1
|
Pluta A, Rola-Łuszczak M, Hoffmann FG, Donnik I, Petropavlovskiy M, Kuźmak J. Genetic Variability of Bovine Leukemia Virus: Evidence of Dual Infection, Recombination and Quasi-Species. Pathogens 2024; 13:178. [PMID: 38392916 PMCID: PMC10893129 DOI: 10.3390/pathogens13020178] [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: 11/22/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
We have characterized the intrahost genetic variation in the bovine leukemia virus (BLV) by examining 16 BLV isolates originating from the Western Siberia-Tyumen and South Ural-Chelyabinsk regions of Russia. Our research focused on determining the genetic composition of an 804 bp fragment of the BLV env gene, encoding for the entire gp51 protein. The results provide the first indication of the quasi-species genetic nature of BLV infection and its relevance for genome-level variation. Furthermore, this is the first phylogenetic evidence for the existence of a dual infection with BLV strains belonging to different genotypes within the same host: G4 and G7. We identified eight cases of recombination between these two BLV genotypes. The detection of quasi-species with cases of dual infection and recombination indicated a higher potential of BLV for genetic variability at the intra-host level than was previously considered.
Collapse
Affiliation(s)
- Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.R.-Ł.); (J.K.)
| | - Marzena Rola-Łuszczak
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.R.-Ł.); (J.K.)
| | - Federico G. Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, USA
| | - Irina Donnik
- Ural State Agrarian University, Ekaterinburg 620075, Russia;
| | - Maxim Petropavlovskiy
- Ural Federal Agrarian Scientific Research Centre of the Ural Branch of the Russian Academy of Sciences, Ekaterinburg 620049, Russia;
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.R.-Ł.); (J.K.)
| |
Collapse
|
2
|
Mullick R, Sutar J, Hingankar N, Deshpande S, Thakar M, Sahay S, Ringe RP, Mukhopadhyay S, Patil A, Bichare S, Murugavel KG, Srikrishnan AK, Goyal R, Sok D, Bhattacharya J. Neutralization diversity of HIV-1 Indian subtype C envelopes obtained from cross sectional and followed up individuals against broadly neutralizing monoclonal antibodies having distinct gp120 specificities. Retrovirology 2021; 18:12. [PMID: 33990195 PMCID: PMC8120817 DOI: 10.1186/s12977-021-00556-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The potential use of the broadly neutralizing monoclonal antibodies (bnAbs) towards prophylaxis and treatment to HIV-1 is currently being explored. While a number of promising bnAbs have been discovered and a few of them have progressed towards clinical development, their extent of neutralization coverage with respect to global HIV-1 variants given the existence of genetically distinct subtypes and recombinants circulating globally is not clearly known. In the present study, we examined the variation in the neutralization susceptibility of pseudoviruses expressing 71 full length primary HIV-1 subtype C envs obtained from limited cross-sectional individuals over different time points against four bnAbs that target gp120 with distinct specificities: VRC01, CAP256-VRC26.25, PGDM1400 and PGT121. RESULTS We found significant variations in the susceptibility of Indian clade C to these four bnAbs. These variations were found to be distinct to that observed in African subtype C based on the existing datasets and concordant with their sequence diversity. Trend analysis indicated an increasing neutralization resistance observed over time with CAP25-VRC26.25, PGDM1400 and PGT121 when tested on pseudoviruses expressing envs obtained from 1999 to 2016. However, inconsistent trend in neutralization susceptibility was observed, when pseudoviruses expressing envs obtained from three followed up individuals were examined. Finally, through predictive analysis of the 98 Indian subtype C including those assessed in the present study by employing additive model implemented in CombiNAber ( http://www.hiv.lanl.gov ), we observed two possibilities where combinations of three bnAbs (VRC01/CAP56-VRC26.25/PGT121 and PGDM1400/CAP256-VRC26.25/PGT121) could achieve near 100% neutralization coverage. CONCLUSIONS Our findings not only indicate disparate intra-clade C genetic vis-à-vis neutralization diversities but also warrant the need for more comprehensive study using additional isolates towards comparing inter and intra-clade neutralization diversities which will be necessary for selecting the bnAb combinations suitable for optimal coverage of the region-specific HIV-1 circulating subtypes. Expanding these efforts is imperative for designing efficacious bnAb based intervention strategies for India as well as subtype C in general.
