Giuseppe
Emeritus
[Source: mBio, full page: (LINK). Abstract, edited.]
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Using Sequence Data To Infer the Antigenicity of Influenza Virus
Hailiang Sun<SUP>a</SUP>, Jialiang Yang<SUP>a</SUP>, Tong Zhang<SUP>b</SUP>, Li-Ping Long<SUP>a</SUP>, Kun Jia<SUP>a</SUP>, Guohua Yang<SUP>a</SUP>, Richard J. Webby<SUP>c</SUP>, Xiu-Feng Wan<SUP>a</SUP>
<SUP></SUP>
Author Affiliations: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA<SUP>a </SUP>Department of Statistics, Rutgers University, Piscataway, New Jersey, USA<SUP>b </SUP>Department of Infectious Diseases, St. Jude Children?s Research Hospital, Memphis, Tennessee, USA<SUP>c </SUP>
<SUP></SUP>
Address correspondence to Xiu-Feng Wan, wan@cvm.msstate.edu.
H.S. and J.Y. contributed equally to this work.
Invited Editor Stanley Perlman, University of Iowa Editor Christine Biron, Brown University
ABSTRACT
The efficacy of current influenza vaccines requires a close antigenic match between circulating and vaccine strains. As such, timely identification of emerging influenza virus antigenic variants is central to the success of influenza vaccination programs. Empirical methods to determine influenza virus antigenic properties are time-consuming and mid-throughput and require live viruses. Here, we present a novel, experimentally validated, computational method for determining influenza virus antigenicity on the basis of hemagglutinin (HA) sequence. This method integrates a bootstrapped ridge regression with antigenic mapping to quantify antigenic distances by using influenza HA1 sequences. Our method was applied to H3N2 seasonal influenza viruses and identified the 13 previously recognized H3N2 antigenic clusters and the antigenic drift event of 2009 that led to a change of the H3N2 vaccine strain.
IMPORTANCE
This report supplies a novel method for quantifying antigenic distance and identifying antigenic variants using sequences alone. This method will be useful in influenza vaccine strain selection by significantly reducing the human labor efforts for serological characterization and will increase the likelihood of correct influenza vaccine candidate selection.
Footnotes
Citation Sun H, Yang J, Zhang T, Long L-P, Jia K, Yang G, Webby RJ, Wan X-F. 2013. Using sequence data to infer the antigenicity of influenza virus. mBio 4(4):e00230-13. doi:10.1128/mBio.00230-13.
Received 1 April 2013 Accepted 10 June 2013 Published 2 July 2013
Copyright ? 2013 Sun et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
-Hailiang Sun<SUP>a</SUP>, Jialiang Yang<SUP>a</SUP>, Tong Zhang<SUP>b</SUP>, Li-Ping Long<SUP>a</SUP>, Kun Jia<SUP>a</SUP>, Guohua Yang<SUP>a</SUP>, Richard J. Webby<SUP>c</SUP>, Xiu-Feng Wan<SUP>a</SUP>
<SUP></SUP>
Author Affiliations: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA<SUP>a </SUP>Department of Statistics, Rutgers University, Piscataway, New Jersey, USA<SUP>b </SUP>Department of Infectious Diseases, St. Jude Children?s Research Hospital, Memphis, Tennessee, USA<SUP>c </SUP>
<SUP></SUP>
Address correspondence to Xiu-Feng Wan, wan@cvm.msstate.edu.
H.S. and J.Y. contributed equally to this work.
Invited Editor Stanley Perlman, University of Iowa Editor Christine Biron, Brown University
ABSTRACT
The efficacy of current influenza vaccines requires a close antigenic match between circulating and vaccine strains. As such, timely identification of emerging influenza virus antigenic variants is central to the success of influenza vaccination programs. Empirical methods to determine influenza virus antigenic properties are time-consuming and mid-throughput and require live viruses. Here, we present a novel, experimentally validated, computational method for determining influenza virus antigenicity on the basis of hemagglutinin (HA) sequence. This method integrates a bootstrapped ridge regression with antigenic mapping to quantify antigenic distances by using influenza HA1 sequences. Our method was applied to H3N2 seasonal influenza viruses and identified the 13 previously recognized H3N2 antigenic clusters and the antigenic drift event of 2009 that led to a change of the H3N2 vaccine strain.
IMPORTANCE
This report supplies a novel method for quantifying antigenic distance and identifying antigenic variants using sequences alone. This method will be useful in influenza vaccine strain selection by significantly reducing the human labor efforts for serological characterization and will increase the likelihood of correct influenza vaccine candidate selection.
Footnotes
Citation Sun H, Yang J, Zhang T, Long L-P, Jia K, Yang G, Webby RJ, Wan X-F. 2013. Using sequence data to infer the antigenicity of influenza virus. mBio 4(4):e00230-13. doi:10.1128/mBio.00230-13.
Received 1 April 2013 Accepted 10 June 2013 Published 2 July 2013
Copyright ? 2013 Sun et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
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