Taveira N. HIV-1 drug resistance and genetic diversity in people with HIV-1 in Cape Verde. AIDS 2024; 38:1101-1110. [PMID: 38349224 DOI: 10.1097/qad.0000000000003866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
OBJECTIVES To characterize the genetic diversity and drug resistance profiles of people with HIV-1 failing ART in Cape Verde (CV). DESIGN Cross-sectional study conducted between January 2019 and December 2021 in 24 health centres on the islands of Santiago and São Vicente. METHODS The HIV-1 pol gene was sequenced in individuals with a detectable viral load. HIV-1 genetic diversity was determined by phylogenetic analysis. Drug resistance mutation patterns and resistance phenotypes were estimated using the Stanford algorithm. RESULTS Viral load was detected in 73 of 252 (29%) enrolled participants and sequencing data were produced for 58 (79%) participants. CRF02 AG strains predominated (46.5%), followed by subtype G (22.4%). Most patients (80%) had mutations conferring resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs) (67%), nucleoside reverse transcriptase inhibitors (55%), integrase inhibitors (10%) and/or protease inhibitors (7%) used in Cape Verde, a significant increase compared with a study conducted in 2010-2011. The most common mutations were M184V/I (43%), K103N/S (36%) and G190A/S (19%). NNRTI resistance was associated with younger age and exposure to two or more drug regimens. CONCLUSION The HIV-1 epidemic in Cape Verde is mainly driven by CRF02_AG and subtype G. Resistance to NNRTIs and/or NRTIs is highly prevalent and resistance to LPV/r and DTG is emerging. Our results support the use of DTG-based first-line ART and protease inhibitor-based regimens for patients with virological failure, but emerging resistance to LPV/r and DTG is a concern. Continued monitoring of drug resistance is essential to ensure adequate healthcare for PWH in Cape Verde.
Collapse
Affiliation(s)
- Paloma Gonçalves
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | | | - Menilita Santos
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - Silvania Leal
- Instituto Nacional de Saúde Pública de Cabo Verde, Praia, Cape Verde
| | - José Marcelino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
| | - Ana Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical/Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
| | - Claudia Palladino
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
| | - Nuno Taveira
- Instituto de Investigação do Medicamento (iMed.Ulisboa), Faculdade de Farmácia de Lisboa, Lisbon, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica
| |
Collapse
|
4
|
Liu Z, Julius P, Mudenda V, Kang G, Del Valle L, West JT, Wood C. Limited HIV-associated neuropathologies and lack of immune activation in sub-saharan African individuals with late-stage subtype C HIV-1 infection. J Neurovirol 2024:10.1007/s13365-024-01219-6. [PMID: 38943022 DOI: 10.1007/s13365-024-01219-6] [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: 03/19/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
Although previous studies have suggested that subtype B HIV-1 proviruses in the brain are associated with physiological changes and immune activation accompanied with microgliosis and astrogliosis, and indicated that both HIV-1 subtype variation and geographical location might influence the neuropathogenicity of HIV-1 in the brain. The natural course of neuropathogenesis of the most widespread subtype C HIV-1 has not been adequately investigated, especially for people living with HIV (PLWH) in sub-Saharan Africa. To characterize the natural neuropathology of subtype C HIV-1, postmortem frontal lobe and basal ganglia tissues were collected from nine ART-naïve individuals who died of late-stage AIDS with subtype C HIV-1 infection, and eight uninfected deceased individuals as controls. Histological staining was performed on all brain tissues to assess brain pathologies. Immunohistochemistry (IHC) against CD4, p24, Iba-1, GFAP, and CD8 in all brain tissues was conducted to evaluate potential viral production and immune activation. Histological results showed mild perivascular cuffs of lymphocytes only in a minority of the infected individuals. Viral capsid p24 protein was only detected in circulating immune cells of one infected individual, suggesting a lack of productive HIV-1 infection of the brain even at the late-stage of AIDS. Notably, similar levels of Iba-1 or GFAP between HIV + and HIV- brain tissues indicated a lack of microgliosis and astrogliosis, respectively. Similar levels of CD8 + cytotoxic T lymphocyte (CTL) infiltration between HIV + and HIV- brain tissues indicated CTL were not likely to be involved within subtype C HIV-1 infected participants of this cohort. Results from this subtype C HIV-1 study suggest that there is a lack of productive infection and limited neuropathogenesis by subtype C HIV-1 even at late-stage disease, which is in contrast to what was reported for subtype B HIV-1 by other investigators.
Collapse
Affiliation(s)
- Zhou Liu
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Peter Julius
- Department of Pathology and Microbiology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Victor Mudenda
- Department of Pathology, University Teaching Hospital, Lusaka, Zambia
| | - Guobin Kang
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Luis Del Valle
- Department of Pathology and Medicine, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - John T West
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Charles Wood
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Department of Interdisciplinary Oncology, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
- , 1700 Tulane Avenue, LCRC Rm 614, New Orleans, LA, 70112, USA.
| |
Collapse
|
5
|
Gotora PT, Brown K, Martin DR, van der Sluis R, Cloete R, Williams ME. Impact of subtype C-specific amino acid variants on HIV-1 Tat-TAR interaction: insights from molecular modelling and dynamics. Virol J 2024; 21:144. [PMID: 38918875 PMCID: PMC11202254 DOI: 10.1186/s12985-024-02419-6] [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: 03/19/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND HIV-1 produces Tat, a crucial protein for transcription, viral replication, and CNS neurotoxicity. Tat interacts with TAR, enhancing HIV reverse transcription. Subtype C Tat variants (C31S, R57S, Q63E) are associated with reduced transactivation and neurovirulence compared to subtype B. However, their precise impact on Tat-TAR binding is unclear. This study investigates how these substitutions affect Tat-TAR interaction. METHODS We utilized molecular modelling techniques, including MODELLER, to produce precise three-dimensional structures of HIV-1 Tat protein variants. We utilized Tat subtype B as the reference or wild type, and generated Tat variants to mirror those amino acid variants found in Tat subtype C. Subtype C-specific amino acid substitutions were selected based on their role in the neuropathogenesis of HIV-1. Subsequently, we conducted molecular docking of each Tat protein variant to TAR using HDOCK, followed by molecular dynamic simulations. RESULTS Molecular docking results indicated that Tat subtype B (TatWt) showed the highest affinity for the TAR element (-262.07), followed by TatC31S (-261.61), TatQ63E (-256.43), TatC31S/R57S/Q63E (-238.92), and TatR57S (-222.24). However, binding free energy analysis showed higher affinities for single variants TatQ63E (-349.2 ± 10.4 kcal/mol) and TatR57S (-290.0 ± 9.6 kcal/mol) compared to TatWt (-247.9 ± 27.7 kcal/mol), while TatC31S and TatC31S/R57SQ/63E showed lower values. Interactions over the protein trajectory were also higher for TatQ63E and TatR57S compared to TatWt, TatC31S, and TatC31S/R57SQ/63E, suggesting that modifying amino acids within the Arginine/Glutamine-rich region notably affects TAR interaction. Single amino acid mutations TatR57S and TatQ63E had a significant impact, while TatC31S had minimal effect. Introducing single amino acid variants from TatWt to a more representative Tat subtype C (TatC31S/R57SQ/63E) resulted in lower predicted binding affinity, consistent with previous findings. CONCLUSIONS These identified amino acid positions likely contribute significantly to Tat-TAR interaction and the differential pathogenesis and neuropathogenesis observed between subtype B and subtype C. Additional experimental investigations should prioritize exploring the influence of these amino acid signatures on TAR binding to gain a comprehensive understanding of their impact on viral transactivation, potentially identifying them as therapeutic targets.
Collapse
Affiliation(s)
- Piwai T Gotora
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Keaghan Brown
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Darius R Martin
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, University of the Western Cape, Bellville, South Africa
| | | | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Monray E Williams
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
| |
Collapse
|
6
|
Yang W, Wang H, Li Z, Zhang L, Liu J, Kirchhoff F, Huan C, Zhang W. RPLP1 restricts HIV-1 transcription by disrupting C/EBPβ binding to the LTR. Nat Commun 2024; 15:5290. [PMID: 38906865 PMCID: PMC11192919 DOI: 10.1038/s41467-024-49622-1] [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: 09/30/2023] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Long-term non-progressors (LTNPs) of HIV-1 infection may provide important insights into mechanisms involved in viral control and pathogenesis. Here, our results suggest that the ribosomal protein lateral stalk subunit P1 (RPLP1) is expressed at higher levels in LTNPs compared to regular progressors (RPs). Functionally, RPLP1 inhibits transcription of clade B HIV-1 strains by occupying the C/EBPβ binding sites in the viral long terminal repeat (LTR). This interaction requires the α-helixes 2 and 4 domains of RPLP1 and is evaded by HIV-1 group M subtype C and group N, O and P strains that do not require C/EBPβ for transcription. We further demonstrate that HIV-1-induced translocation of RPLP1 from the cytoplasm to the nucleus is essential for antiviral activity. Finally, knock-down of RPLP1 promotes reactivation of latent HIV-1 proviruses. Thus, RPLP1 may play a role in the maintenance of HIV-1 latency and resistance to RPLP1 restriction may contribute to the effective spread of clade C HIV-1 strains.
Collapse
Affiliation(s)
- Weijing Yang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Hong Wang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chen Huan
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China.
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China.
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
| |
Collapse
|
7
|
Lamami Y, Abulayha AM, Altabal S, Elbasir M, Elbnnani AS, Aghil L, Ebrahim F, Elzagheid A. Absolute CD4 count and percentage values among Libyan patients with HIV by single-platform flow cytometry. Lab Med 2024:lmae046. [PMID: 38902933 DOI: 10.1093/labmed/lmae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Single-platform flow cytometry technology together with CD45-gating is becoming the method of choice for absolute CD4 T cell enumeration. Immunological assessment of HIV patients by monitoring CD4 can provide valuable information on antiviral treatment response and disease progression. METHODS A total of 97 HIV-positive individuals were recruited from 2 hospitals in Tripoli, Libya, and 14 healthy blood donors. The HIV-infected individuals were classified by CD4+ count into HIV-positive (>200 cells/µL) or AIDS (≤200 cells/µL) groups. CD4+ and CD8+ cell counts were determined and compared among the groups and with similar published data. RESULTS The mean ± SD CD4+ cell counts were 1106 ± 442.8 cells/µL in healthy individuals, 460 ± 219.7 cells/µL in the HIV-positive group, and 78 ± 64.3 cells/µL in the AIDS group. The mean ± SD CD4+/CD8+ ratio was 1.6 ± 0.58, 0.4 ± 0.22, and 0.1 ± 0.1, respectively. CD4+ counts in Libyan healthy adults might be higher than those reported in several studies in other regions, whereas CD4+ counts in Libyan AIDS patients seem lower. CONCLUSION Reference values for T lymphocyte counts in Libyan healthy individuals should be investigated more extensively, and the reasons why Libyan AIDS patients seem to have such lower CD4+ counts should be examined.
Collapse
Affiliation(s)
- Yosra Lamami
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Abdulmunem M Abulayha
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Salah Altabal
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Mohamed Elbasir
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Abdulrhman S Elbnnani
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Laila Aghil
- National Center for Disease Control, Tripoli, Libya
| | - Fawzi Ebrahim
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| | - Adam Elzagheid
- Libyan Biotechnology Research Center, Department of Human Cells and Tissues, Tripoli, Libya
| |
Collapse
|
8
|
Fan W, Zhang Z, Shi H, Jia J, Shi P, Chen S, Lu X. Identification of a new HIV-1 circulating recombinant form (CRF159_01103) derived from CRF103_01B and CRF01_AE in Hebei Province, China. Sci Rep 2024; 14:13182. [PMID: 38849496 PMCID: PMC11161575 DOI: 10.1038/s41598-024-64156-8] [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: 02/29/2024] [Accepted: 06/05/2024] [Indexed: 06/09/2024] Open
Abstract
Recombinant HIV-1 genomes identified in three or more epidemiological unrelated individuals are defined as circulating recombinant forms (CRFs). CRFs can further recombine with other pure subtypes or recombinants to produce secondary recombinants. In this study, a new HIV-1 intersubtype CRF, designated CRF159_01103, isolated from three men who have sex with men with no epidemiological linkage, was identified in Baoding city, Hebei Province, China. CRF159_01103 was derived from CRF103_01B and CRF01_AE. Bayesian molecular clock analysis was performed on the CRF01-AE and CRF103_01B regions of CRF159_01103. The time of origin of CRF159_01103 was predicted to be 2018-2019, indicating that it is a recent recombinant virus. The emergence of CRF159_01103 has increased the complexity of the HIV-1 epidemic in Hebei Province.
