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1.
J Hazard Mater ; 399: 122841, 2020 11 15.
Article in English | MEDLINE | ID: mdl-32526441

ABSTRACT

Novel amine functionalized composite membranes were prepared over tubular ceramic substrate using facile dip-coating and cross-flow filtration approach. The two fabricated membranes, P-60S and P-60S-EDTA with polyethyleneimine (PEI) and EDTA-modified PEI as functional layers respectively, were characterized in terms of EDX, FTIR, XPS, FESEM, AFM and contact angle analyses which confirmed their stable physical and chemical structure for use in high pressure application. Clean water permeability and MWCO study revealed the superior permeability and rejection efficiency of the P-60S-EDTA compared to the P-60S membrane. Incorporation of bulky EDTA molecules in the membrane functional layer simultaneously decreased pore size and increased membrane hydrophilicity. The removal of As(V), Cr(VI) and Cu(II) heavy metals by both membranes were found to be highly pH dependent and overall rejection improved in case of P-60S-EDTA membrane [99.82% for Cu(II), 96.75% for As(V) and 97.22% for Cr(VI)]. Interestingly, rejection of As(V) and Cr(VI) was significantly improved in presence of Cu(II) due to volume resistance provided by EDTA-Cu(II) complex towards the passage of other heavy metal ions. Excellent stability of P-60S-EDTA membrane in continuous operation of 36 h in both ideal and practical water environment suggests its promising application in real field heavy metal contaminated waste water treatment.

2.
J Infect Chemother ; 25(5): 325-329, 2019 May.
Article in English | MEDLINE | ID: mdl-30770182

ABSTRACT

Influenza virus is a common human pathogenic agent that has caused serious respiratory illness and death over the past century and in recent year. Treatment options against pandemic influenza strain A/H1N1 are very limited and unsatisfactory. Therefore we have developed iron oxide nanoparticles (IO-NPs) with particle size in the range of 10-15 nm against pandemic influenza strain A/H1N1/Eastern India/66/PR8-H1N1. Cell viability and anti-influenza activity was measured by MTT assay, plaque inhibition and quantifying viral transcripts using quantitative real-time PCR with Iron oxide nanoparticles in a dose- and time-dependent manner. 50% cell viability (TD50) was observed at 4.25 pg ± .2 pg of Iron oxide nanoparticles. The percentage of plaque inhibition relative to the infection and the IC50 (50% virus reduction) of PR8-H1N1strain (0.5 moi) were measured in vitro by the plate forming unit (pfu) in MA104 cells. Finding were observed at 01 pg after 72 h. The Antiviral activity determined by change in viral RNA transcripts within 24 h of virus infection by RT-PCR, 08 fold reductions in virus found when treated with Iron oxide nanoparticles Thus; it opens a new avenue for use of IP-NPs against virus infections.


Subject(s)
Antiviral Agents/administration & dosage , Ferric Compounds/administration & dosage , Influenza A Virus, H1N1 Subtype/drug effects , Influenza, Human/drug therapy , Metal Nanoparticles/administration & dosage , Animals , Cell Line , Cell Survival/drug effects , Haplorhini , Humans , Influenza, Human/virology , Inhibitory Concentration 50 , Microbial Sensitivity Tests
3.
Mater Sci Eng C Mater Biol Appl ; 75: 1465-1471, 2017 Jun 01.
Article in English | MEDLINE | ID: mdl-28415438

ABSTRACT

Visceral leishmaniasis, a protozoan disease transmitted by phlebotomine sandflies which affect mostly in Indian sub-continent. The treatment for visceral leishmaniasis (VL) caused by Leishmania donovani are limited and unsatisfactory. Currently available drug against such as miltefosine and polymer based drugs amBisome has high efficacy against VL but found serious side effects and poor absorbance. To overcome this, we developed peptide (glycine) coated iron oxide (Fe3O4) nanoparticles (GINPs) encapsulated amphoterecin B (AmB) drug against visceral leishmaniasis. Synthesis of GINPs was carried out and different characterization technique used to confirm the synthesis and size of GINPs GINPs-AmB showed that particle size in the range of 10-15nm and closed to spherical in shaped. GINPs-AmB showed release rate of AmB is higher at lower pH. Significantly two fold higher efficacies of GINP encapsulated AmB during in vitro study. There was a substantial reduction in the total parasite burden in spleen in treated groups (GINPs encapsulate AmB), compare to AmB alone. The results obtained from this study revealed that AmB loaded GINPs is twofold effective than AmB and therefore, it opens a new avenue for use of AmB loaded GINPs against VL.


