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Adesola RO, Onoja BA, Adamu AM, Agbaje ST, Abdulazeez MD, Akinsulie OC, Bakre A, Adegboye OA. Molecular epidemiology and genetic evolution of avian influenza H5N1 subtype in Nigeria, 2006 to 2021. Virus Genes 2024; 60:501-509. [PMID: 38896308 PMCID: PMC11383836 DOI: 10.1007/s11262-024-02080-9] [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: 10/15/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Nigeria recorded one of the earliest outbreaks of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1 in 2006, which spread to other African countries. In 2023, 18 countries reported outbreaks of H5N1 in poultry, with human cases documented in Egypt, Nigeria, and Djibouti. There is limited information on the molecular epidemiology of HPAI H5N1 in Nigeria. We determined the molecular epidemiology and genetic evolution of the virus from 2006 to 2021. We investigated the trend and geographical distribution across Nigeria. The evolutionary history of 61 full-length genomes was performed from 13 countries worldwide, and compared with sequences obtained from the early outbreaks in Nigeria up to 2021. MEGA 11 was used to determine the phylogenetic relationships of H5N1 strains, which revealed close ancestry between sequences in Nigeria and those from other African countries. Clade classification was performed using the subspecies classification tool for Bacterial and Viral Bioinformatics Research Center (BV-BRC) version 3.35.5. H5N1 Clade 2.2 was observed in 2006, with 2.3.2, 2.3.2.1f clades observed afterwards and 2.3.4.4b in 2021. Our findings underscore the need for genomics surveillance to track antigenic variation and clades switching to monitor the epidemiological of the virus and safeguard human and animal health.Impacts Specific variations in the hemagglutinin (HA) and neuraminidase (NA) genes of Avian influenza virus are consistent in different geographical regions. H5N1 Clade 2.2 was reported in 2006, with 2.3.2, 2.3.2.1f afterwards and 2.3.4.4b in 2021. Nigeria is an epicentre for avian influenza with three major migratory routes for wild birds transversing the country. It is plausible that the Avian influenza in Northern Nigeria may be linked to wild bird sanctuaries in the region.
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Affiliation(s)
- Ridwan O Adesola
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Bernard A Onoja
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Andrew M Adamu
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
- Australia Institute of Tropic Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- Department of Veterinary Public Health and Preventive Medicine, University of Abuja, Abuja, 900105, Nigeria
| | - Sheriff T Agbaje
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Modinat D Abdulazeez
- Department of Statistics, Faculty of Science, University of Ibadan, Ibadan, 200005, Nigeria
| | | | - Adetolase Bakre
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Oyelola A Adegboye
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
- Australia Institute of Tropic Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, 0811, Australia.
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Wu Y, Wang J, Xue J, Xiang Z, Guo J, Zhan L, Wei Q, Kong Q. Flu-CED: A comparative transcriptomics database of influenza virus-infected human and animal models. Animal Model Exp Med 2024. [PMID: 38379334 DOI: 10.1002/ame2.12384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/18/2023] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND The continuing emergence of influenza virus has highlighted the value of public databases and related bioinformatic analysis tools in investigating transcriptomic change caused by different influenza virus infections in human and animal models. METHODS We collected a large amount of transcriptome research data related to influenza virus-infected human and animal models in public databases (GEO and ArrayExpress), and extracted and integrated array and metadata. The gene expression matrix was generated through strictly quality control, balance, standardization, batch correction, and gene annotation. We then analyzed gene expression in different species, virus, cells/tissues or after antibody/vaccine treatment and imported sample metadata and gene expression datasets into the database. RESULTS Overall, maintaining careful processing and quality control, we collected 8064 samples from 103 independent datasets, and constructed a comparative transcriptomics database of influenza virus named the Flu-CED database (Influenza comparative expression database, https://flu.com-med.org.cn/). Using integrated and processed transcriptomic data, we established a user-friendly website for realizing the integration, online retrieval, visualization, and exploration of gene expression of influenza virus infection in different species and the biological functions involved in differential genes. Flu-CED can quickly query single and multi-gene expression profiles, combining different experimental conditions for comparative transcriptome analysis, identifying differentially expressed genes (DEGs) between comparison groups, and conveniently finding DEGs. CONCLUSION Flu-CED provides data resources and tools for analyzing gene expression in human and animal models infected with influenza virus that can deepen our understanding of the mechanisms underlying disease occurrence and development, and enable prediction of key genes or therapeutic targets that can be used for medical research.
