tetano
Editor, Senior Moderator
Published online February 4, 2013 doi: 10.1098/rstb.2012.0382 Phil. Trans. R. Soc. B 19 March 2013 vol. 368 no. 1614 20120382
The evolutionary dynamics of influenza A virus adaptation to mammalian hosts
S. Bhatt1,2,
T. T. Lam1,
S. J. Lycett3,
A. J. Leigh Brown3,
T. A. Bowden4,
E. C. Holmes5,6,
Y. Guan7,
J. L. N. Wood8,
I. H. Brown9,
P. Kellam2,
Combating Swine Influenza Consortium and
O. G. Pybus1⇓
+ Author Affiliations
1Department of Zoology, University of Oxford, Oxford, UK
2Wellcome Trust Sanger Institute, Hinxton, UK
3Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
4Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
5Mueller Laboratory, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
6Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
7Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People's Republic of China
8Cambridge Infectious Diseases Consortium, University of Cambridge, Cambridge, UK
9Animal Health and Veterinary Laboratories Agency, Weybridge, UK
e-mail: oliver.pybus@zoo.ox.ac.uk
Abstract
Few questions on infectious disease are more important than understanding how and why avian influenza A viruses successfully emerge in mammalian populations, yet little is known about the rate and nature of the virus? genetic adaptation in new hosts. Here, we measure, for the first time, the genomic rate of adaptive evolution of swine influenza viruses (SwIV) that originated in birds. By using a curated dataset of more than 24 000 human and swine influenza gene sequences, including 41 newly characterized genomes, we reconstructed the adaptive dynamics of three major SwIV lineages (Eurasian, EA; classical swine, CS; triple reassortant, TR). We found that, following the transfer of the EA lineage from birds to swine in the late 1970s, EA virus genes have undergone substantially faster adaptive evolution than those of the CS lineage, which had circulated among swine for decades. Further, the adaptation rates of the EA lineage antigenic haemagglutinin and neuraminidase genes were unexpectedly high and similar to those observed in human influenza A. We show that the successful establishment of avian influenza viruses in swine is associated with raised adaptive evolution across the entire genome for many years after zoonosis, reflecting the contribution of multiple mutations to the coordinated optimization of viral fitness in a new environment. This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts.
http://rstb.royalsocietypublishing.org/content/368/1614/20120382.short?rss=1
The evolutionary dynamics of influenza A virus adaptation to mammalian hosts
S. Bhatt1,2,
T. T. Lam1,
S. J. Lycett3,
A. J. Leigh Brown3,
T. A. Bowden4,
E. C. Holmes5,6,
Y. Guan7,
J. L. N. Wood8,
I. H. Brown9,
P. Kellam2,
Combating Swine Influenza Consortium and
O. G. Pybus1⇓
+ Author Affiliations
1Department of Zoology, University of Oxford, Oxford, UK
2Wellcome Trust Sanger Institute, Hinxton, UK
3Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
4Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
5Mueller Laboratory, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
6Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
7Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People's Republic of China
8Cambridge Infectious Diseases Consortium, University of Cambridge, Cambridge, UK
9Animal Health and Veterinary Laboratories Agency, Weybridge, UK
e-mail: oliver.pybus@zoo.ox.ac.uk
Abstract
Few questions on infectious disease are more important than understanding how and why avian influenza A viruses successfully emerge in mammalian populations, yet little is known about the rate and nature of the virus? genetic adaptation in new hosts. Here, we measure, for the first time, the genomic rate of adaptive evolution of swine influenza viruses (SwIV) that originated in birds. By using a curated dataset of more than 24 000 human and swine influenza gene sequences, including 41 newly characterized genomes, we reconstructed the adaptive dynamics of three major SwIV lineages (Eurasian, EA; classical swine, CS; triple reassortant, TR). We found that, following the transfer of the EA lineage from birds to swine in the late 1970s, EA virus genes have undergone substantially faster adaptive evolution than those of the CS lineage, which had circulated among swine for decades. Further, the adaptation rates of the EA lineage antigenic haemagglutinin and neuraminidase genes were unexpectedly high and similar to those observed in human influenza A. We show that the successful establishment of avian influenza viruses in swine is associated with raised adaptive evolution across the entire genome for many years after zoonosis, reflecting the contribution of multiple mutations to the coordinated optimization of viral fitness in a new environment. This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts.
http://rstb.royalsocietypublishing.org/content/368/1614/20120382.short?rss=1