Genomic characterization of Nipah virus, West Bengal, India.
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ABSTRACT:
SUBMITTER: Arankalle VA
PROVIDER: S-EPMC3321761 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
| S-EPMC2666291 | biostudies-literature
Project description:Northern West Bengal, popularly known as North Bengal, is a dengue-endemic area, which has been severely affected by Dengue in the past few years resulting in massive hospitalizations and deaths. Genetic characterization of the circulating endemic dengue virus (DENV) serotypes is of paramount importance for the epidemiological understanding of the infection and subsequent vaccine development. The present study was conceived to characterize circulating dengue serotypes and to undertake phylogenetic study. EDTA blood samples of all (N = 83) NS1-positive cases of patients with acute febrile illness referred to different health care facilities were collected and processed for RNA isolation followed by the complementary DNA (cDNA) preparation. Serotype determination of dengue infection was done using conventional PCR by targeting the viral C-prM region. Phylogenetic tree was constructed by implementing the Maximum likelihood method. Out of 83 blood samples 17 were detected to be positive for the presence of dengue viral RNA. DENV3 was found to be the predominant serotype in the single-infection cases; however, we have detected multi-serotypic co-infections throughout the study. Joint pain was found to be the most valuable symptom for the prognosis of dengue. Sequence analyses suggested that both DENV1- and DENV3-circulating genotypes are in the genotype III group and remain closely related to the Indian clade. To the best of our knowledge, this is the first report on the genetic characterization of circulating DENVs in North Bengal, which may contribute to the study of dengue epidemic and pathogenesis.
| S-EPMC9630820 | biostudies-literature
Project description:Subclinical mastitis in bovines is mainly responsible for the huge economic loss of the dairy farmers, of which Pseudomonas aeruginosa is one of the causative agents. The study was aimed at a screening of suspected milk samples from different cattle farms of West Bengal for detection and confirmation of P. aeruginosa strains followed by their characterization.Around 422 milk samples were screened from different dairy farms primarily by on-spot bromothymol blue (BTB) test and then in the lab by somatic cell counts (SCC) to finally consider 352 samples for detection of P. aeruginosa. Selective isolation and confirmation of the isolates were done using selective media, viz., cetrimide and Pseudomonas agar followed by confirmation by fluorescent technique. Molecular characterization of the strains was done by polymerase chain reaction for the presence of toxA (enterotoxin A, 352 bp) and exoS (exoenzyme S, 504 bp) genes.Approximately, 371 (87.9%) samples were positive in on-spot BTB test among which 352 (94.8%) samples revealed high SCC values (more than 3 lakh cells/ml) showing infection when screened. Among these, 23 (6.5%) samples yielded typical Pseudomonas sp. isolates out of which only 19 (5.4%) isolates were confirmed to be P. aeruginosa which showed characteristic blue-green fluorescence due to the presence of pigment pyoverdin under ultraviolet light. Out of these 19 isolates, 11 isolates were positive for toxA, 6 isolates for exoS, and 2 for both these pathogenic genes.Approximately, 5.4% cases of bovine subclinical mastitis infections in South Bengal were associated with P. aeruginosa which possess pathogenic genes such as toxA (63.2%) and exoS (36.8%).
| S-EPMC5553139 | biostudies-other
Project description:Background & objectivesJapanese encephalitis (JE), caused by a mosquito-borne virus JE virus (JEV), is a serious health problem in West Bengal, India. In this study, we report the complete genome sequence of two JEV isolates from West Bengal. The amino acid and nucleotide sequence homology was compared with other Indian strains.MethodsTwo JEV isolates (IND-WB-JE1 and IND-WB-JE2) obtained in 2008 and 2010, respectively, from two districts of the State of West Bengal, respectively were analyzed for genetic variations by sequencing the 10934 bp whole genome of the virus. Of these two districts, one was covered under JE vaccination programme in 2007.ResultsPhylogenetic analysis showed that both the isolates belonged to the genotype III. A total of 16 mutations were identified in the two isolates studied with respect to Vellore P20778 strain. One unique mutation A3215S was only found in IND-WB-JE2 isolate, but not in the isolate IND-WB-JE1. These two isolates showed maximum homology with P20778 strain of India.Interpretation & conclusionsThis study reports on complete gene based phylogenetic analysis of JEV isolates from the State of West Bengal. It was evident from the results that JEV was still under circulation in both vaccine covered and not covered districts of West Bengal.
