Finding a virus is not all bad news

Questions around the movement and population size changes of Kiwis, Tuatara and other New Zealand wildlife over the past hundred years have been continually studied by conservationists and scientists. It now seems the answers might all be found in the viruses that infect them.

Dr Alexei Drummond, from The University of Auckland’s Faculty of Science, has been part of a global research team analysing the genetic sequences of viruses in animals.

This pioneering technique has so far proved to be more effective than the traditional technique of using genetic material directly from the animal.

“Analysing a virus in a group of animals enables us to determine such things as their population size, the population changes, rate of evolution and rate of movement in the past hundred years,” says Alexei, who is a lecturer in Computer Science and Bioinformatics.

Studying cougars in the Rocky Mountains in North America the research team took blood samples from 352 cougars along with a GPS reading from where the sample was collected.

The blood samples were then tested for the FIV virus, which is passed from cougar to cougar through physical contact or at birth.

“Viruses evolve rapidly so once you have a common virus such as FIV infecting a large percentage of cougars you are able to analyse its genetic sequence to learn about the cat population.

“Every virus strain has its own unique mutations and as the virus is passed from cougar to cougar these mutations in the virus accumulate, leaving a valuable trail of information about the host animal’s relationships to each other. Because of the way the virus is transmitted, closely related cougars will have closely related viruses. It is for that reason we can use the viruses to track the cats and learn about their recent history.”

Once the viruses have been sequenced the data, GPS readings and sample dates were entered into a computer programme, designed by Alexei.

The software analysed the data by comparing the genetic information from the different virus strains with their geographic positions and the date that they were sampled. Together with a mathematical model of how the virus evolves this information was used to estimate the cougar’s population size, the changes in the population over time, rate of evolution and rate of movement.

“This new technique of analysing the genetic data from a virus in an animal rather than the animals own genes has been more effective for short term information and is both cheaper and a far quicker process,” says Alexei.

The research team’s findings were recently published in Science, one of the worlds leading science journals for new research.