The invasion of a host germline by infectious retroviruses has been a common evolutionary event that shaped the genomes of all vertebrates, including humans. Endogenous retroviruses (ERVs) comprise ca. 8% of the human genome, where they play a role in placentation and in a number of diseases. Despite their ubiquity, until recently all identified ERVs had entered their host germline thousands or millions of years ago. Many ERVs have undergone mutations, deletions and recombination, and many retroviruses that gave rise to ERVs may be extinct. Thus, the evolutionary events that occurred as retroviruses invaded host genomes can be difficult to infer. Recently, an emerging koala retrovirus (KoRV), linked to a high incidence of leukemia and immune system suppression in Australian koalas, was discovered to be in the midst of transitioning from being an infectious exogenous virus to becoming an endogenous part of the koala genome. To date, KoRV is the only known exogenous retrovirus that is currently in the midst of invading a host germ line. Our objective is to use KoRV to understand the process by which an infectious retrovirus invades its host germline, a process that has shaped the human genome, as it actually happens. We will determine how the genetic diversity of KoRV is evolving across loci, individuals, and populations. Museum samples of koalas will be used to determine how the genetic diversity of KoRV has evolved over time. Differences between ancient and modern KoRV will be determined, and examined for their effects on functional properties of the virus.
The specific aims are: (1) Examine the sequence diversity and insertional polymorphisms of KoRV across the geographic range of the host population, from which the origins, spread and evolution of KoRV may be inferred. (2) Use archival samples of koalas to directly determine the evolution of genetic and functional diversity of KoRV across the time period during which KoRV emerged in a new host and invaded the germline. (3) Use complete proviral genomes and known host pedigrees to examine the evolutionary events that are shaping KoRV. The complete genomes of individual KoRVs will be sequenced and analyzed to determine the degree to which KoRVs invading their host germ line are being affected by selection, recombination, open reading frame disruptions, host anti-viral mechanisms, and host population structure.

Public Health Relevance

Retrovirus-like elements that comprise 8% of the human genome play a role in health and disease, yet the process by which endogenous retroviruses (ERVs) invaded and shaped the genomes of humans is difficult to study since human ERVs are millions of years old. There is only one known infectious retrovirus currently in the midst of invading the germ line of its host, a koala retrovirus (KoRV) linked to leukemias and immune suppression. Understanding the evolutionary events affecting the genetic diversity of KoRV, and how KoRV changed as it invaded the host germ line provides an opportunity for research into how ERVs evolve and affect the genomes of all vertebrates, including humans.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Eckstrand, Irene A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Illinois Urbana-Champaign
Veterinary Sciences
Schools of Earth Sciences/Natur
United States
Zip Code
Hobbs, Matthew; King, Andrew; Salinas, Ryan et al. (2017) Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Sci Rep 7:15838
Ruiz-Rodriguez, Christina T; Ishida, Yasuko; Murray, Neil D et al. (2016) Koalas (Phascolarctos cinereus) From Queensland Are Genetically Distinct From 2 Populations in Victoria. J Hered 107:573-580
Rosenfeld, Jeffrey A; Reeves, Darryl; Brugler, Mercer R et al. (2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun 7:10164
Alfano, Niccolò; Michaux, Johan; Morand, Serge et al. (2016) Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia). J Virol 90:8169-80
Alfano, Niccolò; Kolokotronis, Sergios-Orestis; Tsangaras, Kyriakos et al. (2016) Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses. J Virol 90:1757-72
Slater, Graham J; Cui, Pin; Forasiepi, Analía M et al. (2016) Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses. Genome Biol Evol 8:607-21
Guiblet, Wilfried M; Zhao, Kai; O'Brien, Stephen J et al. (2015) SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations. Gigascience 4:1
Alfano, Niccoló; Courtiol, Alexandre; Vielgrader, Hanna et al. (2015) Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep 5:10189
Ishida, Yasuko; McCallister, Chelsea; Nikolaidis, Nikolas et al. (2015) Sequence variation of koala retrovirus transmembrane protein p15E among koalas from different geographic regions. Virology 475:28-36
Hartmann, Stefanie; Hasenkamp, Natascha; Mayer, Jens et al. (2015) Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse. BMC Genomics 16:613

Showing the most recent 10 out of 17 publications