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Affiliation(s)
- Yue Wu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Jue Wang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Jing Xue
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Zhiguang Xiang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Jianguo Guo
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Lingjun Zhan
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Qiang Wei
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
| | - Qi Kong
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, National Human Diseases Animal Model Resource Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Beijing, China
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Moeini S, Mohebbi A, Farahmand B, Mehrbod P, Fotouhi F. Phylogenetic analysis and docking study of neuraminidase gene of influenza A/H1N1 viruses circulating in Iran from 2010 to 2019. Virus Res 2023; 334:199182. [PMID: 37490957 PMCID: PMC10407273 DOI: 10.1016/j.virusres.2023.199182] [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: 02/06/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023]
Abstract
Influenza A viruses (H1N1) have been consistently one of the most evolving viruses that escape from vaccine-induced immunity. Although there has been a rapid rise in human influenza virus knowledge since the 2009 pandemic, the molecular information about Iranian strains is still inadequate. The aim of this study was to analyze the neuraminidase (NA) segment of the Iranian isolates in terms of phylogenetic, antiviral resistance, and vaccine efficiency. Ninety-three NA sequences collected among 1758 nasopharyngeal swab samples during the 2015-2016 influenza season were sequenced and submitted to NCBI. Moreover, all the submitted Iranian influenza H1N1 NA sequences since 2010 till 2019 were included in the study. Software including MEGA-X, MODELLER, UCSF ChimeraX, Auto-Dock 4.2, and other online tools were used to analyze the phylogenetic relationship, vaccine efficiency, and binding affinity to sialic acid of the selected NA proteins. Moreover, the information about antiviral drug resistance mutations of NA were gathered and compared to the Iranian NA segments to check the presence of antiviral drug-resistant strains. The phylogenetic study showed that most Iranian NA sequences (between 2015 and 2016) were located in a single clade and following years were located in its subclade by 3 major mutations (G77R/K, V81A, and J188T). Resistant mutations in drug targets of NA including I117M, D151E, I223V, and S247N were ascertained in 10 isolates during the 2015-2016 flu seasons. Investigation of vaccination effect revealed that Iranian isolates in 2017 and 2018 were best matched to A/Brisbane/02/2018 (H1N1), and in 2019 to A/Guangdong-Maonan/SWL1536/2019 (H1N1). Furthermore, we performed an in-silico analysis of NA enzymatic activity of all Iranian sequences by assessment of enzyme stability, ligand affinity, and active site availability. Overall, the enzyme activity of four Iranian strains (AUG84119, AUG84157, AUG84095, and AUG84100) was assumed as the maximum enzyme activity. This study highlighted the evolutionary trend of influenza A virus/H1N1 circulating in Iran, which provides a preliminary viewpoint for a better comprehension of new emerging strains' virulence and thus, more appropriate monitoring of influenza virus A/H1N1 during each outbreak season.
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Affiliation(s)
- Sina Moeini
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Mohebbi
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Fotouhi
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran, Iran.
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Ritsch M, Cassman NA, Saghaei S, Marz M. Navigating the Landscape: A Comprehensive Review of Current Virus Databases. Viruses 2023; 15:1834. [PMID: 37766241 PMCID: PMC10537806 DOI: 10.3390/v15091834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.
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Affiliation(s)
- Muriel Ritsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Noriko A. Cassman
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Shahram Saghaei
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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5
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Gao Q, Levi R, Renegar N. Leveraging machine learning to assess market-level food safety and zoonotic disease risks in China. Sci Rep 2022; 12:21650. [PMID: 36522373 PMCID: PMC9755119 DOI: 10.1038/s41598-022-25817-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
While many have advocated for widespread closure of Chinese wet and wholesale markets due to numerous zoonotic disease outbreaks (e.g., SARS) and food safety risks, this is impractical due to their central role in China's food system. This first-of-its-kind work offers a data science enabled approach to identify market-level risks. Using a massive, self-constructed dataset of food safety tests, market-level adulteration risk scores are created through machine learning techniques. Analysis shows that provinces with more high-risk markets also have more human cases of zoonotic flu, and specific markets associated with zoonotic disease have higher risk scores. Furthermore, it is shown that high-risk markets have management deficiencies (e.g., illegal wild animal sales), potentially indicating that increased and integrated regulation targeting high-risk markets could mitigate these risks.
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Affiliation(s)
- Qihua Gao
- Sloan School of Management, Massachusetts Institute of Technology, 100 Main Street, E62, Cambridge, MA, 02142, USA
| | - Retsef Levi
- Sloan School of Management, Massachusetts Institute of Technology, 100 Main Street, E62, Cambridge, MA, 02142, USA.
| | - Nicholas Renegar
- Sloan School of Management, Massachusetts Institute of Technology, 100 Main Street, E62, Cambridge, MA, 02142, USA
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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Duvaud S, Gabella C, Lisacek F, Stockinger H, Ioannidis V, Durinx C. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. Nucleic Acids Res 2021; 49:W216-W227. [PMID: 33849055 PMCID: PMC8265094 DOI: 10.1093/nar/gkab225] [Citation(s) in RCA: 310] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/11/2021] [Accepted: 04/01/2021] [Indexed: 12/16/2022] Open
Abstract
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for the storage, analysis and interpretation of biological data. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. In 2020, Expasy was redesigned through a user-centric approach, known as User-Centred Design (UCD), whose aim is to create user interfaces that are easy-to-use, efficient and targeting the intended community. This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. In total, around 50 people were actively involved, including internal stakeholders and end-users. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources.
