Molecular Characteristics of the Envelope of Vertically Transmitted HIV-1 Strains from Infants with HIV Infection

Ashokkumar, Manickam; Nesakumar, Manohar; Cheedarla, Narayaniah; Vidyavijayan, K K; Babu, Hemalatha; Tripathy, Srikanth; Hanna, Luke Elizabeth

doi:10.1089/aid.2016.0260

Cited by 9 publications

(10 citation statements)

References 41 publications

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“…Sequence alignment and analysis. Genotyping was performed using the method described previously (10). In brief, the gp120 sequence data were aligned using SeqScape software (v2.5) with the prescribed default parameters.…”

Section: Methodsmentioning

confidence: 99%

“…Nearly half of the global HIV infections are caused by the subtype C strain (HIV-1C), which is the most predominant among the nine pure HIV-1 subtypes and numerous unique and circulating recombinant forms (6). In India, approximately 2.1 million people were reported to be living with HIV in the middle of 2017 (UNAIDS global AIDS update, 2017), with more than 99% of infections being caused by HIV-1 subtype C (HIV-1C) strains alone (7)(8)(9)(10)(11). Despite the unique characteristics of HIV-1C, there are considerable differences in the features of viruses within the quasispecies, especially in the transmission efficiency of the virus in vivo.…”

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confidence: 99%

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Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

Ashokkumar

Aralaguppe

Tripathy

et al. 2018

J Virol

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Adequate information on the precise molecular and biological composition of the viral strains that establish HIV infection in the human host will provide effective means of immunization against HIV infection. In an attempt to identify the transmitted founder (TF) virus and differentiate the biological properties and infectious potential of the TF virus from those of the population of the early transmitted viruses, 250 patient-derived gp120 envelope glycoproteins were cloned in pMN-K7-Luc-IRESs-NefΔgp120 to obtain chimeric viruses. Samples were obtained from eight infants who had recently become infected with HIV through mother-to-child transmission (MTCT) and two adults who acquired infection through the heterosexual route and were in the chronic stage of infection. Among the 250 clones tested, 65 chimeric viruses were infectious, and all belonged to HIV-1 subtype C. The 65 clones were analyzed for molecular features of the envelope, per-infectious-particle infectivity, coreceptor tropism, drug sensitivity, and sensitivity to broadly neutralizing antibodies. Based on genotypic and phenotypic analysis of the viral clones, we identified 10 TF viruses from the eight infants. The TF viruses were characterized by shorter V1V2 regions, a reduced number of potential N-linked glycosylation sites, and a higher infectivity titer compared to the virus variants from the adults in the chronic stage of infection. CXCR6 coreceptor usage, in addition to that of the CCR5 coreceptor, which was used by all 65 chimeric viruses, was identified in 13 viruses. The sensitivity of the TF variants to maraviroc and a standard panel of neutralizing monoclonal antibodies (VRC01, PG09, PG16, and PGT121) was found to be much lower than that of the virus variants from the adults in the chronic stage of infection. Tremendous progress has been made during the last three and half decades of HIV research, but some significant gaps continue to exist. One of the frontier areas of HIV research which has not seen a breakthrough yet is vaccine research, which is because of the enormous genetic diversity of HIV-1 and the unique infectious fitness of the virus. Among the repertoire of viral variants, the virus that establishes successful infection (transmitted founder [TF] virus) has not been well characterized yet. An insight into the salient features of the TF virus would go a long way toward helping with the design of an effective vaccine against HIV. Here we studied the biological properties of recently transmitted viruses isolated from infants who acquired infection from the mother and have come up with unique characterizations for the TF virus that establishes infection in the human host.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

Ashokkumar

Aralaguppe

Tripathy

et al. 2018

J Virol

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“…Targeting the functional envelopes responsible for the acquisition of clinical HIV-1 infection 9 can block the spread of the virus 10 . Within a few weeks of natural HIV infection, most patients develop envelope-specific autologous neutralizing antibodies, but these antibodies fail to neutralize heterologous isolates 11 .…”

