Whole-genome studies of viruses: future studies of people?

Viral evolution is different from human evolution chiefly because viruses mutate faster, exist in larger populations, have much shorter generations, and have a sharp multifold population structure, including within-host subpopulations and global (and potentially local, regional, or species-specific) metapopulations.

So maybe we shouldn't read too much into this free PLoS essay by Eddie Holmes, "Viral Evolution in the Genomic Age."

But then again, viral evolution sets the context for much of recent human adaptation, including strong recent selection on genes related to pathogen defense.

If there is a lesson to be learned from the history of population genetics, it is that the more fine-scaled the data available for analysis -- from allozymes to genomes -- the more powerful the biological inference. Not only does the comparison of complete genomes invariably provide greater resolution of the spatial and temporal dynamics of viral spread, but it obviously enables the study of genome-wide interactions. As a case in point, the complex evolutionary processes that underpin the recent dramatic rise of resistance to adamantane drugs in influenza A virus, including the central role played by epistasis, were not revealed until an analysis of complete genome sequences was undertaken [10]. Rather than focusing on single genes in isolation, it is therefore essential that we examine the similarities and differences in evolutionary patterns among all the genes in a viral genome.

Holmes begins his essay by noting that the influenza A virus project has so far generated "around 2,500 complete viral genomes." Of course, such widespread sequencing is essential for studying the processes of virus evolution and the rise of new virulent strains.

But it also gives a hint of what will happen to human population genetics when large numbers of complete genomes start coming online. Considering that humans have rather less genomic diversity than influenza A, SNP surveys already have much of the power to detect polymorphisms. Coming attractions: larger and larger samples of people from different populations.


Holmes EC. 2007. Viral evolution in the genomic age. PLoS Biol 5:e278. doi:10.1371/journal.pbio.0050278