Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses
Identifieur interne : 000669 ( Ncbi/Checkpoint ); précédent : 000668; suivant : 000670Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses
Auteurs : Jianpeng Xu ; Mary C. Christman ; Ruben O. Donis ; Guoqing LuSource :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-1348 ] ; 2011.
Abstract
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 7,517 NP nucleotide sequences revealed eight distinct evolutionary lineages, including three host-specific lineages (human, classic 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 Dec 17, 2008. A marked time gap was found between the times when the viruses emerged and were firstly 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.
Url:
DOI: 10.1016/j.meegid.2011.07.002
PubMed: 21763464
PubMed Central: 3204331
Affiliations:
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<front><div type="abstract" xml:lang="en"><p id="P1">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 7,517 NP nucleotide sequences revealed eight distinct evolutionary lineages, including three host-specific lineages (human, classic 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<sup>−3</sup>
substitutions per site per year, with the highest value observed in pandemic H1N1 2009 (3.4 × 10<sup>−3</sup>
) and the lowest in equine (0.9 × 10<sup>−3</sup>
). 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 Dec 17, 2008. A marked time gap was found between the times when the viruses emerged and were firstly 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.</p>
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<name sortKey="Lu, Guoqing" sort="Lu, Guoqing" uniqKey="Lu G" first="Guoqing" last="Lu">Guoqing Lu</name>
<name sortKey="Xu, Jianpeng" sort="Xu, Jianpeng" uniqKey="Xu J" first="Jianpeng" last="Xu">Jianpeng Xu</name>
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