Molecular epidemiology of a familial cluster of SARS-CoV-2 infection during lockdown period in Sant Kabir Nagar, Uttar Pradesh, India
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SUBMITTER: Zaman K
PROVIDER: S-EPMC8438426 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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: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 emergence and rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a global crisis that required a detailed characterization of the dynamics of mutational pattern of the viral genome for comprehending its epidemiology, pathogenesis and containment. We investigated the molecular evolution of the SASR-CoV-2 genome during the first, second and third waves of COVID-19 in Uttar Pradesh, India. Nanopore sequencing of the SARS-CoV-2 genome was undertaken in 544 confirmed cases of COVID-19, which included vaccinated and unvaccinated individuals. In the first wave (unvaccinated population), the 20A clade (56.32%) was superior that was replaced by 21A Delta in the second wave, which was more often seen in vaccinated individuals in comparison to unvaccinated (75.84% versus 16.17%, respectively). Subsequently, 21A delta got outcompeted by Omicron (71.8%), especially the 21L variant, in the third wave. We noticed that Q677H appeared in 20A Alpha and stayed up to Delta, D614G appeared in 20A Alpha and stayed in Delta and Omicron variants (got fixed), and several other mutations appeared in Delta and stayed in Omicron. A cross-sectional analysis of the vaccinated and unvaccinated individuals during the second wave revealed signature combinations of E156G, F157Del, L452R, T478K, D614G mutations in the Spike protein that might have facilitated vaccination breach in India. Interestingly, some of these mutation combinations were carried forward from Delta to Omicron. In silico protein docking showed that Omicron had a higher binding affinity with the host ACE2 receptor, resulting in enhanced infectivity of Omicron over the Delta variant. This work has identified the combinations of key mutations causing vaccination breach in India and provided insights into the change of [virus's] binding affinity with evolution, resulting in more virulence in Delta and more infectivity in Omicron variants of SARS-CoV-2. Our findings will help in understanding the COVID-19 disease biology and guide further surveillance of the SARS-CoV-2 genome to facilitate the development of vaccines with better efficacies.
| S-EPMC9929466 | 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:Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes-49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.
| S-EPMC8777020 | 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:During 2018 an intensive study was conducted to determine the viruses associated with cucurbitaceous crops in nine agroclimatic zones of the state of Uttar Pradesh, India. Total of 563 samples collected and analysed across 14 different cucurbitaceous crops. The results showed the dominance of Begomovirus (93%) followed by Potyvirus (46%), cucumber green mottle mosaic virus (CGMMV-39%), Polerovirus (9%), cucumber mosaic virus (CMV-2%) and Orthotospovirus (2%). Nearly 65% of samples were co-infected with more than one virus. Additionally, host range expansion of CMV, CGMMV and polerovirus was also observed on cucurbit crops. A new potyvirus species, zucchini tigre mosaic virus, earlier not documented from India has also been identified on five crops during the study. Risk map generated using ArcGIS for virus disease incidence predicted the virus severity in unexplored areas. The distribution pattern of different cucurbit viruses throughout Uttar Pradesh will help identify the hot spots for viruses and will facilitate to devise efficient and eco-friendly integrated management strategies for the mitigation of viruses infecting cucurbit crops. Molecular diversity and evolutionary relationship of the virus isolates infecting cucurbits in Uttar Pradesh with previously reported strains were understood from the phylogenetic analysis. Diverse virus infections observed in the Eastern Plain zone, Central zone and North-Eastern Plain zone indicate an alarming situation for the cultivation of cucurbits in the foreseeable future.
| S-EPMC8429706 | biostudies-literature