Somi Sankaran Prakash

Envelope diversity, characteristics of V3 region and predicted co-receptor usage of human immunodeficiency viruses infecting north indians

Subtypes of human immunodeficiency virus type 1 circulating in 21 north Indian patients were characterized based on the partial sequence of the gp120 envelope protein. A majority of viruses (85.7%, 18/21) were subtype C, while 14.3% (3/21) were subtype A. Sequence analysis revealed that the V3 region was highly conserved compared with V4 and V5. The predicted use of co-receptors indicated exclusive usage of R5, except for two subtype A viruses (AIIMS279 and AIIMS281). Our results demonstrate conservation within the V3 loop of subtype C viruses, and suggest the emergence of non-clade C viruses in the north Indian population.

Erratum to: Neutralization Potential of the Plasma of HIV-1 Infected Indian Patients in the Context of Anti-V3 Antibody Content and Antiretroviral Theraphy

We assessed the anti-V3 antibody content and viral neutralization potential of the plasma of 63 HIV-1-infected patients (antiretroviral naïve=39, treated=24) against four primary isolates (PIs) of clade C and a tier 1 clade B isolate SF162. Depletion and inhibition of anti-V3 antibodies in the plasma of five patients with high titers of anti-V3 antibodies led to modest change in the neutralization percentage against two PIs (range 0–21%). The plasma of antiretroviral-treated patients exhibited higher neutralization potential than that of the drug-naïve plasmas against the four PIs tested which was further evidenced by a follow-up study.

A novel strategy for efficient production of anti-V3 human scFvs against HIV-1 clade C

BackgroundProduction of human monoclonal antibodies that exhibit broadly neutralizing activity is needed for preventing HIV-1 infection, however only a few such antibodies have been generated till date. Isolation of antibodies by the hybridoma technology is a cumbersome process with fewer yields. Further, the loss of unstable or slowly growing clones which may have unique binding specificities often occurs during cloning and propagation and the strongly positive clones are often lost. This has been avoided by the process described in this paper, wherein, by combining the strategy of EBV transformation and recombinant DNA technology, we constructed human single chain variable fragments (scFvs) against the third variable region (V3) of the clade C HIV-1 envelope.ResultsAn antigen specific phage library of 7000 clones was constructed from the enriched V3- positive antibody secreting EBV transformed cells. By ligation of the digested scFv DNA into phagemid vector and bio panning against the HIV-1 consensus C and B V3 peptides followed by random selection of 40 clones, we identified 15 clones that showed V3 reactivity in phage ELISA. DNA fingerprinting analysis and sequencing showed that 13 out of the 15 clones were distinct. Expression of the positive clones was tested by SDS-PAGE and Western blot. All the 13 anti-V3 scFvs showed cross-reactivity against both the clade C and B V3 peptides and did not show any reactivity against other unrelated peptides in ELISA. Preliminary neutralization assays indicated varying degrees of neutralization of clade C and B viruses. EBV transformation, followed by antigen selection of lines to identify specific binders, enabled the selection of phage from un-cloned lines for scFv generation, thus avoiding the problems of hybridoma technology. Moreover, as the clones were pretested for antigen binding, a comparatively small library sufficed for the selection of a considerable number of unique antigen binding phage. After selection, the phage clones were propagated in a clonal manner.ConclusionsThis strategy can be efficiently used and is cost effective for the generation of diverse recombinant antibodies. This is the first study to generate anti-V3 scFvs against HIV-1 Clade C.

Efficient neutralization of primary isolates by the plasma from HIV-1 infected Indian children.

We tested the plasma of 51 HIV-1-infected children (23 naïve and 28 ART treated) for neutralization against five primary isolates (PIs) generated from adult Indian HIV-1-infected patients. The plasma exhibited neutralization potential with significantly higher neutralizing antibody titers in ART-treated children than naïve children against three out of five PIs (p<0.0001). Further, in treated children, neutralizing antibody titers were higher in those children with suppressed viremia (<1000 RNA copies/mL) than non-suppressors against two of the three PIs. We report here for the first time the neutralization potential of the plasma of HIV-1-infected Indian children.

IL-8 Alterations in HIV-1 Infected Children With Disease Progression

AbstractDisease progression in HIV-1 infected children is faster than in adults. Less than 5% of the infected children maintain stable CD4 counts beyond 7 years of infection and are termed long-term nonprogressors (LTNPs). Delineating the host immune response in antiretroviral naïve (ART) and treated HIV-1 infected children at different disease stages will help in understanding the immunopathogenesis of the disease.A total of 79 asymptomatic, perinatally HIV-1 infected children (50 ART naïve and 29 ART treated) and 8 seronegative donors were recruited in this study. T- and B-cell activation PCR arrays were performed from the cDNA, using total RNA extracted from the peripheral blood mononuclear cells (PBMCs) of 14 HIV-1 infected children at different stages of the disease. The differentially expressed genes were identified. Quantitative RT-PCR was performed for the (interleukin-8) IL-8 gene and its transcriptional mediators, that is, SHP2, GRB2, and IL-8R (IL-8 receptor/CXCR1). Plasma levels of IL-8 were measured by flow cytometry.Gene array data revealed a higher expression of IL-8 in the ART naïve HIV-1 infected progressors and in ART nonresponders than LTNPs and ART responders, respectively. Quantitative RT-PCR analysis demonstrated a significant higher expression of IL-8 (P < 0.001), its receptor CXCR1 (P = 0.03) and the upstream signaling molecule SHP2 (P = 0.04) in the progressors versus LTNPs. Plasma levels of IL-8 were significantly higher in progressors versus LTNPs (P < 0.001), and ART nonresponders versus ART responders (P < 0.001). A significant negative correlation of plasma levels of IL-8 with CD4 counts (cells/&mgr;L) was observed in HIV-1 infected ART naïve subjects (r = −0.488; P < 0.001), while the IL-8 levels positively correlated with viral load in the ART treated children (r = 0.5494; P < 0.001). ART naïve progressors on follow up demonstrated a significant reduction in the mRNA expression (P = 0.05) and plasma levels of IL-8 (P = 0.05) post 6 months of ART initiation suggesting the beneficial role of ART therapy in reducing inflammation in infected children.Our data suggest that IL-8 may serve as a potential prognostic marker in adjunct with CD4 counts to monitor disease progression in the HIV-1 infected children and the efficacy of ART.

