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Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

Lars Steinbrück, Alice Carolyn McHardy, Neil Ferguson
2012 PLoS Computational Biology  
Additionally, it identified both known and novel sites, and amino acid changes with antigenic impact in the evolution of influenza A (H3N2) viruses from 1968 to 2003.  ...  For human influenza viruses, recognizing changes in the antigenic phenotype and a strains' capability to evade pre-existing host immunity is important for the production of efficient vaccines.  ...  Acknowledgments We thank Derek Smith for providing antigenic data. Author Contributions Conceived and designed the experiments: ACM. Performed the experiments: LS. Analyzed the data: LS ACM.  ... 
doi:10.1371/journal.pcbi.1002492 pmid:22532796 pmcid:PMC3330098 fatcat:3cn4p26z75g27dnj2gqhxd6yqq

Genomic events underlying the changes in adamantane resistance among influenza A(H3N2) viruses during 2006-2008

Varough Deyde, Rebecca Garten, Tiffany Sheu, Catherine Smith, Allison Myrick, John Barnes, Xiyan Xu, Michael Shaw, Alexander Klimov, Larisa Gubareva
2009 Influenza and Other Respiratory Viruses  
Our findings emphasize the importance of complete genome sequencing in understanding the complex nature of the relationship between influenza virus evolution and antiviral resistance.  ...  1 Contributed equally to the manuscript. Conclusions The decrease in adamantane resistance at that time was due to transient co-circulation of genotypes that emerged through reassortment.  ...  , for their active involvement in virus surveillance activities, Dr Carolyn Bridges from the Influenza Division, Centers for Disease Control and Prevention, for critical review of the manuscript, the National  ... 
doi:10.1111/j.1750-2659.2009.00103.x pmid:19903212 pmcid:PMC4984730 fatcat:snb2nvxsyva7bf52plg2y3eboa

A Bayesian approach to incorporate structural data into the mapping of genotype to antigenic phenotype of influenza A(H3N2) viruses [article]

William T Harvey, Vinny Davies, Rodney S Daniels, Lynne Whittaker, Victoria Gregory, Alan J Hay, Dirk Husmeier, John W McCauley, Richard Reeve
2022 bioRxiv   pre-print
For example, influenza A(H3N2) entered the human population in 1968 causing a pandemic and has since been monitored, along with other seasonal influenza viruses, for the emergence of antigenic drift variants  ...  Here, using a sparse hierarchical Bayesian analogue of an experimentally validated model for integrating genetic and antigenic data, we identify the genetic changes in influenza A(H3N2) virus that underpin  ...  The work perfomed at the London-based CC was supported by the Medical Research Council (1990-2014) and, subsequently, the Francis Crick Institute which receives its core funding from Cancer Research UK  ... 
doi:10.1101/2022.03.26.485931 fatcat:5sah6kpgnzhtbdktpafs6p2e6a

Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses

Haifen Chen, Xinrui Zhou, Jie Zheng, Chee-Keong Kwoh
2016 BMC Medical Genomics  
Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution.  ...  The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune  ...  A Bayesian approach was applied in [24] to predict the antigenic relationships of H3N2 viruses, which were used to identify the antigenic clusters and infer the dynamics of antigenic evolution.  ... 
doi:10.1186/s12920-016-0230-5 pmid:28117657 pmcid:PMC5260787 fatcat:j2ie5taxlndydiyyzpmgpv3qai

Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape

Nicholas C. Wu, Jakub Otwinowski, Andrew J. Thompson, Corwin M. Nycholat, Armita Nourmohammad, Ian A. Wilson
2020 Nature Communications  
However, HA antigenic site B, which has become immunodominant in recent human H3N2 influenza viruses, is also evolutionarily constrained by its involvement in receptor binding.  ...  Here, we employ deep mutational scanning to probe the local fitness landscape of HA antigenic site B in six different human H3N2 strains spanning from 1968 to 2016.  ...  This work was supported by National Institutes of Health (NIH) R56 AI127371, R01 AI114730, K99 AI139445, Bill and Melinda Gates Foundation OPP1170236, DFG grant (SFB1310) for Predictability in Evolution  ... 
doi:10.1038/s41467-020-15102-5 pmid:32144244 fatcat:x5fjjbkeqjb7nmxnhbzsfqbgqa