Collapse
Affiliation(s)
- Ranajoy Mullick
- HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India
- International AIDS Vaccine Initiative, New Delhi, India
| | - Jyoti Sutar
- HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India
- International AIDS Vaccine Initiative, New Delhi, India
| | - Nitin Hingankar
- HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India
| | - Suprit Deshpande
- HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India
| | - Madhuri Thakar
- ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | - Seema Sahay
- ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | - Rajesh P Ringe
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sampurna Mukhopadhyay
- ICMR-National AIDS Research Institute, Pune, Maharashtra, India
- , Mississauga, ON, L5B3Y9, Canada
| | - Ajit Patil
- ICMR-National AIDS Research Institute, Pune, Maharashtra, India
| | | | | | | | - Rajat Goyal
- International AIDS Vaccine Initiative, New Delhi, India
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Sciences & Technology Institute, Faridabad, Haryana, India.
- International AIDS Vaccine Initiative, New Delhi, India.
| |
Collapse
|
3
|
Das S, Bansal M, Bhattacharya J. Characterization of the membrane-bound form of the chimeric, B/C recombinant HIV-1 Env, LT5.J4b12C. J Gen Virol 2018; 99:1438-1443. [PMID: 30129918 DOI: 10.1099/jgv.0.001141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) diversity is a significant challenge in developing a vaccine against the virus. B/C recombinants have been found in India and other places but are the predominant clade prevalent in China. HIV-1 envelopes (Envs) are the target of broadly neutralizing antibodies (bNAbs) which develop spontaneously in some HIV-1 infected patients. It has been previously reported with efficiently cleaved clade A, B and C Envs that preferential binding of Envs to bNAbs as opposed to non-NAbs, a desirable property for immunogens, is correlated with efficient cleavage of the Env precursor polypeptide into constituent subunits. These Envs are suitable for designing immunogens as soluble proteins, virus-like particles or for delivery by viral vectors/plasmid DNA. However, a B/C recombinant Env with similar properties has not been reported. Here we show that the chimeric, recombinant B/C clade Env LT5.J4b12C is efficiently cleaved on the plasma membrane and selectively binds to bNAbs.
Collapse
Affiliation(s)
- Supratik Das
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Manish Bansal
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India
| | - Jayanta Bhattacharya
- 1THSTI-IAVI HIV Vaccine Design Program, Translational Health Science and Technology Institute, Faridabad-121001, Haryana, India.,2International AIDS Vaccine Initiative, New York, USA
| |
Collapse
|
4
|
Park SY, Love TMT, Reynell L, Yu C, Kang TM, Anastos K, DeHovitz J, Liu C, Kober KM, Cohen M, Mack WJ, Lee HY. The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards. Sci Rep 2017; 7:7480. [PMID: 28785052 PMCID: PMC5547093 DOI: 10.1038/s41598-017-07490-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022] Open
Abstract
HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. HIV incidence assay performance is evaluated via false recency rate (FRR) and mean duration of recent infection (MDRI). We conducted a meta-analysis of 438 incident and 305 chronic specimens' HIV envelope genes from a diverse global cohort. The genome similarity index (GSI) accurately characterized infection stage across diverse host and viral factors. All except one chronic specimen had GSIs below 0.67, yielding a FRR of 0.33 [0-0.98] %. We modeled the incidence assay biomarker dynamics with a logistic link function assuming individual variabilities in a Beta distribution. The GSI probability density function peaked close to 1 in early infection and 0 around two years post infection, yielding MDRI of 420 [361, 467] days. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 21 subjects who followed from HIV negative status. Both standardized residuals and Anderson-Darling tests showed that the test dataset was statistically consistent with the model biomarker dynamics. This is the first reported incidence assay meeting the optimal FRR and MDRI performance standards. Signatures of HIV gene diversification can allow precise cross-sectional surveillance with a desirable temporal range of incidence detection.
