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Kotokwe K, Moyo S, Zahralban-Steele M, Holme MP, Melamu P, Koofhethile CK, Choga WT, Mohammed T, Nkhisang T, Mokaleng B, Maruapula D, Ditlhako T, Bareng O, Mokgethi P, Boleo C, Makhema J, Lockman S, Essex M, Ragonnet-Cronin M, Novitsky V, Gaseitsiwe S. Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana. Viruses 2023; 15:403. [PMID: 36851617 PMCID: PMC9963705 DOI: 10.3390/v15020403] [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: 12/31/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
It remains unknown whether the C-C motif chemokine receptor type 5 (CCR5) coreceptor is still the predominant coreceptor used by Human Immunodeficiency Virus-1 (HIV-1) in Botswana, where the HIV-1 subtype C predominates. We sought to determine HIV-1C tropism in Botswana using genotypic tools, taking into account the effect of antiretroviral treatment (ART) and virologic suppression. HIV-1 gp120 V3 loop sequences from 5602 participants were analyzed for viral tropism using three coreceptor use predicting algorithms/tools: Geno2pheno, HIV-1C Web Position-Specific Score Matrices (WebPSSM) and the 11/25 charge rule. We then compared the demographic and clinical characteristics of people living with HIV (PLWH) harboring R5- versus X4-tropic viruses using χ2 and Wilcoxon rank sum tests for categorical and continuous data analysis, respectively. The three tools congruently predicted 64% of viruses as either R5-tropic or X4-tropic. Geno2pheno and the 11/25 charge rule had the highest concordance at 89%. We observed a significant difference in ART status between participants harboring X4- versus R5-tropic viruses. X4-tropic viruses were more frequent among PLWH receiving ART (χ2 test, p = 0.03). CCR5 is the predominant coreceptor used by HIV-1C strains circulating in Botswana, underlining the strong potential for CCR5 inhibitor use, even in PLWH with drug resistance. We suggest that the tools for coreceptor prediction should be used in combination.
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Affiliation(s)
- Kenanao Kotokwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Melissa Zahralban-Steele
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Molly Pretorius Holme
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Pinkie Melamu
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Catherine Kegakilwe Koofhethile
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | | | - Terence Mohammed
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tapiwa Nkhisang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Tsotlhe Ditlhako
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Ontlametse Bareng
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Patrick Mokgethi
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Corretah Boleo
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Manon Ragonnet-Cronin
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
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Rodgers MA, Gomathi S, Vallari A, Saravanan S, Lucas GM, Mehta S, Solomon SS, Cloherty GA. Diverse HCV Strains And HIV URFS Identified Amongst People Who Inject Drugs In India. Sci Rep 2020; 10:7214. [PMID: 32350342 PMCID: PMC7190742 DOI: 10.1038/s41598-020-64309-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/27/2020] [Indexed: 12/22/2022] Open
Abstract
Although the prevalences of HIV and HCV are significantly higher amongst PWID in India compared to the general population, the strains circulating within this group have not been well-characterized. Through subgenomic sequencing of viruses present in residual plasma from an HIV/HCV prevalence study conducted amongst PWID across five cities in India in 2016-2017, a total of N = 498 HCV and N = 755 HIV strains were classified from N = 975 study participants. Considerable HCV diversity was identified, with different strains predominating in each region of the country. Overall, the most common strain was genotype 3a (39.0%), with genotypes 1a (26.9%), 1b (3.0%), 1c (0.2%), 3b (20.7%), 3i (2.0%), 4a (0.2%), 4d (1.0%), 6 (1.8%), 6n (4.8%), 6 v (0.2%) and one unclassifiable recombinant specimen (0.2%) also identified. The majority of the HIV specimens were subtype C (96.7%), although subtype A (0.4%), CRF01_AE (0.4%) and unique recombinant forms (URFs, 2.5%) were also detected. Notably, the geographical restriction of HIV subtype A and CRF01_AE, and HCV genotypes 4 and 6 to specific sites suggests distinct novel introductions of HIV and HCV into PWID populations, potentially via drug trafficking routes from neighboring countries where these strains are common.
