Long-read Koala Assembly Provides Insight into Ongoing Retroviral Invasion
Thursday, December 7, 2017
What can one koala tell us about an endemic that threatens the survival of its species? A great deal, it turns out.
While doing a deep dive into the genome of a wild female koala, a team of Australian scientists led by Matthew Hobbs and Andrew King of the Australian Museum Research Institute were able to unravel some of the complexity of the species-specific gammaretrovirus KoRV.
The results, published recently in Nature, paint a picture of a rapidly evolving and diversifying virus, with implications for the long-term survival of the koala, as well as our understanding of retroviral-host species interactions.
The study allowed the researchers to see interspecies transmission, multimerization of sequences in the long terminal repeats, and recombination between different retroviruses, processes which have been reported for other retroviruses but occurred millions of years ago, rather than in very recent times, as for the koala.
KoRV is a retrovirus closely related to gibbon ape leukemia virus, and is thought to be the result of an interspecies transmission. Implicated in the pathogenesis of two major koala diseases, hematopoietic neoplasia and the endemic chlamydiosis, it is considered to be a significant threat to the survival of the species.
Several KoRV subtypes have been proposed. Presumed to be the original transmitted strain, KoRV-A is endogenous and widespread in northern Australian koalas, which are thought to be 100 percent infected. KoRV-B is a more recent, more virulent subtype believed to be the result of recombination. Additional variants — KoRV-C, D, E, F, G, H and I — have also recently been identified, but it has been difficult to examine the population of KoRV and KoRV-like insertions in any koala genome.
PacBio long-read sequencing technology finally made it possible. DNA from the koala’s spleen was sequenced to give an estimated overall coverage of 57.3-fold based on a genome size of 3.5 Gb. The authors used SMRT Sequencing due to its capacity to generate sequences of up to ~70 kb that carry full-length (8.4 kb) KoRV insertions and substantial flanking koala genome sequence. This provided a considerable advantage over short reads, which could not resolve the different KoRV insertion sites or types.
“Obtaining sequence data from elements (such as retroviruses) that are repeated throughout the genome cannot be done with short read sequencing technology, which is why we used long read PacBio sequencing in our study,” the authors add.
The team reported putative somatic integrations of five distinct forms of KoRV (KoRV-A, KoRV-B, KoRV-D, KoRV-E), as well as germline evidence of KoRV-A. They also found an endogenous recombinant element (recKoRV) in which most of the KoRV protein-coding region was replaced with an ancient, endogenous retroelement.
“This diverse pool of viral variants in the same animal highlights the range of strategies being used by this retrovirus as it invades, or comes to equilibrium with its new host,” the authors add.
“As KoRV-A, B and potentially other more pathogenic KoRV types sweep through koala populations, we might expect to see worsening effects of chlamydial disease. This highlights the importance of understanding the complex mix of KoRV types present in an individual animal.”
Read the full report and learn more about the project in this video presentation from a PAG 2017 Workshop by Rebecca Johnson, a co-author on the paper and the Director of the Australian Museum Research Institute. Johnson will also be presenting her work at the Advances in Genome Biology and Technology meeting in February 2018.