Collapse
Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Lucy Reynell
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Carl Yu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Tina Manzhu Kang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kathryn Anastos
- Department of Medicine, and Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States
| | - Jack DeHovitz
- Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
| | - Chenglong Liu
- Department of Medicine, Georgetown University, Washington, DC, United States
| | - Kord M Kober
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, United States
| | - Mardge Cohen
- Department of Medicine, Stroger Hospital, Chicago, IL, United States
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
| |
Collapse
|
5
|
Kumar R, Ozorowski G, Kumar V, Holden LG, Shrivastava T, Patil S, Deshpande S, Ward AB, Bhattacharya J. Characterization of a stable HIV-1 B/C recombinant, soluble, and trimeric envelope glycoprotein (Env) highly resistant to CD4-induced conformational changes. J Biol Chem 2017; 292:15849-15858. [PMID: 28743743 PMCID: PMC5612115 DOI: 10.1074/jbc.m117.803056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/22/2017] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 envelope (Env) is a glycoprotein consisting of a trimer of heterodimers containing gp120 and gp41 subunits that mediates virus entry and is a major target of broadly neutralizing antibodies (bnAbs) developed during infection in some individuals. The engagement of the HIV-1 gp120 glycoprotein to the host CD4 protein triggers conformational changes in gp120 that allow its binding to co-receptors and is necessary for virus entry to establish infection. Native-like HIV-1 Env immunogens representing distinct clades have been proposed to improve immunogenicity. In the present study, we examined the basis of resistance of an HIV-1 B/C recombinant Env (LT5.J4b12C) to non-neutralizing antibodies targeting CD4-induced Env epitopes in the presence of soluble CD4 (sCD4). Using native polyacrylamide gel shift assay and negative-stain EM, we found that the prefusion conformational state of LT5.J4b12C trimeric Env was largely unaffected in the presence of excess sCD4 with most Env trimers appearing to be in a ligand-free state. This resistance to CD4-induced conformational changes was associated with a lower affinity for CD4. Moreover, the LT5.J4b12C trimeric Env preferentially bound to the neutralizing antibodies compared with non-neutralizing antibodies. Taken together, we report on an HIV-1 B/C recombinant, native-like trimeric Env protein that is highly resistant to CD4-induced conformational changes but displays epitopes recognized by a diverse array of bnAbs. Such features make this B/C recombinant trimeric Env a useful addition to the pool of other recently identified native-like HIV-1 Env trimers suitable for use as antigenic bait for bnAb isolation, structural studies, and use as potential immunogens.
Collapse
Affiliation(s)
- Rajesh Kumar
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Vivek Kumar
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Lauren G Holden
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Tripti Shrivastava
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Shilpa Patil
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Suprit Deshpande
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Jayanta Bhattacharya
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India, .,International AIDS Vaccine Initiative, New York, New York 10004
| |
Collapse
|
6
|
Hussain SI, Panneerselvam N, Solomon S, Solomon SS, Adam K, Chandrasekaran E, Montefiori DC, Pachamuthu B. Broadly Neutralizing Antibody Responses in a Subset of HIV-1-Infected Individuals in Chennai, India. J Int Assoc Provid AIDS Care 2013; 16:201-208. [PMID: 23422744 DOI: 10.1177/1545109712467695] [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: 11/16/2022] Open
Abstract
Identification of broadly neutralizing antibodies (NAbs) generated during the course of HIV-1 infection is essential for effective HIV-1 vaccine design. The magnitude and breadth of neutralizing activity in the sera from 46 antiretroviral treatment-naive HIV-1 clade C-infected individuals was measured in a single round infection assay using TZM-bl cells and multisubtype panel of env-pseudotyped viruses. Higher levels of NAb response (NAb titer 500 to >40 000) were measured in these patients against tier 1 and tier 2 viruses. The average magnitude of the NAb responses of chronically infected individuals against heterologous viruses was consistently higher than the response observed from individuals with long-term nonprogressor ( P = .086). To conclude, high titers of HIV-1 cross-neutralizing activity were observed in the sera from a subset of HIV-1-infected individuals in Chennai, India. Additional studies of the epitopes recognized by these antibodies may facilitate the discovery of an effective vaccine immunogen.
Collapse
Affiliation(s)
- Syed Iqbal Hussain
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Nandagopal Panneerselvam
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Suniti Solomon
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | - Sunil S Solomon
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India.,2 Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Ezhilarasi Chandrasekaran
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| | | | - Balakrishnan Pachamuthu
- 1 YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services Hospital Campus, Taramani, Chennai, India
| |
Collapse
|