Subject(s)
Amphotericin B , Coated Materials, Biocompatible , Ferric Compounds , Leishmania donovani , Leishmaniasis, Visceral/drug therapy , Magnetite Nanoparticles/chemistry , Peptides , Amphotericin B/chemistry , Amphotericin B/pharmacokinetics , Amphotericin B/pharmacology , Animals , Coated Materials, Biocompatible/chemistry , Coated Materials, Biocompatible/pharmacokinetics , Coated Materials, Biocompatible/pharmacology , Ferric Compounds/chemistry , Ferric Compounds/pharmacokinetics , Ferric Compounds/pharmacology , Humans , Mice , Mice, Inbred BALB C , Peptides/chemistry , Peptides/pharmacology
4.
J Biomol Struct Dyn ; 35(1): 128-140, 2017 Jan.
Article in English | MEDLINE | ID: mdl-26727289

ABSTRACT

Protein disulphide isomerase (PDI) is one of the key enzymes essential for the survival of Leishmania donovani in the host. Our study suggested that PDI is associated with the generation of Th1-type of cellular responses in treated Visceral leishmaniasis (VL) subjects. The stimulation of Peripheral blood mononuclear cells (PBMCs) with recombinant Protein Disulphide Isomerase upregulated the reactive oxygen species generation, Nitric oxide release, IL12 and IFN-γ production indicating its pivotal role in protective immune response. Further, a pre-stimulation of PBMCs with Protein disulphide isomerase induced a strong IFN-γ response through CD8+ T cells in treated VL subjects. These findings also supported through the evidence that this antigen was processed and presented by major histocompatibility complex class I (MHC-1) dependent pathway and had an immunoprophylactic potential which can induce CD8+ T cell protective immune response in MHC class I dependent manner against VL. To find out the possible epitopes that might be responsible for CD8+ T cell specific IFN-γ response, computational approach was adopted. Six novel promiscuous epitopes were predicted to be highly immunogenic and can be presented by 32 different HLA allele to CD8+ T cells. Further investigation will explore more about their immunological relevance and usefulness as vaccine candidates.


Subject(s)
Epitopes, T-Lymphocyte/chemistry , Histocompatibility Antigens Class I/chemistry , Leishmania donovani/enzymology , Protein Disulfide-Isomerases/chemistry , Adolescent , Adult , Amino Acid Sequence , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cytokines/metabolism , Epitopes, T-Lymphocyte/immunology , Female , Histocompatibility Antigens Class I/immunology , Humans , Immunomodulation , Leishmania donovani/immunology , Leishmaniasis, Visceral/immunology , Male , Protein Disulfide-Isomerases/immunology , Protozoan Proteins/chemistry , Protozoan Proteins/immunology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Young Adult
5.
PLoS Negl Trop Dis ; 10(9): e0004970, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27681709

