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Infection & disease

Phylogenetic diversity of koala retrovirus within a wild koala population

Chappell, KJ, Brearley, JC, Amarilla, AA, Watterson, D, Hulse, L, Palmieri, C, Johnston, SD, Holmes, EC, Meers, J & Young, PR 2017, Journal of Virology, vol. 91, no. 3, e01820-16.

Koala retrovirus (KoRV) is widespread throughout koala populations, both wild and captive, and yet only nine different KoRV envelope sequences have thus far been described. From 18 koalas sampled from free-ranging populations in south-east Queensland, 108 unique sequences and four potentially new KoRV subtypes have been described here for the first time.

  KoRV is ubiquitous throughout koala populations, yet the genetic diversity of the virus is poorly understood. The authors of this study collected samples from 18 wild south-east Queensland koalas infected with KoRV and examined the genetic diversity of the virus. Using deep sequencing of the ~500-nucleotide region of the KoRV envelope gene, 108 unique sequences were detected, building substantially upon the nine sequences described previously. These 108 sequences could be categorised into three phylogenetically-distinct groups: two that were congruent with the previously identified subtypes KoRV-A and -B, and another that matched the previously described subtype KoRV-D but consisting of several unique sequence types newly termed KoRV-F, -G, -H and -I. These sequence types differ within the hypervariable region of the envelope gene’s receptor binding domain. KoRV-B also exhibited some intra-subtype genetic diversity. KoRV-A, on the other hand, was genetically identical in 96% of sequence reads. This finding supports the proposal that KoRV-A is endogenous (incorporated into the host’s DNA and transmitted vertically from parent to offspring) because in genomic DNA the mutations that might evolve genetic diversity are acquired only very slowly. By comparison, the rich intra-subtype diversity of KoRV-B, -D and -F suggests that these subtypes are exogenous (transmitted horizontally between individuals) as genetic diversity can be rapidly produced via replication with a highly error-prone reverse transcriptase that undergoes point mutations, deletions and insertions. Notably, every koala tested positive for two or more unique KoRV sequences. All koalas were positive for KoRV-A, while subtypes B, D and F were also highly prevalent with at least one of these subtypes detected in all koalas sampled. Subtypes G, H and I were detected in a small number of koalas. KoRV-C and -E were not detected in any of the sampled koalas, though these subtypes also fit into the paraphyletic group KoRV-D. Koalas that tested positively for KoRV-B, -D and -F, and that were also from the same geographic area, had either very similar or identical sequences of the respective subtype. This similarity may suggest either very recent horizontal transmission or a unique endogenisation event that occurred in a common ancestor. Likewise, unique subtype sequences were more likely to be detected between koalas from different areas, which indicates that even greater genetic diversity may be identified as a result of more spatially-extensive sampling.

  Our growing understanding of the subtype prevalence, transmission patterns and genetic diversity of KoRV will support the development of strategic conservation actions to mitigate the effects of the virus. Future studies should build upon the developments presented here by exploring potential associations between individual KoRV subtypes and disease.

 

Summarised by Joanna Horsfall

 

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