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Affiliation(s)
- Séverine Duvaud
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland
| | - Chiara Gabella
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, and Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland.,Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Heinz Stockinger
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland
| | - Vassilios Ioannidis
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland
| | - Christine Durinx
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland
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A Conceptual Model for Geo-Online Exploratory Data Visualization: The Case of the COVID-19 Pandemic. INFORMATION 2021. [DOI: 10.3390/info12020069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Responding to the recent COVID-19 outbreak, several organizations and private citizens considered the opportunity to design and publish online explanatory data visualization tools for the communication of disease data supported by a spatial dimension. They responded to the need of receiving instant information arising from the broad research community, the public health authorities, and the general public. In addition, the growing maturity of information and mapping technologies, as well as of social networks, has greatly supported the diffusion of web-based dashboards and infographics, blending geographical, graphical, and statistical representation approaches. We propose a broad conceptualization of Web visualization tools for geo-spatial information, exceptionally employed to communicate the current pandemic; to this end, we study a significant number of publicly available platforms that track, visualize, and communicate indicators related to COVID-19. Our methodology is based on (i) a preliminary systematization of actors, data types, providers, and visualization tools, and on (ii) the creation of a rich collection of relevant sites clustered according to significant parameters. Ultimately, the contribution of this work includes a critical analysis of collected evidence and an extensive modeling effort of Geo-Online Exploratory Data Visualization (Geo-OEDV) tools, synthesized in terms of an Entity-Relationship schema. The COVID-19 pandemic outbreak has offered a significant case to study how and how much modern public communication needs spatially related data and effective implementation of tools whose inspection can impact decision-making at different levels. Our resulting model will allow several stakeholders (general users, policy-makers, and researchers/analysts) to gain awareness on the assets of structured online communication and resource owners to direct future development of these important tools.
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Mohebbi A, Fotouhi F, Jamali A, Yaghobi R, Farahmand B, Mohebbi R. Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran. Virus Res 2018; 259:38-45. [PMID: 30336188 DOI: 10.1016/j.virusres.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 11/17/2022]
Abstract
In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting novel genetic variants causing epidemic potential. This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015/2016 season. In order to investigate the genetic pattern of influenza A/H1N1 pdm09, a total of 1758 nasopharyngeal swabs were screened by real-time RT-PCR. Of those, 510 cases were found to be positive for A/H1N1/pdm09 virus. Evolution of the approximately 100 positive specimens with high virus load was conducted via genomic phylogeny. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. The N-glycosylation of HA protein is post or co-translational modification that affect the evolution of influenza viruses. For influenza A(H1N1) pdm09 viruses, we found more mutations in the antigenic sites than in the stem region. The results of this study confirmed the necessity of constant regular antigenic and molecular surveillance of circulating seasonal influenza viruses.
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Affiliation(s)
- Atefeh Mohebbi
- Department of Microbiology, College of Science Agriculture and Modern Technology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Abbas Jamali
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Behrokh Farahmand
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Borges V, Pinheiro M, Pechirra P, Guiomar R, Gomes JP. INSaFLU: an automated open web-based bioinformatics suite "from-reads" for influenza whole-genome-sequencing-based surveillance. Genome Med 2018; 10:46. [PMID: 29954441 PMCID: PMC6027769 DOI: 10.1186/s13073-018-0555-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/07/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. RESULTS We developed and implemented INSaFLU ("INSide the FLU"), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line "genetic requests" for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants' annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. This platform additionally flags samples as "putative mixed infections" if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional "consensus-based" influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. CONCLUSIONS In summary, INSaFLU supplies public health laboratories and influenza researchers with an open "one size fits all" framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus. INSaFLU can be accessed through https://insaflu.insa.pt .
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Pedro Pechirra
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Raquel Guiomar
- National Reference Laboratory for Influenza and other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal
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Contalbrigo L, Borgo S, Pozza G, Marangon S. Data distribution in public veterinary service: health and safety challenges push for context-aware systems. BMC Vet Res 2017; 13:397. [PMID: 29273034 PMCID: PMC5741927 DOI: 10.1186/s12917-017-1320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/13/2017] [Indexed: 11/16/2022] Open
Abstract
Background Today’s globalised and interconnected world is characterized by intertwined and quickly evolving relationships between animals, humans and their environment and by an escalating number of accessible data for public health. The public veterinary services must exploit new modeling and decision strategies to face these changes. The organization and control of data flows have become crucial to effectively evaluate the evolution and safety concerns of a given situation in the territory. This paper discusses what is needed to develop modern strategies to optimize data distribution to the stakeholders. Main text If traditionally the system manager and knowledge engineer have been concerned with the increase of speed of data flow and the improvement of data quality, nowadays they need to worry about data overflow as well. To avoid this risk an information system should be capable of selecting the data which need to be shown to the human operator. In this perspective, two aspects need to be distinguished: data classification vs data distribution. Data classification is the problem of organizing data depending on what they refer to and on the way they are obtained; data distribution is the problem of selecting which data is accessible to which stakeholder. Data classification can be established and implemented via ontological analysis and formal logic but we claim that a context-based selection of data should be integrated in the data distribution application. Data distribution should provide these new features: (a) the organization of situation types distinguishing at least ordinary vs extraordinary scenarios (contextualization of scenarios); (b) the possibility to focus on the data that are really important in a given scenario (data contextualization by scenarios); and (c) the classification of which data is relevant to which stakeholder (data contextualization by users). Short conclusion Public veterinary services, to efficaciously and efficiently manage the information needed for today’s health and safety challenges, should contextualize and filter the continuous and growing flow of data by setting suitable frameworks to classify data, users’ roles and possible situations.