Binding Antibody Responses to the Immunogenic Regions Of Viral Envelope in HIV-1-Infected Indian Children

Limited information exists on the antibody responses elicited against the viral envelope in HIV-1-infected children. In this cross-sectional study, we assessed the antibody responses against three different immunogenic regions of HIV-1 envelope, namely V3 region of gp120, membrane proximal external region (MPER), and immunodominant loop (IDL) of gp41 in HIV-1-infected children from north India. We recruited 75 HIV-1-infected (40 antiretroviral naive and 35 treated) children, with age ranging from 1.5 to 16 y. Antibodies to V3 and the IDL region were found in a majority of the infected children, whereas antibodies to MPER were found in approximately one-third of the children studied. Higher antibody titers to the immunogenic regions corresponded to the symptomatic stages of HIV-1 infection in both naive and antiretroviral therapy (ART)-treated children. High titers of anti-V3C and anti-IDL antibodies were observed in a subset of antiretroviral-naive patients with suppressed viremia (<47 RNA copies/mL), suggesting that antibodies to these immunogenic regions are present regardless of their viremic status. Further, the antibody titers were significantly lower in the plasma of treated patients compared to naive patients, regardless of whether they were virologically suppressed or not. This is the first report on the antibody responses elicited in HIV-1-infected children in India. The study may help to understand the humoral antibody responses directed against viral envelope in HIV-1-infected children.

Mutations in the reverse transcriptase and protease genes of human immunodeficiency virus-1 from antiretroviral naïve and treated pediatric patients.

The success of highly active antiretroviral therapy (HAART) is challenged by the emergence of resistance-associated mutations in human immunodeficiency virus-1 (HIV-1). In this study, resistance associated mutations in the reverse transcriptase (RT) and protease (PR) genes in antiretroviral therapy (ART) naïve and treated HIV-1 infected pediatric patients from North India were evaluated. Genotyping was successfully performed in 46 patients (30 ART naive and 16 treated) for the RT gene and in 53 patients (27 ART naive and 26 treated) for PR gene and mutations were identified using Stanford HIV Drug Resistance Database. A major drug resistant mutation in RT gene, L74I (NRTI), and two such mutations, K101E and G190A (NNRTI), were observed in two ART naïve patients, while M184V was detected in two ART treated patients. Overall, major resistance associated mutations in RT gene were observed in nine (30%) and seven (36%) of ART naïve and treated children respectively. Minor mutations were identified in PR gene in five children. Few non-clade C viral strains (≈30%) were detected, although subtype C was most predominant. The screening of ART naïve children for mutations in HIV-1 RT and protease genes, before and after initiation of ART is desirable for drug efficacy and good prognosis.

Production of cross neutralizing single chain fragment variables (scFv) from HIV-1 infected Indian children

Methods Nine ART drug naive HIV-1 subtype c infected children were recruited. PBMCs were isolated from all the subjects and pooled. RNA was isolated and cDNA was synthesized followed by amplification of VH and VL chain genes and scFv construction. A human recombinant scFv phage display library of 108 clones was constructed. Diversity of the phage library was checked by DNA sequencing and biopanned with RSC3 core antigen. 60 random clones were screened by phage ELISA. Expression of the scFvs was assessed by SDS-PAGE and Western blotting.

Production and expression of recombinant anti-V3 scFvs from HIV-1 clade C infected Indian patient

Neutralizing antibodies are an important component of the humoral immune response directed against viral infections So far the few available anti HIV-1 broadly neutralizing antibodies have a limited breadth and potency against clade C viruses. More than 50% of the HIV-1 infections worldwide belong to clade C. Clade C is the most prevalent subtype in India.

Generation and characterization of human monoclonal single chain variable fragments (scFvs) against envelope third variable region (V3) of HIV-1 clade C

Methods A phage library of 7000 clones was constructed from a drug naive HIV-1 clade C infected Indian patient whose plasma exhibited high potential neutralizing potential against a panel of viruses and also displayed cross-reactive anti-V3 antibodies. PBMCs were isolated and EBV transformed. Cells (wells) producing anti-V3 antibodies were preselected with V3-CTB fusion protein and expanded. Total RNA was isolated and cDNA was constructed followed by VH and VL amplification. scFvs were constructed, cloned into phagemid vector and expressed in Escherichia coli. We assessed the expression of the scFvs by SDSPAGE and Western blotting. Specificity was examined by ELISA.