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Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

Olivo Miotto, AT Heiny, Tin Tan, J Thomas August, Vladimir Brusic
2008 BMC Bioinformatics  
The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the  ...  Conclusion: By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful  ...  protein Figure 6 Timeline of adaptation to human-to-human transmission for the influenza A PB2 protein.  ... 
doi:10.1186/1471-2105-9-s1-s18 pmid:18315849 pmcid:PMC2259419 fatcat:cvvp2vos4feyhj3fd5p5jyrw6q

Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains

Olivo Miotto, A. T. Heiny, Randy Albrecht, Adolfo García-Sastre, Tin Wee Tan, J. Thomas August, Vladimir Brusic, Art F. Y. Poon
2010 PLoS ONE  
We performed a large-scale comparative analysis of proteins from avian and human strains, to produce a catalogue of mutations associated with H2H transmissibility, and to detect their presence in avian  ...  There is widespread concern that H5N1 avian influenza A viruses will emerge as a pandemic threat, if they become capable of human-to-human (H2H) transmission.  ...  Conclusions In this study, we performed analysis based on mutual information to a dataset of over 40,000 influenza protein sequences, to identify adaptive mutations associated with human-to-human transmissibility  ... 
doi:10.1371/journal.pone.0009025 pmid:20140252 pmcid:PMC2815782 fatcat:bwhr6n25ujgadoydf2dmzyyo5u

Emergence and pandemic potential of swine-origin H1N1 influenza virus

Gabriele Neumann, Takeshi Noda, Yoshihiro Kawaoka
2009 Nature  
A prime example is the recent emergence of swine-origin H1N1 viruses that have transmitted to and spread among humans, resulting in outbreaks internationally.  ...  of the factors that determine viral pathogenicity and/or transmissibility.  ...  the National Institute of Allergy and Infectious Diseases (Contract HHSN266200700010C), Grant-in-Aid for Specially Promoted Research, by a contract research fund for the Program of Founding Research Centers  ... 
doi:10.1038/nature08157 pmid:19525932 pmcid:PMC2873852 fatcat:xgfcycwedje3nb5jck6mg7mhzq

Identification and Chronological Analysis of Genomic Signatures in Influenza A Viruses

Yuh-Jyh Hu, Po-Chin Tu, Chun-Sheng Lin, Szu-Ting Guo, Yue Wang
2014 PLoS ONE  
An increase in the availability of data on the influenza A viruses (IAV) has enabled the identification of the potential determinants of IAV host specificity using computational approaches.  ...  We identified novel signatures that could be mapped to known functional domains, and introduced a chronological analysis to investigate the changes in host-specific genomic signatures over time.  ...  Thanks also go to Editor Yue Wang, and the anonymous reviewers for their comments and suggestions.  ... 
doi:10.1371/journal.pone.0084638 pmid:24416256 pmcid:PMC3885579 fatcat:lrrwhsd7ibcenlaitelxb5vu7u

Viral factors in influenza pandemic risk assessment

Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J Russell, Jessica A Belser, Sarah Cobey, Peter M Kasson, James O Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine AA Beauchemin, Trevor Bedford (+7 others)
2016 eLife  
To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human.  ...  The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans.  ...  assistance in improving the manuscript.  ... 
doi:10.7554/elife.18491 pmid:27834632 pmcid:PMC5156527 fatcat:pffupgrfxbc7fp32rlyjyge64m

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

Emily HM Wong, David K Smith, Raul Rabadan, Malik Peiris, Leo LM Poon
2010 BMC Evolutionary Biology  
The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20 th century.  ...  As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission.  ...  PB2 Codon usage trends in human influenza viruses To better understand the change in codon usage over time that was seen in human influenza viruses (Figure 1 ), a CA analysis of all 6 viral genes in  ... 
doi:10.1186/1471-2148-10-253 pmid:20723216 pmcid:PMC2933640 fatcat:sbfj4xc5rzacnh4hown6x75ad4

Identifying Changes in Selective Constraints: Host Shifts in Influenza

Asif U. Tamuri, Mario dos Reis, Alan J. Hay, Richard A. Goldstein, Christophe Fraser
2009 PLoS Computational Biology  
The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population.  ...  Identifying which mutations allow viruses from avian origin to spread successfully in the human population is of great importance in predicting and controlling influenza pandemics.  ...  Contributed reagents/materials/analysis tools: MdR. Wrote the paper: MdR AJH RAG.  ... 
doi:10.1371/journal.pcbi.1000564 pmid:19911053 pmcid:PMC2770840 fatcat:7ydu5ot2eze5zcl7mflruwbi64

Evolution of canine and equine influenza (H3N8) viruses co-circulating between 2005 and 2008

Pierre Rivailler, Ijeoma A. Perry, Yunho Jang, C. Todd Davis, Li-Mei Chen, Edward J. Dubovi, Ruben O. Donis
2010 Virology  
Acknowledgments We thank the staff of the Animal Health Diagnostic Center for viral isolate logistics and epidemiologic information.  ...  The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention or the Agency for Toxic Substances and  ...  Third, interspecies transmission does not occur due to viral dependence on a mutually exclusive species-specific function.  ... 
doi:10.1016/j.virol.2010.08.022 pmid:20880564 fatcat:clagax37qjgedjcrzwwquauhfy