Collapse
Affiliation(s)
- Weiguang Fan
- Clinical Laboratory of the People's Hospital of Baoding, Baoding, 071000, Hebei, China
| | - Zhen Zhang
- Infection Division of the People's Hospital of Baoding, Baoding, 071000, Hebei, China
| | - Haoxi Shi
- Clinical Laboratory of the People's Hospital of Baoding, Baoding, 071000, Hebei, China
| | - Jianru Jia
- Infection Division of the People's Hospital of Baoding, Baoding, 071000, Hebei, China
| | - Penghui Shi
- Clinical Laboratory of the People's Hospital of Baoding, Baoding, 071000, Hebei, China
| | - Sisi Chen
- Clinical Laboratory of the People's Hospital of Baoding, Baoding, 071000, Hebei, China.
| | - Xinli Lu
- Department of AIDS Research, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, 050021, Hebei, China.
| |
Collapse
|
9
|
Alencar CS, Sabino EC, Diaz RS, Mendrone-Junior A, Nishiya AS. Genetic diversity in the partial sequence of the HIV-1 gag gene among people living with multidrug-resistant HIV-1 infection. Rev Inst Med Trop Sao Paulo 2024; 66:e35. [PMID: 38865573 PMCID: PMC11164046 DOI: 10.1590/s1678-9946202466035] [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: 12/05/2023] [Accepted: 04/02/2024] [Indexed: 06/14/2024] Open
Abstract
The group-specific antigen (gag) plays a crucial role in the assembly, release, and maturation of HIV. This study aimed to analyze the partial sequence of the HIV gag gene to classify HIV subtypes, identify recombination sites, and detect protease inhibitor (PI) resistance-associated mutations (RAMs). The cohort included 100 people living with HIV (PLH) who had experienced antiretroviral treatment failure with reverse transcriptase/protease inhibitors. Proviral HIV-DNA was successfully sequenced in 96 out of 100 samples for gag regions, specifically matrix (p17) and capsid (p24). Moreover, from these 96 sequences, 82 (85.42%) were classified as subtype B, six (6.25%) as subtype F1, one (1.04%) as subtype C, and seven (7.29%) exhibited a mosaic pattern between subtypes B and F1 (B/F1), with breakpoints at p24 protein. Insertions and deletions of amino acid at p17 were observed in 51 samples (53.13%). The prevalence of PI RAM in the partial gag gene was observed in 78 out of 96 PLH (81.25%). Among these cases, the most common mutations were R76K (53.13%), Y79F (31.25%), and H219Q (14.58%) at non-cleavage sites, as well as V128I (10.42%) and Y132F (11.46%) at cleavage sites. While B/F1 recombination was identified in the p24, the p17 coding region showed higher diversity, where insertions, deletions, and PI RAM, were observed at high prevalence. In PLH with virological failure, the analysis of the partial gag gene could contribute to more accurate predictions in genotypic resistance to PIs. This can aid guide more effective HIV treatment strategies.
Collapse
Affiliation(s)
- Cecília Salete Alencar
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Medicina Laboratorial (LIM-03), São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, São Paulo, São Paulo, Brazil
| | - Ricardo Sobhie Diaz
- Universidade Federal de São Paulo, Laboratório de Retrovirologia, São Paulo, São Paulo, Brazil
| | - Alfredo Mendrone-Junior
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Departamento de Hematologia, Laboratório de Investigação Médica em Patogênese e Terapia Dirigida em Onco-Imuno-Hematologia (LIM-31), São Paulo, São Paulo, Brazil
| | - Anna Shoko Nishiya
- Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Departamento de Hematologia, Laboratório de Investigação Médica em Patogênese e Terapia Dirigida em Onco-Imuno-Hematologia (LIM-31), São Paulo, São Paulo, Brazil
| |
Collapse
|
10
|
Zhao J, Zhang L, Li L, Xie X, Li J, Wei Y, Feng Y, Huang A, Huang H, Qin Q. Growth of infants delivered by mothers with HIV in Guangxi, China: An 18-month longitudinal follow-up study, 2015-2021. HIV Med 2024; 25:737-745. [PMID: 38479841 DOI: 10.1111/hiv.13624] [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: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 06/06/2024]
Abstract
OBJECTIVES The prevention of mother-to-child transmission of HIV has been a global success. But little is known about the growth parameters of infants delivered by mothers with HIV or the drug resistance of infants with HIV in China. The study aimed to assess growth parameters and drug resistance in Chinese infants exposed to HIV. METHODS We conducted an 18-month longitudinal follow-up study of 3283 infants (3222 without HIV; 61 with HIV) born to mothers with HIV in the Guangxi Zhuang Autonomous Region between January 2015 and December 2021. The weight and length of all participants was recorded. In addition, genetic subtypes and drug resistance analysis were performed for infants with HIV. RESULTS Compared with infants without HIV, those with HIV had significantly lower weight/length Z-scores, except at 18 months of age. The length/age Z-scores of infants with HIV was significantly reduced, except at 1 month of age. The weight/age Z-scores of infants with HIV were significantly lower at all follow-up time points. The weight/length Z-scores of male infants without HIV were significantly lower than for female infants without HIV at all follow-up time points. Male infants without HIV had lower length/age and weight/age Z-scores than female infants at the remaining follow-up points, except at 1 month of age. Of a total of 61 infants with HIV, subtype and drug-resistance data were obtained from 37 (60.66%) samples. Infants with HIV were dominated by the CRF01_AE genotype and showed a diversity of mutation sites dominated by non-nucleoside reverse transcriptase inhibitor resistance. CONCLUSION Our study demonstrates the growth of infants exposed to HIV in southwest China and provides detailed information on subtype distribution and drug resistance of those with HIV. Nutritional support and drug-resistance surveillance for infants exposed to HIV need to be strengthened.
Collapse
Affiliation(s)
- Jiangyang Zhao
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lingling Zhang
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Linlin Li
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaohua Xie
- Department of Maternal Health, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jianjun Li
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning, China
| | - Yuchen Wei
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yuanyuan Feng
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Aidan Huang
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Haifeng Huang
- Department of Clinical Laboratory, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qinghua Qin
- Department of Maternal Health, The Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| |
Collapse
|
11
|
Liu X, Wang Y, Yang Z, Wu Z, Li J, Tong Z, Li X, Ren F, Zhu X, Jin M, Mao G. Analysis of the immunological response to antiviral therapy in patients with different subtypes of HIV/AIDS: a retrospective cohort study. BMJ Open 2024; 14:e072597. [PMID: 38749684 PMCID: PMC11097878 DOI: 10.1136/bmjopen-2023-072597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE To evaluate the effectiveness of standardised antiretroviral therapy (ART) among different HIV subtypes in people living with HIV/AIDS (PLWHA), and to screen the best ART regimen for this patient population. DESIGN A retrospective cohort study was performed, and PLWHA residing in Huzhou, China, between 2018 and 2020, were enrolled. SETTING AND PARTICIPANTS Data from 625 patients, who were newly diagnosed with HIV/AIDS in the AIDS Prevention and Control Information System in Huzhou between 2018 and 2020, were reviewed. ANALYSIS AND OUTCOME MEASURES Data regarding demographic characteristics and laboratory investigation results were collected. Immune system recovery was used to assess the effectiveness of ART, and an increased percentage of CD4+ T lymphocyte counts >30% after receiving ART for >1 year was determined as immunopositive. A multiple logistic regression model was used to comprehensively quantify the association between PLWHA immunological response status and virus subtype. In addition, the joint association between different subtypes and treatment regimens on immunological response status was investigated. RESULTS Among 326 enrolled PLWHA with circulating recombinant forms (CRFs) CRF01_AE, CRF07_BC and other HIV/AIDS subtypes, the percentages of immunopositivity were 74.0%, 65.6% and 69.6%, respectively. According to multivariate logistic regression models, there was no difference in the immunological response between patients with CRF01_AE, CRF07_BC and other subtypes of HIV/AIDS who underwent ART (CRF07_BC: adjusted OR (aOR) (95% CI) = 0.8 (0.4 to 1.4); other subtypes: aOR (95% CI) = 1.2 (0.6 to 2.3)). There was no evidence of an obvious joint association between HIV subtypes and ART regimens on immunological response. CONCLUSIONS Standardised ART was beneficial to all PLWHA, regardless of HIV subtypes, although it was more effective, to some extent, in PLWHA with CRF01_AE.
Collapse
Affiliation(s)
- Xiaoqi Liu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Yanan Wang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhongrong Yang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Zhenqian Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Jing Li
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Zhaowei Tong
- Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Xiaofeng Li
- Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Feilin Ren
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Xiaojuan Zhu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Meihua Jin
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Guangyun Mao
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| |
Collapse
|
12
|
Liu ZY, Tang F, Yang JZ, Chen X, Wang ZF, Li ZQ. The Role of Beta2-Microglobulin in Central Nervous System Disease. Cell Mol Neurobiol 2024; 44:46. [PMID: 38743119 PMCID: PMC11093819 DOI: 10.1007/s10571-024-01481-6] [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: 01/06/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Central nervous system (CNS) disorders represent the leading cause of disability and the second leading cause of death worldwide, and impose a substantial economic burden on society. In recent years, emerging evidence has found that beta2 -microglobulin (B2M), a subunit of major histocompatibility complex class I (MHC-I) molecules, plays a crucial role in the development and progression in certain CNS diseases. On the one hand, intracellular B2M was abnormally upregulated in brain tumors and regulated tumor microenvironments and progression. On the other hand, soluble B2M was also elevated and involved in pathological stages in CNS diseases. Targeted B2M therapy has shown promising outcomes in specific CNS diseases. In this review, we provide a comprehensive summary and discussion of recent advances in understanding the pathological processes involving B2M in CNS diseases (e.g., Alzheimer's disease, aging, stroke, HIV-related dementia, glioma, and primary central nervous system lymphoma).
Collapse
Affiliation(s)
- Zhen-Yuan Liu
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Feng Tang
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jin-Zhou Yang
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xi Chen
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ze-Fen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, Hubei, China.
| | - Zhi-Qiang Li
- Brain Glioma Center & Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
13
|
Khairunisa SQ, Indriati DW, Megasari NLA, Ueda S, Kotaki T, Fahmi M, Ito M, Rachman BE, Hidayati AN, Nasronudin, Kameoka M. Spatial-temporal transmission dynamics of HIV-1 CRF01_AE in Indonesia. Sci Rep 2024; 14:9917. [PMID: 38730038 PMCID: PMC11087524 DOI: 10.1038/s41598-024-59820-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: 11/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) remains a serious health threat in Indonesia. In particular, the CRF01_AE viruses were the predominant HIV-1 strains in various cities in Indonesia. However, information on the dynamic transmission characteristics and spatial-temporal transmission of HIV-1 CRF01_AE in Indonesia is limited. Therefore, the present study examined the spatial-temporal transmission networks and evolutionary characteristics of HIV-1 CRF01_AE in Indonesia. To clarify the epidemiological connection between CRF01_AE outbreaks in Indonesia and the rest of the world, we performed phylogenetic studies on nearly full genomes of CRF01_AE viruses isolated in Indonesia. Our results showed that five epidemic clades, namely, IDN clades 1-5, of CRF01_AE were found in Indonesia. To determine the potential source and mode of transmission of CRF01_AE, we performed Bayesian analysis and built maximum clade credibility trees for each clade. Our study revealed that CRF01_AE viruses were commonly introduced into Indonesia from Southeast Asia, particularly Thailand. The CRF01_AE viruses might have spread through major pandemics in Asian countries, such as China, Vietnam, and Laos, rather than being introduced directly from Africa in the early 1980s. This study has major implications for public health practice and policy development in Indonesia. The contributions of this study include understanding the dynamics of HIV-1 transmission that is important for the implementation of HIV disease control and prevention strategies in Indonesia.
