Document Detail

Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses.
MedLine Citation:
PMID:  21763464     Owner:  NLM     Status:  MEDLINE    
Influenza A viral nucleoprotein (NP) plays a critical role in virus replication and host adaptation, however, the underlying molecular evolutionary dynamics of NP lineages are less well-understood. In this study, large-scale analyses of 5094 NP nucleotide sequences revealed eight distinct evolutionary lineages, including three host-specific lineages (human, classical swine and equine), two cross-host lineages (Eurasian avian-like swine and swine-origin human pandemic H1N1 2009) and three geographically isolated avian lineages (Eurasian, North American and Oceanian). The average nucleotide substitution rate of the NP lineages was estimated to be 2.4 × 10(-3) substitutions per site per year, with the highest value observed in pandemic H1N1 2009 (3.4 × 10(-3)) and the lowest in equine (0.9 × 10(-3)). The estimated time of most recent common ancestor (TMRCA) for each lineage demonstrated that the earliest human lineage was derived around 1906, and the latest pandemic H1N1 2009 lineage dated back to December 17, 2008. A marked time gap was found between the times when the viruses emerged and were first sampled, suggesting the crucial role for long-term surveillance of newly emerging viruses. The selection analyses showed that human lineage had six positive selection sites, whereas pandemic H1N1 2009, classical swine, Eurasian avian and Eurasian swine had only one or two sites. Protein structure analyses revealed several positive selection sites located in epitope regions or host adaptation regions, indicating strong adaptation to host immune system pressures in influenza viruses. Along with previous studies, this study provides new insights into the evolutionary dynamics of influenza A NP lineages. Further lineage analyses of other gene segments will allow better understanding of influenza A virus evolution and assist in the improvement of global influenza surveillance.
Jianpeng Xu; Mary C Christman; Ruben O Donis; Guoqing Lu
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2011-07-07
Journal Detail:
Title:  Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases     Volume:  11     ISSN:  1567-7257     ISO Abbreviation:  Infect. Genet. Evol.     Publication Date:  2011 Dec 
Date Detail:
Created Date:  2011-12-05     Completed Date:  2012-03-26     Revised Date:  2013-06-28    
Medline Journal Info:
Nlm Unique ID:  101084138     Medline TA:  Infect Genet Evol     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  2125-32     Citation Subset:  IM    
Copyright Information:
Copyright © 2011 Elsevier B.V. All rights reserved.
Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182-0040, United States.
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MeSH Terms
Base Sequence
Evolution, Molecular*
Influenza A Virus, H1N1 Subtype / classification,  genetics*
Influenza, Human / genetics,  virology
Molecular Sequence Data
Nucleoproteins / chemistry,  classification*,  genetics*
Orthomyxoviridae Infections / genetics,  virology
Protein Conformation
Sequence Alignment
Sequence Analysis, RNA
Viral Proteins / chemistry,  classification*,  genetics*
Grant Support
R01 LM009985-01A1/LM/NLM NIH HHS; R01 LM009985-02/LM/NLM NIH HHS; R01LM009985-01A1/LM/NLM NIH HHS
Reg. No./Substance:
0/Nucleoproteins; 0/Viral Proteins

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