The DNA Puzzle
DNA encodes a gold mine of information about macroorganisms and microorganisms. It is a blueprint to life that many scientists worldwide are working to unravel.
There are numerous examples of sudden infectious disease outbreaks of unknown cause where sequencing helped identify the disease agent and track down a point-source. Many people also have their own DNA analyzed for potential disease markers such as ones that indicate an increased susceptibility to cancer. Others are curious to investigate their genealogy.
In the Molecular Diagnostics Lab of the ICR Disease Investigations group we are sequencing the DNA of herpesviruses in hoofed animals at the Safari Park. While herpesviruses are known to infect many different host species, including humans, without or with sporadic clinical signs, some herpesviruses can cause severe disease or even be fatal to susceptible animals.
So which herpesviruses are infecting the Safari Park animals? Which hoofstock are susceptible to which of these viruses? And which hosts carry and spread them without being clinically affected?
Don’t hold your breath, this is a work in progress. But did you know that getting to the answers involves using several algorithms to piece together a large puzzle?
Distinguishing between the different herpesviruses can be computationally challenging. It is like a big puzzle with millions of pieces. We used a method called next generation sequencing to sequence herpesvirus DNA in each of the samples obtained from the individual animals. Technology has progressed in great strides when it comes to sequencing DNA but only short stretches of DNA can be sequenced with a low error rate (not the whole genome). That’s why the DNA of interest (herpesvirus DNA in our case) is chopped up into small pieces first, sequenced, and then put back together.
Imagine shredding an encyclopedia and then reconstructing the text. But we are not fluent in DNA language yet. So imagine shredding a foreign language encyclopedia and putting it back together.
Many computer hours later, Teagen Partin, the Bud Heller Conservation Fellow who crunched through the sequencing data of over 100 animals, made an interesting discovery. The diversity of herpesviruses in the population is even greater than initially imagined, even within some of the individual animals.