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Khachab Y, Saab A, El Morr C, El-Lahib Y, Sokhn ES. Identifying the panorama of potential pandemic pathogens and their key characteristics: a systematic scoping review. Crit Rev Microbiol 2024:1-21. [PMID: 38900695 DOI: 10.1080/1040841x.2024.2360407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/22/2024] [Indexed: 06/22/2024]
Abstract
The globe has recently seen several terrifying pandemics and outbreaks, underlining the ongoing danger presented by infectious microorganisms. This literature review aims to explore the wide range of infections that have the potential to lead to pandemics in the present and the future and pave the way to the conception of epidemic early warning systems. A systematic review was carried out to identify and compile data on infectious agents known to cause pandemics and those that pose future concerns. One hundred and fifteen articles were included in the review. They provided insights on 25 pathogens that could start or contribute to creating pandemic situations. Diagnostic procedures, clinical symptoms, and infection transmission routes were analyzed for each of these pathogens. Each infectious agent's potential is discussed, shedding light on the crucial aspects that render them potential threats to the future. This literature review provides insights for policymakers, healthcare professionals, and researchers in their quest to identify potential pandemic pathogens, and in their efforts to enhance pandemic preparedness through building early warning systems for continuous epidemiological monitoring.
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Affiliation(s)
- Yara Khachab
- Laboratory Department, Lebanese Hospital Geitaoui-University Medical Center, Beirut, Lebanon
| | - Antoine Saab
- Quality and Safety Department, Lebanese Hospital Geitaoui-UMC, Beirut, Lebanon
| | - Christo El Morr
- School of Health Policy and Management, York University, Toronto, Canada
| | - Yahya El-Lahib
- Faculty of Social Work, University of Calgary, Calgary, Canada
| | - Elie Salem Sokhn
- Laboratory Department, Lebanese Hospital Geitaoui-University Medical Center, Beirut, Lebanon
- Molecular Testing Laboratory, Medical Laboratory Department, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
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2
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Rahim AA, Chandran P, Bindu V, Radhakrishnan C, Moorkoth AP, Ramakrishnan LV. Recurrent Nipah outbreaks in Kerala: implications for health policy and preparedness. Front Public Health 2024; 12:1356515. [PMID: 38966708 PMCID: PMC11222320 DOI: 10.3389/fpubh.2024.1356515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Affiliation(s)
- Asuma Ayesha Rahim
- Department of Community Medicine, Government Medical College Kozhikode, Kozhikode, India
| | - Priya Chandran
- Department of Community Medicine, Government Medical College Kozhikode, Kozhikode, India
| | - V. Bindu
- Department of Community Medicine, Government Medical College Kozhikode, Kozhikode, India
| | - Chandini Radhakrishnan
- Department of Emergency Medicine, Government Medical College Kozhikode, Kozhikode, India
| | - Anitha P. Moorkoth
- Department of Microbiology, Government Medical College Kozhikode, Kozhikode, India
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Caruso S, Edwards SJ. Recently Emerged Novel Henipa-like Viruses: Shining a Spotlight on the Shrew. Viruses 2023; 15:2407. [PMID: 38140648 PMCID: PMC10747904 DOI: 10.3390/v15122407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Henipaviruses are zoonotic viruses, including some highly pathogenic and capable of serious disease and high fatality rates in both animals and humans. Hendra virus and Nipah virus are the most notable henipaviruses, resulting in significant outbreaks across South Asia, South-East Asia, and Australia. Pteropid fruit bats have been identified as key zoonotic reservoirs; however, the increased discovery of henipaviruses outside the geographic distribution of Pteropid fruit bats and the detection of novel henipa-like viruses in other species such as the shrew, rat, and opossum suggest that Pteropid bats are not the sole reservoir for henipaviruses. In this review, we provide an update on henipavirus spillover events and describe the recent detection of novel unclassified henipaviruses, with a strong focus on the shrew and its emerging role as a key host of henipaviruses.