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Affiliation(s)
- Laura Contalbrigo
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy.
| | - Stefano Borgo
- Laboratory for Applied Ontology, ISTC-CNR, Via alla Cascata, 56/C, 38123, Trento, Italy
| | - Giandomenico Pozza
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy
| | - Stefano Marangon
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale Dell'Università 10, 35020, Legnaro, (PD), Italy
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12
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María RR, Arturo CJ, Alicia JA, Paulina MG, Gerardo AO. The Impact of Bioinformatics on Vaccine Design and Development. Vaccines (Basel) 2017. [DOI: 10.5772/intechopen.69273] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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13
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Stano M, Beke G, Klucar L. viruSITE-integrated database for viral genomics. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw162. [PMID: 28025349 PMCID: PMC5199161 DOI: 10.1093/database/baw162] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 11/14/2022]
Abstract
Viruses are the most abundant biological entities and the reservoir of most of the genetic diversity in the Earth's biosphere. Viral genomes are very diverse, generally short in length and compared to other organisms carry only few genes. viruSITE is a novel database which brings together high-value information compiled from various resources. viruSITE covers the whole universe of viruses and focuses on viral genomes, genes and proteins. The database contains information on virus taxonomy, host range, genome features, sequential relatedness as well as the properties and functions of viral genes and proteins. All entries in the database are linked to numerous information resources. The above-mentioned features make viruSITE a comprehensive knowledge hub in the field of viral genomics. The web interface of the database was designed so as to offer an easy-to-navigate, intuitive and user-friendly environment. It provides sophisticated text searching and a taxonomy-based browsing system. viruSITE also allows for an alternative approach based on sequence search. A proprietary genome browser generates a graphical representation of viral genomes. In addition to retrieving and visualising data, users can perform comparative genomics analyses using a variety of tools. Database URL: http://www.virusite.org/
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Affiliation(s)
- Matej Stano
- Laboratory of Bioinformatics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Gabor Beke
- Laboratory of Bioinformatics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubos Klucar
- Laboratory of Bioinformatics, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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14
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Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw130. [PMID: 27694207 PMCID: PMC5045858 DOI: 10.1093/database/baw130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
Abstract
The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated. The 3DFlu database contains well annotated HA representatives: 1192 models and 263 crystallographic structures. The relations between these proteins are defined using different metrics and are visualized as a network in the provided web interface. Moreover structural and sequence comparison of the proteins can be explored. Metadata information (e.g. protein identifier, IVA strain, year and location of infection) can enhance the exploration of the presented data. With our database researchers gain a useful tool for the exploration of high quality HA models, viewing and comparing changes in the HA viral subtypes at several information levels (sequence, structure, ESP). The complete and integrated view of those relations might be useful to determine the efficiency of transmission, pathogenicity and for the investigation of evolutionary tendencies of the influenza virus. Database URL: http://nucleus3d.cent.uw.edu.pl/influenza
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Affiliation(s)
- Giovanni Mazzocco
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Migdał
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Jan P Radomski
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
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15
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Artois J, Newman SH, Dhingra MS, Chaiban C, Linard C, Cattoli G, Monne I, Fusaro A, Xenarios I, Engler R, Liechti R, Kuznetsov D, Pham TL, Nguyen T, Pham VD, Castellan D, Von Dobschuetz S, Claes F, Dauphin G, Inui K, Gilbert M. Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors. Sci Rep 2016; 6:30316. [PMID: 27453195 PMCID: PMC4958987 DOI: 10.1038/srep30316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/04/2016] [Indexed: 11/16/2022] Open
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Asia since 2003 and diversified into several genetic lineages, or clades. Although the spatial distribution of its outbreaks was extensively studied, differences in clades were never previously taken into account. We developed models to quantify associations over time and space between different HPAI H5N1 viruses from clade 1, 2.3.4 and 2.3.2 and agro-ecological factors. We found that the distribution of clades in the Mekong region from 2004 to 2013 was strongly regionalised, defining specific epidemiological zones, or epizones. Clade 1 became entrenched in the Mekong Delta and was not supplanted by newer clades, in association with a relatively higher presence of domestic ducks. In contrast, two new clades were introduced (2.3.4 and 2.3.2) in northern Viet Nam and were associated with higher chicken density and more intensive chicken production systems. We suggest that differences in poultry production systems in these different epizones may explain these associations, along with differences in introduction pressure from neighbouring countries. The different distribution patterns found at the clade level would not be otherwise apparent through analysis treating all outbreaks equally, which requires improved linking of disease outbreak records and genetic sequence data.