ABSTRACT

BACKGROUND: Visceral Leishmaniasis, commonly known as kala-azar, is widely prevalent in Bihar. The National Kala-azar Control Program has applied house-to-house survey approach several times for estimating Kala-azar incidence in the past. However, this approach includes huge logistics and operational cost, as occurrence of kala-azar is clustered in nature. The present study aims to compare efficiency, cost and feasibility of snowball sampling approach to house-to-house survey approach in capturing kala-azar cases in two endemic districts of Bihar, India. METHODOLOGY/PRINCIPAL FINDINGS: A community based cross-sectional study was conducted in two highly endemic Primary Health Centre (PHC) areas, each from two endemic districts of Bihar, India. Snowball technique (used to locate potential subjects with help of key informants where subjects are hard to locate) and house-to-house survey technique were applied to detect all the new cases of Kala-azar during a defined reference period of one year i.e. June, 2010 to May, 2011. The study covered a total of 105,035 households with 537,153 populations. Out of total 561 cases and 17 deaths probably due to kala-azar, identified by the study, snowball sampling approach captured only 221 cases and 13 deaths, whereas 489 cases and 17 deaths were detected by house-to-house survey approach. Higher value of McNemar's χ² statistics (64; p<0.0001) for house-to-house survey approach than snowball sampling and relative difference (>1) indicates that most of the kala-azar cases missed by snowball sampling were captured by house-to-house approach with 13% of omission. CONCLUSION/SIGNIFICANCE: Snowball sampling was not found sensitive enough as it captured only about 50% of VL cases. However, it captured about 77% of the deaths probably due to kala-azar and was found more cost-effective than house-to-house approach. Standardization of snowball approach with improved procedure, training and logistics may enhance the sensitivity of snowball sampling and its application in national Kala-azar elimination programme as cost-effective approach for estimation of kala-azar burden.

6.
Curr Pharm Biotechnol ; 17(12): 1089-1099, 2016.
Article in English | MEDLINE | ID: mdl-27633891

ABSTRACT

Glucose-1-Phosphate Thymidylyltransferase (RmlA) is one of the enzymes in rhamnose biosynthesis pathway, where rhamnose acts as linker of peptidoglycan and arabinogalacton in the cell wall, therefore RmlA is a potential enzyme for the survival of Mycobacterium tuberculosis (Mtb). To go into the depth of the structure for exploring binding regions, homology model of RmlA was built in Prime, Schrodinger v9.2. The model with lowest Discrete Optimized Potential Energy (DOPE) score of -35524.17 kcal/mol and RMSD of 0.1 Å with the template (1H5R_B) was subjected to Molecular Dynamics Simulation (MDS) for 5 ns to achieve its stable folding state. The tertiary structure of the proposed model is composed of α/ß/α sandwich type protein with quasi-Rossmann type folding pattern. The substrate, deoxy Thymidine tri phosphate (dTTP) comprises of triphosphate (R1) and methyl (R2) side chains where, R1 is highly essential for the survival of Mtb. Therefore, nineteen side chain analogues of dTTP were designed by substituting R1 and R2 chain of dTTP using Combi Glide, Schrodinger v9.2 and docked with the target RmlA protein. Out of which two analogues such as, 6-[(2R,3S,5R)-5-[5-(2- aminoethyl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl]-3-hydroxyoxolan-2 yl] hexanoic acid (COMP- 11) and 4-(2-{1-[(1S,3S,4S)-3-(5-carboxypentyl)-4-hydroxy-2-methylidenecyclopentyl]-2,4-dioxo- 1,2,3,4-tetrahydropyrimidin-5-yl}ethyl)morpholin-4-ium (COMP-12) showed the highest GLIDE score (-12.55 Kcal/mol and -11.58 Kcal/mol respectively) than that of substrate (-9.725 Kcal/mol). During simulations, hydrogen bonding profile between the two top hits and protein ranges up to 5 strong polar contacts which were much stronger than that of substrate. Similarly, the computational binding free energy of both the analogues was found to be less than -70 Kcal/mol which is much lower than that of substrate (-52.84 Kcal/mol). All these results suggest that these two compounds have more stable interaction than that of substrate inside the solvent condition and can be used as competitive inhibitors.


Subject(s)
Mycobacterium tuberculosis/metabolism , Nucleotidyltransferases/chemistry , Ligands , Molecular Dynamics Simulation , Thymine Nucleotides/chemistry
7.
Infect Genet Evol ; 45: 187-197, 2016 11.
Article in English | MEDLINE | ID: mdl-27590716