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Affiliation(s)
| | - Sarah J. Edwards
- Australian Centre for Disease Preparedness, Health & Biosecurity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, East Geelong, VIC 3219, Australia;
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Srivastava S, Kolbe M. Novel "GaEl Antigenic Patches" Identified by a "Reverse Epitomics" Approach to Design Multipatch Vaccines against NIPAH Infection, a Silent Threat to Global Human Health. ACS OMEGA 2023; 8:31698-31713. [PMID: 37692250 PMCID: PMC10483669 DOI: 10.1021/acsomega.3c01909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Nipah virus (NiV) is a zoonotic virus that causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. Several NiV outbreaks have been reported since 1999 with nearly annual occurrences in Bangladesh. The outbreaks had high mortality rates ranging from 40 to 90%. No specific vaccine has yet been reported against NiV. Recently, several vaccine candidates and different designs of vaccines composed of epitopes against NiV were proposed. Most of the vaccines target single protein or protein complex subunits of the pathogen. The multiepitope vaccines proposed also cover a largely limited number of epitopes, and hence, their efficiency is still uncertain. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have utilized the "reverse epitomics" approach ("overlapping-epitope-clusters-to-patches" method) to identify "antigenic patches" (Ag-Patches) and utilize them as immunogenic composition for multipatch vaccine (MPV) design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties, and interaction with Toll-like receptor 3 ectodomain. In total, 30 CTL (cytotoxic T lymphocyte) and 27 HTL (helper T lymphocyte) antigenic patches were identified from the entire NiV proteome based on the clusters of overlapping epitopes. These identified Ag-Patches cover a total of discrete 362 CTL and 414 HTL epitopes from the entire proteome of NiV. The antigenic patches were utilized as immunogenic composition for the design of two CTL and two HTL multipatch vaccines. The 57 antigenic patches utilized here cover 776 overlapping epitopes targeting 52 different HLA class I and II alleles, providing a global ethnically distributed human population coverage of 99.71%. Such large number of epitope coverage resulting in large human population coverage cannot be reached with single-protein/subunit or multiepitope based vaccines. The reported antigenic patches also provide potential immunogenic composition for early detection diagnostic kits for NiV infection. Further, all the MPVs and Toll-like receptor ectodomain complexes show a stable nature of molecular interaction with numerous hydrogen bonds, salt bridges, and nonbounded contact formation and acceptable root mean square deviation and fluctuation. The cDNA analysis shows a favorable large-scale expression of the MPV constructs in a human cell line. By utilizing the novel "reverse epitomics" approach, highly immunogenic novel "GaEl antigenic patches" (GaEl Ag-Patches), a synonym term for "antigenic patches", were identified and utilized as immunogenic composition to design four MPVs against NiV. We conclude that the novel multipatch vaccines are potential candidates to combat NiV, with greater effectiveness, high specificity, and large human population coverage worldwide.
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Affiliation(s)
- Sukrit Srivastava
- Infection
Biology Group, Indian Foundation for Fundamental
Research Trust, Raebareli, Uttar Pradesh 229316, India
- Department
for Structural Infection Biology, Centre
for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection
Research, Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Kolbe
- Department
for Structural Infection Biology, Centre
for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection
Research, Notkestraße 85, 22607 Hamburg, Germany
- Faculty
of Mathematics, Informatics and Natural Sciences, University of Hamburg, Rothenbaumchaussee 19, 20148 Hamburg, Germany
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5
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Barua S, Dénes A. Global dynamics of a compartmental model for the spread of Nipah virus. Heliyon 2023; 9:e19682. [PMID: 37809375 PMCID: PMC10558937 DOI: 10.1016/j.heliyon.2023.e19682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/18/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Nipah virus, which originated in South-East Asia is a bat-borne virus causing Nipah virus infection in humans. This emerging infectious disease has become one of the most alarming threats to public health due to its periodic outbreaks and extremely high mortality rate. We establish and study a novel SIRS model to describe the dynamics of Nipah virus transmission, considering human-to-human as well as zoonotic transmission from bats and pigs as well as loss of immunity. We determine the basic reproduction number which can be obtained as the maximum of three threshold parameters corresponding to various ways of disease transmission and determining in which of the three species the disease becomes endemic. By constructing appropriate Lyapunov functions, we completely describe the global dynamics of our model depending on these threshold parameters. Numerical simulations are shown to support our theoretical results and assess the effect of various intervention measures.
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Affiliation(s)
- Saumen Barua
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., Szeged, 6720, Hungary
| | - Attila Dénes
- National Laboratory for Health Security, Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., Szeged, 6720, Hungary
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6
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Orosco FL. Advancing the frontiers: Revolutionary control and prevention paradigms against Nipah virus. Open Vet J 2023; 13:1056-1070. [PMID: 37842102 PMCID: PMC10576574 DOI: 10.5455/ovj.2023.v13.i9.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/22/2023] [Indexed: 10/17/2023] Open
Abstract
Nipah Virus (NiV) is a highly virulent pathogen that poses a significant threat to human and animal populations. This review provides a comprehensive overview of the latest control and prevention strategies against NiV, focusing on vaccine development, antiviral drug discovery, early diagnosis, surveillance, and high-level biosecurity measures. Advancements in vaccine research, including live-attenuated vaccines, virus-like particles, and mRNA-based vaccines, hold promise for preventing NiV infections. In addition, antiviral drugs, such as remdesivir, ribavirin, and favipiravir, have the potential to inhibit NiV replication. Early diagnosis through molecular and serological assays, immunohistochemistry, and real-time reverse transcription polymerase chain reaction plays a crucial role in timely detection. Surveillance efforts encompassing cluster-based and case-based systems enhance outbreak identification and provide valuable insights into transmission dynamics. Furthermore, the implementation of high-level biosecurity measures in agriculture, livestock practices, and healthcare settings is essential to minimize transmission risks. Collaboration among researchers, public health agencies, and policymakers is pivotal in refining and implementing these strategies to effectively control and prevent NiV outbreaks and safeguard public health on a global scale.
