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A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2

William D. Lees, David S. Moss, Adrian J. Shepherd
2010 Computer applications in the biosciences : CABIOS  
Motivation: Modelling antigenic shift in influenza A H3N2 can help to predict the efficiency of vaccines.  ...  We introduce a class of predictive models based on the analysis of amino acid changes in these binding regions, and extend the principle to changes in HA1 as a whole by dividing the molecule into regional  ...  We are grateful to reviewers for helpful comments received, particularly in relation to refinement of the model.  ... 
doi:10.1093/bioinformatics/btq160 pmid:20388627 pmcid:PMC2913667 fatcat:wcj355alqzddzdtpmoxpu4gnjm

The human Transmembrane Protease Serine 2 is necessary for the production of Group 2 influenza A virus pseudotypes

Francesca Ferrara, Eleonora Molesti, Giovanni Cattoli
2013 Journal of Molecular and Genetic Medicine  
The monomer of influenza haemagglutinin is synthesized as a single polypeptide precursor that during maturation is cleaved by proteases into two active subunits.  ...  This demonstrates that TMPRSS2 is necessary for the functional activation, in vitro, of both the HA of human seasonal influenza and other Group 2 HA influenza strains.  ...  ACKNOWLEDGEMENTS We thank the Animal Health and Veterinary Laboratories Agency for the reference antisera provided. This work was funded by the University of Kent.  ... 
doi:10.4172/1747-0862.1000055 fatcat:shk6v4y2b5axfdy443eadgbknu

Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas

K M Stucker, S A Schobel, R J Olsen, H L Hodges, X Lin, R A Halpin, N Fedorova, T B Stockwell, A Tovchigrechko, S R Das, D E Wentworth, J M Musser
2015 Eurosurveillance  
Phylogenetic analyses indicated that multiple co-circulating clades and continual antigenic drift in the haemagglutinin (HA) of clades 5, 3A, and 3C, with the evolution of a new 3C subgroup (3C-2012/13  ...  While the early start and higher intensity of the 2012/13 influenza A virus (IAV) epidemic was not unprecedented, it was the first IAV epidemic season since the 2009 H1N1 influenza pandemic where the H3N2  ...  The authors gratefully acknowledge the 32 originating and submitting laboratories who directly contributed sequences used in the constellation analysis to GISAID: Alaska State Virology Lab; Arizona Department  ... 
doi:10.2807/1560-7917.es2015.20.18.21122 fatcat:ri3ae2l4wfg33nnekxt4wsx3om

Phylogenetic Properties of RNA Viruses

Simone Pompei, Vittorio Loreto, Francesca Tria, Yamir Moreno
2012 PLoS ONE  
Our thorough quantitative analysis allows for a deeper understanding of the evolutionary dynamics of the considered RNA viruses, which is crucial in order to provide a valuable framework for a quantitative  ...  In our work, we reconstruct and analyze the phylogenetic trees of six RNA viruses, with a special emphasis on the human Influenza A virus, due to its relevance for vaccine preparation as well as for the  ...  The inferred phylogenetic tree of the haemagglutinin (HA) gene of human Influenza A virus, H3N2 subtype [29, 30, 31, 28] , shown in Fig. 1 , displays a strong temporal pattern.  ... 
doi:10.1371/journal.pone.0044849 pmid:23028645 pmcid:PMC3447819 fatcat:alicflzhrjdhhc2dxvxjixy5om

Comparison of 10 influenza A (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell- and egg-grown viruses

E. P. Rocha, X. Xu, H. E. Hall, J. R. Allen, H. L. Regnery, N. J. Cox
1993 Journal of General Virology  
PCR was used to amplify and sequence the complete HA1 region of the haemagglutinin (HA)-encoding genes of 10 clinical isolates of influenza virus of the H1N1 or H3N2 subtypes.  ...  Amino acid substitutions in the egg-derived HA sequences were found in nine out of the 10 specimens analysed, whereas seven out of eight of the MDCK-derived HA sequences were identical to those in the  ...  Since it was observed that propagation of influenza viruses in eggs may lead to isolation of viruses bearing haemagglutinins (HAs) that differ in both their antigenic properties and molecular sequences  ... 
doi:10.1099/0022-1317-74-11-2513 pmid:8245870 fatcat:qfjsdwwiyndxhlvgilsw2zxukq