ABSTRACT

The Zika virus disease is an Aedes mosquito-borne disease caused by the ZIKA virus. The unavailability of vaccines or proper chemotherapeutic treatment emphasizes the need for the development of preventive and therapeutic vaccines. T cell specific epitopes have been used as vaccine candidates to generate desired immune responses against a variety of viral pathogens. Herein, the immune-informatics approach was used for the screening of potential major histocompatibility complex class I restricted epitopes, which may be competent to generate a cell-mediated immune response in humans. A total of 63 epitopes were identified, which revealed a comprehensive binding affinity to the 42 different human leukocyte antigen class I supertypes: A01, A02, A08, A23, A24, A25, A26, A29, A30, A32, A66, A68, A69, A80, B07, B08, B14, B15, B27, B35, B39, B40, B42, B45, B46, B48, B51, B53, B54, B57, B58, B83, C12, C03, C04, C05, C06, C07, C08, C12, C14, and C15, and which had no homologs in humans. By combining the human leukocyte antigen binding specificity and population coverage, nine promiscuous epitopes located in Capsid 1 Protein (MVLAILAFL(P1)), Envelop Protein (RLKGVSYSL (P2) and RLITANPVI (P3)), NS2A (AILAALTPL (P4)), NS4B (LLVAHYMYL (P5) and LVAHYMYLI (P6)) and NS5 (SLINGVVRL (P7), ALNTFTNLV (P8) and YLSTQVRYL (P9)) were shortlisted. Most of these consensus epitopes revealed 100% conservancy in all Zika virus strains and were very less conserved against the human proteome. The combination of the selected epitopes accounted for an optimal coverage in the world wide population (>99%) independent of ethnicity. Structural analysis of these selected epitopes by the PatchDock web server showed their preferential mode of presentation to the T cell receptor. All these results recommended the possibility of a combined epitope vaccine strategy and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.


Subject(s)
Antigens, Viral , Computational Biology/methods , Epitopes, T-Lymphocyte , Zika Virus , Antigens, Viral/chemistry , Antigens, Viral/genetics , Antigens, Viral/immunology , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/immunology , Humans , Models, Molecular , Models, Statistical , T-Lymphocytes, Cytotoxic/immunology , Viral Vaccines/genetics , Zika Virus/genetics , Zika Virus/immunology , Zika Virus Infection/immunology , Zika Virus Infection/prevention & control , Zika Virus Infection/virology
8.
Drug Des Devel Ther ; 10: 1753-61, 2016.
Article in English | MEDLINE | ID: mdl-27307706

ABSTRACT

New treatments for visceral leishmaniasis, caused by Leishmania donovani, are needed to overcome sustained toxicity, cost, and drug resistance. The aim of this study was to evaluate the therapeutic effects of 2-nitro-N-(pyridin-2-ylmethyl)benzenesulfonamide (2NB) against promastigote and amastigote forms of L. donovani and examine its effect in combination with amphotericin B (AmB) against AmB-resistant clinical isolates. Effects were assessed against extracellular promastigotes in vitro and intracellular amastigotes in L. donovani-infected macrophages. Levels of inducible nitric oxide and Th1 and Th2 cytokines were measured in infected 2NB-treated macrophages, and levels of reactive oxygen species and NO were measured in 2NB-treated macrophages. 2NB was active against promastigotes and intracellular amastigotes with 50% inhibitory concentration values of 38.5±1.5 µg/mL and 86.4±2.4 µg/mL, respectively. 2NB was not toxic to macrophages. Parasite titer was reduced by >85% in infected versus uninfected macrophages at a 2NB concentration of 120 µg/mL. The parasiticidal activity was associated with increased levels of Th1 cytokines, NO, and reactive oxygen species. Finally, 2NB increased the efficacy of AmB against AmB-resistant L. donovani. These results demonstrate 2NB to be an antileishmanial agent, opening up a new avenue for the development of alternative chemotherapies against visceral leishmaniasis.


Subject(s)
Amphotericin B/administration & dosage , Amphotericin B/pharmacology , Antiprotozoal Agents/pharmacology , Leishmania donovani/drug effects , Leishmaniasis, Visceral/drug therapy , Macrophages/drug effects , Nitric Oxide/chemistry , Pyridines/therapeutic use , Sulfonamides/therapeutic use , Antiprotozoal Agents/administration & dosage , Humans , Inhibitory Concentration 50 , Macrophages/chemistry , Pyridines/chemistry , Pyridines/pharmacology , Sulfonamides/chemistry , Sulfonamides/pharmacology
9.
Infect Genet Evol ; 36: 369-375, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26462623

