Investigations on annual spreading of viruses infecting cucurbit crops in Uttar Pradesh State, India.
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SUBMITTER: Kumari S
PROVIDER: S-EPMC8429706 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:An outbreak of viral encephalitis occurred in northern India in 2006. Attempts to identify an etiologic agent in cerebrospinal fluid by using reverse transcription-PCR showed positivity to enterovirus (EV) in 66 (21.6%) of 306 patients. Sequencing and phylogenetic analyses of PCR products from 59 (89.3%) of 66 specimens showed similarity with EV-89 and EV-76 sequences.
| S-EPMC2657625 | biostudies-literature
Project description:The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
| S-EPMC10491582 | biostudies-literature
Project description:Scrub typhus (ST) caused by Orientia tsutsugamushi (OT), has long been known to cause acute encephalitis syndrome (AES) and acute febrile illness (AFI). The immunodominant 56 kDa protein of OT, which is encoded by the 56 kDa gene (1600 bp encoding 516-541 amino acids) is a commonly studied antigen for genotype and serotype assignment. Previous studies from India have utilized partial type specific antigen (TSA) 56 kDa sequences for OT strain characterisation. On the other hand, understanding the antigenic diversity of current OT strains, is critical for developing specific diagnostic tests and vaccines against ST. As a result, the current study analyses antigenic variants using the entire TSA56 ORF of OT from AES cases. Phylogenetic investigation using complete TSA56 ORF sequences revealed Karp and Gilliam were the circulating predominant strains of OT. Furthermore, Immuno-informatical analysis demonstrated that the majority of high-binding affinity CD4 TCEs against the most prevalent Indian human leukocyte antigen alleles were present in the S-VDIII/IV and S-VDIV spacer regions of TSA56 ORF. TSA56 conserved spacer is crucial for OT immunological response investigations. Further, the pathophysiological effects of spacer domains in ST require further investigation. Furthermore, the characterization of the TSA56 spacer region of the OT from different parts of India is critical for developing region-specific ST diagnostic assays and vaccines.
| S-EPMC10082565 | biostudies-literature
Project description:BackgroundThe sustainable development goals (SDG) aim at satisfying three-fourths of family planning needs through modern contraceptive methods by 2030. However, the traditional methods (TM) of family planning use are on the rise, along with modern contraception in Uttar Pradesh (UP), the most populous Indian state. This study attempts to explore the dynamics of rising TM use in the state.MethodsWe used a state representative cross-sectional survey conducted among 12,200 Currently Married Women (CMW) aged 15-49 years during December 2020-February 2021 in UP. Using a multistage sampling technique, 508 primary sampling units (PSU) were selected. These PSU were ASHA areas in rural settings and Census Enumeration Blocks in urban settings. About 27 households from each PSU were randomly selected. All the eligible women within the selected households were interviewed. The survey also included the nearest public health facilities to understand the availability of family planning methods. Univariate and bivariate analyses were conducted. Appropriate sampling weights were applied.ResultsOverall, 33.9% of CMW were using any modern methods and 23.7% any TM (Rhythm and withdrawal) at the time of survey. The results show that while the modern method use has increased by 2.2 percentage points, the TM use increased by 9.9 percentage points compared to NFHS-4 (2015-16). The use of TM was almost same across women of different socio-demographic characteristics. Of 2921 current TM users, 80.7% started with TM and 78.3% expressed to continue with the same in future. No side effects (56.9%), easy to use (41.7%) and no cost incurred (38.0%) were the main reasons for the continuation of TM. TM use increased despite a significant increase (66.1 to 81.3%) in the availability of modern reversible methods and consistent availability of limiting methods (84.0%) in the nearest public health facilities.ConclusionInitial contraceptive method was found to have significant implications for current contraceptive method choice and future preferences. Program should reach young and zero-parity women with modern method choices by leveraging front-line workers in rural UP. Community and facility platforms can also be engaged in providing modern method choices to women of other parities to increase modern contraceptive use further to achieve the SDG goals.
| S-EPMC9817250 | biostudies-literature
Project description:Outbreaks of acute encephalitis syndrome (AES) have been occurring in Gorakhpur Division, Uttar Pradesh, India, for several years. In 2016, we conducted a case-control study. Our findings revealed a high proportion of AES cases with Orientia tsutsugamushi IgM and IgG, indicating that scrub typhus is a cause of AES.
