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Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective.

Fucheng Guo1, Jinjin Yang1, Junbin Pan1

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Frontiers in Microbiology
|August 8, 2020
PubMed
Summary

The H1N1/pdm2009 virus adapted to humans through specific gene segments from swine influenza viruses. Ongoing evolution further optimized these genes for better replication and transmission in the human population.

Keywords:
Eurasian avian-like swine virusesH1N1/pdm2009codon usageinfluenza A virusswine influenza virustriple-reassortant swine viruses

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Area of Science:

  • Virology
  • Molecular Biology
  • Evolutionary Biology

Background:

  • The H1N1/pdm2009 influenza virus emerged from a complex pool of swine influenza viruses, including Eurasian avian-like and triple-reassortant lineages.
  • The precise genetic factors enabling the H1N1/pdm2009 virus's successful emergence and transmission in humans remain incompletely understood.

Purpose of the Study:

  • To investigate the adaptability of swine influenza virus gene segments to the human expression system.
  • To identify specific genes contributing to the H1N1/pdm2009 virus's replication and transmission efficiency in humans.
  • To analyze the evolutionary trajectory of H1N1/pdm2009 gene codon usage post-emergence.

Main Methods:

  • Analysis of codon usage patterns of swine influenza virus genes (Eurasian avian-like and triple-reassortant).
  • Estimation of gene segment adaptability to the human codon usage pattern.
  • Detection of changes in H1N1/pdm2009 gene codon usage between 2009 and 2019.

Main Results:

  • Specific genes from Eurasian avian-like (MP, NA) and triple-reassortant (PB2, PB1, PA) swine influenza viruses showed high adaptability to human codon usage.
  • These adaptable genes likely contributed to the H1N1/pdm2009 virus's replication and competitiveness during its emergence.
  • A significant optimization of H1N1/pdm2009 codon usage patterns towards the human system was observed between 2009 and 2019.

Conclusions:

  • The H1N1/pdm2009 virus's emergence was facilitated by pre-existing gene segments with high adaptability to the human expression system.
  • Ongoing adaptive evolution has further enhanced the overall gene cassette's compatibility with human hosts.
  • Codon usage analysis provides insights into viral adaptation and the emergence of novel influenza strains.