ABSTRACT

Cell-mediated immunity is important for the control of Ebola virus infection. We hypothesized that those HLA A0201 and HLA B40 restricted epitopes derived from Ebola virus proteins, would mount a good antigenic response. Here we employed an immunoinformatics approach to identify specific 9mer amino acid which may be capable of inducing a robust cell-mediated immune response in humans. We identified a set of 28 epitopes that had no homologs in humans. Specifically, the epitopes derived from NP, RdRp, GP and VP40 share population coverage of 93.40%, 84.15%, 74.94% and 77.12%, respectively. Based on the other HLA binding specificity and population coverage, seven novel promiscuous epitopes were identified. These 7 promiscuous epitopes from NP, RdRp and GP were found to have world-wide population coverage of more than 95% indicating their potential significance as useful candidates for vaccine design. Epitope conservancy analysis also suggested that most of the peptides are highly conserved (100%) in other virulent Ebola strain (Mayinga-76, Kikwit-95 and Makona-G3816- 2014) and can therefore be further investigated for their immunological relevance and usefulness as vaccine candidates.


Subject(s)
Antigens, Viral/chemistry , Antigens, Viral/immunology , Ebolavirus/immunology , Epitopes, T-Lymphocyte/chemistry , Epitopes, T-Lymphocyte/immunology , Hemorrhagic Fever, Ebola/immunology , Models, Molecular , T-Lymphocytes, Cytotoxic/immunology , Alleles , Amino Acid Sequence , HLA-A2 Antigen/chemistry , HLA-A2 Antigen/genetics , HLA-A2 Antigen/immunology , HLA-B Antigens/chemistry , HLA-B Antigens/genetics , HLA-B Antigens/immunology , Hemorrhagic Fever, Ebola/genetics , Hemorrhagic Fever, Ebola/virology , Humans , Molecular Docking Simulation , Peptides/chemistry , Peptides/immunology , Protein Binding/immunology , Protein Conformation , Proteomics/methods
10.
Article in English | MEDLINE | ID: mdl-25125444

ABSTRACT

A Leishmania Microsatellite Database (LeishMicrosatDB) is reported for genome wise mining of microsatellites in six Leishmania species, using in silico techniques. This was created to provide parasitologists a platform to understand the genome characterization, mapping, phylogeny and evolutionary analysis. The present version of the database contains 1,738,669 simple sequence repeats of which 181 s756 repeats are present in compound form. The repeats can be sought in a chromosome using input parameters such as repeat type (mono- hexa), coding status, repeat unit length and repeat sequence motif. The genic repeats have been further hyperlinked with their corresponding locus id, and the database is appended with primer3 plus for primer designing of selected repeats with left and right flanking sequences up to 250 bp. Information on clustering and polymorphic repeats can also be retrieved. This database may also be adopted as a tool to study the relative occurrence and distribution of microsatellites across the parasitic genome. The database can enable a biologist to select markers at desired intervals over the chromosomes, and can be accessed as an open source repository at http://biomedinformri.com/leishmicrosat. DATABASE URL: http://biomedinformri.com/leishmicrosat.


Subject(s)
Databases, Genetic , Genome, Protozoan/genetics , Internet , Leishmania/genetics , Genomics , User-Computer Interface
11.
Biomed Res Int ; 2013: 609289, 2013.
Article in English | MEDLINE | ID: mdl-23984386

ABSTRACT

Enzyme adenosine kinase is responsible for phosphorylation of adenosine to AMP and is crucial for parasites which are purine auxotrophs. The present study describes development of robust homology model of Leishmania donovani adenosine kinase to forecast interaction phenomenon with inhibitory molecules using structure-based drug designing strategy. Docking calculation using reported organic small molecules and natural products revealed key active site residues such as Arg131 and Asp16 for ligand binding, which is consistent with previous studies. Molecular dynamics simulation of ligand protein complex revealed the importance of hydrogen bonding with active site residues and solvent molecules, which may be crucial for successful development of drug candidates. Precise role of Phe168 residue in the active site was elucidated in this report that provided stability to ligand-protein complex via aromatic- π contacts. Overall, the present study is believed to provide valuable information to design a new compound with improved activity for antileishmanial therapeutics development.


