Quantifying influenza virus diversity and transmission in humans (original) (raw)

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NCBI Reference Sequence

References

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Acknowledgements

T.S. was a predoctoral trainee supported by US National Institutes of Health T32 training grant T32 EB009403 as part of the HHMI-NIBIB Interfaces Initiative. This research was supported with a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (project T11-705/14N) (L.L.M.P., Y.G., J.S.M.P. and B.J.C.), federal funds from the National Institute of Allergy and Infectious Diseases, US National Institutes of Health, US Department of Health and Human Services, under contract numbers HHS-N272201400006C (L.L.M.P., Y.G. and J.S.M.P.), HHS-N266200700005C (B.J.C.) and HHS-N272200900007C (E.G., X.L., R.A.H., T.B.S. and D.E.W.), the National Institute of General Medical Science, US National Institutes of Health, under award numbers U54 GM088491 (E.G., R.R. and J.V.D.) and U54 GM088558 (B.J.C.), and National Health and Medical Research Council of Australia Fellowship AF30 (E.C.H.). The data for this manuscript were generated and prepared while D.E.W. was employed at the J. Craig Venter Institute. The opinions expressed in this article are the authors' own and do not reflect the views of the Centers for Disease Control and Prevention, the US Department of Health and Human Services or the US government.

Author information

Author notes

  1. Matthew B Rogers & David E Wentworth
    Present address: Present addresses: Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA (M.B.R.) and Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA (D.E.W.).,
  2. Leo L M Poon and Timothy Song: These authors contributed equally to this work.
  3. Benjamin J Cowling and Elodie Ghedin: These authors jointly supervised this work.

Authors and Affiliations

  1. Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China
    Leo L M Poon, Yi Guan & Joseph S M Peiris
  2. Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
    Timothy Song & Matthew B Rogers
  3. Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
    Timothy Song, Bin Zhou, Alan Twaddle & Elodie Ghedin
  4. School of Computer Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
    Roni Rosenfeld
  5. J. Craig Venter Institute, Rockville, Maryland, USA
    Xudong Lin, Rebecca A Halpin, Timothy B Stockwell & David E Wentworth
  6. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
    Robert Sebra
  7. Pittsburgh Supercomputer Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
    Jay V DePasse
  8. Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia
    Edward C Holmes
  9. Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
    Edward C Holmes
  10. Departments of Medicine, Tisch Cancer Institute, Hematology and Medical Oncology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
    Benjamin Greenbaum
  11. Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong, China
    Benjamin J Cowling
  12. College of Global Public Health, New York University, New York, New York, USA
    Elodie Ghedin

Authors

  1. Leo L M Poon
  2. Timothy Song
  3. Roni Rosenfeld
  4. Xudong Lin
  5. Matthew B Rogers
  6. Bin Zhou
  7. Robert Sebra
  8. Rebecca A Halpin
  9. Yi Guan
  10. Alan Twaddle
  11. Jay V DePasse
  12. Timothy B Stockwell
  13. David E Wentworth
  14. Edward C Holmes
  15. Benjamin Greenbaum
  16. Joseph S M Peiris
  17. Benjamin J Cowling
  18. Elodie Ghedin

Contributions

All the authors read and approved the manuscript. L.L.M.P. and E.G. conceived and designed the experiments, supervised research, performed analyses and wrote the manuscript. T.S. analyzed the deep sequence data, performed the variant codon and clustering analyses, and wrote the manuscript. B.G. and R.R. supervised research on the inoculum size estimates and wrote the manuscript. X.L., R.A.H., D.E.W., B.Z. and R.S. performed the sample preparation and sequencing. T.B.S., A.T. and J.V.D. performed the bioinformatic analyses. M.B.R. performed phylogenetic analyses. E.C.H. performed phylogenetic analyses and wrote the manuscript. Y.G. and J.S.M.P. conceived and designed the experiments. B.J.C. conceived and designed the experiments and supervised research.

Corresponding authors

Correspondence toBenjamin J Cowling or Elodie Ghedin.

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Competing interests

The authors declare no competing financial interests.

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Poon, L., Song, T., Rosenfeld, R. et al. Quantifying influenza virus diversity and transmission in humans.Nat Genet 48, 195–200 (2016). https://doi.org/10.1038/ng.3479

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