@article {48995, title = {Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India}, journal = {Environmental Science and Pollution Research }, volume = {30}, year = {2023}, month = {DEC}, pages = {118976-118988}, type = {Article}, abstract = {

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.

}, keywords = {Bioinformatics pipeline, COVID-19, Early warning, India, Next-generation sequencing, Omicron, Public health, SARS-CoV-2, wastewater, Wastewater-based epidemiology}, issn = {0944-1344}, doi = {10.1007/s11356-023-30709-z}, author = {Rajput, Vinay and Pramanik, Rinka and Malik, Vinita and Yadav, Rakeshkumar and Samson, Rachel and Kadam, Pradnya and Bhalerao, Unnati and Tupekar, Manisha and Deshpande, Dipti and Shah, Priyanki and Shashidhara, L. S. and Boargaonkar, Radhika and Patil, Dhawal and Kale, Saurabh and Bhalerao, Asim and Jain, Nidhi and Kamble, Sanjay and Dastager, Syed and Karmodiya, Krishanpal and Dharne, Mahesh} } @article {48323, title = {Histidinal-based potent antimalarial agents}, journal = {ChemMedChem}, volume = {18}, year = {2023}, month = {MAY }, type = {Article}, abstract = {

Herein we report the synthesis and evaluation of peptide-histidinal conjugated drug scaffolds, which have the potential to target the hemoglobin-degrading proteases falcipain-2/3 from the human malaria parasite. Scaffolds with various substitutions were tested for antimalarial activity, and compounds 8 g, 8 h, and 15 exhibited EC50 values of similar to 0.018 mu M, similar to 0.069 mu M, and similar to 0.02 mu M, respectively. Structure-based docking studies on falcipain-2/3 proteases (PDB:2GHU and PDB:3BWK) revealed that compounds 8 g, 8 h, and 15 interact strongly with binding sites of falcipain-2/3 in a substrate-like manner. In silico ADME studies revealed that the molecules of interest showed no or minimal violations of drug-likeness parameters. Further, phenotypic assays revealed that compound 8 g and its biotinylated version inhibit hemoglobin degradation in the parasite food vacuole. The identification of falcipain-2/3 targeting potent inhibitors of the malaria parasite can serve as a starting point for the development of lead compounds as future antimalarial drug candidates.

}, keywords = {artemisinin, chloroquine, digestive vacuole, docking, falcipains, falciparum, P}, issn = {1860-7179}, doi = {10.1002/cmdc.202200709}, author = {Meena, Chhuttan L. and Hingamire, Tejashri and Gupta, Tanya and Deshmukh, Bhagyashree and Karmodiya, Krishanpal and Joshi, Rakesh and Shanmugam, Dhanasekaran and Sanjayan, Gangadhar J.} } @article {48819, title = {Tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India}, journal = {Journal of Infection and Public Health}, volume = {16}, year = {2023}, month = {AUG}, pages = {1290-1300}, type = {Article}, abstract = {

Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data.Methods: A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a {\textquoteleft}{\textquoteleft}band of five{\textquoteright}{\textquoteright} outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5).Results: The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. Conclusions: The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implica-tions for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.\& COPY; 2023 Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

}, keywords = {COVID-19, Delta, Omicron, SARS-CoV-2 genomic surveillance, Variant of concern, Whole Genome Sequencing (WGS)}, issn = {1876-0341}, doi = {10.1016/j.jiph.2023.06.004}, author = {Niveditha, Divya and Khan, Soumen and Khilari, Ajinkya and Nadkarni, Sanica and Bhalerao, Unnati and Kadam, Pradnya and Yadav, Ritu and Kanekar, Jugal B. and Shah, Nikita and Likhitkar, Bhagyashree and Sawant, Rutuja and Thakur, Shikha and Tupekar, Manisha and Nagar, Dhriti and Rao, Anjani G. and Jagtap, Rutuja and Jogi, Shraddha and Belekar, Madhuri and Pathak, Maitreyee and Shah, Priyanki and Ranade, Shatakshi and Phadke, Nikhil and Das, Rashmita and Joshi, Suvarna and Karyakarte, Rajesh and Ghose, Aurnab and Kadoo, Narendra and Shashidhara, L. S. and Monteiro, Joy Merwin and Shanmugam, Dhanasekaran and Raghunathan, Anu and Karmodiya, Krishanpal} } @article {49538, title = {32nd National Congress of Parasitology, Pune: bringing together India{\textquoteright}s parasitologists}, journal = {Trends in Parasitology}, volume = {41}, year = {2025}, month = {JAN}, pages = {1-7}, type = {Article}, abstract = {

The 32nd National Congress of Parasitology (NCP) was held in person, 3-5 October 2024, at the Indian Institute of Science Education and Research Pune (IISER Pune), jointly organized by IISER Pune; the Council of Scientific and Industrial Research - National Chemical Laboratory, Pune; and Savitribai Phule Pune University (formerly University of Pune) in association with the Indian Society for Parasitology. The conference brought together around 250 attendees from across the country and abroad, including a diverse group of researchers, clinicians, industry experts, and students. The event provided a collaborative environment for exchanging research ideas relevant to the field of parasitology. The congress emphasized the concept of One Health, a holistic approach to address parasitic infections affecting humans and animals to promote overall health and well-being. In this TrendsTalk, the organizers provide an overview of the conference proceedings, which brought together India{\textquoteright}s vast and diverse parasitology community.

}, issn = {1471-4922}, doi = {10.1016/j.pt.2024.10.022}, author = {Purkayastha, Devatrisha and Pandit, Kushankur and Upadrasta, Sindhuri and Khilari, Ajinkya and Shanmugam, Dhanasekaran and Karmodiya, Krishanpal} }