Collapse
Affiliation(s)
- Siti Qamariyah Khairunisa
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Health, Vocational Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Luh Ayu Megasari
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Postgraduate School, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
| | - Tomohiro Kotaki
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Muhamad Fahmi
- Research Department, Research Institute for Humanity and Nature, Kyoto, Japan
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Brian Eka Rachman
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Afif Nurul Hidayati
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Nasronudin
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
| | - Masanori Kameoka
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan.
| |
Collapse
|
14
|
Lebedev A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A, Kuznetsova A. Rev Protein Diversity in HIV-1 Group M Clades. Viruses 2024; 16:759. [PMID: 38793640 PMCID: PMC11125641 DOI: 10.3390/v16050759] [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: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The HIV-1 Rev protein expressed in the early stage of virus replication is involved in the nuclear export of some forms of virus RNA. Naturally occurring polymorphisms in the Rev protein could influence its activity. The association between the genetic features of different virus variants and HIV infection pathogenesis has been discussed for many years. In this study, Rev diversity among HIV-1 group M clades was analyzed to note the signatures that could influence Rev activity and, subsequently, clinical characteristics. From the Los Alamos HIV Sequence Database, 4962 Rev sequences were downloaded and 26 clades in HIV-1 group M were analyzed for amino acid changes, conservation in consensus sequences, and the presence of clade-specific amino acid substitutions (CSSs) and the Wu-Kabat protein variability coefficient (WK). Subtypes G, CRF 02_AG, B, and A1 showed the largest amino acid changes and diversity. The mean conservation of the Rev protein was 80.8%. In consensus sequences, signatures that could influence Rev activity were detected. In 15 out of 26 consensus sequences, an insertion associated with the reduced export activity of the Rev protein, 95QSQGTET96, was identified. A total of 32 CSSs were found in 16 clades, wherein A6 had the 41Q substitution in the functionally significant region of Rev. The high values of WK coefficient in sites 51 and 82, located on the Rev interaction surface, indicate the susceptibility of these positions to evolutionary replacements. Thus, the noted signatures require further investigation.
Collapse
Affiliation(s)
- Aleksey Lebedev
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
- Mechnikov Scientific Research Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - Kristina Kim
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Ekaterina Ozhmegova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anastasiia Antonova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Elena Kazennova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Aleksandr Tumanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| | - Anna Kuznetsova
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia; (K.K.); (E.O.); (A.A.); (E.K.); (A.T.)
| |
Collapse
|
15
|
Selvam D, D'silva A, Panchapakesan A, Gohil Y, Singh J, Hanna LE, Ranga U. The expression of HIV-1 tat in Lactococcus lactis. Protein Expr Purif 2024; 217:106443. [PMID: 38360084 DOI: 10.1016/j.pep.2024.106443] [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: 11/21/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Efficient expression of functional proteins in heterologous hosts has become the pivotal focus of modern biotechnology and biomedical research. To this end, multiple alternatives to E. coli are being explored for recombinant protein expression. L. lactis, being a gram-positive organism, circumvents the need for an endotoxin removal step during protein purification. We report here the optimisation of the expression of HIV-1 Tat, a notoriously difficult protein, in Lactococcus lactis system. We evaluated five different promoters in two different Lactococcus lactis strains and examined the effect of pH, glucose, and induction time on the yield and purity of Tat. Finally, the recombinant Tat was functionally competent in transactivating the HIV-1 promoter in HLM-1 reporter cells. Our work provides a scaffold for future work on the expression of toxic proteins in Lactococcus lactis.
Collapse
Affiliation(s)
- Deepak Selvam
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India; National Institute for Research in Tuberculosis, Chennai, India
| | - Anish D'silva
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Arun Panchapakesan
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Yuvrajsinh Gohil
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Jayendra Singh
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | | | - Udaykumar Ranga
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India.
| |
Collapse
|
16
|
De Meyer A, Meuleman P. Preclinical animal models to evaluate therapeutic antiviral antibodies. Antiviral Res 2024; 225:105843. [PMID: 38548022 DOI: 10.1016/j.antiviral.2024.105843] [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: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 04/05/2024]
Abstract
Despite the availability of effective preventative vaccines and potent small-molecule antiviral drugs, effective non-toxic prophylactic and therapeutic measures are still lacking for many viruses. The use of monoclonal and polyclonal antibodies in an antiviral context could fill this gap and provide effective virus-specific medical interventions. In order to develop these therapeutic antibodies, preclinical animal models are of utmost importance. Due to the variability in viral pathogenesis, immunity and overall characteristics, the most representative animal model for human viral infection differs between virus species. Therefore, throughout the years researchers sought to find the ideal preclinical animal model for each virus. The most used animal models in preclinical research include rodents (mice, ferrets, …) and non-human primates (macaques, chimpanzee, ….). Currently, antibodies are tested for antiviral efficacy against a variety of viruses including different hepatitis viruses, human immunodeficiency virus (HIV), influenza viruses, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rabies virus. This review provides an overview of the current knowledge about the preclinical animal models that are used for the evaluation of therapeutic antibodies for the abovementioned viruses.
Collapse
Affiliation(s)
- Amse De Meyer
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Philip Meuleman
- Laboratory of Liver Infectious Diseases, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| |
Collapse
|
17
|
Li X, Tamim S, Trovão NS. The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C. J Med Microbiol 2024; 73. [PMID: 38757423 DOI: 10.1099/jmm.0.001827] [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] [Indexed: 05/18/2024] Open
Abstract
Introduction. Human immunodeficiency virus (HIV)-1 subtype C is the most prevalent globally and is thought to have originated in non-human primates in the Democratic Republic of Congo.Hypothesis/Gap Statement. Although the global dominance of HIV-1 subtype C is well established, a thorough understanding of its evolutionary history and transmission dynamics across various risk populations remains elusive. The current knowledge is insufficient to fully capture the global diversification and dissemination of this subtype.Aim. We for the first time sought to investigate the global evolutionary history and spatiotemporal dynamics of HIV-1 subtype C using a selection of maximum-likelihood-based phylodynamic approaches on a total of 1210 near full-length genomic sequences sampled from 32 countries, collected in 4 continents, with sampling dates between 1986-2019 among various risk groups were analysed.Methodology. We subsampled the HIV-1 subtype C genomic datasets based on continent and risk group traits, and performed nucleotide substitution model selection analysis, maximum likelihood (ML) phylogenetic reconstruction, phylogenetic tree topology similarity analysis, temporal signal analysis and traced the timings of viral spread both geographically and by risk group.Results. Based on the phylodynamic analyses of four datasets (full1210, locrisk626, loc562 and risk393), we inferred the time to the most recent common ancestor (TMRCA) in the 1930s and an evolutionary rate of 0.0023 substitutions per site per year. The total number of introduction events of HIV-1 subtype C between continents and between risk groups is estimated to be 71 and 115, respectively. The largest number of introductions occurred from Africa to Europe (n=32), from not-recorded to heterosexual (n=40) and from heterosexual to not-recorded (n=51) risk groups.Conclusion. Our results emphasize that HIV subtype C has mainly spread from Africa to Europe, likely through heterosexual transmission.
Collapse
Affiliation(s)
- Xingguang Li
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, 315000, PR China
| | - Sana Tamim
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| |
Collapse
|
18
|
Acchioni C, Sandini S, Acchioni M, Sgarbanti M. Co-Infections and Superinfections between HIV-1 and Other Human Viruses at the Cellular Level. Pathogens 2024; 13:349. [PMID: 38787201 PMCID: PMC11124504 DOI: 10.3390/pathogens13050349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Co-infection or superinfection of the host by two or more virus species is a common event, potentially leading to viral interference, viral synergy, or neutral interaction. The simultaneous presence of two or more viruses, even distantly related, within the same cell depends upon viral tropism, i.e., the entry of viruses via receptors present on the same cell type. Subsequently, productive infection depends on the ability of these viruses to replicate efficiently in the same cellular environment. HIV-1 initially targets CCR5-expressing tissue memory CD4+ T cells, and in the absence of early cART initiation, a co-receptor switch may occur, leading to the infection of naïve and memory CXCR4-expressing CD4+ T cells. HIV-1 infection of macrophages at the G1 stage of their cell cycle also occurs in vivo, broadening the possible occurrence of co-infections between HIV-1 and other viruses at the cellular level. Moreover, HIV-1-infected DCs can transfer the virus to CD4+ T cells via trans-infection. This review focuses on the description of reported co-infections within the same cell between HIV-1 and other human pathogenic, non-pathogenic, or low-pathogenic viruses, including HIV-2, HTLV, HSV, HHV-6/-7, GBV-C, Dengue, and Ebola viruses, also discussing the possible reciprocal interactions in terms of virus replication and virus pseudotyping.
Collapse
Affiliation(s)
| | | | | | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (C.A.); (S.S.); (M.A.)
| |
Collapse
|
19
|
Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303990. [PMID: 38558994 PMCID: PMC10980117 DOI: 10.1101/2024.03.14.24303990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was estimated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Evolutionary dynamics were assessed among demographic and behavioral sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by more than four-fold. Inter-subtype HIV diversity has generally increased. While p24 intra-subtype genetic diversity and divergence leveled off after 2014, diversity and divergence of gp41 increased through 2017. Inter- and intra-subtype viral diversity increased across all population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics in declining African HIV epidemics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.
Collapse
Affiliation(s)
- Seungwon Kim
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Michael A. Martin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Thomas C. Quinn
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Redd
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Joshua T. Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven J. Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, England, United Kingdom
| | - Joseph Kagaayi
- Rakai Health Sciences Program, Kalisizo, Uganda
- Makerere University School of Public Health, Kampala, Uganda
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - M. Kate Grabowski
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Rakai Health Sciences Program, Kalisizo, Uganda
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| |
Collapse
|
20
|
Li K, Chen H, Li J, Feng Y, Liang S, Rashid A, Liu M, Li S, Chu Q, Ruan Y, Xing H, Lan G, Qiao W, Shao Y. Distinct genetic clusters in HIV-1 CRF01_AE-infected patients induced variable degrees of CD4 + T-cell loss. mBio 2024; 15:e0334923. [PMID: 38385695 PMCID: PMC10936439 DOI: 10.1128/mbio.03349-23] [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: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
CRF01_AE strains have been shown to form multiple transmission clusters in China, and some clusters have disparate pathogenicity in Chinese men who have sex with men. This study focused on other CRF01_AE clusters prevalent in heterosexual populations. The CD4+ T-cell counts from both cross-section data in National HIV Molecular Epidemiology Survey and seropositive cohort data were used to evaluate the pathogenicity of the CRF01_AE clusters and other HIV-1 sub-types. Their mechanisms of pathogenicity were evaluated by co-receptor tropisms, predicted by genotyping and confirmed with virus isolate phenotyping, as well as inflammation parameters. Our research elucidated that individuals infected with CRF01_AE clusters 1 and 2 exhibited significantly lower baseline CD4+ T-cell counts and greater CD4+ T-cell loss in cohort follow-up, compared with other HIV-1 sub-types and CRF01_AE clusters. The increased pathogenesis of cluster 1 or 2 was associated with higher CXCR4 tropisms, higher inflammation/immune activation, and increased pyroptosis. The protein structure modeling analysis revealed that the envelope V3 loop of clusters 1 and 2 viruses is favorable for CXCR4 co-receptor usage. Imbedded with the most mutating reverse transcriptase, HIV-1 is one of the most variable viruses. CRF01_AE clusters 1 and 2 have been found to have evolved into more virulent strains in regions with predominant heterosexual infections. The virulent strains increased the pressure for early diagnosis and treatment in HIV patients. To save more lives, HIV-1 surveillance systems should be upgraded from serology and genotyping to phenotyping, which could support precision interventions for those infected by virulent viruses. IMPORTANCE Retroviruses swiftly adapt, employing error-prone enzymes for genetic and phenotypic evolution, optimizing survival strategies, and enhancing virulence levels. HIV-1 CRF01_AE has persistently undergone adaptive selection, and cluster 1 and 2 infections display lower counts and fast loss of CD4+ T cells than other HIV-1 sub-types and CRF01_AE clusters. Its mechanisms are associated with increased CXCR4 tropism due to an envelope structure change favoring a tropism shift from CCR5 to CXCR4, thereby shaping viral phenotype features and impacting pathogenicity. This underscores the significance of consistently monitoring HIV-1 genetic evolution and phenotypic transfer to see whether selection bias across risk groups alters the delicate balance of transmissible versus toxic trade-offs, since virulent strains such as CRF01_AE clusters 1 and 2 could seriously compromise the efficacy of antiviral treatment. Only through such early warning and diagnostic services can precise antiviral treatments be administered to those infected with more virulent HIV-1 strains.