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confidence: 99%

In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

Ashokkumar

Sonawane

Sperk

et al. 2020

Sci Rep

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Type I interferons, particularly interferon-alpha (IFN-α), play a vital role in the host's anti-viral defensesby interfering with viral replication. However, the virus rapidly evolves to exploit the IFN-α response for its replication, spread, and pathogenic function. In this study, we attempted to determine IFN-α susceptibility and productivity of infectious transmitted/founder (TF) (n = 8) and non-transmitted (NT) viruses (n = 8) derived from HIV-1 infected infants. Independent experiments were carried out to determine IFN-α resistance, replication fitness, and viral productivity in CD4 + T cells over a short period. In vitro studies showed that TF viruses were resistant to IFN-α during the very near moment of transmission, but in the subsequent time points, they became susceptible to IFN-α. We did not observe much difference in replicative fitness of the TF viruses in cultures treated with and without IFN-α, but the difference was significant in the case of NT viruses obtained from the same individual. Despite increased susceptibility to IFN-α, NT viruses produced more viral particles than TF viruses. Similar results were also obtained in cultures treated with maraviroc (MVC). The study identified unique characteristics of TF viruses thus prompting further investigation into virus-host interaction occurring during the early stages of HIV infection. Determination of saturation point for maraviroc. TZM-bl and GHOST (3) CCR5+ (Hi-5) celllines were employed to assess the sensitivity of chimeric viruses to the CCR5 antagonist, maraviroc. Briefly, 10 4 TZM-bl and Hi-5 cells were plated in each well of a 96-well plate 24 hours before infection. Cells were incubated with different dilutions of MVC (10-fold dilutions starting from 10 μM up to 10 −3 nM) overnight at 37 °C before inoculation with chimeric viruses. Virus infected cells cultured in the absence of MVC served as negative control. At 48 hours post-infection, cells were lysed with 1X passive lysis buffer (Bright-Glo luciferase assay system) and luciferase expression was measured using an Infinite M200Pro plate reader (Tecan, Switzerland) as the number of relative light units (RLU). All conditions were tested in triplicate in each of at least two independent experiments.Single round virus replication kinetics assay. For single cycle infectivity assay, virus stocks normalized by TCID 50 and further diluted to 0.01 MOI were used to infect TZM-bl cells (1 × 10 4 cells/well) in triplicates in the presence of DEAE dextran (10 μg/mL). Cells were pre-incubated for 2 hours with different concentrations (0, 250, 500 and 750 IU/mL) of IFN-α at 37 °C before infection with chimeric viruses. 48 hours after infection, luciferase activity was measured using the Bright-Glo luciferase assay system (Promega). Multiple round virus replication kinetics assay. CD4 + T cells were isolated from buffy coats by deplet-ing CD8 + T cells and stimulated with PHA (20 μg/mL) in the presence of 20 U/mL IL-2 in RPMI medium containing 10% FBS at a concentration of 1 × 10 6 cells per milliliter....

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“…Sequencing of amplicons was performed using 20 HIV-1 subtype C Env sequencing primers 13 on an ABI 3100 Genetic Analyzer (model 3100; Applied Biosystems, Inc.) following the procedure recommended by the manufacturer. Nucleotide and deduced amino acid sequence of full-length gp160 were formatted using SeqScape v2.5 (Applied Biosystems, Inc.), aligned using clustal X and imported into MEGA 6.06 for molecular phylogenetic tree construction using maximum likelihood algorithm.…”

Section: Dna Sequencing and Sequence Analysismentioning

confidence: 99%

“…A total of 117 critical amino acids have been identified as potential epitopes on the Env of HIV by in vitro testing, this list is provided in the HIV database (https://www.hiv.lanl .gov/components/sequence/HIV/featuredb/search/env_ab_ search_pub.comp). The list categorizes the critical amino acids on the basis of the class of antibodies they bind to, namely, CD4BS (63), N160 (13), and N332 (41) classspecific epitopes. There are several online bioinformatics tools and methods that can be used to identify potential epitopes from protein sequence and structure.…”

Section: Introductionmentioning

confidence: 99%

Mapping of Neutralizing Antibody Epitopes on the Envelope of Viruses Obtained from Plasma Samples Exhibiting Broad Cross-Clade Neutralization Potential Against HIV-1

Cheedarla

Sundaramurthi

Babu

et al. 2019

AIDS Research and Human Retroviruses

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Several broadly neutralizing antibodies (bNAbs) that can target HIV strains with large degrees of variability have recently been identified. However, efforts to induce synthesis of such bNAbs that can protect against HIV infection have not met with much success. Identification of specific epitopes encoded in the HIV-1 envelope (Env) that can direct the host to synthesize bNAbs remains a challenge. In a previous study, we identified 12 antiretroviral therapy-naive HIV-1-infected individuals whose plasma exhibited broad cross-clade neutralization property against different clades of HIV-1. In this study, we sequenced the full-length HIV-1 gp160 from 11 of these individuals and analyzed the sequences to identify bNAb epitopes. We identified critical residues in the viral envelopes that contribute to the formation of conformational epitopes and possibly induce the production of bNAbs, using in silico methods. We found that many of the sequences had conserved glycans at positions N160 (10/11) and N332 (9/11), which are known to be critical for the binding of PG9/PG16-like and PGT128-like bNAbs, respectively. We also observed conservation of critical glycans at positions N234 and N276 critical for the interaction with CD4 binding site bNAbs in 8/11 and 11/11 sequences, respectively. We modeled the three-dimensional structure of the 11 HIV-1 envelopes and found that though each had structural differences, the critical residues were mostly present on the surface of the Env structures. The identified critical residues are proposed as candidates for further evaluation as bNAb epitopes.

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Molecular Characteristics of the Envelope of Vertically Transmitted HIV-1 Strains from Infants with HIV Infection

Cited by 9 publications

References 41 publications

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

Mapping of Neutralizing Antibody Epitopes on the Envelope of Viruses Obtained from Plasma Samples Exhibiting Broad Cross-Clade Neutralization Potential Against HIV-1

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