Subject(s)
Adenosine Kinase/chemistry , Adenosine Kinase/metabolism , Leishmania donovani/enzymology , Molecular Dynamics Simulation , Amino Acid Sequence , Hydrogen Bonding , Molecular Sequence Data , Reproducibility of Results , Structural Homology, Protein
12.
J Hazard Mater ; 211-212: 281-7, 2012 Apr 15.
Article in English | MEDLINE | ID: mdl-22137174

ABSTRACT

PEEK-WC nanostructured capsules were prepared by the phase inversion technique and used as support for the coating of a manganese dioxide layer. The coating was done by a chemical treatment of the capsules followed by a thermal one. The presence of the MnO(2) layer was confirmed by scanning electron microscopy (SEM), back scattering electron (BSE), energy dispersive X-ray (EDX) and X-ray diffraction (XRD) analysis. The produced capsules were, then, tested for As(III) oxidation in batch. The experiments consisted in treating 165 ml of As(III) solution with 1g of coated capsules at fixed temperature (15°C) and pH (5.7-5.8). In particular, the efficiency of the system was investigated for different As(III) concentrations (0.1, 0.3, 0.7 and 1 ppm). For feeds at lower As(III) content (0.1-0.3 ppm), tests lasted for 8h, while prolonged runs (up to 48 h) were carried out on more concentrated solutions (0.7 and 1 ppm). The produced capsules were able to oxidize As(III) into As(V) leading to complete conversion after 3 and 4h for feed concentrations of 0.1 and 0.3 ppm, respectively.


Subject(s)
Arsenic/chemistry , Manganese Compounds/chemistry , Nanostructures/chemistry , Oxides/chemistry , Polymers/chemistry , Water Pollutants, Chemical/chemistry , Capsules , Oxidation-Reduction , Waste Disposal, Fluid/methods , Water Purification/methods
13.
J Biomed Res ; 25(2): 100-10, 2011 Mar.
Article in English | MEDLINE | ID: mdl-23554678

ABSTRACT

EMR2 is an EGF-like module containing mucin-like hormone receptor-2 precursor, a G-protein coupled receptor (G-PCR). Mutation in EMR2 causes complicated disorders like polycystic kidney disease (PKD). The structure of EMR2 shows that the fifth domain is comprised of EGF-TM7 helices. Functional assignment of EMR2 by support vector machine (SVM) revealed that along with transporter activity, several novel functions are predicted. A twenty amino acid sequence "MGGRVFLVFLAFCVWLTLPG" acts as the signal peptide responsible for posttranslational transport. Eight amino acids are involved in N-glycosylation sites and two cleavage sites are Leu517 and Ser518 in EMR2. The residue Arg241 is responsible for interaction with glycosaminoglycan and chondroitin sulfate. On the basis of structure, function and ligand binding sites, competitive EMR2 inhibitors designed may decrease the rate of human diseases like Usher's syndrome, bilateral frontoparietal polymicrogyria and PKD.

14.
Virology ; 377(1): 117-23, 2008 Jul 20.
Article in English | MEDLINE | ID: mdl-18555887

ABSTRACT

Mutation and recombination are recognized as important driving forces of evolution among RNA viruses. An intergenogroup recombinant norovirus strain [Hu/Kol/NLV/L8775/AB290150/2006/India] was detected in the faecal specimen of a 17 year old male, who had suffered from acute watery diarrhea and severe dehydration. Sequence analysis confirmed that this novel recombinant strain had a polymerase gene fragment that closely resembled a Norovirus (NoV) genogroup-I genotype-3 virus (HuCV/NLV/GI.3/VA98115/AY038598/1998/USA) and a capsid gene resembling NoV genogroup-II genotype-4 virus (NoV/Hu/GII.4/Terneuzen70/EF126964/2006/NL). The crossing over and recombination was observed at nucleotide (nt) 790 of NoV GI VA98115 strain and nt808 of NoV GII Terneuzen70 strain. In both parent strains conserved nucleotide sequence and hairpin structure (DNA secondary structure) were reported at the junction point of ORF1 and ORF2, exhibiting the mechanism of recombination in these viruses. Thus this novel recombinant NoV is another step in evolution among NoVs, indicating that constant surveillance is important to successfully monitor emergence of these strains.


