The variable codons of H3 influenza A virus haemagglutinin genes
- First Online:
- 48 Downloads
We have analyzed several sets of well-studied haemagglutinin (HA) gene sequences of H3 subtype influenza A viruses to identify codons that are unusually variable, using a simple pairwise sliding window method, DnDscanning. For two of the sets there were results of detailed phylogenetic modeling studies of selection already published. A third set had been the subject of an antigen mapping study, the results of which provide a completely independent benchmark of selected changes in H3 HA genes. Our analyses show that the codons with greatest DnDscan scores (i.e. the most variable) were mostly those reported in the published studies as being positively selected; indeed the DnDscan results matched the antigenic mapping results more closely than did those of the phylogenetic modeling methods. These results suggest that codons under selection can be found even when, as with some sets of virus sequences, a phylogeny is uncertain or cannot be obtained because, for example, the sequences are recombinants, or when selection is not necessarily linked with phylogeny, as in host-switching events. The program DnDscan is available at http://biojanus.anu.edu.au.
Unable to display preview. Download preview PDF.
- Darwin C (1859) On the origin of species by means of natural selection. John Murray, London, 1st edn. (van Wyhe, J. The writings of Charles Darwin on the web. http://pages.britishlibrary.net/charles.darwin2/texts.html)
- Kimura, M 1983The Neutral Theory of Molecular EvolutionCambridge University PressNew YorkGoogle Scholar
- Li, WH, Wu, CI, Luo, CC 1985A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changesMol Evol Biol2150174Google Scholar
- Luscombe N, Qian J, Zhang Z, Johnson T, Gerstein M (2002) The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol 3(8)Google Scholar
- Nei, M 1987Molecular Evolutionary GeneticsColumbia University PressNew YorkGoogle Scholar