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Affiliation(s)
- Jean Artois
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Scott H. Newman
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam
| | - Madhur S. Dhingra
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Animal Husbandry & Dairying, Government of Haryana, India
| | - Celia Chaiban
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium
| | - Catherine Linard
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Geography, Université de Namur, Namur, Belgium
| | - Giovanni Cattoli
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Seibersdorf, Austria
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy
| | - Ioannis Xenarios
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland
| | - Robin Engler
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Robin Liechti
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Dmitri Kuznetsov
- Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Thanh Long Pham
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Tung Nguyen
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Van Dong Pham
- Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - David Castellan
- Emergency Center for Transboundary Animal Diseases (ECTAD), FAO Regional Office for Asia and the Pacific (FAO-RAP), Bangkok, Thailand
| | - Sophie Von Dobschuetz
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Filip Claes
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Gwenaëlle Dauphin
- Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy
| | - Ken Inui
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium
- Fonds National de la Recherche Scientifique, Brussels, Belgium
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16
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McWhite CD, Meyer AG, Wilke CO. Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evol 2016; 2:vew026. [PMID: 27713835 PMCID: PMC5049878 DOI: 10.1093/ve/vew026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical influenza A virus isolates are frequently not sequenced directly. Instead, a majority of these isolates (~70% in 2015) are first subjected to passaging for amplification, most commonly in non-human cell culture. Here, we find that this passaging leaves distinct signals of adaptation, which can confound evolutionary analyses of the viral sequences. We find distinct patterns of adaptation to Madin-Darby (MDCK) and monkey cell culture absent from unpassaged hemagglutinin sequences. These patterns also dominate pooled datasets not separated by passaging type, and they increase in proportion to the number of passages performed. By contrast, MDCK-SIAT1 passaged sequences seem mostly (but not entirely) free of passaging adaptations. Contrary to previous studies, we find that using only internal branches of influenza virus phylogenetic trees is insufficient to correct for passaging artifacts. These artifacts can only be safely avoided by excluding passaged sequences entirely from subsequent analysis. We conclude that future influenza virus evolutionary analyses should appropriately control for potentially confounding effects of passaging adaptations.
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Affiliation(s)
- Claire D. McWhite
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin,
Austin, TX 78712, USA
| | - Austin G. Meyer
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Center for Computational Biology and Bioinformatics, The University of Texas
at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin,
Austin, TX 78712, USA
| | - Claus O. Wilke
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Center for Computational Biology and Bioinformatics, The University of Texas
at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin,
Austin, TX 78712, USA
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17
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Simon C, Kudahl UJ, Sun J, Olsen LR, Zhang GL, Reinherz EL, Brusic V. FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses. J Immunol Res 2015; 2015:380975. [PMID: 26504853 PMCID: PMC4609449 DOI: 10.1155/2015/380975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/12/2015] [Indexed: 01/01/2023] Open
Abstract
FluKB is a knowledge-based system focusing on data and analytical tools for influenza vaccine discovery. The main goal of FluKB is to provide access to curated influenza sequence and epitope data and enhance the analysis of influenza sequence diversity and the analysis of targets of immune responses. FluKB consists of more than 400,000 influenza protein sequences, known epitope data (357 verified T-cell epitopes, 685 HLA binders, and 16 naturally processed MHC ligands), and a collection of 28 influenza antibodies and their structurally defined B-cell epitopes. FluKB was built using a modular framework allowing the implementation of analytical workflows and includes standard search tools, such as keyword search and sequence similarity queries, as well as advanced tools for the analysis of sequence variability. The advanced analytical tools for vaccine discovery include visual mapping of T- and B-cell vaccine targets and assessment of neutralizing antibody coverage. FluKB supports the discovery of vaccine targets and the analysis of viral diversity and its implications for vaccine discovery as well as potential T-cell breadth and antibody cross neutralization involving multiple strains. FluKB is representation of a new generation of databases that integrates data, analytical tools, and analytical workflows that enable comprehensive analysis and automatic generation of analysis reports.