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Affiliation(s)
- Fredmoore L. Orosco
- Virology and Vaccine Institute of the Philippines Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
- S&T Fellows Program, Department of Science and Technology, Taguig City, Philippines
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7
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Satter SM, Aquib WR, Sultana S, Sharif AR, Nazneen A, Alam MR, Siddika A, Akther Ema F, Chowdhury KIA, Alam AN, Rahman M, Klena JD, Rahman MZ, Banu S, Shirin T, Montgomery JM. Tackling a global epidemic threat: Nipah surveillance in Bangladesh, 2006-2021. PLoS Negl Trop Dis 2023; 17:e0011617. [PMID: 37756301 PMCID: PMC10529576 DOI: 10.1371/journal.pntd.0011617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Human Nipah virus (NiV) infection is an epidemic-prone disease and since the first recognized outbreak in Bangladesh in 2001, human infections have been detected almost every year. Due to its high case fatality rate and public health importance, a hospital-based Nipah sentinel surveillance was established in Bangladesh to promptly detect Nipah cases and respond to outbreaks at the earliest. The surveillance has been ongoing till present. The hospital-based sentinel surveillance was conducted at ten strategically chosen tertiary care hospitals distributed throughout Bangladesh. The surveillance staff ensured that routine screening, enrollment, data, and specimen collection from suspected Nipah cases were conducted daily. The specimens were then processed and transported to the reference laboratory of Institute of Epidemiology, Disease Control and Research (IEDCR) and icddr,b for confirmation of diagnosis through serology and molecular detection. From 2006 to 2021, through this hospital-based surveillance platform, 7,150 individuals were enrolled and tested for Nipah virus. Since 2001, 322 Nipah infections were identified in Bangladesh, 75% of whom were laboratory confirmed cases. Half of the reported cases were primary cases (162/322) having an established history of consuming raw date palm sap (DPS) or tari (fermented date palm sap) and 29% were infected through person-to-person transmission. Since the initiation of surveillance, 68% (218/322) of Nipah cases from Bangladesh have been identified from various parts of the country. Fever, vomiting, headache, fatigue, and increased salivation were the most common symptoms among enrolled Nipah patients. Till 2021, the overall case fatality rate of NiV infection in Bangladesh was 71%. This article emphasizes that the overall epidemiology of Nipah virus infection in Bangladesh has remained consistent throughout the years. This is the only systematic surveillance to detect human NiV infection globally. The findings from this surveillance have contributed to early detection of NiV cases in hospital settings, understanding of Nipah disease epidemiology, and have enabled timely public health interventions for prevention and containment of NiV infection. Although we still have much to learn regarding the transmission dynamics and risk factors of human NiV infection, surveillance has played a significant role in advancing our knowledge in this regard.
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Affiliation(s)
| | | | - Sharmin Sultana
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Ahmad Raihan Sharif
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | | | | | | | | | | | - Ahmed Nawsher Alam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | | | - John D. Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | | | | | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
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8
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Kadir AKMS, Umar TP, Rabbi AA, Chowdhury MS, Shemanto MU. Preparedness of South Asian countries regarding Langya virus emergence: A view on the current situation. HEALTH CARE SCIENCE 2023; 2:194-197. [PMID: 38939109 PMCID: PMC11080717 DOI: 10.1002/hcs2.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2024]
Affiliation(s)
- Al Kamal Muhammad Shafiul Kadir
- Biomedical Research Division, Institute of Biological Sciences (IBSc)University of RajshahiRajshahiNorthern RegionBangladesh
| | - Tungki Pratama Umar
- Medical Profession Program, Faculty of MedicineSriwijaya UniversityPalembangSouth SumateraIndonesia
| | - Abdullah Al Rabbi
- Biomedical Research Division, Institute of Biological Sciences (IBSc)University of RajshahiRajshahiNorthern RegionBangladesh
| | - Md. Suza Chowdhury
- Health Education DivisionCentral Medical Assistant Training SchoolRangpurNorth BengalBangladesh
- Health Education DivisionSmart Living Nursing CollegeRangpurNorth BengalBangladesh
| | - Mohammad Ullah Shemanto
- Healthcare Services DivisionAhsania Mission Cancer and General Hospital (AMCGH)DhakaCentral RegionBangladesh
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9
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Yang S, Kar S. Are we ready to fight the Nipah virus pandemic? An overview of drug targets, current medications, and potential leads. Struct Chem 2023:1-19. [PMID: 37363045 PMCID: PMC9993391 DOI: 10.1007/s11224-023-02148-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/16/2023] [Indexed: 03/11/2023]
Abstract
Nipah virus (NiV) is a high-lethality RNA virus from the family of Paramyxoviridae and genus Henipavirus, classified under Biosafety Level-4 (BSL-4) pathogen due to the severity of pathogenicity and lack of medications and vaccines. Direct contacts or the body fluids of infected animals are the major factor of transmission of NiV. As it is not an airborne infection, the transmission rate is relatively low. Still, mutations of the NiV in the animal reservoir over the years, followed by zoonotic transfer, can make the deadliness of the virus manifold in upcoming years. Therefore, there is no denial of the possibility of a pandemic after COVID-19 considering the severe pathogenicity of NiV, and that is why we need to be prepared with possible drugs in upcoming days. Considering the time constraints, computational aided drug design (CADD) is an efficient way to study the virus and perform the drug design and test the HITs to lead experimentally. Therefore, this review focuses primarily on NiV target proteins (covering NiV and human), experimentally tested repurposed drug details, and latest computational studies on potential lead molecules, which can be explored as potential drug candidates. Computationally identified drug candidates, including their chemical structures, docking scores, amino acid level interaction with corresponding protein, and the platform used for the studies, are thoroughly discussed. The review will offer a one-stop study to access what had been performed and what can be performed in the CADD of NiV.
