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Abhinand CS, Ibrahim J, Keshava Prasad TS, Raju R, Oommen OV, Nair AS. Molecular docking and dynamics studies for the identification of Nipah virus glycoprotein inhibitors from Indian medicinal plants. J Biomol Struct Dyn 2023; 41:9211-9218. [PMID: 36473711 DOI: 10.1080/07391102.2022.2153169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
The infection by Nipah Virus (NiV), a zoonotic paramyxovirus, is fatal and several outbreaks have been reported in humans in various countries. No effective vaccines or drugs are developed till date to control this infection. The NiV-Glycoprotein (NiV-G) is one of the essential proteins for viral entry by binding to the Ephrin-B receptors. The present study screens the potential phytocompounds that can target NiV-G and thereby inhibit the viral entry to human. Computer-aided virtual screening of 1426 phytocompounds from various medicinal plants was carried out to investigate their efficacy as potential therapeutics. Ribavirin, the currently used drug, was also docked to compare the docking score and intermolecular interactions between ligand and target protein. Further, molecular dynamics simulations and MM-PBSA binding free energy calculations were performed to understand the stability of the docked complexes. Radius of gyrations and Solvent Accessible Surface Area were also performed to evaluate the compactness and solvent behaviour of ligand-receptor complexes during the 100 ns simulation. Our analysis revealed that the alkaloid, Serpentinine, has the highest potency to block NiV-G with favourable binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chandran S Abhinand
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Junaida Ibrahim
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India
| | - Oommen V Oommen
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, India
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Lewis CE, Pickering B. Livestock and Risk Group 4 Pathogens: Researching Zoonotic Threats to Public Health and Agriculture in Maximum Containment. ILAR J 2022; 61:86-102. [PMID: 34864994 PMCID: PMC8759435 DOI: 10.1093/ilar/ilab029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 09/12/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Maximum-containment laboratories are a unique and essential component of the bioeconomy of the United States. These facilities play a critical role in the national infrastructure, supporting research on a select set of especially dangerous pathogens, as well as novel, emerging diseases. Understanding the ecology, biology, and pathology at the human-animal interface of zoonotic spillover events is fundamental to efficient control and elimination of disease. The use of animals as human surrogate models or as target-host models in research is an integral part of unraveling the interrelated components involved in these dynamic systems. These models can prove vitally important in determining both viral- and host-factors associated with virus transmission, providing invaluable information that can be developed into better risk mitigation strategies. In this article, we focus on the use of livestock in maximum-containment, biosafety level-4 agriculture (BSL-4Ag) research involving zoonotic, risk group 4 pathogens and we provide an overview of historical associated research and contributions. Livestock are most commonly used as target-host models in high-consequence, maximum-containment research and are routinely used to establish data to assist in risk assessments. This article highlights the importance of animal use, insights gained, and how this type of research is essential for protecting animal health, food security, and the agriculture economy, as well as human public health in the face of emerging zoonotic pathogens. The utilization of animal models in high-consequence pathogen research and continued expansion to include available species of agricultural importance is essential to deciphering the ecology of emerging and re-emerging infectious diseases, as well as for emergency response and mitigation preparedness.
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Affiliation(s)
- Charles E Lewis
- Corresponding Author: Dr Charles E. Lewis, DVM, MPH, MS, National Centre for Foreign Animal Diseases, Canadian Food Inspection Agency, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3M4, Canada. E-mail:
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Sudeep AB, Yadav PD, Gokhale MD, Balasubramanian R, Gupta N, Shete A, Jain R, Patil S, Sahay RR, Nyayanit DA, Gopale S, Pardeshi PG, Majumdar TD, Patil DR, Sugunan AP, Mourya DT. Detection of Nipah virus in Pteropus medius in 2019 outbreak from Ernakulam district, Kerala, India. BMC Infect Dis 2021; 21:162. [PMID: 33563231 PMCID: PMC7871573 DOI: 10.1186/s12879-021-05865-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Background In June 2019, Nipah virus (NiV) infection was detected in a 21-year-old male (index case) of Ernakulum, Kerala, India. This study was undertaken to determine if NiV was in circulation in Pteropus species (spp) in those areas where the index case had visit history in 1 month. Methods Specialized techniques were used to trap the Pteropus medius bats (random sampling) in the vicinity of the index case area. Throat and rectal swabs samples of 141 bats along with visceral organs of 92 bats were collected to detect the presence of NiV by real-time reverse transcriptase-polymerase chain reaction (qRTPCR). Serum samples of 52 bats were tested for anti-NiV Immunoglobulin (Ig) G antibodies by Enzyme-Linked Immunosorbent Assay (ELISA). The complete genome of NiV was sequenced by next-generation sequencing (NGS) from the tissues and swab samples of bats. Results One rectal swab sample and three bats visceral organs were found positive for the NiV. Interestingly, 20.68% (12/58) of Pteropus were positive for anti-NiV IgG antibodies. NiV sequences of 18,172; 17,200 and 15,100 nucleotide bps could be retrieved from three Pteropus bats. Conclusion A distinct cluster of NiV sequences, with significant net-evolutionary nucleotide divergence, was obtained, suggesting the circulation of new genotype (I-India) in South India. NiV Positivity in Pteropus spp. of bats revealed that NiV is circulating in many districts of Kerala state, and active surveillance of NiV should be immediately set up to know the hotspot area for NiV infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05865-7.
