Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
Kyriakos Tsangaras1, Matthew C. Siracusa2, Nikolas Nikolaidis2, Yasuko Ishida3, Pin Cui2, Hanna Vielgrader4, Kristofer M. Helgen5, Alfred L. Roca3, Alex D. Greenwood2*
1Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
2Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, California, United States of America
3Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America,
4Zoo Vienna, Vienna, Austria
5National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.