Moving H5N1 studies into the era of systems biology

Laurence Josset, Jennifer Tisoncik-Go, Michael G. Katze
2013 Virus Research  
This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis.  ...  and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response.  ...  This project was funded in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract HHSN272200800060C  ... 
doi:10.1016/j.virusres.2013.02.011 pmid:23499671 pmcid:PMC3834220 fatcat:dzmpbx4hnzd35mjqarlsv2xh3u

Understanding infectious agents from an in silico perspective

Joo Chuan Tong, Lisa F.P. Ng
2011 Drug Discovery Today  
Here, we describe how considerable advances in computational methods of data mining, mathematical modeling in epidemiology and simulation have been used to enhance our understanding of infectious agents  ...  Knowledge of infectious diseases now emerging from genomic, proteomic, epidemiological and clinical data can provide insights into the mechanisms of immune function, disease pathogenesis and epidemiology  ...  [23] applied mutual information, an information theoretical statistic that measures the strength of association between a pair of variables, to identify characteristic sites in influenza A proteins  ... 
doi:10.1016/j.drudis.2010.10.007 pmid:20974283 pmcid:PMC7185741 fatcat:vf7f3ruebrc43ca6pyy2dz3co4

Expanded Cocirculation of Stable Subtypes, Emerging Lineages, and New Sporadic Reassortants of Porcine Influenza Viruses in Swine Populations in Northwest Germany

T. C. Harder, E. grosse Beilage, E. Lange, C. Meiners, S. Dohring, S. Pesch, T. Noe, C. Grund, M. Beer, E. Starick
2013 Journal of Virology  
In addition, a more exhaustive tracing of the formation, transmission, and spread of new reassortant influenza A viruses with unknown zoonotic potential is urgently required. Harder et al.  ...  European avian influenza virus-derived H1N1 (H1N1av) viruses dominated the epidemiology, followed by human-derived subtypes H1N2 and H3N2.  ...  result of mutual adaptations to the new partner protein.  ... 
doi:10.1128/jvi.00381-13 pmid:23824819 pmcid:PMC3807404 fatcat:uy7i2ly5bbdrvk5rggarie5ytq

Antiviral agents targeting the influenza virus: a review and publication analysis

L. Eyer, K. Hruska
2013 Veterinární Medicína  
In addition to vaccination, the development of new anti-influenza agents represents a crucial defence strategy to combat seasonal and pandemic influenza strains.  ...  In this review article, an analysis of publications describing anti-influenza agents indexed in the Web of Science<sup>&reg;</sup> database has been carried out.  ...  large-scale mutual information analysis.  ... 
doi:10.17221/6746-vetmed fatcat:3jyjelrmdvevlgikn4tjhllfkm

Advances in respiratory virus therapeutics – A meeting report from the 6th isirv Antiviral Group conference

John H. Beigel, Hannah H. Nam, Peter L. Adams, Amy Krafft, William L. Ince, Samer S. El-Kamary, Amy C. Sims
2019 Antiviral Research  
The aim of this report is to provide a summary of the presentations given at this meeting.  ...  The International Society for Influenza and other Respiratory Virus Diseases held its 6th Antiviral Group (isirv-AVG) conference in Rockville, Maryland, November 13-15, 2018.  ...  All speakers were given an opportunity to review the summary of the presentations.  ... 
doi:10.1016/j.antiviral.2019.04.006 pmid:30974127 pmcid:PMC7132446 fatcat:s2qn3ez3mjfw5bfvfr7llql554

Influenza A viruses are transmitted via the air from the nasal respiratory epithelium of ferrets

Mathilde Richard, Judith M. A. van den Brand, Theo M. Bestebroer, Pascal Lexmond, Dennis de Meulder, Ron A. M. Fouchier, Anice C. Lowen, Sander Herfst
2020 Nature Communications  
Human influenza A viruses are known to be transmitted via the air from person to person. It is unknown from which anatomical site of the respiratory tract influenza A virus transmission occurs.  ...  These results indicate that virus replication in the upper respiratory tract, the nasal respiratory epithelium in particular, of donors is a driver for transmission of influenza A viruses via the air.  ...  This work was supported by NIH/NIAID contracts HHSN272201400008C and HHSN27220140004C. S.H. was funded in part by an NWO VIDI grant (contract number 91715372).  ... 
doi:10.1038/s41467-020-14626-0 pmid:32034144 pmcid:PMC7005743 fatcat:a4iycyzf5vbedlkfdddm3vwcca

Inactivation of influenza A viruses in the environment and modes of transmission: A critical review

Thomas P. Weber, Nikolaos I. Stilianakis
2008 Journal of Infection  
We systematically review available information on the environmental inactivation of influenza A viruses and employ information on infectious dose and results from mathematical models to assess transmission  ...  The relative importance of airborne, droplet and contact transmission of influenza A virus and the efficiency of control measures depends among other factors on the inactivation of viruses in different  ...  Influenza A virion structure and tissue tropism Influenza A virions are pleomorphic with shapes ranging from spherical to long filamentous; viral morphology is determined by genetic factors, viral proteins  ... 
doi:10.1016/j.jinf.2008.08.013 pmid:18848358 pmcid:PMC7112701 fatcat:e6ffr7n2kneq7ahoa3csjjhxqu
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