Evolution of Novel Reassortant A/H3N2 Influenza Viruses in North American Swine and Humans, 2009–2011

Martha I. Nelson, Amy L. Vincent, Pravina Kitikoon, Edward C. Holmes, Marie R. Gramer
2012 Journal of Virology  
To understand the evolution of these novel H3N2 viruses in swine and humans, we undertook a phylogenetic analysis of 674 M sequences and 388 HA and NA sequences from influenza viruses isolated from North  ...  Importantly, the N2 segment of all H3N2v viruses isolated from humans is derived from a genetically distinct N2 lineage that has circulated in swine since being acquired by reassortment with seasonal human  ...  This research was conducted within the context of the Multinational Influenza Seasonal Mortality Study (MISMS), an on-going international collaborative effort to understand influenza epidemiology and evolution  ... 
doi:10.1128/jvi.00259-12 pmid:22696653 pmcid:PMC3421719 fatcat:xhis3dbqxvdgxneqfm73ezd2qy

Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses

Edward C Holmes, Elodie Ghedin, Naomi Miller, Jill Taylor, Yiming Bao, Kirsten St George, Bryan T Grenfell, Steven L Salzberg, Claire M Fraser, David J Lipman, Jeffery K Taubenberger, Simon Levin
2005 PLoS Biology  
Viruses described in this study collected after 2001 include some isolates collected as part of  ...  Acknowledgments The authors wish to acknowledge the excellent technical assistance of Sara Griesemer and Matthew Kleabonas.  ...  Other recent examples of reassortment between human and animal influenza A viruses have resulted in the emergence of novel H3N2 and H1N2 swine viruses in North America and Europe [33, 34] and the evolution  ... 
doi:10.1371/journal.pbio.0030300 pmid:16026181 pmcid:PMC1180517 fatcat:5c2aiws4rzcmxbf536jpqhpvgm

Genomewide Analysis of Reassortment and Evolution of Human Influenza A(H3N2) Viruses Circulating between 1968 and 2011

K. B. Westgeest, C. A. Russell, X. Lin, M. I. J. Spronken, T. M. Bestebroer, J. Bahl, R. van Beek, E. Skepner, R. A. Halpin, J. C. de Jong, G. F. Rimmelzwaan, A. D. M. E. Osterhaus (+5 others)
2013 Journal of Virology  
This study of genotype in relation to antigenic phenotype throughout the period of circulation of human influenza A(H3N2) viruses leads to a better understanding of the evolution of these viruses.  ...  Influenza A(H3N2) viruses became widespread in humans during the 1968 H3N2 virus pandemic and have been a major cause of influenza epidemics ever since.  ...  To study the genotype in relation to the antigenic phenotype throughout the period of circulation of human A(H3N2) influenza viruses, we used a data set comprising 286 full genomes of viruses sampled between  ... 
doi:10.1128/jvi.02163-13 pmid:24371052 pmcid:PMC3958060 fatcat:m4j77gnc3vfstjh7pifmi6oagm

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

2019 Virus Evolution  
The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus's North American diversity falling into the A2 clade.  ...  Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70 per cent of A(H3N2) viruses circulating in North America by early 2018.  ...  The findings and conclusions in this report are those of the author(s) and do not necessarily represent the official position of the Centers for Disease Control and Prevention.  ... 
doi:10.1093/ve/vez046 pmid:33282337 pmcid:PMC6891002 fatcat:dbakqtqbuzcpvnfjnd7gkqgxmi

Novel Reassortant Human-Like H3N2 and H3N1 Influenza A Viruses Detected in Pigs Are Virulent and Antigenically Distinct from Swine Viruses Endemic to the United States

