@article {152898, title = {BharatSim: An agent-based modelling framework for India.}, journal = {PLoS Comput Biol}, volume = {20}, year = {2024}, month = {2024 Dec}, pages = {e1012682}, abstract = {

BharatSim is an open-source agent-based modelling framework for the Indian population. It can simulate populations at multiple scales, from small communities to states. BharatSim uses a synthetic population created by applying statistical methods and machine learning algorithms to survey data from multiple sources, including the Census of India, the India Human Development Survey, the National Sample Survey, and the Gridded Population of the World. This synthetic population defines individual agents with multiple attributes, among them age, gender, home and work locations, pre-existing health conditions, and socio-economic and employment status. BharatSim{\textquoteright}s domain-specific language provides a framework for the simulation of diverse models. Its computational core, coded in Scala, supports simulations of a large number of individual agents, up to 50 million. Here, we describe the design and implementation of BharatSim, using it to address three questions motivated by the COVID-19 pandemic in India: (i) When can schools be safely reopened given specified levels of hybrid immunity?, (ii) How do new variants alter disease dynamics in the background of prior infections and vaccinations? and (iii) How can the effects of varied non-pharmaceutical interventions (NPIs) be quantified for a model Indian city? Through its India-specific synthetic population, BharatSim allows disease modellers to address questions unique to this country. It should also find use in the computational social sciences, potentially providing new insights into emergent patterns in social behaviour.

}, keywords = {Algorithms, Computational Biology, Computer Simulation, COVID-19, Humans, India, Machine Learning, Pandemics, SARS-CoV-2, Systems Analysis}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1012682}, author = {Cherian, Philip and Kshirsagar, Jayanta and Neekhra, Bhavesh and Deshkar, Gaurav and Hayatnagarkar, Harshal and Kapoor, Kshitij and Kaski, Chandrakant and Kathar, Ganesh and Khandekar, Swapnil and Mookherjee, Saurabh and Ninawe, Praveen and Noronha, Riz Fernando and Ranka, Pranjal and Sinha, Vaibhhav and Vinod, Tina and Yadav, Chhaya and Gupta, Debayan and Menon, Gautam I} } @article {150948, title = {Monitoring Influenza A (H1N1, H3N2), RSV, and SARS-CoV-2 Using Wastewater-Based Epidemiology: A 2-Year Longitudinal Study in an Indian Megacity Covering Omicron and Post-Omicron Phases.}, journal = {Food Environ Virol}, volume = {17}, year = {2024}, month = {2024 Nov 19}, pages = {3}, abstract = {

The bourgeoning field of wastewater-based epidemiology (WBE) for the surveillance of several respiratory viruses which includes Influenza A, H1N1pdm09, H3N2, respiratory syncytial viruses (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of interest for public health concerns. However, there are few long-term monitoring studies globally. In this study, respiratory viruses were detected and quantified from 11 sewer sheds by utilizing reverse transcription-quantitative polymerase chain reaction analysis in Pune city, India, from Jan 2022 to Dec 2023. The RNA fragments of respiratory viruses were detected in sewage samples before clinical cases were reported, underscoring the potential of WBE for early detection and monitoring within the population. The Spearman correlation of wastewater viral copies was positively and significantly correlated with the clinically positive case of H1N1pdm09 (ρ = 0.55, p = 1.4 {\texttimes} 10), H3N2 (ρ = 0.25, p = 9.9 {\texttimes} 10), and SARS-CoV-2 (ρ = 0.43, p = 4.1 {\texttimes} 10). The impact of public health interventions on the circulation of infectious respiratory diseases showed a significant difference in the viral load during the period when many preventing measures were carried out against the COVID-19 pandemic (restriction phase), compared to the period when no such preventive measures are followed (no-restriction phase) for Influenza A, H1N1pdm09, H3N2, and RSV with p-value \< 0.05, which indicates the influence of health policy implementation in controlling disease spread. The present study provides an effective approach to detecting multiple respiratory viruses from wastewater and provides insights into the epidemiology of respiratory illnesses. The WBE aids in providing information on the spread of pathogens (viruses) in the community, offering a proactive strategy for public health management, allowing for timely interventions and implementing targeted measures to mitigate the spread of these viruses under one health approach.

}, keywords = {Cities, COVID-19, Humans, India, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H3N2 Subtype, Influenza, Human, Longitudinal Studies, Respiratory Syncytial Virus Infections, Respiratory Syncytial Viruses, SARS-CoV-2, Sewage, Wastewater, Wastewater-Based Epidemiological Monitoring}, issn = {1867-0342}, doi = {10.1007/s12560-024-09618-y}, author = {Pramanik, Rinka and Nannaware, Kiran and Malik, Vinita and Shah, Priyanki and Sangewar, Poornima and Gogate, Niharika 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 Dharne, Mahesh} } @article {137335, title = {Niacinamide enhances cathelicidin mediated SARS-CoV-2 membrane disruption.}, journal = {Front Immunol}, volume = {14}, year = {2023}, month = {2023}, pages = {1255478}, abstract = {

The continual emergence of SARS-CoV-2 variants threatens to compromise the effectiveness of worldwide vaccination programs, and highlights the need for complementary strategies for a sustainable containment plan. An effective approach is to mobilize the body{\textquoteright}s own antimicrobial peptides (AMPs), to combat SARS-CoV-2 infection and propagation. We have found that human cathelicidin (LL37), an AMP found at epithelial barriers as well as in various bodily fluids, has the capacity to neutralise multiple strains of SARS-CoV-2. Biophysical and computational studies indicate that LL37{\textquoteright}s mechanism of action is through the disruption of the viral membrane. This antiviral activity of LL37 is enhanced by the hydrotropic action of niacinamide, which may increase the bioavailability of the AMP. Interestingly, we observed an inverse correlation between LL37 levels and disease severity of COVID-19 positive patients, suggesting enhancement of AMP response as a potential therapeutic avenue to mitigate disease severity. The combination of niacinamide and LL37 is a potent antiviral formulation that targets viral membranes of various variants and can be an effective strategy to overcome vaccine escape.

}, keywords = {Antimicrobial Cationic Peptides, Antiviral Agents, Cathelicidins, COVID-19, Humans, Niacinamide, SARS-CoV-2}, issn = {1664-3224}, doi = {10.3389/fimmu.2023.1255478}, author = {Bhatt, Tanay and Dam, Binita and Khedkar, Sneha Uday and Lall, Sahil and Pandey, Subhashini and Kataria, Sunny and Ajnabi, Johan and Gulzar, Shah-E-Jahan and Dias, Paul M and Waskar, Morris and Raut, Janhavi and Sundaramurthy, Varadharajan and Vemula, Praveen Kumar and Ghatlia, Naresh and Majumdar, Amitabha and Jamora, Colin} }