| S-EPMC5547812 | biostudies-literature
Project description:IntroductionAbortion is legal in India and medication abortion (MA) using a combined regimen of mifepristone and misoprostol is the preferred method. Users increasingly purchase MA kits directly from pharmacies, in some cases experiencing perceived complications and approaching a facility for care. We present findings of a qualitative research tracing the decision-making pathway(s) of MA users in Uttar Pradesh, India, to help understand knowledge and behaviour gaps, and recommend ways to improve the overall quality of care at these service delivery points.MethodsForty in-depth interviews were conducted with recent MA users (20 each of clinic and pharmacy clients) across three districts. Providers were purposively selected in collaboration with an international organization selling MA kits, using their list of pharmacies and clinics. MA users were identified from the clients of the selected providers, and additionally through the snow ball method. Interviews were conducted in Hindi with verbal informed consent in a private place convenient to the respondent. Transcripts were translated to English and analysed thematically.ResultsUsers first sought MA kits at pharmacies out of convenience, low cost and customer anonymity. Men often purchased kits for their partners and trusted the chemist for guidance on dosage, progression and side effects. For side effects or other concerns after using an MA kit, users first visited their neighbourhood doctor or traditional practitioner. These providers either attempted to treat the issue and failed, or directly advised her to consult a gynaecologist. The final point of care was gynaecologists, preferably female private practitioners with their own clinics. They diagnosed most abortion-related cases as incomplete abortions, emptying the uterus using the dilation and curettage method. Comparatively low cost and convenience made users inclined towards repeat use of MA.ConclusionThere are information gaps at various stages in the MA pathway that need to be addressed. Large scale public information programmes are required on safe abortion care- when is it legal, where to obtain MA, dosage, side effects and signs of possible complications. Pharmacists could be trained or incentivized to improve their quality of care to facilitate adequate exchange of information on MA. Since, for most couples, the male partner purchases MA, information approaches or tools are needed that pharmacists can give men to share directly with the MA user.
| S-EPMC6513085 | biostudies-literature
Project description:IntroductionSince ancient times leprosy has had a negative perception, resulting in stigmatization. To improve the lives of persons affected by leprosy, these negative perceptions need to change. The aim of this study is to evaluate interventions to change perceptions and improve knowledge of leprosy.Methodology/principal findingsWe conducted a pre-post intervention study in Fatehpur and Chandauli districts, Uttar Pradesh, India. Based on six steps of quality intervention development (6SQuID) two interventions were designed: (1) posters that provided information about leprosy and challenged misconceptions, and (2) meetings with persons affected by leprosy, community members and influential people in the community. The effect of the interventions was evaluated in a mixed-methods design; in-depth interviews, focus group discussions, and questionnaires containing a knowledge measure (KAP), two perception measures (EMIC-CSS, SDS) and an intervention evaluation tool. 1067 participants were included in Survey 1 and 843 in Survey 2. The interventions were effective in increasing knowledge of all participant groups, and in changing community and personal attitudes of close contacts and community members (changes of 19%, 24% and 13% on the maximum KAP, EMIC-CSS and SDS scores respectively, p<0.05). In Survey 1, 13% of participants had adequate knowledge of leprosy versus 53% in Survey 2. Responses showed stigmatizing community attitudes in 86% (Survey 1) and 61% (Survey 2) of participants and negative personal attitudes in 37% (Survey 1) and 19% (Survey 2). The number of posters seen was associated with KAP, EMIC-CSS and SDS scores in Survey 2 (p<0.001). In addition, during eight post-intervention focus group discussions and 48 interviews many participants indicated that the perception of leprosy in the community had changed.Conclusions/significanceContextualized posters and community meetings were effective in changing the perception of leprosy and in increasing leprosy-related knowledge. We recommend studying the long-term effect of the interventions, also on behavior.
| S-EPMC8412405 | biostudies-literature
Project description:BackgroundAlmost 3 quarters of India's roughly 16 million annual abortions are done through medication abortion purchased from pharmacists outside of healthcare facilities. The quality of information provided by pharmacists about medication abortion is often poor.ObjectiveTo determine whether pharmacists selling medication abortion provide different information or ask different, potentially stigmatizing questions to clients by gender and marital status.Study designMystery clients presenting as 4 profiles (unmarried woman, unmarried man, married woman, and married man) purchasing medication abortion interacted with 111 pharmacists in 3 districts around Lucknow, Uttar Pradesh in 2018. Data were collected immediately after the interaction. The differences in the information conveyed and the questions asked by the pharmacists by mystery client characteristics were analyzed using logistic regression in Stata 15 MP.ResultsPharmacists very rarely asked intrusive, medically irrelevant questions and appeared willing to sell medication abortion to all the mystery clients regardless of gender, age, or marital status. However, the pharmacists were overall less likely to provide the female mystery clients with as comprehensive and correct information on medication abortion as they were to male mystery clients, particularly if female mystery clients presented as unmarried.ConclusionPharmacists are observed to provide differential and poorer quality information about medication abortion to women, especially if they seem unmarried, potentially putting women at risk of having a lower-quality and less supported experience of using the medication. However, the pharmacists' willingness to sell the medication to all mystery clients and the lack of intrusive questions and comments reinforces out-of-facility medication abortion as a way for individuals to access an often-stigmatized service. Interventions must find a way to either address this bias among pharmacists, or more practically, to provide high-quality information directly to the individuals seeking medication abortion.
