Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

This thesis describes the translational genomics of HIV-1subtype C in India from its origin to therapeutic response with the aim to improve our knowledge for better therapeutic and preventive strategies to combat HIV/AIDS. In a systemic approach, we identified the molecular phylogeny of HIV-1 subtypes circulating in India and the time to most recent common ancestors (tMRCA) of predominant HIV-1 subtype C strains. Additionally, this thesis also studied drug resistance mutations in children, adolescents and adults, the role of host factors in evolution of drug resistance, and population dynamics of viremia and viral co-receptor tropism in perinatal transmission. Finally, the long term therapeutic responses on Indian national first-line antiretroviral therapy were also studied. In Paper I, we reported an increase in the HIV-1 recombinant forms in the HIV-1 epidemiology using a robust subtyping methodology. While the study confirmed HIV- 1 subtype C as a dominant subtype, its origin was dated back to the early 1970s from a single or few genetically related strains from South Africa, whereafter, it has evolved independently. In Paper II, the lethal hypermutations due to the activity of human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (hA3G) was significantly associated with antiretroviral therapy (ART) failure in Indian HIV-1 subtype C patients. The presence of M184I and M230I mutations were observed due to the editing of hA3G in the proviral compartment but stop codons were also found in the open reading frames and the same drug resistance mutations were absent in plasma virus. Therefore, it is unlikely that the viral variants which exhibit hypermutated sequences and M184I and/or M230I will mature and expand in vivo and hence are unlikely to have any clinical significance. The high concordance of drug resistance genotyping in the plasma and proviral compartments in therapy-naïve patients, gives weight to the idea of using whole blood for surveillance of drug resistance mutations which precludes logistic challenges of cold chain transport. In Papers III and IV, we identified a substantial proportion of HIV-1 subtype C perinatally-infected older children who had a high burden of plasma viremia but also had high CD4+ T-cell counts. In addition, older children with HIV-1 subtype C infection presented a high prevalence of predicted X4 and R5/X4 tropic strains which indicates that HIV-1 subtype C strains required longer duration of infection and greater disease progression to co-receptor transition from R5- to X4-tropic strains (IV). Our studies also indicate that transmitted drug resistance is low among Indian HIV-1 infected children, adolescents (III) and adults (II). In Paper V, in a longitudinal cohort study, a good long-term response to the Indian national first-line therapy for a median of nearly four years with 2.8% viral failure, indicating the overall success of the Indian ART program. Our study also showed that three immunologically well patients with virological rebound and major viral drug resistance mutations (M184V, K103N and Y181C) during one study visit had undetectable viral load at their next visit. These findings suggest that use of multiple parameters like patients’ immunological (CD4+ T-cell count), virological (viral load) and drug resistance data should all be used to optimize the treatment switch to second line therapy. In conclusion, this translational genomics study enhances our knowledge about the HIV-1 subtype C strains circulating in India which are genetically distinct from prototype African subtype C strains. Considerably more research using appropriate models need to be performed to understand the phenotypic and biological characteristics of these strains to guide efficient disease intervention and management strategies

Genetic Analysis of HIV-1 Subtypes in Nairobi, Kenya

Background: Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution. Objective: In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya. Methodology: 69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database. Results: Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C. Conclusion: Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections

