Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized, and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.
Background: Health care workers are at greater risk of infection during COVID 19 pandemic. This study was carried out to assess the knowledge and attitude toward COVID-19 among healthcare workers at working at Seti Zonal Hospital. Methods: A cross-sectional study was performed between April and May 2020 at Seti Zonal Hospital with purposive sampling technique and self-administered questionnaire of the knowledge and attitude of healthcare workers regarding COVID-19. The demographic characteristics mean knowledge and attitude score of healthcare workers were identified and inferential statistics t-test, ANOVA and Spearman’s correlation were used to show the relationship between variables. Results: A total of 230 healthcare workers (92% response rate) had a mean score of knowledge and attitude of 8±0.88 and 7.88±1.32, respectively with good knowledge and a low positive attitude. Majority (94.7%) were familiar with the sign and symptoms, agreed that chronic diseases patients and HCWs are at a higher risk (97%) and (87.8%) respectively while knowledge related to COVID 19 vaccination, isolation period and treatment by antibiotics was poor with low positive attitude towards information availability about COVID 19 (41%), government ability to control the epidemic (49%), and the family members might get infection (60%). There was a positive correlation between knowledge scores and attitude scores (r=0.28, p<0.0001). Conclusions: We identified a significant gap in information source, sufficient knowledge and low positive attitude about COVID 19 among health care workers. Greater educational efforts about prevention should be directed to different level of health workers. Keywords: Attitude; COVID-19; health care worker; knowledge.
Background Excessive and irrational use of antibiotics as growth promoters in poultry has been one of key factors contributing to increased emergence of antibiotics resistant bacteria. Several alternatives for antibiotic growth promoters are being sought, and the search for effective probiotics to be used as feed additives is amongst the promising ones. Our study aimed to isolate and test potential probiotics bacteria from cloacal swabs of various indigenous chicken (Gallus domesticus) breeds from rural outskirts of the Kathmandu valley (Nepal). Methods Selective isolation of probiotics was conducted by micro-aerophilic enrichment of sample in MRS Broth at 37°C, followed by culturing on MRS agar supplemented with 5 g/L of CaCO3. Isolated bacterial colonies producing transparent halo were selected as potential lactic acid bacteria (LAB), and tested for their antibacterial activity, phenotypic and biochemical characteristics, acidic yield, and tolerance to acid and bile. Results A total of 90 potential LAB were isolated from cloacal samples collected from 41 free-ranging chickens of indigenous breeds. Of these, 52 LAB isolates (57%) showed variable antibacterial activity to at least one bacterial pathogen. Of 52 LAB, 46 isolates fulfilled phenotypic and biochemical criteria of Lactobacillus spp. Of these, 37 isolates produced varying percentage yields of lactic acid, 27 isolates showed survival at pH 3.0, and 17 isolates showed survival tolerances in the presence of 0.3% and 0.5% bile salts for 24 hours. Phylogenetic analysis of 16S rDNA sequencing of LAB isolates fulfilling in vitro probiotics properties showed that 3 isolates had genetic identity of 99.38% with Lactobacillus plantarum, while one isolate was genetically similar (99.85%) with the clade of L. reuteri, L. antri and L. panis. Conclusion Our study identified four Lactobacillus spp. strains having potential probiotics properties. Further investigations are needed to evaluate these isolates to be used as poultry probiotics feed supplement.
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