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Affiliation(s)
- A B Sudeep
- ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India
| | - Pragya D Yadav
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India.
| | - Mangesh D Gokhale
- ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India
| | | | - Nivedita Gupta
- Indian Council of Medical Research, Ansari Nagar, New Delhi, India
| | - Anita Shete
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Rajlaxmi Jain
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Savita Patil
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Rima R Sahay
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Dimpal A Nyayanit
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Sanjay Gopale
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Prachi G Pardeshi
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Triparna D Majumdar
- Maximum Containment Laboratory, Indian Council of Medical Research-National Institute of Virology, Sus Road, Pashan, Pune, 411 021, India
| | - Dilip R Patil
- ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India
| | - A P Sugunan
- ICMR-National Institute of Virology, Kerala unit, Alappuzha, India
| | - Devendra T Mourya
- ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, Maharashtra, 411001, India
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Epstein JH, Anthony SJ, Islam A, Kilpatrick AM, Ali Khan S, Balkey MD, Ross N, Smith I, Zambrana-Torrelio C, Tao Y, Islam A, Quan PL, Olival KJ, Khan MSU, Gurley ES, Hossein MJ, Field HE, Fielder MD, Briese T, Rahman M, Broder CC, Crameri G, Wang LF, Luby SP, Lipkin WI, Daszak P. Nipah virus dynamics in bats and implications for spillover to humans. Proc Natl Acad Sci U S A 2020; 117:29190-29201. [PMID: 33139552 PMCID: PMC7682340 DOI: 10.1073/pnas.2000429117] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Nipah virus (NiV) is an emerging bat-borne zoonotic virus that causes near-annual outbreaks of fatal encephalitis in South Asia-one of the most populous regions on Earth. In Bangladesh, infection occurs when people drink date-palm sap contaminated with bat excreta. Outbreaks are sporadic, and the influence of viral dynamics in bats on their temporal and spatial distribution is poorly understood. We analyzed data on host ecology, molecular epidemiology, serological dynamics, and viral genetics to characterize spatiotemporal patterns of NiV dynamics in its wildlife reservoir, Pteropus medius bats, in Bangladesh. We found that NiV transmission occurred throughout the country and throughout the year. Model results indicated that local transmission dynamics were modulated by density-dependent transmission, acquired immunity that is lost over time, and recrudescence. Increased transmission followed multiyear periods of declining seroprevalence due to bat-population turnover and individual loss of humoral immunity. Individual bats had smaller host ranges than other Pteropus species (spp.), although movement data and the discovery of a Malaysia-clade NiV strain in eastern Bangladesh suggest connectivity with bats east of Bangladesh. These data suggest that discrete multiannual local epizootics in bat populations contribute to the sporadic nature of NiV outbreaks in South Asia. At the same time, the broad spatial and temporal extent of NiV transmission, including the recent outbreak in Kerala, India, highlights the continued risk of spillover to humans wherever they may interact with pteropid bats and the importance of limiting opportunities for spillover throughout Pteropus's range.
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Affiliation(s)
| | - Simon J Anthony
- Center for Infection and Immunity, Columbia University, New York, NY 10032
| | | | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Shahneaz Ali Khan
- EcoHealth Alliance, New York, NY 10018
- Chattogram Veterinary and Animal Sciences University, Chattogram, Khulshi 4225, Bangladesh
| | - Maria D Balkey
- Center for Infection and Immunity, Columbia University, New York, NY 10032
- Center for Food Safety & Applied Nutrition, U.S. Food & Drug Administration, College Park, MD 20740
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018
| | - Ina Smith
- CSIRO Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3219, Australia
| | | | - Yun Tao
- EcoHealth Alliance, New York, NY 10018
| | - Ausraful Islam
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Phenix Lan Quan
- Center for Infection and Immunity, Columbia University, New York, NY 10032
| | | | - M Salah Uddin Khan
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Emily S Gurley
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka 1212, Bangladesh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - M Jahangir Hossein
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Mark D Fielder
- School of Life Sciences, Science, Engineering and Computing Faculty, Kingston University, London KT1 2EE, United Kingdom
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, NY 10032
| | - Mahmudur Rahman
- Institute of Epidemiology, Disease Control, and Research, Government of Bangladesh, Dhaka 1212, Bangladesh
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD 20814
| | - Gary Crameri
- CSIRO Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3219, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857
| | - Stephen P Luby
- International Centre for Diarrhoeal Diseases Research, Bangladesh, Dhaka 1212, Bangladesh
- Department of Infectious Diseases & Geographic Medicine, Stanford University, Stanford, CA 94305
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY 10032
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