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Affiliation(s)
- Christian Simon
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ulrich J. Kudahl
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Sun
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lars Rønn Olsen
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ellis L. Reinherz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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18
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Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia. Prev Vet Med 2015; 120:96-105. [DOI: 10.1016/j.prevetmed.2015.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 11/23/2022]
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19
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Nolte N, Kurzawa N, Eils R, Herrmann C. MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences. Nucleic Acids Res 2015; 43:W547-51. [PMID: 25940623 PMCID: PMC4489300 DOI: 10.1093/nar/gkv417] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/18/2015] [Indexed: 11/13/2022] Open
Abstract
Understanding the molecular dynamics of viral spreading is crucial for anticipating the epidemiological implications of disease outbreaks. In the case of influenza, reassortments or point mutations affect the adaption to new hosts or resistance to anti-viral drugs and can determine whether a new strain will result in a pandemic infection or a less severe progression. To this end, tools integrating molecular information with epidemiological parameters are important to understand how molecular characteristics reflect in the infection dynamics. We present a new web tool, MapMyFlu, which allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. The tool is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service, and is available at http://mapmyflu.ipmb.uni-heidelberg.de
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Affiliation(s)
- Nicholas Nolte
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Nils Kurzawa
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Roland Eils
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
| | - Carl Herrmann
- Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, Heidelberg 69120, Germany
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20
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Arafa AS, Naguib MM, Luttermann C, Selim AA, Kilany WH, Hagag N, Samy A, Abdelhalim A, Hassan MK, Abdelwhab EM, Makonnen Y, Dauphin G, Lubroth J, Mettenleiter TC, Beer M, Grund C, Harder TC. Emergence of a novel cluster of influenza A(H5N1) virus clade 2.2.1.2 with putative human health impact in Egypt, 2014/15. ACTA ACUST UNITED AC 2015; 20:2-8. [PMID: 25860390 DOI: 10.2807/1560-7917.es2015.20.13.21085] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A distinct cluster of highly pathogenic avian influenzaviruses of subtype A(H5N1) has been found to emergewithin clade 2.2.1.2 in poultry in Egypt since summer2014 and appears to have quickly become predominant.Viruses of this cluster may be associated withincreased incidence of human influenza A(H5N1) infectionsin Egypt over the last months.
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Affiliation(s)
- A S Arafa
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt
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21
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Unraveling the web of viroinformatics: computational tools and databases in virus research. J Virol 2014; 89:1489-501. [PMID: 25428870 DOI: 10.1128/jvi.02027-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain--viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article.
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22
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Castelán-Vega JA, Magaña-Hernández A, Jiménez-Alberto A, Ribas-Aparicio RM. The hemagglutinin of the influenza A(H1N1)pdm09 is mutating towards stability. Adv Appl Bioinform Chem 2014; 7:37-44. [PMID: 25328411 PMCID: PMC4198066 DOI: 10.2147/aabc.s68934] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The last influenza A pandemic provided an excellent opportunity to study the adaptation of the influenza A(H1N1)pdm09 virus to the human host. Particularly, due to the availability of sequences taken from isolates since the beginning of the pandemic until date, we could monitor amino acid changes that occurred in the hemagglutinin (HA) as the virus spread worldwide and became the dominant H1N1 strain. HA is crucial to viral infection because it binds to sialidated cell-receptors and mediates fusion of cell and viral membranes; because antibodies that bind to HA may block virus entry to the cell, this protein is subjected to high selective pressure. Multiple alignment analysis of sequences of the HA from isolates taken since 2009 to date allowed us to find amino acid changes that were positively selected as the pandemic progressed. We found nine changes that became prevalent: HA1 subunits D104N, K166Q, S188T, S206T, A259T, and K285E; and HA2 subunits E47K, S124N, and E172K. Most of these changes were located in areas involved in inter- and intrachain interactions, while only two (K166Q and S188T) were located in known antigenic sites. We conclude that selective pressure on HA was aimed to improve its functionality and hence virus fitness, rather than at avoidance of immune recognition.
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Affiliation(s)
- Juan A Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Anastasia Magaña-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Mexico City, Mexico
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23
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Claes F, Kuznetsov D, Liechti R, Von Dobschuetz S, Truong BD, Gleizes A, Conversa D, Colonna A, Demaio E, Ramazzotto S, Larfaoui F, Pinto J, Le Mercier P, Xenarios I, Dauphin G. The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau008. [PMID: 24608033 PMCID: PMC3945526 DOI: 10.1093/database/bau008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO’s global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored. Database OpenfluDB URL:http://openflu.vital-it.ch Database EMPRES-i URL:http://EMPRES-i.fao.org/
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Affiliation(s)
- Filip Claes
- Animal Health Service, Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 10532 Rome, Italy and Vital-IT/Swiss-Prot Groups, SIB, Swiss Institute for Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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Jiménez-Alberto A, Alvarado-Facundo E, Ribas-Aparicio RM, Castelán-Vega JA. Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. PLoS One 2013; 8:e70005. [PMID: 23894575 PMCID: PMC3720954 DOI: 10.1371/journal.pone.0070005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/17/2013] [Indexed: 12/17/2022] Open
Abstract
Hemagglutinin is the major surface glycoprotein of influenza viruses. It participates in the initial steps of viral infection through receptor binding and membrane fusion events. The influenza pandemic of 2009 provided a unique scenario to study virus evolution. We performed molecular dynamics simulations with four hemagglutinin variants that appeared throughout the 2009 influenza A (H1N1) pandemic. We found that variant 1 (S143G, S185T) likely arose to avoid immune recognition. Variant 2 (A134T), and variant 3 (D222E, P297S) had an increased binding affinity for the receptor. Finally, variant 4 (E374K) altered hemagglutinin stability in the vicinity of the fusion peptide. Variants 1 and 4 have become increasingly predominant, while variants 2 and 3 declined as the pandemic progressed. Our results show some of the different strategies that the influenza virus uses to adapt to the human host and provide an example of how selective pressure drives antigenic drift in viral proteins.