Mapping of H3N2 influenza antigenic evolution in China reveals a strategy for vaccine strain recommendation

Xiangjun Du, Libo Dong, Yu Lan, Yousong Peng, Aiping Wu, Ye Zhang, Weijuan Huang, Dayan Wang, Min Wang, Yuanji Guo, Yuelong Shu, Taijiao Jiang
2012 Nature Communications  
Here we have developed a computational method, denoted as PREDAC, to predict antigenic clusters of influenza A (H3n2) viruses with high accuracy from viral HA sequences.  ...  one of the primary efforts in influenza vaccine strain recommendation is to monitor through gene sequencing the viral surface protein haemagglutinin (HA) variants that lead to viral antigenic changes.  ...  Acknowledgements Author contributions T.J. and Y.S. conceived and directed the project. X.D., A.W. and Y.P. performed the computation.  ... 
doi:10.1038/ncomms1710 pmid:22426230 fatcat:ayu5peuajvgixasjykd5j5aexy

Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses

Emily J. Goldstein, William T. Harvey, Gavin S. Wilkie, Samantha J. Shepherd, Alasdair R. MacLean, Pablo R. Murcia, Rory N. Gunson
2018 Microbial Genomics  
Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and  ...  Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene.  ...  Fig. 1 . 1 Phylogenetic tree of the haemagglutinin gene of influenza A(H3N2) viruses obtained from the 2014/15 influenza season.  ... 
doi:10.1099/mgen.0.000137 pmid:29310750 pmcid:PMC5857367 fatcat:dshnkq7s3vhxpbmnvgjt4rzzcq

Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution

K. B. Westgeest, M. de Graaf, M. Fourment, T. M. Bestebroer, R. van Beek, M. I. J. Spronken, J. C. de Jong, G. F. Rimmelzwaan, C. A. Russell, A. D. M. E. Osterhaus, G. J. D. Smith, D. J. Smith (+1 others)
2012 Journal of General Virology  
In 2004, the antigenic evolution of HA of human influenza A (H3N2) viruses was mapped (Smith et al., Science 305, 371-376, 2004) from its introduction in humans in 1968 until 2003.  ...  Each year, influenza viruses cause epidemics by evading pre-existing humoral immunity through mutations in the major glycoproteins: the haemagglutinin (HA) and the neuraminidase (NA).  ...  part of the influenza A (H3N2) virus isolates.  ... 
doi:10.1099/vir.0.043059-0 pmid:22718569 pmcid:PMC3542130 fatcat:gobwyw47xjhs3jdey7xab2rol4

Intense interseasonal influenza outbreaks, Australia, 2018/19

Ian G Barr, Yi Mo Deng, Miguel L Grau, Alvin X Han, Robin Gilmour, Melissa Irwin, Peter Markey, Kevin Freeman, Geoff Higgins, Mark Turra, Naomi Komadina, Heidi Peck (+4 others)
2019 Eurosurveillance  
/19 interseasonal influenza outbreaks in Australia epidemiologically and examine the genetic, antigenic and structural properties of the viruses responsible for these outbreaks.MethodsThis observational  ...  and resulted in a very early start to the 2019 influenza season across Australia.  ...  Thank you to all the Australian laboratories that supplied the influenza samples/ isolates used in this study.  ... 
doi:10.2807/ pmid:31431210 pmcid:PMC6702793 fatcat:5t4lqf5oure6dlbi2skjewr3xu

Scientific Opinion on monitoring for the emergence of possible new pandemic strains of influenza in animals

2011 EFSA Journal  
Current influenza vaccines are recommended to contain antigens protecting against two influenza A subtypes, H3N2 and H1N1, and one of the two lineages of the type B virus.  ...  Type A influenza viruses are further divided into subtypes based on the antigenic relationships in the surface glycoproteins haemagglutinin (HA) and neuraminidase (NA).  ...  change in the environment.  ... 
doi:10.2903/j.efsa.2011.2109 fatcat:a7khiojgzzgbzmtiofg7byizwu