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Affiliation(s)
- Mary A Rodgers
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA.
| | | | - Ana Vallari
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA
| | | | | | - Shruti Mehta
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Sunil S Solomon
- YR Gaitonde Centre for AIDS Research and Education, Chennai, India
- Johns Hopkins University School of Medicine, Baltimore, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Gavin A Cloherty
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, USA
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Makhdoomi MA, Khan L, Kumar S, Aggarwal H, Singh R, Lodha R, Singla M, Das BK, Kabra SK, Luthra K. Evolution of cross-neutralizing antibodies and mapping epitope specificity in plasma of chronic HIV-1-infected antiretroviral therapy-naïve children from India. J Gen Virol 2017; 98:1879-1891. [PMID: 28696188 DOI: 10.1099/jgv.0.000824] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Delineating the factors leading to the development of broadly neutralizing antibodies (bnAbs) during natural HIV-1 infection and dissecting their epitope specificities generates useful information for vaccine design. This is the first longitudinal study to assess the plasma-neutralizing antibody response and neutralizing determinants in HIV-1-infected children from India. We enrolled 26 and followed up 20 antiretroviral therapy (ART)-naïve, asymptomatic, chronic HIV-1-infected children. Five (19.2 %) baseline and 10 (50 %) follow-up plasma samples neutralized ≥50 % of subtypes A, B and C tier 2 viruses at an ID50 titre ≥150. A modest improvement in neutralization breadth and potency was observed with time. At baseline, subtype C-specific neutralization predominated (P=0.026); interestingly, follow-up samples exhibited cross-neutralizing activity. Epitope mapping revealed V3C reactive antibodies with significantly increased Max50 binding titres in follow-up samples from five infected children; patient #4's plasma antibodies exhibited V3-directed neutralization. A salient observation was the presence of CD4 binding site (CD4bs)-specific NAbs in patient #18 that improved with time (1.76-fold). The RSC3 wild-type (RSC3WT) protein-depleted plasma eluate of patient #18 demonstrated a more than 50% ID50 decrease in neutralization capacity against five HIV-1 pseudoviruses. Further, the presence of CD4bs-neutralizing determinants in patient #18's plasma was confirmed by the neutralizing activity demonstrated by the CD4bs-directed IgG fraction purified from this plasma, and competition with sCD4 against JRFLgp120, identifying this paediatric donor as a potential candidate for the isolation of CD4bs-directed bnAbs. Overall, we observed a relative increase in plasma-neutralizing activity with time in HIV-1-infected children, which suggests that the bnAbs evolve.
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Affiliation(s)
- Muzamil A Makhdoomi
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Lubina Khan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Heena Aggarwal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ravinder Singh
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Bimal K Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
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Khan L, Kumar R, Thiruvengadam R, Parray HA, Makhdoomi MA, Kumar S, Aggarwal H, Mohata M, Hussain AW, Das R, Varadarajan R, Bhattacharya J, Vajpayee M, Murugavel KG, Solomon S, Sinha S, Luthra K. Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library. Sci Rep 2017; 7:45163. [PMID: 28332627 PMCID: PMC5362912 DOI: 10.1038/srep45163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/15/2017] [Indexed: 11/30/2022] Open
Abstract
More than 50% of HIV-1 infection globally is caused by subtype_C viruses. Majority of the broadly neutralizing antibodies (bnAbs) targeting HIV-1 have been isolated from non-subtype_C infected donors. Mapping the epitope specificities of bnAbs provides useful information for vaccine design. Recombinant antibody technology enables generation of a large repertoire of monoclonals with diverse specificities. We constructed a phage recombinant single chain variable fragment (scFv) library with a diversity of 7.8 × 108 clones, using a novel strategy of pooling peripheral blood mononuclear cells (PBMCs) of six select HIV-1 chronically infected Indian donors whose plasma antibodies exhibited potent cross neutralization efficiency. The library was panned and screened by phage ELISA using trimeric recombinant proteins to identify viral envelope specific clones. Three scFv monoclonals D11, C11 and 1F6 selected from the library cross neutralized subtypes A, B and C viruses at concentrations ranging from 0.09 μg/mL to 100 μg/mL. The D11 and 1F6 scFvs competed with mAbs b12 and VRC01 demonstrating CD4bs specificity, while C11 demonstrated N332 specificity. This is the first study to identify cross neutralizing scFv monoclonals with CD4bs and N332 glycan specificities from India. Cross neutralizing anti-HIV-1 human scFv monoclonals can be potential candidates for passive immunotherapy and for guiding immunogen design.