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MESH Headings
- Adaptation, Physiological/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza Pandemic, 1918-1919
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Molecular Dynamics Simulation
- Molecular Epidemiology
- Static Electricity
- Surface Properties
- Thermodynamics
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Affiliation(s)
- Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Esmeralda Alvarado-Facundo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
| | - Juan A. Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Distrito Federal, Mexico City, Mexico
- * E-mail:
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Characterization of the 2012 highly pathogenic avian influenza H7N3 virus isolated from poultry in an outbreak in Mexico: pathobiology and vaccine protection. J Virol 2013; 87:9086-96. [PMID: 23760232 DOI: 10.1128/jvi.00666-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In June of 2012, an H7N3 highly pathogenic avian influenza (HPAI) virus was identified as the cause of a severe disease outbreak in commercial laying chicken farms in Mexico. The purpose of this study was to characterize the Mexican 2012 H7N3 HPAI virus (A/chicken/Jalisco/CPA1/2012) and determine the protection against the virus conferred by different H7 inactivated vaccines in chickens. Both adult and young chickens intranasally inoculated with the virus became infected and died at between 2 and 4 days postinoculation (p.i.). High virus titers and viral replication in many tissues were demonstrated at 2 days p.i. in infected birds. The virus from Jalisco, Mexico, had high sequence similarity of greater than 97% to the sequences of wild bird viruses from North America in all eight gene segments. The hemagglutinin gene of the virus contained a 24-nucleotide insert at the hemagglutinin cleavage site which had 100% sequence identity to chicken 28S rRNA, suggesting that the insert was the result of nonhomologous recombination with the host genome. For vaccine protection studies, both U.S. H7 low-pathogenic avian influenza (LPAI) viruses and a 2006 Mexican H7 LPAI virus were tested as antigens in experimental oil emulsion vaccines and injected into chickens 3 weeks prior to challenge. All H7 vaccines tested provided ≥90% protection against clinical disease after challenge and decreased the number of birds shedding virus and the titers of virus shed. This study demonstrates the pathological consequences of the infection of chickens with the 2012 Mexican lineage H7N3 HPAI virus and provides support for effective programs of vaccination against this virus in poultry.
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Schweizer F, Bodenhausen N, Lassueur S, Masclaux FG, Reymond P. Differential Contribution of Transcription Factors to Arabidopsis thaliana Defense Against Spodoptera littoralis. FRONTIERS IN PLANT SCIENCE 2013; 4:13. [PMID: 23382734 PMCID: PMC3563046 DOI: 10.3389/fpls.2013.00013] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/18/2013] [Indexed: 05/18/2023]
Abstract
In response to insect herbivory, Arabidopsis plants activate the synthesis of the phytohormone jasmonate-isoleucine, which binds to a complex consisting of the receptor COI1 and JAZ repressors. Upon proteasome-mediated JAZ degradation, basic helix-loop-helix transcription factors (TFs) MYC2, MYC3, and MYC4 become activated and this results in the expression of defense genes. Although the jasmonate (JA) pathway is known to be essential for the massive transcriptional reprogramming that follows herbivory, there is however little information on other TFs that are required for defense against herbivores and whether they contribute significantly to JA-dependent defense gene expression. By transcriptome profiling, we identified 41 TFs that were induced in response to herbivory by the generalist Spodoptera littoralis. Among them, nine genes, including WRKY18, WRKY40, ANAC019, ANAC055, ZAT10, ZAT12, AZF2, ERF13, and RRTF1, were found to play a significant role in resistance to S. littoralis herbivory. Compared to the triple mutant myc234 that is as sensitive as coi1-1 to herbivory, knockout lines of these nine TFs were only partially more sensitive to S. littoralis but, however, some displayed distinct gene expression changes at the whole-genome level. Data thus reveal that MYC2, MYC3, and MYC4 are master regulators of Arabidopsis resistance to a generalist herbivore and identify new genes involved in insect defense.