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Affiliation(s)
- Siyun Yang
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083 USA
| | - Supratik Kar
- Chemometrics and Molecular Modeling Laboratory, Department of Chemistry, Kean University, 1000 Morris Avenue, Union, NJ 07083 USA
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10
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Roy P, Deb N. Marburg virus outbreak in Equatorial Guinea- what are the implications for India? New Microbes New Infect 2023; 53:101120. [PMID: 37090949 PMCID: PMC10113826 DOI: 10.1016/j.nmni.2023.101120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
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Srivastava S, Verma S, Kamthania M, Saxena AK, Pandey KC, Pande V, Kolbe M. Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health. PLoS One 2023; 18:e0282580. [PMID: 36920996 PMCID: PMC10016716 DOI: 10.1371/journal.pone.0282580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Nipah virus (NiV) is an emerging zoonotic virus that caused several serious outbreaks in the south asian region with high mortality rates ranging from 40 to 90% since 2001. NiV infection causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. No specific and effective vaccine has yet been reported against NiV. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have designed two Multi-Epitope Vaccines (MEVs) composed of 33 Cytotoxic T lymphocyte (CTL) epitopes and 38 Helper T lymphocyte (HTL) epitopes. Out of those CTL and HTL combined 71 epitopes, 61 novel epitopes targeting nine different NiV proteins were not used before for vaccine design. Codon optimization for the cDNA of both the designed MEVs might ensure high expression potential in the human cell line as stable proteins. Both MEVs carry potential B cell linear epitope overlapping regions, B cell discontinuous epitopes as well as IFN-γ inducing epitopes. Additional criteria such as sequence consensus amongst CTL, HTL and B Cell epitopes was implemented for the design of final constructs constituting MEVs. Hence, the designed MEVs carry the potential to elicit cell-mediated as well as humoral immune response. Selected overlapping CTL and HTL epitopes were validated for their stable molecular interactions with HLA class I and II alleles and in case of CTL epitopes with human Transporter Associated with antigen Processing (TAP) cavity. The structure based epitope cross validation for interaction with TAP cavity was used as another criteria choosing final epitopes for NiV MEVs. Finally, human Beta-defensin 2 and Beta-defensin 3 were used as adjuvants to enhance the immune response of both the MEVs. Molecular dynamics simulation studies of MEVs-TLR3 ectodomain (Human Toll-Like Receptor 3) complex indicated the stable molecular interaction. We conclude that the MEVs designed and in silico validated here could be highly potential vaccine candidates to combat NiV infections, with great effectiveness, high specificity and large human population coverage worldwide.
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Affiliation(s)
- Sukrit Srivastava
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- * E-mail: (SS); (MK)
| | - Sonia Verma
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Kailash C. Pandey
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Kumaun University, Bheemtal, Nainital, Uttarakhand, India
| | - Michael Kolbe
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
- * E-mail: (SS); (MK)
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Abstract
Nipah virus is an acute febrile illness that can cause fatal encephalitis. It is an emerging zoonotic paramyxovirus endemic to south-east Asia and the western Pacific, and can be transmitted by its primary reservoir of fruit bats, through intermediate animal vectors and by human-to-human spread. Outbreaks of Nipah virus encephalitis have occurred in Malaysia, Singapore, Philippines, India and Bangladesh, with the most recent outbreak occurring in Kerala, India in late 2021. Extremely high case fatality rates have been reported from these outbreaks, and to date no vaccines or therapeutic management options are available. Combining this with its propensity to present non-specifically, Nipah virus encephalitis presents a challenging diagnosis that should not be missed in patients returning from endemic regions. Raising awareness of the epidemiology, clinical presentation and risk factors of contracting Nipah virus is vital to recognise and manage potential outbreaks of this disease in the UK.
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Affiliation(s)
- Ali M Alam
- Foundation year 2 doctor, Institute of Infection, Veterinary, and Ecological Science, University of Liverpool, UK.