The receptor-binding and membrane-fusion properties of influenza virus variants selected using anti-haemagglutinin monoclonal antibodies

P S Daniels, S Jeffries, P Yates, G C Schild, G N Rogers, J C Paulson, S A Wharton, A R Douglas, J J Skehel, D C Wiley
1987 EMBO Journal  
A monoclonal antibody raised against X-31 influenza virus reacted with the majority of natural H3N2 viruses isolated between 1968 and 1982.  ...  A number of variants of X-31 and of a receptor-binding mutant of X-31 were selected by the antibody during virus replication in eggs and MDCK cells.  ...  ., for computing hardware) and NIAID AI20591 (G.C.S.)  ... 
pmid:3608984 pmcid:PMC553952 fatcat:m32j3cr5grbbjddael7tirriea

Explaining the geographical origins of seasonal influenza A (H3N2)

Frank Wen, Trevor Bedford, Sarah Cobey
2016 Proceedings of the Royal Society of London. Biological Sciences  
Most antigenically novel and evolutionarily successful strains of seasonal influenza A (H3N2) originate in East, South and Southeast Asia.  ...  To understand this pattern, we simulated the ecological and evolutionary dynamics of influenza in a host metapopulation representing the temperate north, tropics and temperate south.  ...  Influenza A/H3N2, A/H1N1 and two B lineages currently circulate in the human population, with the H3N2 subtype causing the most disease [5] .  ... 
doi:10.1098/rspb.2016.1312 pmid:27629034 pmcid:PMC5031657 fatcat:uxqnzlmahfgp5muhfweskbyzly

Changing Selective Pressure during Antigenic Changes in Human Influenza H3

Benjamin P. Blackburne, Alan J. Hay, Richard A. Goldstein, Bruce Levin
2008 PLoS Pathogens  
In addition, the role of changing glycosylation of the haemagglutinin in these shifts in antigenic properties is unknown.  ...  Interestingly, while amino acid substitutions occur at a relatively constant rate, the antigenic properties of H3 move in a discontinuous, step-wise manner.  ...  Author Contributions Conceived and designed the experiments: BB AH RG. Performed the experiments: BB. Analyzed the data: BB. Contributed reagents/materials/ analysis tools: BB.  ... 
doi:10.1371/journal.ppat.1000058 pmid:18451985 pmcid:PMC2323114 fatcat:zxywicaquzdbzdm3fbh4qw4omm

Complete structure of A/duck/Ukraine/63 influenza hemagglutinin gene: Animal virus as progenitor of human H3 Hong Kong 1968 influenza hemagglutinin

Rongxiang Fang, Willy Min Jou, Danny Huylebroeck, René Devos, Walter Fiers
1981 Cell  
Influenza A can undergo radical changes (antigenic shift) in the properties of its two surface antigens, hemagglutinin and neuraminidase, resulting in the appearance of a new human influenza A subtype  ...  A. (1980). The haemagglutinin gene of influenza A virus: nucleotide sequence analysis of cloned DNA copies. In Structure and Variation in Influenza Virus, G. Laver and G. Air, eds.  ...  These rather extensive differences presumably have to be explained on the basis of the origins and histories of the virus stocks used in these studies.  ... 
doi:10.1016/0092-8674(81)90049-0 pmid:6169439 fatcat:tbyea3p7njfirpm5zrl2iiat7i

Vaccination and antigenic drift in influenza

Maciej F. Boni
2008 Vaccine  
If antigenic drift occurs on the time scale of a single influenza season, it may be associated with the presence of herd immunity at the beginning of the season and may indicate a need to monitor for vaccine  ...  The relationship between antigenic drift and vaccination must also be viewed in the context of the global circulation of influenza strains and the seeding of local and regional epidemics.  ...  Holmes for providing the New York sequences, to A. Lavenu for providing the French sequences, and to C. Viboud for pointing me to the New Zealand data. Thanks to E. C. Holmes, C. Viboud, D. L.  ... 
doi:10.1016/j.vaccine.2008.04.011 pmid:18773534 pmcid:PMC2603026 fatcat:odgzjhyqjfg3ja3g2yvk5wqe4u
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