Abstract
The koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus). KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an individual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites. Most integrations contain full-length, endogenous provirus; KoRV-A subtype. The second most frequent integrations contain an endogenous recombinant element (recKoRV) in which most of the KoRV protein-coding region has been replaced with an ancient, endogenous retroelement. A third set of integrations, with very low sequence coverage, may represent somatic cell integrations of KoRV-A, KoRV-B and two recently designated additional subgroups, KoRV-D and KoRV-E. KoRV-D and KoRV-E are missing several genes required for viral processing, suggesting they have been transmitted as defective viruses. Our results represent the first comprehensive analyses of KoRV integration and variation in a single animal and provide further insights into the process of retroviral-host species interactions.
Highlights
koala retrovirus (KoRV) is a gammaretrovirus, most closely related to gibbon ape leukaemia virus (GALV)[1] and is thought to be the result of an interspecies transmission[2]
We found a total of 133 KoRV integration sites (Table 1; Supplementary Figure 1; Supplementary Table 1)
We have reported putative somatic integrations of five distinct forms of KoRV (KoRV-A, KoRV-B, KoRV-D, KoRV-E) as well as of recKoRV1
Summary
KoRV is a gammaretrovirus, most closely related to gibbon ape leukaemia virus (GALV)[1] and is thought to be the result of an interspecies transmission[2]. Several KoRV sub-types have been proposed, based primarily on the amino acid sequence of the receptor binding domain (RBD) of the viral envelope protein. KoRV-B is a more recent retroviral subtype that is presumably the result of recombination, which, to date, has not been shown to be endogenized and is thought to be more virulent[5,6]. Many recently discovered additional variants (KoRV-C, D, E, F, G, H and I)[9,10,11] have been. RecKoRV3 in koala genome contigs only in pacbio reads total identified based on the RBD of the viral envelope protein, but as yet, no corresponding cell surface receptor has been identified[11]. We discover that KoRV-D and E have been integrated as incomplete provirus and suggest a mechanism that could explain their presence in this koala
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