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13
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Ruszczyk HA, Castán Broto V, McFarlane C. Urban health challenges: Lessons from COVID-19 responses. GEOFORUM; JOURNAL OF PHYSICAL, HUMAN, AND REGIONAL GEOSCIENCES 2022; 131:105-115. [PMID: 35291575 PMCID: PMC8913332 DOI: 10.1016/j.geoforum.2022.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/02/2023]
Abstract
The COVID-19 pandemic has forced a re-examination of our societies and in particular urban health. We argue that urban health needs to address three inter-related challenge areas - the unequal impacts of climate change, changing patterns of urbanization, and the changing role of the local government - across multiple spatial scales: from individual, households to neighbourhoods, cities, and urban hinterlands. Urban health calls for nimble institutions to provide a range of responses while adapting to crisis situations, and which operate beyond any one spatial scale. We illustrate our argument by drawing on South and Southeast Asian examples where responses to the pandemic have confronted these challenges across scales. A multiscalar definition of urban health offers an opportunity to challenge dominant approaches to urban health in research, policy, and practice.
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Affiliation(s)
- Hanna A Ruszczyk
- Department of Geography, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Vanesa Castán Broto
- Climate Urbanism at the Urban Institute, ICOSS, University of Sheffield, 219 Portobello, Sheffield S1 4DP, UK
| | - Colin McFarlane
- Department of Geography, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
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Skowron K, Bauza-Kaszewska J, Grudlewska-Buda K, Wiktorczyk-Kapischke N, Zacharski M, Bernaciak Z, Gospodarek-Komkowska E. Nipah Virus-Another Threat From the World of Zoonotic Viruses. Front Microbiol 2022; 12:811157. [PMID: 35145498 PMCID: PMC8821941 DOI: 10.3389/fmicb.2021.811157] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022] Open
Abstract
Among the diseases that pose a serious threat to public health, those caused by viruses are of great importance. The Nipah virus (NiV) belonging to the Paramyxoviridae family was reported in Malaysia in 1998/1999. Due to its high mortality in humans, its zoonotic nature, the possibility of human-to-human transmission, and the lack of an available vaccine, the World Health Organization (WHO) has recognized it as a global health problem. Depending on strain specificity, neurological symptoms and severe respiratory disorders are observed in NiV infection. In most confirmed cases of NiV epidemics, the appearance of the virus in humans was associated with the presence of various animal species, but generally, bats of Pteropus species are considered the most important natural animal NiV reservoir and vector. Consumption of contaminated food, contact with animals, and “human-to-human” direct contact were identified as NiV transmission routes. Due to the lack of vaccines and drugs with proven effectiveness against NiV, treatment of patients is limited to supportive and prophylactic.
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Affiliation(s)
- Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, Jan and Jędrzej Śniadecki University of Technology in Bydgoszcz, Bydgoszcz, Poland
| | - Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Maciej Zacharski
- Department of Biochemistry and Molecular Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Zuzanna Bernaciak
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
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Abstract
In this review, we highlight the risk to livestock and humans from infections with henipaviruses, which belong to the virus family Paramyxoviridae. We provide a comprehensive overview of documented outbreaks of Nipah and Hendra virus infections affecting livestock and humans and assess the burden on the economy and health systems. In an increasingly globalized and interconnected world, attention must be paid to emerging viruses and infectious diseases, as transmission routes can be rapid and worldwide.
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Affiliation(s)
- Susann Kummer
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- * E-mail:
| | - Denise-Carina Kranz
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
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16
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Chinnaswamy S. SARS-CoV-2 infection in India bucks the trend: Trained innate immunity? Am J Hum Biol 2021; 33:e23504. [PMID: 32965717 PMCID: PMC7536963 DOI: 10.1002/ajhb.23504] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/26/2020] [Accepted: 08/24/2020] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19 pandemic caught the world unawares by its sudden onset in early 2020. Memories of the 1918 Spanish Flu were rekindled raising extreme fear for the virus, but in essence, it was the host and not the virus, which was deciding the outcome of the infection. Age, gender, and preexisting conditions played critical roles in shaping COVID-19 outcome. People of lower socioeconomic strata were disproportionately affected in industrialized countries such as the United States. India, a developing country with more than 1.3 billion population, a large proportion of it being underprivileged and with substandard public health provider infrastructure, feared for the worst outcome given the sheer size and density of its population. Six months into the pandemic, a comparison of COVID-19 morbidity and mortality data between India, the United States, and several European countries, reveal interesting trends. While most developed countries show curves expected for a fast-spreading respiratory virus, India seems to have a slower trajectory. As a consequence, India may have gained on two fronts: the spread of the infection is unusually prolonged, thus leading to a curve that is "naturally flattened"; concomitantly the mortality rate, which is a reflection of the severity of the disease has been relatively low. I hypothesize that trained innate immunity, a new concept in immunology, may be the phenomenon behind this. Biocultural, socioecological, and socioeconomic determinants seem to be influencing the outcome of COVID-19 in different regions/countries of the world.