The importance of nerve microenvironment for schwannoma development

Schwannomas are predominantly benign nerve sheath neoplasms caused by Nf2 gene inactivation. Presently, treatment options are mainly limited to surgical tumor resection due to the lack of effective pharmacological drugs. Although the mechanistic understanding of Nf2 gene function has advanced, it has so far been primarily restricted to Schwann cell-intrinsic events. Extracellular cues determining Schwann cell behavior with regard to schwannoma development remain unknown. Here we show pro-tumourigenic microenvironmental effects on Schwann cells where an altered axonal microenvironment in cooperation with injury signals contribute to a persistent regenerative Schwann cell response promoting schwannoma development. Specifically in genetically engineered mice following crush injuries on sciatic nerves, we found macroscopic nerve swellings in mice with homozygous nf2 gene deletion in Schwann cells and in animals with heterozygous nf2 knockout in both Schwann cells and axons. However, patient-mimicking schwannomas could only be provoked in animals with combined heterozygous nf2 knockout in Schwann cells and axons. We identified a severe re-myelination defect and sustained macrophage presence in the tumor tissue as major abnormalities. Strikingly, treatment of tumor-developing mice after nerve crush injury with medium-dose aspirin significantly decreased schwannoma progression in this disease model. Our results suggest a multifactorial concept for schwannoma formation-emphasizing axonal factors and mechanical nerve irritation as predilection site for schwannoma development. Furthermore, we provide evidence supporting the potential efficacy of anti-inflammatory drugs in the treatment of schwannomas

Improvement of nutritional quality of live feed for aquaculture: An overview

In hatcheries, the adequate supply of live feed has a vital role in feeding fish larvae, fry and fingerlings. Furthermore, the enhancement of the nutritional quality of live feeds is well-developed techniques in aquaculture. Essential fatty acids (EFA) such as docosahexaenoic acid (DHA; C22:6 n-3), eicosapentaenoic acid (EPA; 20:5(n-3) and arachidonic acid (ARA; 20:4(n-6) and amino acids are an essential source of proteins for larval rearing of fish. However, the common practised live feeds used for the primary feeding such as rotifers and Artemia are naturally deficient in essential nutrient components. Hence, the improvement of the nutritional quality of live feeds with different oil emulsions and commercial diets, and manipulation of the feed are necessary for fish production. The production protocols of copepods, Moina and fairy shrimps as live feed are still underdeveloped in hatcheries. The different lipid sources using for the enrichment of Artemia and rotifers are not effective on other live feeds, especially copepods and cladocerans (Moina, Daphnia) and fairy shrimps. This review focuses on the importance of live feeds by the techniques of feed enhancement or enrichment of zooplankton by direct incorporation of nutrients for feeding of early stages of fish

Human Immunodeficiency Virus Infection and Levels of Dehydroepiandrosterone Sulfate in Plasma among Indians

The shift in cytokine profile during human immunodeficiency virus (HIV) disease progression is influenced by dehydroepiandrosterone sulfate (DHEAS) level. Radioimmunoassay was used to measure plasma DHEAS for 30 treatment-naïve HIV-infected and 30 uninfected individuals. There was a significant negative correlation of viral load with DHEAS level (P < 0.05). Further studies of the use of DHEAS levels for monitoring HIV patients economically are warranted

Grazing rates of freshwater copepod Thermocyclops decipiens (Kiefer, 1929) on Chlorella vulgaris under different light intensities

Light is one of the most important structuring factors for life in aquactic biology. For zooplankton grazers, including copepods, light offers a behavioral dilemma that is potentially present at both small and large scales. We investigated the grazing rate, clearance rate, fecal pellet production rate, egg production rate, percertage of egg hatching and survival percentage of the freshwater copepod Thermocyclops deceipiens under different light intensities (0 lx, 500 lx, 1500 lx) over periods of 15 days. For the grazing experiment the fresh water microalgae Chlorella vulgaris was used at concentrations 2-6 x 10(6) cells/mL(-1). The grazing rates of the copepod decreased at higher light intensities when compared to other treatments. Maximum grazing rate and the clearance rate occurred in the treatment with 500 lx (70,490 cells copepod(-1) h(-1), 0.23 mL copepod(-1) h(-1)). Egg production rate and hatching rate percentage (17.4 eggs female(-1) day(-1), 99 +/- 0.98%) were also higher at the algae fed with 500 lx light intensity. Copepods survived well and continuously produced fecal pellets on a 500 lx light intensity diet of Chlorella vulgaris. The results suggest that low light intensity influenced the grazing rate, fecundity and survival of copepod T.decipiens