| S-EPMC4557254 | biostudies-literature
Project description:During January and February 2001, an outbreak of febrile illness associated with altered sensorium was observed in Siliguri, West Bengal, India. Laboratory investigations at the time of the outbreak did not identify an infectious agent. Because Siliguri is in close proximity to Bangladesh, where outbreaks of Nipah virus (NiV) infection were recently described, clinical material obtained during the Siliguri outbreak was retrospectively analyzed for evidence of NiV infection. NiV-specific immunoglobulin M (IgM) and IgG antibodies were detected in 9 of 18 patients. Reverse transcription-polymerase chain reaction (RT-PCR) assays detected RNA from NiV in urine samples from 5 patients. Sequence analysis confirmed that the PCR products were derived from NiV RNA and suggested that the NiV from Siliguri was more closely related to NiV isolates from Bangladesh than to NiV isolates from Malaysia. NiV infection has not been previously detected in India.
| S-EPMC3373078 | biostudies-literature
Project description:The 2018 outbreak of Nipah virus in Kerala, India, highlights the need for global surveillance of henipaviruses in bats, which are the reservoir hosts for this and other viruses. Nipah virus, an emerging paramyxovirus in the genus Henipavirus, causes severe disease and stuttering chains of transmission in humans and is considered a potential pandemic threat. In May 2018, an outbreak of Nipah virus began in Kerala, > 1800 km from the sites of previous outbreaks in eastern India in 2001 and 2007. Twenty-three people were infected and 21 people died (16 deaths and 18 cases were laboratory confirmed). Initial surveillance focused on insectivorous bats (Megaderma spasma), whereas follow-up surveys within Kerala found evidence of Nipah virus in fruit bats (Pteropus medius). P. medius is the confirmed host in Bangladesh and is now a confirmed host in India. However, other bat species may also serve as reservoir hosts of henipaviruses. To inform surveillance of Nipah virus in bats, we reviewed and analyzed the published records of Nipah virus surveillance globally. We applied a trait-based machine learning approach to a subset of species that occur in Asia, Australia, and Oceana. In addition to seven species in Kerala that were previously identified as Nipah virus seropositive, we identified at least four bat species that, on the basis of trait similarity with known Nipah virus-seropositive species, have a relatively high likelihood of exposure to Nipah or Nipah-like viruses in India. These machine-learning approaches provide the first step in the sequence of studies required to assess the risk of Nipah virus spillover in India. Nipah virus surveillance not only within Kerala but also elsewhere in India would benefit from a research pipeline that included surveys of known and predicted reservoirs for serological evidence of past infection with Nipah virus (or cross reacting henipaviruses). Serosurveys should then be followed by longitudinal spatial and temporal studies to detect shedding and isolate virus from species with evidence of infection. Ecological studies will then be required to understand the dynamics governing prevalence and shedding in bats and the contacts that could pose a risk to public health.
| S-EPMC6597033 | biostudies-literature
Project description:Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV and the substitutions observed were mostly not present in the region of any functional significance except for the phosphoprotein gene. The differential expression of viral genes was observed following infection in Vero (ATCC® CCL-81™) and BHK-21 cells. Intraperitoneal infection in the 10-12-week-old, Syrian hamster model induced dose dependant multisystemic disease characterized by prominent vascular lesions in lungs, brain, kidney and extra vascular lesions in brain and lungs. Congestion, haemorrhages, inflammatory cell infiltration, thrombosis and rarely endothelial syncitial cell formation were seen in the blood vessels. Intranasal infection resulted in respiratory tract infection characterised by pneumonia. The model showed disease characteristics resembling the human NiV infection except that of myocarditis similar to that reported by NiV-Malaysia and NiV-Bangladesh isolates in hamster model. The variation observed in the genome of the Indian isolate at the amino acid levels should be explored further for any functional significance.
