A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive evolution, RNA-based viruses can quickly evolve resistance to antiviral drugs.

Comparing Mutations Allows Us to Reconstruct Evolution

A major goal in modern biology is to reveal evolutionary history by comparing genome sequences. An important practical application of these analyses is the study of evolution in disease-causing viruses. Genome sequencing has become so rapid and inexpensive that it is now possible to investigate the origins and ongoing evolution of viruses during a disease outbreak.

For example, in 2013, a new strain of avian influenza called H7N9 emerged in China that caused severe respiratory illness in humans. By comparing the mutations in viruses isolated from humans and several bird species, researchers were able to show that the ancestor of this flu strain probably originated in Chinese domestic duck populations before it was transmitted to chickens. The ancestral strain subsequently recombined with other bird viruses to generate the H7N9 strain that infected humans. These analyses identified live poultry markets as the likely source of human infections. Furthermore, while investigating the evolution of the H7N9 strain, researchers found an additional strain of avian flu that can likely infect humans. This work demonstrates how evolutionary analyses of mutations can provide critical information to epidemiologists during an epidemic.