Subject(s)
Norovirus/genetics , Norovirus/isolation & purification , Recombination, Genetic , Adolescent , Base Sequence , Caliciviridae Infections/virology , Capsid Proteins/genetics , DNA Primers/genetics , DNA, Viral/chemistry , DNA, Viral/genetics , Gastroenteritis/virology , Humans , India , Male , Molecular Sequence Data , Norovirus/classification , Nucleic Acid Conformation , Open Reading Frames , Phylogeny , Sequence Homology, Nucleic Acid
15.
Infect Genet Evol ; 7(2): 229-38, 2007 Mar.
Article in English | MEDLINE | ID: mdl-17049316

ABSTRACT

Picobirnaviruses (PBVs) with bisegmented small RNA genome profile (1.75 and 1.55kbp for segment 1 and 2, respectively) were detected from 1999 to 2003 in faecal specimens of acute watery diarrhoea cases, largely children (n=20) and an adult in Kolkata, India. Varying degrees of dehydration necessitated their visit to hospital for further treatment and management of acute watery diarrhoea. PBV was associated with rotavirus (n=3) or astrovirus (n=3) and with both in one case. No co-infection with norovirus, sapovirus or adenovirus was detected in the picobirnavirus positive cases. No co-infection with parasites (Cryptosporidium spp., Giardia spp., Entamoeba spp., helminths) or bacteria (Vibrio spp., Shigella spp., Escherichia coli) was detected among the picobirnavirus positive cases. There was a single instance of co-infection with Salmonella spp. (n=1). PBVs not associated with serious diarrhoea illness and showing large genome profile (2.3-2.6 and 1.5-1.9kbp for segment 1 and 2, respectively) have earlier been reported in adult individuals and recently among children from a slum community in Kolkata, India. The short genome profile PBVs associated with acute watery diarrhoea may be another emerging diarrhoeagenic virus in Kolkata, India. Molecular characterization using reported primers PicoB25-PicoB43 for Genogroup I and PicoB23-PicoB24 for Genogroup II in RT-PCR showed the presence of Genogroup I PBVs (n=6) and Genogroup II PBVs (n=5), while some could not be amplified (n=3) with these primers. Sequence analysis of Genogroup I amplicons indicated remarkable sequence heterogeneity. After more than a decade, four PBV positives of Genogroup II were detected during this study. Phylogenetic analysis showed varying degree of genetic diversity amongst PBV strains from Kolkata and other countries.


Subject(s)
Diarrhea/virology , Genome, Viral , Picobirnavirus/isolation & purification , RNA Virus Infections/virology , RNA, Viral/genetics , Adult , Age Factors , Child, Preschool , Diarrhea/epidemiology , Diarrhea/physiopathology , Diarrhea, Infantile/epidemiology , Diarrhea, Infantile/physiopathology , Diarrhea, Infantile/virology , Feces/virology , Humans , India/epidemiology , Infant , Molecular Sequence Data , Phylogeny , Picobirnavirus/classification , Picobirnavirus/genetics , Prevalence , Reverse Transcriptase Polymerase Chain Reaction , Rotavirus/isolation & purification
16.
Infect Genet Evol ; 6(6): 453-8, 2006 Nov.
Article in English | MEDLINE | ID: mdl-16616879