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Affiliation(s)
- Lubina Khan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Hilal Ahmad Parray
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Heena Aggarwal
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Madhav Mohata
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Abdul Wahid Hussain
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Raksha Das
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Jayanta Bhattacharya
- HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.,International AIDS Vaccine initiative, USA
| | - Madhu Vajpayee
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - K G Murugavel
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Suniti Solomon
- Y.R. Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.,National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Makhdoomi MA, Singh D, Nair Pananghat A, Lodha R, Kabra SK, Luthra K. Neutralization resistant HIV-1 primary isolates from antiretroviral naïve chronically infected children in India. Virology 2016; 499:105-113. [PMID: 27643887 DOI: 10.1016/j.virol.2016.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 10/21/2022]
Abstract
Anti-HIV-1 broadly neutralizing antibodies (bnAbs) have been extensively tested against pesudoviruses of diverse strains. We generated and characterized HIV-1 primary isolates from antiretroviral naïve infected Indian children, and determined their susceptibility to known NAbs. All the 8 isolates belonged to subtype-C and were R5 tropic. Majority of these viruses were resistant to neutralization by NAbs, suggesting that the bnAbs, known to efficiently neutralize pseudoviruses (adult and pediatric) of different strains, are less effective against pediatric primary isolates. Interestingly, AIIMS_329 isolate displayed high susceptibility to neutralization by PG9 and PG16bnAbs, with IC50 titer of 1.3 and 0.97μg/ml, suggesting exposure of this epitope on this virus. All isolates except AIIMS_506 were neutralized by contemporaneous plasma antibodies. Our findings suggest that primary isolates, due to close resemblance to viruses in natural infection, should be used to evaluate NAbs as effective vaccine candidates in both children and adults.
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Affiliation(s)
| | - Deepti Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ambili Nair Pananghat
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India; Department of Biochemistry, Jamia Hamdard University, 110062 New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sushil Kumar Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India.
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Pandey SS, Cherian S, Thakar M, Paranjape RS. Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1. AIDS Res Hum Retroviruses 2016; 32:489-502. [PMID: 26756665 DOI: 10.1089/aid.2015.0207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
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Affiliation(s)
| | - Sarah Cherian
- Bioinformatics Group, National Institute of Virology (ICMR), Pune, India
| | - Madhuri Thakar
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
| | - Ramesh S. Paranjape
- Department of Immunology, National AIDS Research Institute (ICMR), Pune, India
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Etemad B, Ghulam-Smith M, Gonzalez O, White LF, Sagar M. Single genome amplification and standard bulk PCR yield HIV-1 envelope products with similar genotypic and phenotypic characteristics. J Virol Methods 2015; 214:46-53. [PMID: 25681527 DOI: 10.1016/j.jviromet.2015.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 01/25/2015] [Indexed: 11/19/2022]
Abstract
Recent studies suggest that single genome amplification (SGA) as compared to standard bulk PCR and virus stocks from 293T transfection versus short term passage in peripheral blood mononuclear cells (PBMC) yield a less biased representation of HIV-1 envelope characteristics. In 9 different subjects, genetic diversity, divergence, and population structure were not significantly different among SGA or bulk PCR amplified envelope V1-V3 segments. In these subjects, 293T transfection derived virus stocks with SGA or bulk PCR amplified envelopes have similar infectivity, replication kinetics, co-receptor usage, and neutralization susceptibility. While PBMC passage as compared to the 293T derived virus stocks had similar co-receptor usage, PBMC viruses were less neutralization susceptible to some specific antibodies. Our results suggest that the method of envelope sequence amplification, either SGA or bulk PCR, does not have a significant impact on the genotypic and phenotypic properties of the virus envelope quasispecies.
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Affiliation(s)
- Behzad Etemad
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Oscar Gonzalez
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Laura F White
- Boston University School of Public Health, Boston, MA, USA
| | - Manish Sagar
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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Andrabi R, Makhdoomi MA, Kumar R, Bala M, Parray H, Gupta A, Kotnala A, Thirumurthy V, Luthra K. Highly Efficient Neutralization by Plasma Antibodies from Human Immunodeficiency Virus Type-1 Infected Individuals on Antiretroviral Drug Therapy. J Clin Immunol 2014; 34:504-13. [DOI: 10.1007/s10875-014-0010-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 02/25/2014] [Indexed: 07/19/2023]
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