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New article on a statistical analysis of phylogeography of the spread of H5N1 until 2006, published in the open-source journal PLoS one
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001697
Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
Robert G. Wallace*, Walter M. Fitch
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
Abstract
Background
Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space.
Methodology and Principal Findings
We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus.
Conclusions
The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone.
Citation: Wallace RG, Fitch WM (2008) Influenza A H5N1 Immigration Is Filtered Out at Some International Borders. PLoS ONE 3(2): e1697. doi:10.1371/journal.pone.0001697
Academic Editor: Philip Awadalla, University of Montreal, Canada
Received: October 16, 2007; Accepted: January 17, 2008; Published: February 27, 2008
Copyright: ? 2008 Wallace, Fitch. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The work was supported by National Institutes of Health NIAID grant 1R21AI063275-01.
Competing interests: The authors have declared that no competing interests exist.
* To whom correspondence should be addressed. E-mail: rwallace@uci.edu
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001697
Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
Robert G. Wallace*, Walter M. Fitch
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
Abstract
Background
Geographic spread of highly pathogenic influenza A H5N1, the bird flu strain, appears a necessary condition for accelerating the evolution of a related human-to-human infection. As H5N1 spreads the virus diversifies in response to the variety of socioecological environments encountered, increasing the chance a human infection emerges. Genetic phylogenies have for the most part provided only qualitative evidence that localities differ in H5N1 diversity. For the first time H5N1 variation is quantified across geographic space.
Methodology and Principal Findings
We constructed a statistical phylogeography of 481 H5N1 hemagglutinin genetic sequences from samples collected across 28 Eurasian and African localities through 2006. The MigraPhyla protocol showed southern China was a source of multiple H5N1 strains. Nested clade analysis indicated H5N1 was widely dispersed across southern China by both limited dispersal and long distance colonization. The UniFrac metric, a measure of shared phylogenetic history, grouped H5N1 from Indonesia, Japan, Thailand and Vietnam with those from southeastern Chinese provinces engaged in intensive international trade. Finally, H5N1's accumulative phylogenetic diversity was greatest in southern China and declined beyond. The gradient was interrupted by areas of greater and lesser phylogenetic dispersion, indicating H5N1 migration was restricted at some geopolitical borders. Thailand and Vietnam, just south of China, showed significant phylogenetic clustering, suggesting newly invasive H5N1 strains have been repeatedly filtered out at their northern borders even as both countries suffered recurring outbreaks of endemic strains. In contrast, Japan, while successful in controlling outbreaks, has been subjected to multiple introductions of the virus.
Conclusions
The analysis demonstrates phylogenies can provide local health officials with more than hypotheses about relatedness. Pathogen dispersal, the functional relationships among disease ecologies across localities, and the efficacy of control efforts can also be inferred, all from viral genetic sequences alone.
Citation: Wallace RG, Fitch WM (2008) Influenza A H5N1 Immigration Is Filtered Out at Some International Borders. PLoS ONE 3(2): e1697. doi:10.1371/journal.pone.0001697
Academic Editor: Philip Awadalla, University of Montreal, Canada
Received: October 16, 2007; Accepted: January 17, 2008; Published: February 27, 2008
Copyright: ? 2008 Wallace, Fitch. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The work was supported by National Institutes of Health NIAID grant 1R21AI063275-01.
Competing interests: The authors have declared that no competing interests exist.
* To whom correspondence should be addressed. E-mail: rwallace@uci.edu