ABSTRACT

Picobirnaviruses are a group of unclassified, non-enveloped, small spherical viruses, 35-41 nm in diameter without any apparent surface morphology. They have characteristic bisegmented double stranded RNA genome of two types namely large profile (2.3-2.6 kbp for the larger and 1.5-1.9 kbp for the smaller segment, respectively) or small profile (1.75 and 1.55 kbp for segments 1 and 2, respectively). Human picobirnaviruses (n=12 positives; 2/56 diarrhoeic children and 10/607 non-diarrhoeic children) with large (n=11) or small (n=1) genome pattern were observed in faecal specimens of children from a slum community by silver stained PAGE gels. Faecal specimen from four asymptomatic cases (P597_02_IND, K135_02_IND, A373_03_IND, A356_03_IND) and one diarrhoeic case (K135_03_IND) had genogroup I picobirnaviruses (1-CHN-97 like) showing amplicons within the 201 bp region, with primers PicoB25-PicoB43, targeting the conserved domain of RNA-dependent RNA polymerase (RdRp) gene. It was interesting to note that only the PBV strain P597_02_IND from Kolkata with large genome was closely related to a reported strain (similarity with 2-GA-91 from USA was 87% at the nucleotide level and 90% at the amino acid level). Sequence analysis showed three conserved amino acid domains as well as a highly conserved D-S-D motif, characteristic of RNA-dependent RNA polymerase gene of bisegmented, double stranded RNA viruses. Sequence data of the picobirnavirus A356_03_IND indicated strong heterogeneity with all other picobirnavirus strains sequenced till date. After nearly a decade a genogroup II picobirnavirus strain (R227_03_IND) was isolated from a diarrhoea case in the community, with small genome profile and amplified with specific primers PicoB23-PicoB24; but the sequence data showed that it was divergent from the hitherto reported prototype strain 4-GA-91 of genogroup II human picobirnaviruses.


Subject(s)
Picobirnavirus/genetics , Picobirnavirus/isolation & purification , RNA Virus Infections/epidemiology , RNA Virus Infections/virology , Amino Acid Sequence , Child, Preschool , Diarrhea/virology , Feces/virology , Genome, Viral , Humans , India/epidemiology , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Poverty Areas , Viral Proteins/genetics , Viral Proteins/metabolism
17.
Infect Genet Evol ; 6(6): 425-35, 2006 Nov.
Article in English | MEDLINE | ID: mdl-16546454

ABSTRACT

UNLABELLED: The study is aimed to determine the seasonal distribution and clinical characteristics of astroviruses associated with acute watery diarrhoea among children in Kolkata and characterize them at the molecular level. METHOD OF STUDY: Faecal specimens of acute watery diarrhoea cases (n=857) and non-diarrhoeic samples (n=211) from the hospitals and a nearby field community were screened with IDEIA Astrovirus detection kit; astrovirus co-infections with rotavirus and/or picobirnavirus were detected by RNA-PAGE and silver staining. Further RT-PCR was carried out using specific primers, viz. Mon340 (+) and Mon348 (-) targeting a highly conserved domain of ORF1a (289 bp) of human astroviruses. RESULTS: Astrovirus infection was detected in 50 cases (50/857); astroviruses were detected mostly in children aged 6-12 months (50%); all non-diarrhoeic samples (n=211) were negative for astrovirus. In 52% of astrovirus positive cases, the virus was detected as the sole agent; mixed infections were also detected with other diarrhoeic pathogens such as rotavirus (32%), picobirnavirus (2%), rotavirus and picobirnavirus (2%), picobirnavirus and Enterotoxigenic E. coli (ETEC) (2%), rotavirus and ETEC (2%), rotavirus and Enteroaggregative E. coli (EAEC) (2%), Enteropathogenic E. coli (EPEC) (2%), Shigella flexneri type 3a (2%) and Ascaris (2%). RT-PCR and sequencing of amplicons of astroviruses from Kolkata, with specific primers targeted to the conserved domain of ORF1a (289 bp) of the astrovirus genome, showed maximum homology to the astrovirus strain ("5-158") from Seoul (98%). RESULTS AND CONCLUSIONS: Clinical characteristics of the diarrhoeic children in Kolkata indicated that astrovirus infections were detected throughout the year and were associated with varying degree of dehydration and acute watery diarrhoea. In-depth molecular epidemiological surveillance of astroviruses in Kolkata is essential for better understanding of their overall genetic nature.


Subject(s)
Astroviridae Infections/epidemiology , Astroviridae Infections/virology , Mamastrovirus/genetics , Mamastrovirus/isolation & purification , Adult , Child , Child, Preschool , Diarrhea/epidemiology , Diarrhea/virology , Humans , India/epidemiology , Infant , Molecular Epidemiology , Phylogeny , Prevalence , Seasons
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