Collapse
Affiliation(s)
- Kang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Yi Feng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Abdur Rashid
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Nankai University, Tianjin, China
| | - Meiliang Liu
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Sisi Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhua Ruan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xing
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yiming Shao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Medicine, Zhejiang University, Hangzhou, China
- Changping Laboratory, Beijing, China
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Asia LK, Van Vuren EJ, Kruger IM, Williams ME. A Pilot Investigation of the Association Between Vpr Amino Acid Substitutions and Peripheral Immune Marker Levels in People With Human Immunodeficiency Virus: Implications for Neurocognitive Impairment. Open Forum Infect Dis 2024; 11:ofae111. [PMID: 38524224 PMCID: PMC10960601 DOI: 10.1093/ofid/ofae111] [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: 10/02/2023] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Background Subtype-specific amino acid variations in viral proteins of human immunodeficiency virus type 1 (HIV-1) influence disease progression. Furthermore, Vpr sequence variation correlates with chronic inflammation, a central mechanism in HIV-1 (neuro)pathogenesis. Nevertheless, no clinical study has investigated the link between Vpr sequence variation and peripheral inflammation in people with HIV (PWH). The aim of this pilot study was to ascertain whether specific Vpr amino acid variants were associated with immune markers in PWH. Methods We included a unique cohort of 48 treatment-naive South African PWH to determine the association between blood-derived Vpr sequence variation and peripheral immune marker levels using Sanger sequencing and enzyme-linked immunosorbent assay analysis, respectively. Results Our findings indicate that among the many neuropathogenic Vpr amino acid variants and immune markers examined, after applying Bonferroni corrections (P = .05/3) and adjusting for sex and locality, soluble urokinase plasminogen activator receptor (suPAR) was nearing significance for higher levels in participants with the G41 amino acid variant compared to those with the S41 variant (P = .035). Furthermore, amino acid variations at position 41 (between G41 and S41) exhibited a significant association with suPAR (adjusted R2 = 0.089, β = .386 [95% confidence interval, .125-3.251]; P = .035). Conclusions These findings suggest that Vpr amino acid sequence variations might contribute to dysregulated inflammation, which could explain the observed association between specific Vpr variants and HIV-1 (neuro)pathogenesis found in prior research. These Vpr variants merit further investigation to fully understand their roles in HIV-1 pathogenesis and neuropathogenesis.
Collapse
Affiliation(s)
- Levanco K Asia
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Esmé Jansen Van Vuren
- Hypertension in Africa Research Team, North-West University, Potchefstroom, South Africa
- South African Medical Research Council, Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Iolanthé M Kruger
- Africa Unit for Transdisciplinary Health Research, North-West University, Potchefstroom, South Africa
| | - Monray E Williams
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| |
Collapse
|
23
|
Wang D, Feng Y, Ruan Y, Liao L, Hao J, Song C, Hu J, Shao Y, Xing H. Criteria for classification, nomenclature, and reference sequence selection for HIV sub-subtypes of CRF01_AE and CRF07_BC strains in China. AIDS 2024; 38:427-430. [PMID: 38300161 PMCID: PMC10842659 DOI: 10.1097/qad.0000000000003756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/12/2023] [Indexed: 02/02/2024]
Abstract
The available knowledge regarding classification, nomenclature, and reference sequence selection for the various sub-subtypes of circulating recombinant forms (CRFs) is inadequate to fulfill the growing demands of research focused on HIV prevention. We analyzed the spread of CRF01_AE and CRF07_BC strains, mainly in China, to complement and update the existing nomenclature and to propose a reference sequence selection criteria for sub-subtypes of CRFs.
Collapse
Affiliation(s)
- Dong Wang
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Asia LK, Van Vuren EJ, Lindeque Z, Williams ME. A pilot investigation of the association between HIV-1 Vpr amino acid sequence diversity and the tryptophan-kynurenine pathway as a potential mechanism for neurocognitive impairment. Virol J 2024; 21:47. [PMID: 38395987 PMCID: PMC10893664 DOI: 10.1186/s12985-024-02313-1] [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: 11/17/2023] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
HIV infection compromises both the peripheral and central immune systems due to its pathogenic and neuropathogenic features. The mechanisms driving HIV-1 pathogenesis and neuropathogenesis involve a series of events, including metabolic dysregulation. Furthermore, HIV-subtype-specific variations, particularly alterations in the amino acid sequences of key viral proteins, are known to influence the severity of clinical outcomes in people living with HIV. However, the impact of amino acid sequence variations in specific viral proteins, such as Viral protein R (Vpr), on metabolites within the Tryptophan (Trp)-kynurenine (Kyn) pathway in people living with HIV remains unclear. Our research aimed to explore the relationship between variations in the Vpr amino acid sequence (specifically at positions 22, 41, 45, and 55, as these have been previously linked to neurocognitive function) and peripheral Trp-Kyn metabolites. Additionally, we sought to clarify the systems biology of Vpr sequence variation by examining the link between Trp-Kyn metabolism and peripheral inflammation, as a neuropathogenic mechanism. In this preliminary study, we analyzed a unique cohort of thirty-two (n = 32) South African cART naïve people living with HIV. We employed Sanger sequencing to ascertain blood-derived Vpr amino acid sequence variations and a targeted LC-MS/MS metabolomics platform to assess Trp-Kyn metabolites, such as Trp, Kyn, kynurenic acid (KA), and quinolinic acid (QUIN). Particle-enhanced turbidimetric assay and Enzyme-linked immunosorbent assays were used to measure immune markers, hsCRP, IL-6, suPAR, NGAL and sCD163. After applying Bonferroni corrections (p =.05/3) and adjusting for covariates (age and sex), only the Vpr G41 and A55 groups was nearing significance for higher levels of QUIN compared to the Vpr S41 and T55 groups, respectively (all p =.023). Multiple regression results revealed that Vpr amino acid variations at position 41 (adj R2 = 0.049, β = 0.505; p =.023), and 55 (adj R2 = 0.126, β = 0.444; p =.023) displayed significant associations with QUIN after adjusting for age and sex. Lastly, the higher QUIN levels observed in the Vpr G41 group were found to be correlated with suPAR (r =.588, p =.005). These results collectively underscore the importance of specific Vpr amino acid substitutions in influencing QUIN and inflammation (specifically suPAR levels), potentially contributing to our understanding of their roles in the pathogenesis and neuropathogenesis of HIV-1.
Collapse
Affiliation(s)
| | - Esmé Jansen Van Vuren
- Hypertension in Africa Research Team (HART), North-West University, Potchefstroom, South Africa
- South African Medical Research Council, Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Zander Lindeque
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | | |
Collapse
|
25
|
Wan Z, Zhang C. How to report and make sense of a new HIV-1 circulating recombinant form? Front Microbiol 2024; 15:1343143. [PMID: 38450164 PMCID: PMC10915052 DOI: 10.3389/fmicb.2024.1343143] [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: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024] Open
Abstract
Co-circulation of multiple HIV-1 subtypes in the same high-risk groups leads to the on-going generation of various inter-subtype recombinants, including unique (URFs) and circulating (CRFs) recombinant forms, which brings a new challenge for the prevention and eradication of HIV/AIDS. Identification and prompt reporting of new CRFs will provide not only new insights into the understanding of genetic diversity and evolution of HIV-1, but also an early warning of potential prevalence of these variants. Currently, 140 HIV-1 CRFs have been described; however, their prevalence and clinical importance are less concerned. Apart from the mosaic genomic maps, less other valuable information, including the clinical and demographic data, genomic sequence characteristics, origin and evolutionary dynamics, as well as representative genomic fragments for determining the variants, are available for most of these CRFs. Accompanied with the growing increase of HIV-1 full-length genomic sequences, more and more CRFs will be identified in the near future due to the high recombination potential of HIV-1. Here, we discuss the prevalence and clinical importance of various HIV-1 CRFs and propose how to report and make sense of a new HIV-1 CRF.
Collapse
Affiliation(s)
- Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
26
|
Switzer WM, Shankar A, Jia H, Knyazev S, Ambrosio F, Kelly R, Zheng H, Campbell EM, Cintron R, Pan Y, Saduvala N, Panneer N, Richman R, Singh MB, Thoroughman DA, Blau EF, Khalil GM, Lyss S, Heneine W. High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus Evol 2024; 10:veae015. [PMID: 38510920 PMCID: PMC10953796 DOI: 10.1093/ve/veae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.
Collapse
Affiliation(s)
- William M Switzer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Anupama Shankar
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Hongwei Jia
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sergey Knyazev
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Frank Ambrosio
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Reagan Kelly
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA 22042, USA
| | - HaoQiang Zheng
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Roxana Cintron
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Yi Pan
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | | | - Nivedha Panneer
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Rhiannon Richman
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
| | - Manny B Singh
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
| | - Douglas A Thoroughman
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- ORR/Division of State and Local Readiness/Field Services Branch/CEFO Program, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Erin F Blau
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Epidemic Intelligence Service, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - George M Khalil
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| | - Sheryl Lyss
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
- HIV Surveillance Program, Bureau of HIV/STI/Viral Hepatitis, Ohio Department of Health, 246 North High Street, Colombus, OH 43215, USA
- Division of Epidemiology and Health Planning, Kentucky Department for Public Health, Frankfort, KY 40621, USA
- Hamilton County Public Health, 250 William Howard Taft Rd, Cincinnati, OH 45219, USA
- Northern Kentucky Health Department, 8001 Veterans Memorial Drive, Florence, KY 41042, USA
| | - Walid Heneine
- Division of HIV Prevention, CDC, 1600 Clifton Rd, Atlanta, GA 30329, USA
| |
Collapse
|
27
|
Franz BJ, Register H, Sullivan V, Warber K, Granade TC, Cornaby C, Magee ME, Denny TN, Lockwood D, Schmitz JL. Evaluation of the VioOne HIV profile supplemental assay. J Clin Microbiol 2024; 62:e0083623. [PMID: 38206000 PMCID: PMC10865837 DOI: 10.1128/jcm.00836-23] [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: 07/03/2023] [Accepted: 12/02/2023] [Indexed: 01/12/2024] Open
Abstract
HIV is an ongoing global epidemic with estimates of more than a million new infections occurring annually. To combat viral spread, continuous innovations in areas including testing and treatment are necessary. In the United States, the Centers for Disease Control and Prevention recommend that laboratories follow an HIV testing algorithm that first uses a US Food and Drug Administration approved immunoassay to detect antibodies to HIV-1 or HIV-2 as well as HIV-1 p24 antigen in serum or plasma samples. An initially reactive specimen is tested by a supplemental assay for confirmation and to differentiate antibodies to HIV-1 or HIV-2. There are few Food and Drug Administration (FDA)-approved supplemental differentiation tests currently available. A multicenter investigation was conducted to determine the clinical performance for two independent versions of the Avioq VioOne HIV Profile Supplemental Assay (Avioq, Inc., Research Triangle Park, NC). The performance of both assay versions compared favorably with the performance parameters for the Geenius HIV 1/2 Supplemental Assay as published in that assay package insert (Bio-Rad Laboratories, Hercules, CA), the current gold standard for HIV supplemental testing. When comparing the two VioOne assays, version 2 (lacking HIV-2 p27 antibody detection) demonstrated improved reproducibility, specificity, and sensitivity as compared to its predecessor. IMPORTANCE We evaluated the reproducibility, sensitivity, and specificity data for two versions of the VioOne HIV Profile Supplemental Assay and compared these results back to similar results for the Geenius HIV 1/2 Supplemental Assay that are publicly available. Our study concluded that the VioOne HIV Profile Supplemental Assay compared favorably with the Geenius HIV 1/2 Supplemental Assay, thus providing an additional option for clinical laboratories to improve and expand their HIV testing capabilities.
Collapse
Affiliation(s)
- Brian J. Franz
- Department of Pathology and Laboratory Medicine, UNC-Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Heidi Register
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Vickie Sullivan
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kimbrough Warber
- Clinical Reference Laboratory, Clinical Reference Laboratory Inc., Lenexa, Kansas, USA
| | - Timothy C. Granade
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Caleb Cornaby
- Department of Pathology and Laboratory Medicine, UNC-Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Mark E. Magee
- Clinical Reference Laboratory, Clinical Reference Laboratory Inc., Lenexa, Kansas, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Don Lockwood
- Avioq, Inc., Research Triangle Park, North Carolina, USA
| | - John L. Schmitz
- Department of Pathology and Laboratory Medicine, UNC-Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| |
Collapse
|
28
|
Williams ME. HIV-1 Vif protein sequence variations in South African people living with HIV and their influence on Vif-APOBEC3G interaction. Eur J Clin Microbiol Infect Dis 2024; 43:325-338. [PMID: 38072879 PMCID: PMC10821834 DOI: 10.1007/s10096-023-04728-0] [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: 07/24/2023] [Accepted: 11/28/2023] [Indexed: 01/28/2024]
Abstract
PURPOSE Despite extensive research, HIV-1 remains a global epidemic with variations in pathogenesis across regions and subtypes. The Viral Infectivity Factor (Vif) protein, which neutralizes the host protein APOBEC3G, has been implicated in differences in clinical outcomes among people living with HIV (PLHIV). Most studies on Vif sequence diversity have focused on subtype B, leaving gaps in understanding Vif variations in HIV-1C regions like South Africa. This study aimed to identify and compare Vif sequence diversity in a cohort of 51 South African PLHIV and other HIV-1C prevalent regions. METHODS Sanger sequencing was used for Vif analysis in the cohort, and additional sequences were obtained from the Los Alamos database. Molecular modeling and docking techniques were employed to study the influence of subtype-specific variants on Vif-APOBEC3G binding affinity. RESULTS The findings showed distinct genetic variations between Vif sequences from India and Uganda, while South African sequences had wider distribution and closer relatedness to both. Specific amino acid substitutions in Vif were associated with geographic groups. Molecular modeling and docking analyses consistently identified specific residues (ARGR19, LYS26, TYR30, TYR44, and TRP79) as primary contributors to intermolecular contacts between Vif and APOBEC3G, essential for their interaction. The Indian Vif variant exhibited the highest predicted binding affinity to APOBEC3G among the studied groups. CONCLUSIONS These results provide insights into Vif sequence diversity in HIV-1C prevalent regions and shed light on differential pathogenesis observed in different geographical areas. The identified Vif amino acid residues warrant further investigation for their diagnostic, prognostic, and therapeutic potential.
