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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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Zhou P, Ma B, Gao Y, Xu Y, Li Z, Jin H, Luo R. Epidemiology, genetic diversity, and evolutionary dynamics of Tembusu virus. Arch Virol 2023; 168:262. [PMID: 37773423 DOI: 10.1007/s00705-023-05885-5] [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: 12/01/2022] [Accepted: 08/02/2023] [Indexed: 10/01/2023]
Abstract
Tembusu virus (TMUV) is an emerging pathogenic flavivirus associated with acute egg-drop and fatal encephalitis in domestic waterfowl. Since its initial identification in mosquitoes in 1955, TMUV has been confirmed to infect ducks, pigeons, sparrows, geese, and chickens, posing a significant threat to the poultry industry. Here, we sequenced two DTMUV strains isolated in 2019 and systematically investigated the possible origin, genetic relationships, evolutionary dynamics, and transmission patterns of TMUV based on complete virus genome sequences in the public database. We found that TMUV can be divided into four major clusters: TMUV, cluster 1, cluster 2, and cluster 3. Interestingly, we found that cluster 2.2 (within cluster 2) is the most commonly involved in interspecies transmission events, and subcluster 2.1.2 (within cluster 2.1) is currently the most prevalent cluster circulating in Asia. Notably, we also identified three positively selected sites in the E and NS1 proteins, which may be involved in virus replication, immune evasion, and host adaptation. Finally, phylogeographic analysis revealed that cluster dispersal originated in Southeast Asia and that short-distance transmission events have occurred frequently. Altogether, these data provide novel insights into the evolution and dispersal of TMUV, facilitating the development of rapid diagnostics, vaccines, and therapeutics against TMUV infection.
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Affiliation(s)
- Peng Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Bin Ma
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yuan Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yumin Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Zhuofei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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Zeghbib S, Kemenesi G, Jakab F. The importance of equally accessible genomic surveillance in the age of pandemics. Biol Futur 2023:10.1007/s42977-023-00164-5. [PMID: 37199870 DOI: 10.1007/s42977-023-00164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.
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Affiliation(s)
- Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary.
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pecs, Hungary
- Faculty of Sciences, Institute of Biology, University of Pécs, Pecs, Hungary
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Lamkiewicz K, Esquivel Gomez LR, Kühnert D, Marz M. Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2. Curr Top Microbiol Immunol 2023; 439:305-339. [PMID: 36592250 DOI: 10.1007/978-3-031-15640-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA secondary structure features, which are involved in the complex replication mechanism. With a focus on computational methods, we review the emergence of SARS-CoV-2 starting with the 2019 strains. In that context, we also discuss the debated hypothesis of whether SARS-CoV-2 was created in a laboratory. We focus on the molecular evolution and the epidemiological dynamics of this recently emerged pathogen and we explain how variants of concern are detected and characterised. COVID-19, the disease caused by SARS-CoV-2, can spread through different transmission routes and also depends on a number of risk factors. We describe how current computational models of viral epidemiology, or more specifically, phylodynamics, have facilitated and will continue to enable a better understanding of the epidemic dynamics of SARS-CoV-2.
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Affiliation(s)
- Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany.
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745, Jena, Germany.
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Davedow T, Carleton H, Kubota K, Palm D, Schroeder M, Gerner-Smidt P, Al-Jardani A, Chinen I, Kam KM, Smith AM, Nadon C. PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance. Foodborne Pathog Dis 2022; 19:332-340. [PMID: 35325576 PMCID: PMC10863729 DOI: 10.1089/fpd.2021.0110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.