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Affiliation(s)
- Sreedhar Chinnaswamy
- Infectious Disease GeneticsNational Institute of Biomedical GenomicsKalyaniIndia
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17
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M. A. S, Pande N, P. K. SK. Role of effective crisis communication by the government in managing the first wave Covid-19 pandemic - A study of Kerala government's success. JOURNAL OF PUBLIC AFFAIRS 2021; 21:e2721. [PMID: 34512184 PMCID: PMC8420553 DOI: 10.1002/pa.2721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/13/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Effective crisis communication is critical for successful crisis management. The current study is an attempt to unravel the public communication efforts of the Kerala government in its successful Covid-19 crisis management efforts during the first wave of the pandemic. The findings of the study indicate that the government has successfully used pre-crisis communication to inoculate the stakeholders, 'steal thunder', and bolster their crisis management capabilities. Effective crisis communication, by the government, has ensured proper information management, media management, right supportive action, and direct communication with stakeholders. Effective communication has also helped the government in garnering favourable constituent attribution, positive framing, positive affect in stakeholder, and enlist active stakeholder participation in crisis management; resulting in, effective crisis management and enhanced reputation for the government. The study unravels the best practices of the Kerala government, in public crisis communication, during the pre-crisis and crisis stages of the first wave of the pandemic and proposes a Kerala model of crisis communication. The model can be used as a reference for future government communication efforts during a crisis across geographies.
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Affiliation(s)
- Sanjeev M. A.
- Associate Professor ‐ MarketingJaipuria Institute of ManagementLucknowIndia
| | - Neerja Pande
- Professor ‐ Business CommunicationIndian Institute of Management (IIM)LucknowIndia
| | - Santhosh Kumar P. K.
- Assistant Professor ‐ School of Management Studies (SMS)Cochin University of Science and Technology (CUSAT)CochinIndia
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18
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Abstract
PURPOSE OF REVIEW The COVID-19 pandemic has cast increased attention on emerging infections. Clinicians and public health experts should be aware of emerging infectious causes of encephalitis, mechanisms by which they are transmitted, and clinical manifestations of disease. RECENT FINDINGS A number of arthropod-borne viral infections -- transmitted chiefly by mosquitoes and ticks -- have emerged in recent years to cause outbreaks of encephalitis. Examples include Powassan virus in North America, Chikungunya virus in Central and South America, and tick-borne encephalitis virus in Europe. Many of these viruses exhibit complex life cycles and can infect multiple host animals in addition to humans. Factors thought to influence emergence of these diseases, including changes in climate and land use, are also believed to underlie the emergence of the rickettsial bacterium Orientia tsutsugamushi, now recognized as a major causative agent of acute encephalitis syndrome in South Asia. In addition, the COVID-19 pandemic has highlighted the role of bats as carriers of viruses. Recent studies have begun to uncover mechanisms by which the immune systems of bats are poised to allow for viral tolerance. Several bat-borne infections, including Nipah virus and Ebola virus, have resulted in recent outbreaks of encephalitis. SUMMARY Infectious causes of encephalitis continue to emerge worldwide, in part because of climate change and human impacts on the environment. Expansion of surveillance measures will be critical in rapid diagnosis and limiting of outbreaks in the future.
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19
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McEntire CRS, Song KW, McInnis RP, Rhee JY, Young M, Williams E, Wibecan LL, Nolan N, Nagy AM, Gluckstein J, Mukerji SS, Mateen FJ. Neurologic Manifestations of the World Health Organization's List of Pandemic and Epidemic Diseases. Front Neurol 2021; 12:634827. [PMID: 33692745 PMCID: PMC7937722 DOI: 10.3389/fneur.2021.634827] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
The World Health Organization (WHO) monitors the spread of diseases globally and maintains a list of diseases with epidemic or pandemic potential. Currently listed diseases include Chikungunya, cholera, Crimean-Congo hemorrhagic fever, Ebola virus disease, Hendra virus infection, influenza, Lassa fever, Marburg virus disease, Neisseria meningitis, MERS-CoV, monkeypox, Nipah virus infection, novel coronavirus (COVID-19), plague, Rift Valley fever, SARS, smallpox, tularemia, yellow fever, and Zika virus disease. The associated pathogens are increasingly important on the global stage. The majority of these diseases have neurological manifestations. Those with less frequent neurological manifestations may also have important consequences. This is highlighted now in particular through the ongoing COVID-19 pandemic and reinforces that pathogens with the potential to spread rapidly and widely, in spite of concerted global efforts, may affect the nervous system. We searched the scientific literature, dating from 1934 to August 2020, to compile data on the cause, epidemiology, clinical presentation, neuroimaging features, and treatment of each of the diseases of epidemic or pandemic potential as viewed through a neurologist's lens. We included articles with an abstract or full text in English in this topical and scoping review. Diseases with epidemic and pandemic potential can be spread directly from human to human, animal to human, via mosquitoes or other insects, or via environmental contamination. Manifestations include central neurologic conditions (meningitis, encephalitis, intraparenchymal hemorrhage, seizures), peripheral and cranial nerve syndromes (sensory neuropathy, sensorineural hearing loss, ophthalmoplegia), post-infectious syndromes (acute inflammatory polyneuropathy), and congenital syndromes (fetal microcephaly), among others. Some diseases have not been well-characterized from a neurological standpoint, but all have at least scattered case reports of neurological features. Some of the diseases have curative treatments available while in other cases, supportive care remains the only management option. Regardless of the pathogen, prompt, and aggressive measures to control the spread of these agents are the most important factors in lowering the overall morbidity and mortality they can cause.