Collapse
|
29
|
Buchholtz NVEJ, Nühn MM, de Jong TCM, Stienstra TAT, Reddy K, Ndung'u T, Ndhlovu ZM, Fisher K, Palmer S, Wensing AMJ, Symons J, Nijhuis M. Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C. Virol J 2024; 21:36. [PMID: 38297379 PMCID: PMC10832250 DOI: 10.1186/s12985-024-02300-6] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
INTRODUCTION HIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C. METHODS Primer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability. RESULTS The in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region. CONCLUSIONS We developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.
Collapse
Affiliation(s)
- N V E J Buchholtz
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M M Nühn
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T C M de Jong
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - T A T Stienstra
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - K Reddy
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - T Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA, 01238, USA
- Division of Infection and Immunity, University College London, London, UK
| | - Z M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - K Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - S Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - A M J Wensing
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
- ha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J Symons
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands
| | - M Nijhuis
- Translational Virology, Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584C, Utrecht, The Netherlands.
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
| |
Collapse
|
30
|
Dampier W, Berman R, Nonnemacher MR, Wigdahl B. Computational analysis of cas proteins unlocks new potential in HIV-1 targeted gene therapy. Front Genome Ed 2024; 5:1248982. [PMID: 38239625 PMCID: PMC10794619 DOI: 10.3389/fgeed.2023.1248982] [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: 06/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction: The human immunodeficiency virus type 1 (HIV-1) pandemic has been slowed with the advent of anti-retroviral therapy (ART). However, ART is not a cure and as such has pushed the disease into a chronic infection. One potential cure strategy that has shown promise is the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas gene editing system. It has recently been shown to successfully edit and/or excise the integrated provirus from infected cells and inhibit HIV-1 in vitro, ex vivo, and in vivo. These studies have primarily been conducted with SpCas9 or SaCas9. However, additional Cas proteins are discovered regularly and modifications to these known proteins are being engineered. The alternative Cas molecules have different requirements for protospacer adjacent motifs (PAMs) which impact the possible targetable regions of HIV-1. Other modifications to the Cas protein or gRNA handle impact the tolerance for mismatches between gRNA and the target. While reducing off-target risk, this impacts the ability to fully account for HIV-1 genetic variability. Methods: This manuscript strives to examine these parameter choices using a computational approach for surveying the suitability of a Cas editor for HIV-1 gene editing. The Nominate, Diversify, Narrow, Filter (NDNF) pipeline measures the safety, broadness, and effectiveness of a pool of potential gRNAs for any PAM. This technique was used to evaluate 46 different potential Cas editors for their HIV therapeutic potential. Results: Our examination revealed that broader PAMs that improve the targeting potential of editors like SaCas9 and LbCas12a have larger pools of useful gRNAs, while broader PAMs reduced the pool of useful SpCas9 gRNAs yet increased the breadth of targetable locations. Investigation of the mismatch tolerance of Cas editors indicates a 2-missmatch tolerance is an ideal balance between on-target sensitivity and off-target specificity. Of all of the Cas editors examined, SpCas-NG and SPRY-Cas9 had the highest number of overall safe, broad, and effective gRNAs against HIV. Discussion: Currently, larger proteins and wider PAMs lead to better targeting capacity. This implies that research should either be targeted towards delivering longer payloads or towards increasing the breadth of currently available small Cas editors. With the discovery and adoption of additional Cas editors, it is important for researchers in the HIV-1 gene editing field to explore the wider world of Cas editors.
Collapse
Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| |
Collapse
|
31
|
Li QH, Zhang YQ, Li EL, Guo Q, Chen XH, Wang FX, Wang JY. Characterization of an imported HIV-1 A1/A7/G recombinant in China. Virol J 2024; 21:3. [PMID: 38178224 PMCID: PMC10768240 DOI: 10.1186/s12985-023-02274-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: 10/07/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND International migration has accelerated the HIV-1 spread across national borders, gradually reducing the restrictions on the geographical distribution of HIV-1 subtypes. Subtypes A and G are globally recognized as the third and sixth most dominant HIV-1 genotypes, mainly prevalent in Africa, but rarely detected in China. Here we reported an imported HIV-1 recombinant which was composed of sub-subtypes A1 and A7 of subtype A and subtype G genes in a Chinese female. This virus was the first HIV-1 recombinant including A7 genes reported in the world. CASE PRESENTATION The near full-length genome (NFLG) was obtained from the plasma sample of the female in an HIV-1 molecular epidemiological survey with 853 participants in China. Phylogenetic analyses showed that this NFLG sequence contains three A7 segments, four G segments and one A1 segment with seven breakpoints, and all these segments were closely related to HIV-1 references circulating in Africa. The evidence from epidemiological investigation indicated that this female participant had a more-than-two-years heterosexual contact history with a fixed partner from Nigeria, a country in west Africa, which further supported the results of phylogenetic analyses. By the Bayesian phylogenetic analyses, the times of most recent common ancestors (tMRCA) of the partial pol gene (nt2308-3284, A7 region) and full-length vpr-vpu plus partial env gene (nt5534-6858, G region) were estimated around 1989 and 1984, respectively. CONCLUSIONS In this study, by using the NFLG sequencing, we identified an imported HIV-1 A1/A7/G recombinant which was estimated to originate around 1980s in Africa and introduced into China with international migration. This study highlighted the complexity of the global HIV-1 epidemic, the necessity of using genome sequences to determine HIV-1 genotypes and the importance of real-time monitoring of HIV-1 infection among international migrants and travelers.
Collapse
Affiliation(s)
- Qing-Hai Li
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yun-Qi Zhang
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China
| | - En-Long Li
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China
| | - Qi Guo
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xiao-Hong Chen
- Department of Infectious Diseases, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Infectious Diseases, the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Jia-Ye Wang
- Department of Microbiology, Harbin Medical University, 157 Baojian Road, 150001, Harbin, China.
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China.
- Heilongjiang Academy of Medical Sciences, Harbin, China.
| |
Collapse
|
32
|
Sharafi M, Mirahmadizadeh A, Hassanzadeh J, Seif M, Heiran A. Factors associated with late initiation of antiretroviral therapy in Iran's HIV/AIDS surveillance data. Sci Rep 2024; 14:199. [PMID: 38167855 PMCID: PMC10761711 DOI: 10.1038/s41598-023-50713-0] [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: 02/20/2023] [Accepted: 12/23/2023] [Indexed: 01/05/2024] Open
Abstract
Early initiation of Antiretroviral Treatment (ART) in HIV patients is essential for effectively suppressing the viral load and prognosis. This study utilized National HIV/AIDS Surveillance Data in Iran to identify factors associated factors with the duration to initiate ART. This hybrid cross-sectional historical cohort study was conducted on Iran's National HIV/AIDS Surveillance Data from 2001 to 2019. Sociodemographic characteristics, route of transmission, HIV diagnosis date, and ART initiation date were collected. Multivariable linear and quantile regression models were employed to analyze the duration to initiate ART by considering predictor variables. This study included 17,062 patients (mean age 34.14 ± 10.77 years, 69.49% males). Multivariate quantile regression coefficients varied across different distributions of the dependent variable (i.e., duration to initiate ART) for several independent variables. Generally, male gender, injecting drug use (IDU), and having an HIV-positive spouse were significantly associated with an increased duration to initiate ART (p < 0.05). However, a significant decrease was observed in older patients, those with a university level education, men who had sex with men (MSM), and patients diagnosed after 2016 (p < 0.05). Despite improvements in the duration to initiate ART after implementing the WHO's 2016 program in Iran, various sociodemographic groups were still vulnerable to delayed ART initiation in the region. Therefore, programs including early testing, early ART initiation, active care, educational and cultural interventions, and appropriate incentives are required for these groups.
Collapse
Affiliation(s)
- Mehdi Sharafi
- Social Determinants in Health Promotion Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Mirahmadizadeh
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jafar Hassanzadeh
- Department of Epidemiology, Research Centre for Health Sciences, Institute of Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mozhgan Seif
- Non-communicable Diseases Research Center, Department of Epidemiology, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Heiran
- Non-communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
33
|
Epalza C, Valadés-Alcaraz A, González-Alba JM, Beltrán-Pavez C, Gutiérrez-López M, Rubio-Garrido M, Fortuny C, Frick MA, Muñoz Medina L, Moreno S, Sanz J, Rojo P, Navarro ML, Holguín Á. Transmitted Drug Resistance and HIV Diversity Among Adolescents Newly Diagnosed With HIV in Spain. Pediatr Infect Dis J 2024; 43:40-48. [PMID: 37922511 DOI: 10.1097/inf.0000000000004138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
BACKGROUND Virologic characterization of newly HIV-diagnosed adolescents could help to improve their specific needs. The objective was to describe the transmitted drug resistance mutations (TDR) and its transmission by clusters in this population in Spain. METHODS TDR to retrotranscriptase and protease inhibitors included in the WHO TDR list 2009 implemented in the Calibrated Population Resistance tool v8.0 (Stanford) were studied in HIV pol sequences from all HIV-diagnosed adolescents (12-19-year-old) enrolled during 2004-2019 period in the Spanish pediatric and adult (CoRISpe-CoRIS) cohorts. The found TDR were compared with the provided by the Stanford algorithm v9.0 2021. HIV-1 variants and transmission clusters were also studied. RESULTS Among 410 HIV-1 adolescents diagnosed, 141 (34.4%) had available ART-naive sequences. They were mostly male (81.6%), Spanish (55.3%) and with behavioral risk (92.2%), mainly male-to-male sexual contact (63.1%). TDR prevalence was significantly higher by Stanford versus WHO list (18.4% vs. 7.1%; P = 0.004). The most prevalent TDR by the WHO list was K103N (3.6%) and by Stanford E138A (6.6%), both at retrotranscriptase. E138A, related to rilpivirine/etravirine resistance, was absent in the WHO list. One in 4 adolescents carried HIV-1 non-B variants. We described 5 transmission clusters, and 2 carried TDR mutations. CONCLUSIONS Our data suggest a high TDR prevalence in adolescents with a new HIV diagnosis in Spain, similar to adults, 2 active TDR transmission clusters, and the need for the WHO TDR list update. These findings could have implications for the options of the recently available rilpivirine-related long-acting treatment and in first-line regimen election.