Daniela S. Rajão, Phillip C. Gauger, Tavis K. Anderson, Nicola S. Lewis, Eugenio J. Abente, Mary Lea Killian, Daniel R. Perez, Troy C. Sutton, Jianqiang Zhang, Amy L. Vincent, A. García-Sastre
2015 Journal of Virology  
considered.IMPORTANCEPigs are important hosts in the evolution of influenza A viruses (IAV).  ...  Both viruses were antigenically distant from swine H3 viruses that circulate in the United States and from swine vaccine strains and also showed antigenic drift from human seasonal H3N2 viruses.  ...  ACKNOWLEDGMENTS We gratefully acknowledge the pork producers, swine veterinarians, and laboratories for participating in the USDA Swine Influenza A Virus Surveillance System.  ... 
doi:10.1128/jvi.01675-15 pmid:26311895 pmcid:PMC4645639 fatcat:q6tbgcknrrajdkf5oajsnua5fi

Evolution-informed forecasting of seasonal influenza A (H3N2) [article]

Xiangjun Du, Aaron A. King, Robert J. Woods, Mercedes Pascual
2017 bioRxiv   pre-print
Incidence prediction ahead of season remains a challenge largely because of the virus' antigenic evolution.  ...  With a monthly time series of H3N2 incidence in the United States over 10 years, we demonstrate the feasibility of prediction ahead of season and an accurate real-time forecast for the 2016/2017 influenza  ...  For this, we developed and tested a rule based on a published genotype-phenotype map for prediction of new antigenic variants.  ... 
doi:10.1101/198168 fatcat:sd6ht6zvsvg67jobkyeibckjay

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season [article]

Barney I Potter, Rebecca Garten, James Hadfield, John Huddleston, John Barnes, Thomas Rowe, Lizheng Guo, Xiyan Xu, Richard A Neher, Trevor Bedford, David Wentworth
2019 bioRxiv   pre-print
The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus's North American diversity falling into the A2 clade.  ...  Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70% of A(H3N2) viruses circulating in North America by early 2018.  ...  This suggests that NA evolution is a substantial contributor to the changing antigenic properties and dynamics of influenza viruses.  ... 
doi:10.1101/543322 fatcat:j4dye2xv4nhhhlfo273tbj5df4

Evolution-informed forecasting of seasonal influenza A (H3N2)

Xiangjun Du, Aaron A. King, Robert J. Woods, Mercedes Pascual
2017 Science Translational Medicine  
Interpandemic or seasonal influenza A, currently subtypes H3N2 and H1N1, exacts an enormous annual burden both in terms of human health and economic impact.  ...  Incidence prediction ahead of season remains a challenge largely because of the virus' antigenic evolution.  ...  For this, we developed and tested a rule based on a published genotype-phenotype map for prediction of new antigenic variants (40) .  ... 
doi:10.1126/scitranslmed.aan5325 pmid:29070700 pmcid:PMC5805486 fatcat:rnb346wfmfhmhmkk33l3q5wgdm

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses [article]

Johanna West, Juliane Roeder, Tatyana Matrosovich, Jana Beicht, Jan Baumann, Nancy Mounogou Kouassi, Jennifer Doedt, Nicolai Bovin, Gianpiero Zamperin, Michele Gastaldelli, Annalisa Salviato, Francesco Bonfante (+6 others)
2021 bioRxiv   pre-print
The hemagglutinin (HA) of A/H3N2 pandemic influenza viruses (IAVs) of 1968 differed from its inferred avian precursor by eight amino acid substitutions.  ...  To determine their phenotypic effects, we studied recombinant variants of A/Hong Kong/1/1968 virus containing either human-type or avian-type amino acids in the corresponding positions of HA.  ...  Swine influenza a viruses and the tangled relationship with 955 humans.  ... 
doi:10.1101/2021.04.19.439873 fatcat:vocdambionhktoc2jpvov5fcay

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  ...  Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited.  ...  Specific examples of adaptive intra-subtype reassortment include a reassortment event between two antigenically distinct A (H3N2) lineages in 2003 that caused a major change in antigenic phenotype reducing  ... 
doi:10.1099/mgen.0.000137 pmid:29310750 pmcid:PMC5857367 fatcat:dshnkq7s3vhxpbmnvgjt4rzzcq
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