Back to Basics

The list of unanswered questions about the biosphere is long, longer than one might expect. According to Valerie Morley, a PhD candidate at Yale University’s Department of Ecology and Evolutionary Biology, these unanswered questions range from the complex to the surprisingly basic. Her research on the evolution of viral communities tackles some of the most fundamental gaps in our knowledge about how organisms adapt to their surroundings.

“Using viruses as a model system we can ask really basic questions about evolutionary biology and how adaptation happens. For example, we actually don’t have a general understanding of the risks and environmental conditions that make spillovers of viral diseases between host types likely. So, we can’t make predictions about how viruses move from animals to humans, how they deal with complex or diverse host communities or even environmental change. This is science on a very basic level but it has relevance to almost everything from humans to cancer cells to algae and important crops.”

It would be wrong to confuse basic with simple. Though understanding how viruses multiply and change is fundamental to our ability to tackle serious challenges to human health, these questions have not been easy to answer. SARS, HIV and Ebola are just a few of the diseases that have spread to human populations from animals, changing their preferred host tissue types along the way. Despite the impact of these diseases on public health, we still have a way to go before we understand the intricacies of how viral populations react to environmental change, moving from place to place and host to host.

However, recent advances in the technology that scientists can use to study organisms are allowing researchers to revisit some of these fundamental and unanswered questions. Aiming to revisit some of these very basic ideas, Valerie Morley and her colleagues have been using new sequencing technology that is giving them what she says is “an unprecedented ability to see high resolution pictures of what is happening in [viral] populations.”

“Traditional sequencing technology depicts a virus genome that is true for a majority of the population. You can think of it as a consensus genome. But sometimes outliers are actually more interesting and one cell with a mutation can be very important. With high-resolution technology we can actually look at individuals, potentially detecting something like a mutation that exists at a very low frequency but might become common over time. The genomes of viruses are incredibly small but we suddenly have the power to look at these things on a completely new level. The scale is unprecedented,” said Morley.

With this new ability to see how populations change and individual traits rise to dominance, the lab has been asking essential questions about the speed of viral adaptation to environmental shifts. Most theories of adaptation imagine that change will be sudden and acute but, while sudden changes do happen, most environmental shifts happen over substantial periods of time. With unpredictable and rapidly escalating climate change, understanding adaptations of this kind becomes ever more important.

“I have been particularly interested in how viral populations gradually evolve to infect new hosts, just as some diseases have done when moving from animals to humans. We grow viral communities in the lab and add new cell types, gradually increasing the ratio of novel host tissue to old. Then, we watch evolution happening. The really interesting finding we have so far is that these viruses do much better than we might think compared to predictions based on traditional adaptation theory. Under conditions of gradual change they seem much more able to adapt to environmental turnover.”