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Affiliation(s)
- Caleb R. S. McEntire
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Kun-Wei Song
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Robert P. McInnis
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - John Y. Rhee
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Michael Young
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Erika Williams
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Leah L. Wibecan
- Massachusetts General Hospital (MGH)-Brigham Pediatric Neurology Residency Program, Boston, MA, United States
| | - Neal Nolan
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Amanda M. Nagy
- Massachusetts General Hospital (MGH)-Brigham Pediatric Neurology Residency Program, Boston, MA, United States
| | - Jeffrey Gluckstein
- Massachusetts General Hospital (MGH)-Brigham Neurology Residency Program, Boston, MA, United States
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Farrah J. Mateen
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
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20
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Mustafa S, Jayadev A, Madhavan M. COVID-19: Need for Equitable and Inclusive Pandemic Response Framework. INTERNATIONAL JOURNAL OF HEALTH SERVICES 2020; 51:101-106. [PMID: 33076739 PMCID: PMC7576329 DOI: 10.1177/0020731420967630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
When a new infectious disease emerges as an epidemic or pandemic, strict and appropriate mitigation strategies are critical. Appropriate steps that facilitate defining of cases, carrying out accurate clinical diagnoses, and forming a powerful health surveillance that addresses public health policies and procedures are necessary. Tracking the number of COVID-19 cases over time and flattening the curve is another important element to establish research settings and identify therapeutic components to expedite and develop effective interventions. Addressing the various sections of the society in a philanthropic way is crucial to acquiring the public cooperation that is essential to controlling a disease like COVID-19. In this study, we discuss various strategies and measures adopted by Kerala, an Indian state, to combat the COVID-19 outbreak. Regular and timely updates by government public relations and health departments were used in many of the adopted strategies. The engagement of health information systems, together with the application of decentralized governance and community engagement, has contributed to effective population health management and surveillance of the pandemic.
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Affiliation(s)
- Sabeena Mustafa
- Department of Biostatistics and Bioinformatics, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Anishia Jayadev
- Institute of Management in Government, Government of Kerala, Thiruvananthapuram, Kerala, India
| | - Maya Madhavan
- Department of Biochemistry, Government College for Women, Thiruvananthapuram, Kerala, India
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21
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Singh BB, Lowerison M, Lewinson RT, Vallerand IA, Deardon R, Gill JPS, Singh B, Barkema HW. Public health interventions slowed but did not halt the spread of COVID-19 in India. Transbound Emerg Dis 2020; 68:2171-2187. [PMID: 33012088 PMCID: PMC7675717 DOI: 10.1111/tbed.13868] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/08/2020] [Accepted: 09/26/2020] [Indexed: 12/27/2022]
Abstract
The government of India implemented social distancing interventions to contain the COVID‐19 epidemic. However, effects of these interventions on epidemic dynamics are yet to be understood. Rates of laboratory‐confirmed COVID‐19 infections per day and effective reproduction number (Rt) were estimated for 7 periods (Pre‐lockdown, Lockdown Phases 1 to 4 and Unlock 1–2) according to nationally implemented interventions with phased relaxation. Adoption of these interventions was estimated using Google mobility data. Estimates at the national level and for 12 Indian states most affected by COVID‐19 are presented. Daily case rates ranged from 0.03 to 285.60/10 million people across 7 discrete periods in India. From 18 May to 31 July 2020, the NCT of Delhi had the highest case rate (999/10 million people/day), whereas Madhya Pradesh had the lowest (49/10 million/day). Average Rt was 1.99 (95% CI 1.93–2.06) and 1.39 (95% CI 1.38–1.40) for the entirety of India during the period from 22 March 2020 to 17 May 2020 and from 18 May 2020 to 31 July 2020, respectively. Median mobility in India decreased in all contact domains during the period from 22 March 2020 to 17 May 2020, with the lowest being 21% in retail/recreation, except home which increased to 129% compared to the 100% baseline value. Median mobility in the ‘Grocery and Pharmacy’ returned to levels observed before 22 March 2020 in Unlock 1 and 2, and the enhanced mobility in the Pharmacy sector needs to be investigated. The Indian government imposed strict contact mitigation, followed by a phased relaxation, which slowed the spread of COVID‐19 epidemic progression in India. The identified daily COVID‐19 case rates and Rt will aid national and state governments in formulating ongoing COVID‐19 containment plans. Furthermore, these findings may inform COVID‐19 public health policy in developing countries with similar settings to India.
