How the koala retrovirus genome evolved

Unlike other viruses, retroviruses must copy their genetic material into the host genome as part of their life cycle. Occasionally, a retrovirus may integrate into the reproductive cells of the host which give rise to future generations, thus becoming a permanent part of the host genome. The koala retrovirus (KoRV) is the pathogen of the Koala Immune Deficiency Syndrome (KIDS), an AIDS-like immunodeficiency. Many generations of the koala population suffered during the process of retroviral endogenisation, the process of initial germ line invasion. KoRV is ubiquitous among northern Australian koalas, but is less common in southern Australian mainland and island populations.

In order to find out how retroviruses invade the germ lines of their hosts, an international team of scientists from the Leibniz Institute for Zoo and Wildlife Research (IZW) in Berlin, the California State University, the Zoo in Vienna, the National Museum of Natural History in Washington and the University of Illinois at Urbana-Champaign applied a technique known as hybridisation capture. This method permits the identification of entire genome sequences of the KoRV, the only known retrovirus currently invading its host germ line, from koala museum skins from the late 19^th and across the 20^th century and therefore were able to study 130 years of KoRV evolution.

Previous analyses by the team, employing Polymerase Chain Reaction (PCR) based methods, were only able to isolate a single viral gene with a great deal of effort. Using the technique of hybridisation capture, the full retrovirus genome and the location of the retrovirus within the koala genome could be simultaneously examined with far less effort. During hybridisation capture, the “library” DNA which contains the sequence of the KoRV is immobilised on beads and serves as bait. The targeted DNA from different samples binds to them and the non-specific DNA is washed away. With this method, the scientists could find sequences at high coverage across the full length of the KoRV from both museum samples and modern genomic DNA.

The application of complex mathematical protein modelling demonstrated that selection pressure on the virus to change appears to be very mild. This is why the scientists concentrated on the envelope gene which allows the virus to bind to and invade cells. Overall, the virus was very stable and changed little. The results suggest that for ca. 130 years, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. Newly described and possibly more pathogenic variants known as KoRV-B and KoRV-J were not found in museum specimens, supporting the hypothesis that they have arisen only recently. This also indicates that while generally stable, KoRV may be able to change quickly with unforeseen pathological outcome.

“The results suggest that the endogenisation of a retrovirus may happen frequently and rather rapidly, initially without much change inside the virus and that becoming a part of the genome of all members of a host species takes a very long time” said Prof Alex Greenwood, the principal investigator of the study. The findings indicate that the formation of a large part of mammalian genomes involved rapid events within individuals or populations but took a very long time to become a standard feature of the species. This suggests that such processes may be happening right now unobserved in many species.