Collapse
Affiliation(s)
- Cristina Epalza
- From the Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Pediatric Research and Clinical Trials Unit (UPIC) , Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, CoRISpe, Universidad Complutense de Madrid, Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Spain
| | - Ana Valadés-Alcaraz
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal-IRYCIS and CoRISpe, Madrid
| | - José María González-Alba
- Microbiology Department, Hospital Universitario Central de Asturias and Grupo de Investigación Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carolina Beltrán-Pavez
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal-IRYCIS and CoRISpe, Madrid
| | - Miguel Gutiérrez-López
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal-IRYCIS and CoRISpe, Madrid
| | - Marina Rubio-Garrido
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal-IRYCIS and CoRISpe, Madrid
| | - Clàudia Fortuny
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Spain
- Malalties Infeccioses i Resposta Inflamatòria Sistèmica en Pediatria, Unitat d'Infeccions, Servei de Pediatria, Institut de Recerca Pediàtrica Sant Joan de Déu, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
| | - Marie Antoinette Frick
- Unidad de Patología Infecciosa e Inmunodeficiencias de Pediatría, Servicio de Pediatría, Hospital Universitario Vall d´Hebron, Barcelona, Spain
| | - Leopoldo Muñoz Medina
- Unidad de Enfermedades Infecciosas, Hospital Universitario Clinico San Cecilio, Granada, Spain
| | - Santiago Moreno
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal, Madrid, IRYCIS, Universidad Alcalá de Henares, Madrid, Spain
| | - José Sanz
- Servicio de Medicina Interna/Enfermedades Infecciosas, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain
| | - Pablo Rojo
- From the Pediatric Infectious Diseases Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Pediatric Research and Clinical Trials Unit (UPIC) , Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, CoRISpe, Universidad Complutense de Madrid, Madrid, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Spain
| | - María Luisa Navarro
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Spain
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Infectious Disease Unit, Department of Pediatrics, Hospital Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), CoRISpe, Universidad Complutense de Madrid, Madrid, Spain
| | - África Holguín
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Spain
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Hospital Universitario Ramón y Cajal-IRYCIS and CoRISpe, Madrid
- CIBER de Enfermedades Infecciosas (CIBERINFECT), Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
34
|
Ma Y, Wan Z, Zhang M, Zhang C. Genomic Characteristics of the New HIV-1 CRF07_BC K 28E 32 Variant. AIDS Res Hum Retroviruses 2024; 40:42-53. [PMID: 37312534 DOI: 10.1089/aid.2022.0182] [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] [Indexed: 06/15/2023] Open
Abstract
Accompanied with the appearance and prevalence of the new K28E32 variant among men who have sex with men, HIV-1 circulating recombinant form 07_BC (CRF07_BC) was becoming the most predominant subtype circulating in China. The K28E32 variant with five specific mutations in reverse transcriptase coding region appears to have significantly higher in vitro HIV-1 replication ability than the wild-type strain. In this study, we characterized the special mutations/substitutions in the K28E32 variant at the genomic level. Ten specific mutations that rarely appeared in other six main HIV-1 subtypes/CRFs (A-D, CRF01_AE, and CRF02_AG) were identified in the coding genes/regions of the K28E32 variant, including S77L and a novel seven-amino acid detection (32DKELYPL38) (p6Δ7) in p6, I135L in integrase, T189S in Vif, H/Y15L/F in Vpr, I264V/A and LV/LI328-329VG in gp41, and H82C and S97P in Rev. The special locations of the novel p6Δ7, and gp41 mutations I264V/A and LV/LI328-329VG in crucial protein functional domains suggest that these mutations might be functionally important to the K28E32 variant. Furthermore, eight specific substitutions were identified in Rev responsive element (RRE) of the K28E32 variant, and were revealed to increase the stability of RRE structure with a lower minimum free energy. Whether these mutations/substitutions contribute to improved transmissibility of the CRF07_BC K28E32 variant needs to be further confirmed.
Collapse
Affiliation(s)
- Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, China
| | - Min Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
35
|
Paneerselvam N, Khan A, Lawson BR. Broadly neutralizing antibodies targeting HIV: Progress and challenges. Clin Immunol 2023; 257:109809. [PMID: 37852345 PMCID: PMC10872707 DOI: 10.1016/j.clim.2023.109809] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Anti-HIV broadly neutralizing antibodies (bNAbs) offer a novel approach to treating, preventing, or curing HIV. Pre-clinical models and clinical trials involving the passive transfer of bNAbs have demonstrated that they can control viremia and potentially serve as alternatives or complement antiretroviral therapy (ART). However, antibody decay, persistent latent reservoirs, and resistance impede bNAb treatment. This review discusses recent advancements and obstacles in applying bNAbs and proposes strategies to enhance their therapeutic potential. These strategies include multi-epitope targeting, antibody half-life extension, combining with current and newer antiretrovirals, and sustained antibody secretion.
Collapse
Affiliation(s)
| | - Amber Khan
- The Scintillon Research Institute, 6868 Nancy Drive, San Diego, CA 92121, USA
| | - Brian R Lawson
- The Scintillon Research Institute, 6868 Nancy Drive, San Diego, CA 92121, USA.
| |
Collapse
|
36
|
Li Z, Kang Q, Liu Y, Jia L, Li T, Wang X, Li J, Zhang B, Han J, Li H, Li L. Identification of Two Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/CRF07_BC) in Men Who Have Sex with Men in Hebei, China. AIDS Res Hum Retroviruses 2023; 39:681-687. [PMID: 36943286 DOI: 10.1089/aid.2022.0131] [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] [Indexed: 03/23/2023] Open
Abstract
In recent years, men who have sex with men (MSM) have been identified as the primary source of HIV-1 transmission in Hebei Province, China. Co-circulation of multiple subtypes in HIV-1 positive MSM populations may contribute to the emergence of the second generation of recombinant HIV-1 strains, indicating the occurrence of dual infections or superinfections in MSM populations. Thus, the discovery of new recombinant strains is important to indicate the appearance of multiple infected individuals and the prevalence caused by changes in the parent strains. In this study, we present two new unique recombinant forms (URFs) from two HIV-1-positive subjects (HB070052 and HB070056) infected through homosexual contact in Hebei Province, China. The near full-length genome of the two URFs revealed that HB070052 was divided into seven segments by six breakpoints in the gag, pol, vif, and vpr genes; HB070056 was separated into five fragments by four breakpoints, with two regions of CRF07_BC inserted into a CRF01_AE backbone's gag, pol regions. The subregion tree showed CRF01_AE segments were traced back to the cluster 4 and 6 of the CRF01_AE phylogenetic tree, which were prevalent among HIV-1 infections through MSM in China. The continued emergence of the novel CRF01_AE/CRF07_BC recombinant forms indicates the HIV-1 epidemic is complex and long-term surveillance of recombinant strains is necessary among MSM in this region.
Collapse
Affiliation(s)
- Zhengyang Li
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Qian Kang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tianyi Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolin Wang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohan Zhang
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| |
Collapse
|
37
|
Williams A, Menon S, Crowe M, Agarwal N, Biccler J, Bbosa N, Ssemwanga D, Adungo F, Moecklinghoff C, Macartney M, Oriol-Mathieu V. Geographic and Population Distributions of Human Immunodeficiency Virus (HIV)-1 and HIV-2 Circulating Subtypes: A Systematic Literature Review and Meta-analysis (2010-2021). J Infect Dis 2023; 228:1583-1591. [PMID: 37592824 PMCID: PMC10681860 DOI: 10.1093/infdis/jiad327] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 07/13/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND HIV poses significant challenges for vaccine development due to its high genetic mutation and recombination rates. Understanding the distribution of HIV subtypes (clades) across regions and populations is crucial. In this study, a systematic review of the past decade was conducted to characterize HIV-1/HIV-2 subtypes. METHODS A comprehensive search was performed in PubMed, EMBASE, and CABI Global Health, yielding 454 studies from 91 countries. RESULTS Globally, circulating recombinant forms (CRFs)/unique recombinant forms (URFs) accounted for 29% of HIV-1 strains, followed by subtype C (23%) and subtype A (17%). Among studies reporting subtype breakdowns in key populations, 62% of HIV infections among men who have sex with men (MSM) and 38% among people who inject drugs (PWIDs) were CRF/URFs. Latin America and the Caribbean exhibited a 25% increase in other CRFs (excluding CRF01_AE or CRF02_AG) prevalence between 2010-2015 and 2016-2021. CONCLUSIONS This review underscores the global distribution of HIV subtypes, with an increasing prevalence of CRFs and a lower prevalence of subtype C. Data on HIV-2 were limited. Understanding subtype diversity is crucial for vaccine development, which need to elicit immune responses capable of targeting various subtypes. Further research is needed to enhance our knowledge and address the challenges posed by HIV subtype diversity.
Collapse
Affiliation(s)
| | - Sonia Menon
- P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium
| | - Madeleine Crowe
- P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium
| | - Neha Agarwal
- P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium
| | - Jorne Biccler
- P95 Pharmacovigilance and Epidemiological Services, Leuven, Belgium
| | - Nicholas Bbosa
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe
| | | | | | | | | |
Collapse
|
38
|
Antonova A, Kazennova E, Lebedev A, Ozhmegova E, Kuznetsova A, Tumanov A, Bobkova M. Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation. Viruses 2023; 15:2312. [PMID: 38140553 PMCID: PMC10748268 DOI: 10.3390/v15122312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, HIV-1 displays a substantial level of genetic diversity on a global scale, partly attributed to its recombinant variants. This study seeks to identify and analyze HIV-1 recombinants in Russia during the last decade of the epidemic. A comprehensive examination was conducted, encompassing 3178 partial pol sequences. Subtyping was achieved through various programs including COMET, the Stanford Database, REGA, jpHMM, RIP, and RDP4 for recombination analysis. The study also involved phylogenetic analysis to trace the origins of the identified recombinants. Primary resistance (PrimDR) prevalence and Drug Resistance Mutations (DRMs) were assessed. The study uncovered an overall proportion of recombinants at 8.7%, with a statistically significant increase in their frequency observed over time (p < 0.001). The Northwestern (18.5%) and Siberian (15.0%) Federal Districts exhibited a high prevalence of recombinants, while the Volga (1.9%) and Ural (2.8%) Federal Districts had a lower prevalence. Among HIV-1 recombinants, a PrimDR prevalence of 11.4% was identified. Notably, significant differences in DRMs were observed, with a higher prevalence of M184V in sub-subtype A6 (p = 0.018) and K103N in CRF63_02A6 (p = 0.002). These findings underscore the increasing HIV-1 genetic diversity and highlight a substantial prevalence of PrimDR among its recombinant forms, emphasizing the necessity for ongoing systematic monitoring.
Collapse
Affiliation(s)
- Anastasiia Antonova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Elena Kazennova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksey Lebedev
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Ekaterina Ozhmegova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Anna Kuznetsova
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Aleksandr Tumanov
- The National Research Center for Epidemiology and Microbiology Named after Honorary Academician N.F. Gamaleya of the Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (E.K.); (A.L.); (E.O.); (A.K.); (A.T.)
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia;
| |
Collapse
|
39
|
Weibull Wärnberg A, Brännström J, Elvstam O, Gisslén M, Månsson F, Sönnerborg A, van de Klundert MA. The molecular epidemiology of HIV-1 in Sweden 1996 to 2022, and the influence of migration from Ukraine. Euro Surveill 2023; 28:2300224. [PMID: 38037731 PMCID: PMC10690863 DOI: 10.2807/1560-7917.es.2023.28.48.2300224] [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: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023] Open
Abstract
BackgroundThe global distribution of HIV-1 subtypes is evolving, which is reflected in the Swedish HIV cohort. The subtype HIV-1A6, which may be prone to developing resistance to cabotegravir, is the most common subtype in Ukraine.AimWe aimed to examine trends in HIV-1 subtype distribution in Sweden, with a special focus on HIV-1A6, and to describe the virology, demography and treatment of Ukrainian people living with HIV (PLWH) who migrated to Sweden in 2022.MethodsData about PLWH in Sweden are included in a national database (InfCareHIV). We used the online tool COMET to establish HIV-1 subtypes and the Stanford database to define drug resistance mutations. We investigated the relation between virological characteristics and demographic data.ResultsThe early epidemic was predominated by HIV-1 subtype B infections in people born in Sweden. After 1990, the majority of new PLWH in Sweden were PLWH migrating to Sweden, resulting in an increasingly diverse epidemic. In 2022, HIV-1A6 had become the sixth most common subtype in Sweden and 98 of the 431 new PLWH that were registered in Sweden came from Ukraine. We detected HIV RNA in plasma of 32 Ukrainian patients (34%), of whom 17 were previously undiagnosed, 10 had interrupted therapy and five were previously diagnosed but not treated. We found HIV-1A6 in 23 of 24 sequenced patients.ConclusionThe molecular HIV epidemiology in Sweden continues to diversify and PLWH unaware of their HIV status and predominance of HIV-1A6 should be considered when arranging care directed at PLWH from Ukraine.
Collapse
Affiliation(s)
- Anna Weibull Wärnberg
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Brännström
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Södersjukhuset, Stockholm, Sweden
| | - Olof Elvstam
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö
- Department of Infectious Diseases, Växjö Central Hospital, Växjö, Sweden
| | - Magnus Gisslén
- Region Västra Götaland, Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Månsson
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maarten Aa van de Klundert
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
40
|
Priyanka, Abusalah MAH, Chopra H, Sharma A, Mustafa SA, Choudhary OP, Sharma M, Dhawan M, Khosla R, Loshali A, Sundriyal A, Saini J. Nanovaccines: A game changing approach in the fight against infectious diseases. Biomed Pharmacother 2023; 167:115597. [PMID: 37783148 DOI: 10.1016/j.biopha.2023.115597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
The field of nanotechnology has revolutionised global attempts to prevent, treat, and eradicate infectious diseases in the foreseen future. Nanovaccines have proven to be a valuable pawn in this novel technology. Nanovaccines are made up of nanoparticles that are associated with or prepared with components that can stimulate the host's immune system. In addition to their delivery capabilities, the nanocarriers have been demonstrated to possess intrinsic adjuvant properties, working as immune cell stimulators. Thus, nanovaccines have the potential to promote rapid as well as long-lasting humoral and cellular immunity. The nanovaccines have several possible benefits, including site-specific antigen delivery, increased antigen bioavailability, and a diminished adverse effect profile. To avail these benefits, several nanoparticle-based vaccines are being developed, including virus-like particles, liposomes, polymeric nanoparticles, nanogels, lipid nanoparticles, emulsion vaccines, exomes, and inorganic nanoparticles. Inspired by their distinctive properties, researchers are working on the development of nanovaccines for a variety of applications, such as cancer immunotherapy and infectious diseases. Although a few challenges still need to be overcome, such as modulation of the nanoparticle pharmacokinetics to avoid rapid elimination from the bloodstream by the reticuloendothelial system, The future prospects of this technology are also assuring, with multiple options such as personalised vaccines, needle-free formulations, and combination nanovaccines with several promising candidates.
