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Review
. 2009 Oct;5(10):e1000505.
doi: 10.1371/journal.pcbi.1000505. Epub 2009 Oct 26.

Discovering the phylodynamics of RNA viruses

Edward C Holmes  1 , Bryan T Grenfell
Affiliations
Review

Discovering the phylodynamics of RNA viruses

Edward C Holmes et al. PLoS Comput Biol. 2009 Oct.
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Sampling scales for acute RNA viruses and the associated phylodynamic processes that viral genome sequence data and host sampling can elucidate.
Figure 2
Figure 2. Phylodynamic patterns of human and avian influenza viruses.
The left diagram shows the phylogeny of the hemagglutinin (HA) gene of human H3N2 influenza A viruses sampled between 1985 and 2005, revealing the “ladder-like” branching structure indicative of antigenic drift. By comparison, the phylogeny of the HA gene of human influenza B virus sampled over the same interval (center diagram) shows the co-circulation of the antigenically distinct “Victoria 1987” and “Yamagata 1988” lineages, as well a shorter length from root to tip, reflecting a lower rate of evolutionary change. Finally, the phylogeny for the HA gene of H4 avian influenza virus (right diagram) reveals the deep geographic division between the Eurasian and Australian versus North American lineages of this virus.
Figure 3
Figure 3. Fluctuating genetic diversity of influenza A virus.
The figure shows a Bayesian skyline plot of changing levels of genetic diversity through time for the HA gene (165 sequences) of A/H3N2 virus sampled from the state of New York, US, during the period 2001–2003. The y-axes depict relative genetic diversity (N e t, where N e is the effective population size, and t the generation time from infected host to infected host), which can be considered a measure of effective population size under strictly neutral evolution. Peaks of genetic diversity, reflecting the seasonal occurrence of influenza, are clearly visible. See for a more detailed analysis.
See this image and copyright information in PMC

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