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Affiliation(s)
- Taylor Davedow
- Division of Enteric Diseases, Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kristy Kubota
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Daniel Palm
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Morgan Schroeder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Amina Al-Jardani
- Central Public Health Laboratories, Ministry of Health, Muscat, Oman
| | - Isabel Chinen
- Instituto Nacional de Enfermedades Infecciosas, Administracion Nacional del Laboratorios et Institutos de Salud "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Kai Man Kam
- Stanley Ho Centre for Emerging Infectious Diseases, School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anthony M Smith
- National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Celine Nadon
- Division of Enteric Diseases, Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Rodriguez-Morales AJ, Paniz-Mondolfi AE, Faccini-Martínez ÁA, Henao-Martínez AF, Ruiz-Saenz J, Martinez-Gutierrez M, Alvarado-Arnez LE, Gomez-Marin JE, Bueno-Marí R, Carrero Y, Villamil-Gomez WE, Bonilla-Aldana DK, Haque U, Ramirez JD, Navarro JC, Lloveras S, Arteaga-Livias K, Casalone C, Maguiña JL, Escobedo AA, Hidalgo M, Bandeira AC, Mattar S, Cardona-Ospina JA, Suárez JA. The Constant Threat of Zoonotic and Vector-Borne Emerging Tropical Diseases: Living on the Edge. FRONTIERS IN TROPICAL DISEASES 2021; 2:676905. [PMID: 34010366 PMCID: PMC8132189 DOI: 10.3389/fitd.2021.676905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Alfonso J. Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de las Americas, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group, Instituto para la Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
- Coordinación Nacional de Investigación, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia
- Master Program on Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Laboratory of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | | | - Andrés F. Henao-Martínez
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Lucia E. Alvarado-Arnez
- Coordinación Nacional de Investigación, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia
| | - Jorge E. Gomez-Marin
- Grupo de Estudio en Parasitologia Molecular (GEPAMOL) Group, Facultad de Ciencias de la Salud, Universidad del Quindío, Armenia, Colombia
| | - Ruben Bueno-Marí
- Departamento de Investigación y Desarrollo (I+D), Laboratorios Lokímica, Paterna, Spain
- Área de Parasitología, Departamento de Farmacia y Tecnología Farmaceútica y Parasitología, Universidad de Valencia, Burjasot, Spain
| | - Yenddy Carrero
- Facultad de Ciencias de la Salud, Carrera de Medicina, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Wilmer E. Villamil-Gomez
- Infectious Diseases and Infection Control Research Group, Hospital Universitario de Sincelejo, Sincelejo, Colombia
- Programa Del Doctorado de Medicina Tropical, SUE Caribe, Universidad Del Atlántico, Barranquilla, Colombia
| | - D. Katterine Bonilla-Aldana
- Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundacion Universitaria Autonoma de las Americas, Pereira, Colombia
| | - Ubydul Haque
- Department of Biostatistics and Epidemiology, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Juan D. Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan-Carlos Navarro
- Research Group of Emerging Diseases, Ecoepidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito, Ecuador
| | - Susana Lloveras
- Sección Zoopatología Médica, Hospital de Infecciosas FJ Muñiz, Buenos Aires, Argentina
| | - Kovy Arteaga-Livias
- Master Program on Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru
- Faculty of Medicine, Universidad Nacional Hermilio Valdizán, Huánuco, Peru
| | | | - Jorge L. Maguiña
- Master Program on Clinical Epidemiology and Biostatistics, Universidad Científica del Sur, Lima, Peru
| | - Angel A. Escobedo
- Department of Epidemiology, Institute of Gastroenterology, Havana, Cuba
| | - Marylin Hidalgo
- Infectious Diseases Group, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Salim Mattar
- Instituto de Investigaciones Biologicas del Tropico, Universidad de Cordoba, Monteria, Colombia
| | - Jaime A. Cardona-Ospina
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de las Americas, Pereira, Colombia
- Emerging Infectious Diseases and Tropical Medicine Research Group, Instituto para la Investigación en Ciencias Biomédicas - Sci-Help, Pereira, Colombia
| | - Jose A. Suárez
- Investigador SNI Senacyt Panamá, Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
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Sah R, Khatiwada AP, Shrestha S, Bhuvan KC, Tiwari R, Mohapatra RK, Dhama K, Rodriguez-Morales AJ. COVID-19 vaccination campaign in Nepal, emerging UK variant and futuristic vaccination strategies to combat the ongoing pandemic. Travel Med Infect Dis 2021; 41:102037. [PMID: 33781945 PMCID: PMC7997904 DOI: 10.1016/j.tmaid.2021.102037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
With the emergence of the new variants of concern (VOC) of the SARS-CoV-2, the efficacy of certain vaccines against them requires further research and considerations for future scenarios of COVID-19 vaccination. The vaccines' lack of efficacy against VOC will pose at risk to the vaccinated population and is a public health threat. In this commentary, we discuss Nepal's recent experiences and expectations regarding the confirmation of VOC B.1.1.7 from the United Kingdom in the country.
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Affiliation(s)
- Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal; National Public Health Laboratory, Kathmandu, Nepal
| | - Asmita Priyadarshini Khatiwada
- Department of Pharmaceutical and Health Service Research, Nepal Health Research and Innovation Foundation, Lalitpur, Nepal
| | - Sunil Shrestha
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - K C Bhuvan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, 281001, India
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India.
| | - Alfonso J Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundacion Universitaria Autonoma de Las Americas, Pereira, Risaralda, Colombia; School of Medicine, Universidad Privada Franz Tamayo (UNIFRANZ), Cochabamba, Bolivia.
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