Collapse
Affiliation(s)
- Priyanka
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda 151103, Punjab, India
| | - Mai Abdel Haleem Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Hitesh Chopra
- Department of Biosciences, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Abhilasha Sharma
- Department of Life Science, Gujarat University, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat, India
| | - Suhad Asad Mustafa
- Scientific Research Center/ Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda 151103, Punjab, India.
| | - Manish Sharma
- University Institute of Biotechnology, Department of Biotechnology, Chandigarh University, Mohali 140413, Punjab, India
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, Punjab, India; Trafford College, Altrincham, Manchester WA14 5PQ, UK.
| | - Rajiv Khosla
- Department of Biotechnology, Doaba College, Jalandhar 144004, Punjab, India
| | - Aanchal Loshali
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Ankush Sundriyal
- School of Pharmaceutical Sciences and Research, Sardar Bhagwan Singh University, Balawala, Dehradun 248001, India
| | - Jyoti Saini
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda 151103, Punjab, India
| |
Collapse
|
41
|
Togna Pabo WLR, Fokam J, Njume D, Takou D, Santoro MM, Nyasa RB, Chenwi C, Mpouel ML, Beloumou G, Jagni ESN, Nka AD, Ka’e AC, Teto G, Dambaya B, Djupsa S, Gouissi Anguechia DH, Evariste M, Kamta C, Bala L, Lambo V, Halle-Ekane EG, Colizzi V, Perno CF, Ndjolo A, Ndip Ndip R. HIV-1 subtype diversity and immuno-virological outcomes among adolescents failing antiretroviral therapy in Cameroon: A cohort study. PLoS One 2023; 18:e0293326. [PMID: 37878637 PMCID: PMC10599502 DOI: 10.1371/journal.pone.0293326] [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: 11/30/2022] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVE We sought to evaluate the variability of HIV-1 and its effect on immuno-virological response among adolescents living with perinatally acquired HIV (APHI). METHODS A cohort study was conducted from 2018-2020 among 311 APHI receiving antiretroviral therapy (ART) in Cameroon. Sequencing of protease and reverse transcriptase regions was performed for participants experiencing virological failure, VF, (Plasma viral load, PVL ≥ 1000 RNA copies/ml). HIV-1 subtypes were inferred by phylogeny; immuno-virological responses were monitored at 3-time points (T1-T3). Cox regression modeling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4 < 250, and PVL > 5log10, adjusted for acquired drug resistance, gender, ART line, adherence, and duration on treatment; p < 0.05 was considered statistically significant. RESULTS Of the 141 participants in VF enrolled, the male-female ratio was 1:1; mean age was 15 (±3) years; and median [IQR] duration on ART was 51 [46-60] months. In all phases, 17 viral clades were found with a predominant CRF02_AG (58.2%, 59.4%, and 58.3%). From T1-T3 respectively, there was an increasing CD4 count (213 [154-313], 366 [309-469], and 438 [364-569] cells/mm3) and decline log10 PVL (5.23, 4.43, and 4.43), similar across subtypes. Among participants with CRF02_AG infection, duration of treatment was significantly associated with both rates of progression to CD4 < 250, and PVL > 5log10, aHR = 0.02 (0.001-0.52), and aHR = 0.05 (0.01-0.47) respectively. Moreover, four potential new HIV-1 recombinants were identified (CRF02_AG/02D, CRF02_AG/02A1F2, D/CRF02_AG, and AF2/CRF02_AG), indicating a wide viral diversity. CONCLUSION Among APHI in settings like Cameroon, there is a wide genetic diversity of HIV-1, driven by CRF02_AG and with potential novel clades due to ongoing recombination events. Duration of treatment significantly reduces the risk of disease progression.
Collapse
Affiliation(s)
- Willy Le roi Togna Pabo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Science, University of Buea, Buea, Cameroon
| | - Joseph Fokam
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
- National HIV Drug Resistance Group, Ministry of Public Health, Yaoundé, Cameroon
| | - Debimeh Njume
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
- Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Désiré Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | | | | | - Collins Chenwi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Marie Laure Mpouel
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Grace Beloumou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Ezechiel Semengue Ngoufack Jagni
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Alex Durand Nka
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Aude Christelle Ka’e
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
| | - Georges Teto
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Beatrice Dambaya
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Sandrine Djupsa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | - Davy Hyacinthe Gouissi Anguechia
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | - Molimbou Evariste
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
| | | | - Lionel Bala
- Mbalmayo District Hospital, Mbalmayo, Cameroon
| | | | | | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Evangelic University of Cameroon, Bandjoun, Cameroon
| | - Carlo Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- University of Rome Tor Vergata, Rome, Italy
- Bambino Gesu Pediatric Hospital, Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, Yaoundé, Cameroon
| | | |
Collapse
|
42
|
Parkin N, Harrigan PR, Inzaule S, Bertagnolio S. Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001948. [PMID: 37851634 PMCID: PMC10584185 DOI: 10.1371/journal.pgph.0001948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Resistance to antiretroviral drugs used to treat HIV is an important and evolving concern, particularly in low- and middle-income countries (LMICs) which have been impacted to the greatest extent by the HIV pandemic. Efforts to monitor the emergence and transmission of resistance over the past decade have shown that drug resistance-especially to the nucleoside analogue and non-nucleoside reverse transcriptase inhibitors-can (and have) increased to levels that can jeopardize the efficacy of available treatment options at the population level. The global shift to integrase-based regimens as the preferred first-line therapy as well as technological advancements in the methods for detecting resistance have had an impact in broadening and diversifying the landscape of and use case for HIV drug resistance testing. This review estimates the potential demand for HIV drug resistance tests, and surveys current testing methodologies, with a focus on their application in LMICs.
Collapse
Affiliation(s)
- Neil Parkin
- Data First Consulting, Sebastopol, CA, United States of America
| | - P. Richard Harrigan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, and Department of Global Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | |
Collapse
|
43
|
Roshanfekr P, Karimi SE, Narouee S, Moftakhar L, Vameghi M, Ali D, Higgs P, Soleimanvandiazar N. Life-time HIV testing among people who inject drugs in Iran: results from the National Rapid Assessment and Response survey. Front Public Health 2023; 11:1253407. [PMID: 37915820 PMCID: PMC10616789 DOI: 10.3389/fpubh.2023.1253407] [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: 07/05/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
Background HIV testing is recommended for people who inject drugs (PWID). The aim of this study was to determine the prevalence of lifetime HIV testing among PWID and to better understand the predictors for HIV testing in a convenience sample across Iran. Materials and methods This study is a secondary analysis of Iran's National Rapid Assessment and Response survey conducted between October 2016 and March 2017. Analysis includes the 999 people who reported injecting drugs across the capital cities of 21 provinces. Data were collected by using the venue-based application of the Time Location Sampling (TLS) frame. Chi-square tests were used to examine the difference between HIV testing across different quantitative variables. Logistic regression was used to determine the predictors of life-time HIV testing. Analysis was performed using STATA V.12 software with a significance level of 95%. Results Most participants were male (n = 902, 93.50%), and over half (n = 555, 59.17%) were older than 35 years old. About one-third, (n = 326, 38%) of people interviewed were single and another one-third (n = 251, 29%) reported being divorced. Over two-thirds of participants (n = 678, 69.78%) in this study reported lifetime HIV testing. The results from a multiple variable logistic regression showed people with a university education were more likely to have been previously tested for HIV than illiterate people (OR = 18.87, 95%CI 2.85-124.6, value of p = 0.002). Those individuals who reported ever receiving methadone treatment were 2.8 times more likely to have been tested for HIV than individuals without methadone treatment experience (OR = 2.89, 95%CI 1.53-5.42, value of p < 0.001). Needle syringe sharing in last month, was negatively associated with life-time HIV testing (OR = 0.29, 95%CI 0.17-0.48, value of p < 0.001). Conclusion Despite Iran's wide availability and access to counseling services for HIV testing in key populations, the proportion of PWID being tested for HIV could be improved. Developing effective strategies to increase people's understanding and awareness of the importance of and need for HIV prevention and familiarity with HIV testing sites is an essential step in increasing HIV testing for this population. Studies on more recent HIV testing are required to better assess and understand the frequency of HIV testing among PWID in Iran.
Collapse
Affiliation(s)
- Payam Roshanfekr
- Social Welfare Management Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Salah Eddin Karimi
- Social Determinants of Health Research Center, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sakineh Narouee
- Department of Statistics and Epidemiology, Faculty of Health, Kerman University Medical of Sciences, Kerman, Iran
| | - Leila Moftakhar
- Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Meroe Vameghi
- Social Welfare Management Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Delaram Ali
- Social Welfare Management Research Center, Social Health Research Institute, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Peter Higgs
- Department of Public Health, La Trobe University, Melbourne, VIC, Australia
- Behaviours and Health Risks Program, Burnet Institute, Melbourne, VIC, Australia
| | - Neda Soleimanvandiazar
- Preventive Medicine and Public Health Research Center, Psychosocial Health Research Institute, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
44
|
Yucha R, Litchford ML, Fish CS, Yaffe ZA, Richardson BA, Maleche-Obimbo E, John-Stewart G, Wamalwa D, Overbaugh J, Lehman DA. Higher HIV-1 Env gp120-Specific Antibody-Dependent Cellular Cytotoxicity (ADCC) Activity Is Associated with Lower Levels of Defective HIV-1 Provirus. Viruses 2023; 15:2055. [PMID: 37896832 PMCID: PMC10611199 DOI: 10.3390/v15102055] [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: 09/11/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
A cure for HIV-1 (HIV) remains unrealized due to a reservoir of latently infected cells that persist during antiretroviral therapy (ART), with reservoir size associated with adverse health outcomes and inversely with time to viral rebound upon ART cessation. Once established during ART, the HIV reservoir decays minimally over time; thus, understanding factors that impact the size of the HIV reservoir near its establishment is key to improving the health of people living with HIV and for the development of novel cure strategies. Yet, to date, few correlates of HIV reservoir size have been identified, particularly in pediatric populations. Here, we employed a cross-subtype intact proviral DNA assay (CS-IPDA) to quantify HIV provirus between one- and two-years post-ART initiation in a cohort of Kenyan children (n = 72), which had a median of 99 intact (range: 0-2469), 1340 defective (range: 172-3.84 × 104), and 1729 total (range: 178-5.11 × 104) HIV proviral copies per one million T cells. Additionally, pre-ART plasma was tested for HIV Env-specific antibody-dependent cellular cytotoxicity (ADCC) activity. We found that pre-ART gp120-specific ADCC activity inversely correlated with defective provirus levels (n = 68, r = -0.285, p = 0.0214) but not the intact reservoir (n = 68, r = -0.0321, p-value = 0.800). Pre-ART gp41-specific ADCC did not significantly correlate with either proviral population (n = 68; intact: r = -0.0512, p-value = 0.686; defective: r = -0.109, p-value = 0.389). This suggests specific host immune factors prior to ART initiation can impact proviruses that persist during ART.
Collapse
Affiliation(s)
- Ryan Yucha
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Morgan L. Litchford
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zak A. Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi P.O. Box 30197, Kenya
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
45
|
Su C, Ma Y, Liang H, Huang A, Deng W, Zhou J, Liu H. ART and Serum albumin are influencing factors of the 5-year survival rate of people living with HIV undergoing maintenance hemodialysis caused by HIV: A cohort study. Medicine (Baltimore) 2023; 102:e35494. [PMID: 37800798 PMCID: PMC10553035 DOI: 10.1097/md.0000000000035494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection is one of the most prominent public health problems worldwide. The 5-year survival rate of people living with HIV undergoing maintenance hemodialysis (MHD) and the factors related to the survival rate have not been widely studied. This study calculated the 5-year survival rate of people living with HIV who were undergoing MHD and determined the risk factors that may affect the 5-year survival rate. All enrolled participants were followed up for more than 5 years from the first round of MHD. The survival rate of them was calculated, the Cox proportional hazards model was used for multivariate analysis, the Kaplan-Meier method was used to draw the survival curve, and the log-rank test was used to compare the survival time of different groups. A total of 121 participants were included in the study. Statistical analysis showed that the overall 5-year survival rate was 19.0%. The 6-, 12-, 24-, and 36-month survival rates were 71.90%, 56.20%, 41.32%, and 30.58%, respectively. Infection was the leading cause of death, accounting for 55.37%. The Cox proportional hazards model revealed that antiretroviral therapy (ART) and the serum albumin level after dialysis were independent protective factors for patient survival. The log-rank test showed that there was a significant difference in survival time between the ART and non-ART groups.