| S-EPMC9563544 | biostudies-literature
Project description:Abstract Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives Cryptococcosis affects more than one million people per year worldwide. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. The ecological niche of the etiological agents of C. neoformans and C. gattii are not well established yet in various parts of India. Methodology The present study was performed on the C. neoformans isolated from the Eucalyptus terreticornis at Varanasi, India. A total of 265 samples including flowers, leaves, bark, and nearby soil of E. terreticornis. The fungal pathogens were identified by both the conventional and molecular methods. The isolates were also grown in Staib's and tobacco agar medium. In addition, all isolates were identified on the basis of different biochemical tests such as urease test and canavanine-glycine-bromothymol blue (CGB). Further, molecular characterization was carried out by using PCR and DNA sequence analyses. Results Of all the 265 samples, 11 were positive for C. neoformans. 8% (4/50) for E. tereticornis bark, 5% (3/60) for nearby soil, 6.66% (2/30) for debris, and 3.07% (2/65) for decayed wood from tree hollows. C. neoformans was not recovered from the leaves and flowers of E. tereticornis. The presence of brown colonies on Staib's and tobacco agar media confirmed that the isolated pathogen is Cryptococcus. Further the isolates of Cryptococcus were tested for urease production using Christensen urea citrate agar medium in which all isolates were found to hydrolyze urea rapidly and reddish pink color was obtained confirming it to be C. neoformans. All isolated yeast were negative for Canavanine glycinebromothymol blue (CGB) as they fail to produce a color change in the medium. Five strains were identified as C. neoformans var. grubii and one of the isolates was identified as C. neoformans var. neoformans. Molecular typing grouped the isolates into two major genotypes. Five were molecular type VNI (serotype A, var. grubii), one of the isolates was molecular type VNIV (serotype D, var. neoformans). Figure 3 shows the Gel electrophoresis image of ITS1- ITS4 amplicons. The nucleotide sequences were submitted in NCBI GenBank with accession numbers MZ824412, MZ848145, MZ823611, MZ882370, MZ882372, and MZ817986. Conclusion In spite of a major Eucalyptus growing region of India, there is no report of C. neoformans/C. gattii-Eucalyptus association from Eastern Uttar Pradesh. Therefore, the current study would certainly be helpful in the establishment of molecular epidemiology of Cryptococcus in this area.
| S-EPMC9509839 | biostudies-literature
Project description:BackgroundGenetic analysis of measles viruses associated with recent cases and outbreaks has proven to bridge information gaps in routine outbreak investigations and has made a substantial contribution to measles control efforts by helping to identify the transmission pathways of the virus.Materials and methodsThe present study describes the genetic characterization of wild type measles viruses from Uttar Pradesh, India isolated between January 2008 and January 2011. In the study, 526 suspected measles cases from 15 outbreaks were investigated. Blood samples were collected from suspected measles outbreaks and tested for the presence of measles specific IgM; throat swab and urine samples were collected for virus isolation and RT-PCR. Genotyping of circulating measles viruses in Uttar Pradesh was performed by sequencing a 450-bp region encompassing the nucleoprotein hypervariable region and phylogenetic analysis.Results and conclusionBased on serological results, all the outbreaks were confirmed as measles. Thirty eight strains were obtained. Genetic analysis of circulating measles strains (n = 38) in Uttar Pradesh from 235 cases of laboratory-confirmed cases from 526 suspected measles cases between 2008 and 2011 showed that all viruses responsible for outbreaks were within clade D and all were genotype D8.Analysis of this region showed that it is highly divergent (up to 3.4% divergence in the nucleotide sequence and 4.1% divergence in the amino acid sequence between most distant strains). Considerable genetic heterogeneity was observed in the MV genotype D8 viruses in North India and underscores the need for continued surveillance and in particular increases in vaccination levels to decrease morbidity and mortality attributable to measles.
| S-EPMC3544691 | biostudies-literature