| S-EPMC10281463 | biostudies-literature
Project description:Background: The community form of palliative care first constructed in Kerala, India has gained recognition worldwide. Although it is the subject of important claims about its replicability elsewhere, little effort has gone into studying how this might occur. Drawing on translation studies, we attend to under-examined aspects of the transfer of a community palliative care intervention into a new geographic and institutional context. Methods: Over a period of 29 months, we conducted an in-depth case study of Sanjeevani, a community-based palliative care organization in Nadia district, West Bengal (India), that is modelled on the Kerala approach. We draw upon primary (semi-structured interviews and field notes) and secondary data sources. Results: We identify the translator's symbolic power and how it counteracts the organizational challenges relating to socio-economic conditions and weak histories of civil society organizing. We find that unlike the Kerala form, which is typified by horizontal linkages and consensus-oriented decision-making, the translated organizational form in Nadia is a hybrid of horizontal and vertical solidarities. We show how translation is an ongoing, dynamic process, where community participation is infused with values of occupational prestige and camaraderie and shaped by emergent vertical solidarities among members. Conclusions: Our findings have implications for how we understand the relationship between locations, institutional histories, and healthcare interventions. We contribute to translation studies in healthcare, and particularly to conversations about the transfer or 'roll out' of palliative care interventions from one geography to another.
| S-EPMC6069742 | biostudies-literature
Project description:BackgroundFew studies have documented the blood group antigens in the population of eastern India. Frequencies of some common alleles and haplotypes were unknown. We describe phenotype, allele, and haplotype frequencies in the state of West Bengal, India.MethodsWe tested 1,528 blood donors at the Medical College Hospital, Kolkata. The common antigens of the ABO, Rhesus, and Kell blood group systems were determined by standard serologic methods in tubes. Allele and haplotype frequencies were calculated with an iterative method that yielded maximum-likelihood estimates under the assumption of a Hardy-Weinberg equilibrium.ResultsThe prevalence of ABO antigens were B (34%), O (32%), A (25%), and AB (9%) with ABO allele frequencies for O = 0.567, A = 0.189, and B = 0.244. The D antigen (RH1) was observed in 96.6% of the blood donors with RH haplotype frequencies, such as for CDe = 0.688809, cde = 0.16983 and CdE = 0.000654. The K antigen (K1) was observed in 12 donors (0.79%) with KEL allele frequencies for K = 0.004 and k = 0.996. Conclusions: For the Bengali population living in the south of West Bengal, we established the frequencies of the major clinically relevant antigens in the ABO, Rhesus, and Kell blood group systems and derived estimates for the underlying ABO and KEL alleles and RH haplotypes. Such blood donor screening will improve the availability of compatible red cell units for transfusion. Our approach using widely available routine methods can readily be applied in other regions, where the sufficient supply of blood typed for the Rh and K antigens is lacking.
| S-EPMC5836283 | biostudies-literature
Project description:The data represents the bacterial community profile obtained through metagenomic sequencing of soil sample, collected from the 'Rarh' region of West Bengal, which is characterized by the lateritic badlands dating back to the late Pleistocene. Taxonomic binning and operational taxonomic unit (OTU) prediction of the Illumina sequencing data indicated the abundance Proteobacteria (61%) followed closely by Bacterioidetes (35%). The top two most abundant genera identified, were Sphingobacterium and Acinetobacter respectively. Chemical properties of soil, such as pH, organic carbon content, available nitrogen, phosphorus, and potassium were also analyzed for enabling future researchers to correlate the abundance of microbial taxa with the prevalent conditions. These findings can be effectively used to formulate strategic microbiome engineering through bioaugmentation for a sustainable agricultural system.
| S-EPMC8086014 | biostudies-literature