Collapse
Affiliation(s)
- Chunxiong Su
- Department of Blood Purification, the Fourth People’s Hospital of Nanning, Guangxi (Guangxi AIDS Clinical Treatment Center), Nanning, China
| | - Yuting Ma
- Department of Traditional Chinese Medicine, the Fourth People’s Hospital of Nanning, Guangxi (Guangxi AIDS Clinical Treatment Center), Nanning, China
| | - Huiping Liang
- Department of Medicine, GuangXi Medical College, Nanning, China
| | - Aixian Huang
- Department of Blood Purification, the Fourth People’s Hospital of Nanning, Guangxi (Guangxi AIDS Clinical Treatment Center), Nanning, China
| | - Wenhai Deng
- Department of Blood Purification, the Fourth People’s Hospital of Nanning, Guangxi (Guangxi AIDS Clinical Treatment Center), Nanning, China
| | - Jia Zhou
- Department of Blood Purification, the Fourth People’s Hospital of Nanning, Guangxi (Guangxi AIDS Clinical Treatment Center), Nanning, China
| | - Huaying Liu
- Department of Medicine, GuangXi Medical College, Nanning, China
| |
Collapse
|
46
|
De Castro N, Chazallon C, Brites C, Messou E, Khosa C, Laureillard D, Chau GD, Pilotto JH, Eholié S, Delaugerre C, Molina JM, Wittkop L, Grinsztejn B, Marcy O. Virologic response to antiretroviral therapy in people with HIV and tuberculosis in high tuberculosis burden countries. AIDS 2023; 37:1837-1842. [PMID: 36928120 DOI: 10.1097/qad.0000000000003521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
OBJECTIVE We sought to compare virologic outcomes on antiretroviral therapy (ART) between people with HIV (PWH) also treated for tuberculosis in the different countries who participated to two randomized trials. DESIGN Pooled analysis of two randomized clinical trials. METHODS In the phase II Reflate TB and phase III Reflate TB2 trials conducted in Brazil, Côte d'Ivoire, Mozambique and Vietnam, ART-naïve PWH treated for tuberculosis were randomized to receive raltegravir or efavirenz. We assessed country differences in baseline characteristic using Wilcoxon tests and chi-square, or Fisher's exact test. We used logistic regression to analyze determinants of virologic success, defined as week-48 plasma HIV-1 RNA <50 copies/ml. RESULTS Of 550 participants (140 from Brazil, 170 from Côte d'Ivoire, 129 from Mozambique and 111 from Vietnam) with median baseline HIV-1 RNA of 5.4 log 10 copies/ml, 362 (65.8%) achieved virologic success at week 48. Virologic success rates were: 105/140 (75.0%) in Brazil, 99/170 (58.2%) in Côte d'Ivoire, 84/129 (65.1%) in Mozambique and 74/111 (66.7%) in Vietnam ( P = 0.0233). Baseline HIV-1 RNA, but not the country, was independently associated with virologic success: baseline HIV-1 RNA ≥500 000 copies/ml (reference), HIV RNA <100 000 copies/ml odds ratio 3.12 [95% confidence interval (CI) 1.94; 5.01] and HIV-1 RNA 100 000-499 999 copies/ml odds ratio: 1.80 (95% CI 1.19; 2.73). Overall, 177/277 (63.9%) patients treated with raltegravir and 185/273 (67.9%) patients treated with efavirenz had a plasma HIV-1 RNA <50 copies/ml at week 48. CONCLUSIONS Virologic response to antiretroviral therapy in PWH with TB varied across countries but was mainly driven by levels of pretreatment HIV-1 RNA.
Collapse
Affiliation(s)
- Nathalie De Castro
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
- Infectious Diseases Department, AP-HP-Hôpital Saint-Louis Lariboisière, Paris, France
| | - Corine Chazallon
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
| | - Carlos Brites
- Laboratório de Pesquisa em Doenças Infecciosas, Hospital Universitário Prof Edgar Santos, Bahia, Brazil
| | - Eugène Messou
- Programme PACCI/ANRS Research Center
- Centre de Prise en Charge de Recherche et de Formation, CePReF-Aconda-VS, Abidjan, Cote D'Ivoire
- Département de Dermatologie et d'Infectiologie, UFR des Sciences Médicales, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Celso Khosa
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Didier Laureillard
- Department of Infectious and Tropical Diseases, Nimes University Hospital, Nimes
- Research Unit 1058, Pathogenesis and Control Chronical Infections, INSERM, French Blood Center, University of Montpellier, Montpellier, France
| | - Giang D Chau
- Pham Ngoc Thach Hospital, Ho Chi Minh City, Vietnam
| | - José H Pilotto
- Laboratorio de AIDS e Imunologia Molecular-IOC/Fiocruz, Rio de Janeiro, Brazil
| | - Serge Eholié
- Programme PACCI/ANRS Research Center
- Département de Dermatologie et d'Infectiologie, UFR des Sciences Médicales, Université Félix Houphouët Boigny, Abidjan, Cote d'Ivoire
| | - Constance Delaugerre
- Virology department, APHP-Hôpital Saint-Louis
- INSERM U944
- Université Paris Cité, Paris
| | - Jean-Michel Molina
- Infectious Diseases Department, AP-HP-Hôpital Saint-Louis Lariboisière, Paris, France
- INSERM U944
- Université Paris Cité, Paris
| | - Linda Wittkop
- University Bordeaux, INSERM, Institut Bergonié, Bordeaux
- INRIA SISTM team, Talence
- CHU de Bordeaux, Service d'information médicale, INSERM, Institut Bergonié, Bordeaux, France
| | - Beatriz Grinsztejn
- National Institute of Infectious Diseases Evandro Chagas, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Olivier Marcy
- University of Bordeaux, National Institute for Health and Medical Research (INSERM) UMR 1219, Research Institute for Sustainable Development (IRD) EMR 271, Bordeaux Population Health Centre, Bordeaux, France
| |
Collapse
|
47
|
Ostankova YV, Shchemelev AN, Thu HHK, Davydenko VS, Reingardt DE, Serikova EN, Zueva EB, Totolian AA. HIV Drug Resistance Mutations and Subtype Profiles among Pregnant Women of Ho Chi Minh City, South Vietnam. Viruses 2023; 15:2008. [PMID: 37896785 PMCID: PMC10612098 DOI: 10.3390/v15102008] [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: 09/03/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
According to the latest data released by UNAIDS, the global number of people living with HIV (PLHIV) in 2021 was 38.4 million, with 1.5 million new HIV infections. In different countries, a significant proportion of these cases occur in the adult fertile population aged 15-49 years. According to UNAIDS, Vietnam had a national HIV prevalence of 0.3% of the total population at the end of 2019, with approximately 230,000 PLHIV. The most effective way to prevent mother-to-child transmission of HIV is ART to reduce maternal viral load. HIV-infected pregnant women should undergo monthly monitoring, especially before the expected date of delivery. The aim of our work was to analyze subtypic structure and drug-resistant variants of HIV in pregnant women in Ho Chi Minh City. The study material was blood plasma samples from HIV-infected pregnant women: 31 women showed virological failure of ART, and 30 women had not previously received therapy. HIV-1 genotyping and mutation detection were performed based on analysis of the nucleotide sequences of the pol gene region. More than 98% of sequences genotyped as HIV-1 sub-subtype CRF01_AE. When assessing the occurrence of drug resistance mutations, genetic resistance to any drug was detected in 74.41% (95% CI: 62.71-85.54%) of patients. These included resistance mutations to protease inhibitors in 60.66% (95% CI: 47.31-72.93%) of patients, to NRTIs in 8.20% (95% CI: 2.72-18.10%), and to NNRTIs in 44.26% (95% CI: 31.55-57.52%). Mutations associated with NRTI (2) and NNRTI (8) resistance as well as PI mutations (12), including minor ones, were identified. The high prevalence of drug resistance mutations found in this study among pregnant women, both in therapeutically naive individuals and in patients with virological failure of ART, indicates that currently used regimens in Vietnam are insufficient to prevent vertical HIV infection.
Collapse
Affiliation(s)
- Yulia V. Ostankova
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | | | | | | | - Diana E. Reingardt
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Elena N. Serikova
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Elena B. Zueva
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| | - Areg A. Totolian
- Saint Petersburg Pasteur Institute, 19710 St. Petersburg, Russia; (Y.V.O.)
| |
Collapse
|
48
|
Bekker LG, Beyrer C, Mgodi N, Lewin SR, Delany-Moretlwe S, Taiwo B, Masters MC, Lazarus JV. HIV infection. Nat Rev Dis Primers 2023; 9:42. [PMID: 37591865 DOI: 10.1038/s41572-023-00452-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/19/2023]
Abstract
The AIDS epidemic has been a global public health issue for more than 40 years and has resulted in ~40 million deaths. AIDS is caused by the retrovirus, HIV-1, which is transmitted via body fluids and secretions. After infection, the virus invades host cells by attaching to CD4 receptors and thereafter one of two major chemokine coreceptors, CCR5 or CXCR4, destroying the host cell, most often a T lymphocyte, as it replicates. If unchecked this can lead to an immune-deficient state and demise over a period of ~2-10 years. The discovery and global roll-out of rapid diagnostics and effective antiretroviral therapy led to a large reduction in mortality and morbidity and to an expanding group of individuals requiring lifelong viral suppressive therapy. Viral suppression eliminates sexual transmission of the virus and greatly improves health outcomes. HIV infection, although still stigmatized, is now a chronic and manageable condition. Ultimate epidemic control will require prevention and treatment to be made available, affordable and accessible for all. Furthermore, the focus should be heavily oriented towards long-term well-being, care for multimorbidity and good quality of life. Intense research efforts continue for therapeutic and/or preventive vaccines, novel immunotherapies and a cure.
Collapse
Affiliation(s)
- Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, RSA, Cape Town, South Africa.
| | - Chris Beyrer
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Nyaradzo Mgodi
- University of Zimbabwe Clinical Trials Research Centre, Harare, Zimbabwe
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | | | - Babafemi Taiwo
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Mary Clare Masters
- Division of Infectious Diseases, Northwestern University, Chicago, IL, USA
| | - Jeffrey V Lazarus
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic, University of Barcelona, Barcelona, Spain
| |
Collapse
|
49
|
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.
Collapse
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.
| |
Collapse
|
50
|
Nkoy AB, Ekulu PM, Labarque V, Van den Heuvel LP, Levtchenko EN. HIV-associated nephropathy in children: challenges in a resource-limited setting. Pediatr Nephrol 2023; 38:2509-2521. [PMID: 36472655 DOI: 10.1007/s00467-022-05819-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
HIV infection remains one of the leading causes of morbidity and mortality worldwide, especially in children living in resource-limited settings. Although the World Health Organization (WHO) recently recommended antiretroviral therapy (ART) initiation upon diagnosis regardless of the number of CD4, ART access remains limited, especially in children living in sub-Saharan Africa (SSA). HIV-infected children who do not receive appropriate ART are at increased risk of developing HIV-associated nephropathy (HIVAN). Although due to genetic susceptibility, SSA is recognized to be the epicenter of HIVAN, limited information is available regarding the burden of HIVAN in children living in Africa. The present review discusses the information available to date on the prevalence, pathogenesis, risk factors, diagnosis, and management of HIVAN in children, focusing on related challenges in a resource-limited setting.
Collapse
Affiliation(s)
- Agathe B Nkoy
- Division of Nephrology, Department of Pediatrics, University Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of Congo
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Pépé M Ekulu
- Division of Nephrology, Department of Pediatrics, University Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Veerle Labarque
- Department of Pediatric Hematology, University Hospital Leuven, Leuven, Belgium
- Center of Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lambertus P Van den Heuvel
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Pediatric Nephrology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Elena N Levtchenko
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium.
- Department of Pediatric Nephrology, University Hospital Leuven, Leuven, Belgium.
| |
Collapse
|