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Affiliation(s)
- Fabian Schweizer
- Department of Plant Molecular Biology, University of LausanneLausanne, Switzerland
| | - Natacha Bodenhausen
- Department of Plant Molecular Biology, University of LausanneLausanne, Switzerland
| | - Steve Lassueur
- Department of Plant Molecular Biology, University of LausanneLausanne, Switzerland
| | - Frédéric G. Masclaux
- Department of Plant Molecular Biology, University of LausanneLausanne, Switzerland
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of LausanneLausanne, Switzerland
- *Correspondence: Philippe Reymond, Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland. e-mail:
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Masson P, Hulo C, De Castro E, Bitter H, Gruenbaum L, Essioux L, Bougueleret L, Xenarios I, Le Mercier P. ViralZone: recent updates to the virus knowledge resource. Nucleic Acids Res 2012. [PMID: 23193299 PMCID: PMC3531065 DOI: 10.1093/nar/gks1220] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.
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Affiliation(s)
- Patrick Masson
- SIB Swiss Institute of Bioinformatics, Swiss-Prot Group, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland
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Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses 2012; 6:404-16. [PMID: 22260278 PMCID: PMC3345175 DOI: 10.1111/j.1750-2659.2011.00331.x] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6(6), 404–416. Background The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly‐accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user‐friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in‐protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross‐protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.
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Affiliation(s)
- R Burke Squires
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Timpka T, Eriksson H, Gursky EA, Strömgren M, Holm E, Ekberg J, Eriksson O, Grimvall A, Valter L, Nyce JM. Requirements and design of the PROSPER protocol for implementation of information infrastructures supporting pandemic response: a Nominal Group study. PLoS One 2011; 6:e17941. [PMID: 21464918 PMCID: PMC3065450 DOI: 10.1371/journal.pone.0017941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 02/17/2011] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Advanced technical systems and analytic methods promise to provide policy makers with information to help them recognize the consequences of alternative courses of action during pandemics. Evaluations still show that response programs are insufficiently supported by information systems. This paper sets out to derive a protocol for implementation of integrated information infrastructures supporting regional and local pandemic response programs at the stage(s) when the outbreak no longer can be contained at its source. METHODS Nominal group methods for reaching consensus on complex problems were used to transform requirements data obtained from international experts into an implementation protocol. The analysis was performed in a cyclical process in which the experts first individually provided input to working documents and then discussed them in conferences calls. Argument-based representation in design patterns was used to define the protocol at technical, system, and pandemic evidence levels. RESULTS The Protocol for a Standardized information infrastructure for Pandemic and Emerging infectious disease Response (PROSPER) outlines the implementation of information infrastructure aligned with pandemic response programs. The protocol covers analyses of the community at risk, the response processes, and response impacts. For each of these, the protocol outlines the implementation of a supporting information infrastructure in hierarchical patterns ranging from technical components and system functions to pandemic evidence production. CONCLUSIONS The PROSPER protocol provides guidelines for implementation of an information infrastructure for pandemic response programs both in settings where sophisticated health information systems already are used and in developing communities where there is limited access to financial and technical resources. The protocol is based on a generic health service model and its functions are adjusted for community-level analyses of outbreak detection and progress, and response program effectiveness. Scientifically grounded reporting principles need to be established for interpretation of information derived from outbreak detection algorithms and predictive modeling.
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Affiliation(s)
- Toomas Timpka
- Department of Medical and Health Sciences, Linköpings universitet, Linköping, Sweden.
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Maximova V, Kirilov K, Markov S, Ivanov I. Comparative Genomic Studies of Influenza a Viruses Performed on Bluegene P Supercomputer: Part 1. Conservative Nucleotide Sequences in Influenza a Virus Genomes Revealed by Multiple Sequence Alignment. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Pepin KM, Lass S, Pulliam JRC, Read AF, Lloyd-Smith JO. Identifying genetic markers of adaptation for surveillance of viral host jumps. Nat Rev Microbiol 2010; 8:802-13. [PMID: 20938453 PMCID: PMC7097030 DOI: 10.1038/nrmicro2440] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adaptation is often thought to affect the likelihood that a virus will be able to successfully emerge in a new host species. If so, surveillance for genetic markers of adaptation could help to predict the risk of disease emergence. However, adaptation is difficult to distinguish conclusively from the other processes that generate genetic change. In this Review we survey the research on the host jumps of influenza A, severe acute respiratory syndrome-coronavirus, canine parvovirus and Venezuelan equine encephalitis virus to illustrate the insights that can arise from combining genetic surveillance with microbiological experimentation in the context of epidemiological data. We argue that using a multidisciplinary approach for surveillance will provide a better understanding of when adaptations are required for host jumps and thus when predictive genetic markers may be present.
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Affiliation(s)
- Kim M Pepin
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA.
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Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P. ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res 2010; 39:D576-82. [PMID: 20947564 PMCID: PMC3013774 DOI: 10.1093/nar/gkq901] [Citation(s) in RCA: 266] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.
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Affiliation(s)
- Chantal Hulo
- Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland
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