03254nas a2200493   4500008004100000022001400041245016200055210006900217260000800286300001800294490000700312520171400319653002802033653001302061653001802074653001002092653003102102653001202133653001802145653001502163653001502178653003402193100001802227700002002245700001802265700002302283700001902306700001902325700002102344700002102365700002102386700001902407700002402426700002502450700001802475700001802493700001902511700001602530700001902546700001902565700002602584700001902610856013102629       2023                        eng d  a0944-134400aGenomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India0 aGenomic surveillance reveals early detection and transition of d  cDEC  a118976-1189880 v303 a<p>
	The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (similar to 28%), BA.1.X (1.0-72%), BA.2 (1.0-18%), BA.2.X (1.0-97.4%) BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-21.83%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.</p>
10aBioinformatics pipeline10aCOVID-1910aEarly warning10aIndia10aNext-generation sequencing10aOmicron10aPublic health10aSARS-CoV-210awastewater10aWastewater-based epidemiology1 aRajput, Vinay1 aPramanik, Rinka1 aMalik, Vinita1 aYadav, Rakeshkumar1 aSamson, Rachel1 aKadam, Pradnya1 aBhalerao, Unnati1 aTupekar, Manisha1 aDeshpande, Dipti1 aShah, Priyanki1 aShashidhara, L., S.1 aBoargaonkar, Radhika1 aPatil, Dhawal1 aKale, Saurabh1 aBhalerao, Asim1 aJain, Nidhi1 aKamble, Sanjay1 aDastager, Syed1 aKarmodiya, Krishanpal1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/genomic-surveillance-reveals-early-detection-and-transition-delta-omicron-lineages-sars-cov02417nas a2200169   4500008004100000022001400041245014800055210006900203260000800272300001100280490000800291520175900299100002302058700001902081700001902100856012802119       2025                        eng d  a0023-643800aGenome mining, probiotic characteristics, and in-silico safety assessment of Limosilactobacillus fermentum AV7 isolated from Avocado fruit pulp0 aGenome mining probiotic characteristics and insilico safety asse  cJAN  a1172310 v2163 a<p>
	Limosilactobacillus fermentum holds substantial promise for probiotic applications in human health and various industries. Herein, we present the first report of L. fermentum AV7 isolated from the avocado pulp and assessed for its probiotic potentials and safety through probiogenomic analyses and In-vitro probiotic assays. The genomic insights revealed genes associated with acid and bile tolerance and antimicrobial peptide production, highlighting the probiotic potential of the strain AV7. Notably, the in-silico safety analysis showed that the genome of L.fermentum AV7 is devoid of plasmid and lacks any putative antibiotic resistance or pathogenic traits, ensuring its safety for human consumption. Beyond the genomic and in-silico analysis, we also aimed to evaluate the probiotic potentials of AV7 strain using in- vitro tests for acid, gastric juice, intestinal fluid and bile tolerance, resilience to osmotic stress, followed by auto-aggregation and co-aggregation assays with Escherichia coli ATCC 8739. The data obtained through in-vitro studies confirmed the efficacy of L.fermentum AV7 as a probiotic strain, and positions it as a potent probiotic candidate, expanding the scope of probiotic research. Our study investigates avocados, a nutrient-dense fruit, as a novel source of beneficial lactic acid bacteria, thereby attracting innovative dietary and therapeutic applications. By introducing L .fermentum AV7 into the probiotic landscape, we pave the way for new health benefits from this beloved fruit. The research not only adds a new dimension to avocado utilization but also contributes to the relatively unexplored field of isolating beneficial bacteria from avocados, promising exciting advancements in human health.</p>
1 aMahajan, Vaishnavi1 aSamson, Rachel1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/genome-mining-probiotic-characteristics-and-silico-safety-assessment-limosilactobacillus