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Affiliation(s)
- Balbir B Singh
- School of Public Health & Zoonoses, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India.,Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia.,Department of Veterinary Microbiology, University of Saskatchewan, Canada
| | - Mark Lowerison
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Canada.,One Health at UCalgary, University of Calgary, Calgary, Canada
| | - Ryan T Lewinson
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Isabelle A Vallerand
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rob Deardon
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Department of Mathematics and Statistics, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Játinder P S Gill
- School of Public Health & Zoonoses, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Baljit Singh
- One Health at UCalgary, University of Calgary, Calgary, Canada.,Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Canada.,One Health at UCalgary, University of Calgary, Calgary, Canada.,Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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22
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Nambiar D, Sankar H, Negi J, Nair A, Sadanandan R. Field-testing of primary health-care indicators, India. Bull World Health Organ 2020; 98:747-753. [PMID: 33177771 PMCID: PMC7607472 DOI: 10.2471/blt.19.249565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 11/27/2022] Open
Abstract
Objective To develop a primary health-care monitoring framework and health outcome indicator list, and field-test and triangulate indicators designed to assess health reforms in Kerala, India, 2018–2019. Methods We used a modified Delphi technique to develop a 23-item indicator list to monitor primary health care. We used a multistage cluster random sampling technique to select one district from each of four district clusters, and then select both a family and a primary health centre from each of the four districts. We field-tested and triangulated the indicators using facility data and a population-based household survey. Findings Our data revealed similarities between facility and survey data for some indicators (e.g. low birth weight and pre-check services), but differences for others (e.g. acute diarrhoeal diseases in children younger than 5 years and blood pressure screening). We made four critical observations: (i) data are available at the facility level but in varying formats; (ii) established global indicators may not always be useful in local monitoring; (iii) operational definitions must be refined; and (iv) triangulation and feedback from the field is vital. Conclusion We observe that, while data can be used to develop indices of progress, interpretation of these indicators requires great care. In the attainment of universal health coverage, we consider that our observations of the utility of certain health indicators will provide valuable insights for practitioners and supervisors in the development of a primary health-care monitoring mechanism.
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Affiliation(s)
- Devaki Nambiar
- The George Institute for Global Health, 311-312, Third Floor, Elegance Tower, Plot No. 8, Jasola District Centre, New Delhi 110025, India
| | - Hari Sankar
- The George Institute for Global Health, 311-312, Third Floor, Elegance Tower, Plot No. 8, Jasola District Centre, New Delhi 110025, India
| | | | - Arun Nair
- ACCESS Health International, New Delhi, India
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23
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Udhaya Kumar S, Thirumal Kumar D, Siva R, George Priya Doss C. Kerala, India's Front Runner in Novel Coronavirus Disease (COVID-19). Front Med (Lausanne) 2020; 7:355. [PMID: 32714937 PMCID: PMC7343716 DOI: 10.3389/fmed.2020.00355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Affiliation(s)
- S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - D Thirumal Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - R Siva
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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24
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Hassan MZ, Ahmed MS, Khan MM, Uddin MA, Chowdhury F, Kamruzzaman M. Genomic profiling of Nipah virus using NGS driven RNA-Seq expression data. Bioinformation 2019; 15:853-862. [PMID: 32256005 PMCID: PMC7088422 DOI: 10.6026/97320630015853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 01/20/2023] Open
Abstract
Nipah virus (NiV) is an ssRNA, enveloped paramyxovirus in the genus Henipaveridae with a case fatality rate >70%. We analyzed the NGS RNA-Seq gene expression data of NiV to detect
differentially expressed genes (DEGs) using the statistical R package limma. We used the Cytoscape, Ensembl, and STRING tools to construct the gene-gene interaction tree, phylogenetic
gene tree and protein-protein interaction networks towards functional annotation. We identified 2707 DEGs (p-value <0.05) among 54359 NiV genes. The top-up and down-regulated DEGs were
EPST1, MX1, IFIT3, RSAD2, OAS1, OASL, CMPK2 and SLFN13, SPAC977.17 using log2FC criteria with optimum threshold 1.0. The top 20 up-regulated gene-gene interaction trees showed no significant
association between Nipah and Tularemia virus. Similarly, the top 20 down-regulated genes of neither Ebola nor Tularemia virus showed an association with the Nipah virus. Hence, we
document the top-up and down-regulated DEGs for further consideration as biomarkers and candidates for vaccine or drug design against Nipah virus to combat infection.
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Affiliation(s)
- Md Zakiul Hassan
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Shakil Ahmed
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Marufuzzaman Khan
- Department of Public Health, The University of Tennessee, Knoxville, Tennessee, USA
| | | | - Fahmida Chowdhury
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Kamruzzaman
- Institute of Bangladesh Studies, University of Rajshahi, Rajshahi, Bangladesh
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