endogenization

The Koala retrovirus (KoRV) continues to spread within Australia, according to results of a new analysis of a larger sample size from a wider geographical range than was previously studied.

Blood or tissue samples were collected from koalas in different regions of Australia, and polymerase chain reaction (PCR) was used to detect the presence of KoRV proviral DNA,Â a DNA copy of the retroviral genome integrated into host cell DNA. Most of the koalas from the Australian mainland were positive for KoRV proviral DNA (442/466; 94.8%). All samples from animals in Queensland and New South Wales were KoRV positive. In mainland Victoria 65 of 89 animals contained KoRV DNA (73%). On the Victorian islands prevalence of KoRV ranged from 0% on Philip Island (0/11) to 50% on Snake Island (6/12). On the previously KoRV-free Kangaroo Island (link), 24 of 162 animals (14.8%) were KoRV positive. These results suggest that KoRV initially entered the koala population in the north of Australia and has been slowly spreading to the south. There are also other potential explanations for the results: there may be differences in KoRV susceptibility in northern versus southern animals, and the rate of transmission might differ in the two areas.

The genome of Queensland koalas contain far more copies of KoRV per cell, 165, than animals in Victoria, which ranged from less than one to 1.5 copies per cell. The Queensland koalas are likely fully endogenized – that is, the integrated KoRV DNA is passed from parent to offspring in the germline, and hence every koala cell contains viral DNA. In contrast, in Victoria koalas KoRV has either recently entered the germline (1.5 copies/cell) or has not yet entered this state (<1 copy/cell). In animals with less than one proviral copy per cell, KoRV infection was likely acquired exogenously from one animal to another. The mode of transmission of KoRV among koalas is not known, but might involve animal-animal contact or arthropod transmission.

It seems likely that eventually all wild koalas will be endogenized by KoRV. Whether this process will impact the long-term survival of the species is not known, especially since the disease caused by KoRV infection is poorly understood.

GS Simmons, PR Young, JJ Hanger, K Jones, D Clarke, JJ McKeed, J Meersa. 2012. Prevalence of koala retrovirus in geographically diverse populations in Australia. Austr. Vet. J.Â 90(10):404-9.

The genomes of most higher organisms contain sequences from retroviral genomes called endogenous retroviruses (ERVs). These are DNA copies of retroviral RNAs that are integrated into the germ line DNA of the host, and passed from parent to offspring. In most species the infections that lead to germ line ERVs appear to have occurred millions of years ago. The Koala retrovirus, KoRV, is the only retrovirus that we know of that is currently invading the germ line of its host species. A study of Koala pelts preserved in museums suggests how recently the virus infected this animal.

The koala is native to Australia, and all koalas in northern Australia are infected with KoRV. However not all animals in the southeast or on southern islands are infected. It is believed that KoRV crossed into koalas from another species (possibly the Asian mouse Mus caroli) some time within the past two hundred years. To test this hypothesis, DNA was extracted from 28 koala skins that were held in museums and which had been collected from the late 1800s to the 1980s. Polymerase chain reaction was used to detect KoRV DNA in the koala genome. The results show that KoRV was already widespread in Northern Australian koalas by the late 1800s. It has since spread slowly because the virus is not ubiquitous in southern koalas. The slow dispersal may due to the sedentary and solitary nature of koalas. Examination of mitochondrial DNA from the koala skins confirmed that there has been limited movement of the animals with Australia.

The sequence of the KoRV gene encoding the viral glycoprotein, env, was also determined. The results reveal that env sequences from museum specimens are remarkably similar to those of KoRV found in contemporary koalas. At first glance this result might not seem surprising: the endogenous KoRV genomes are evolving at the same slow rate as the host DNA into which they are integrated. However, there appear to have been multiple transmissions and germ line invasions by KoRV, leading the authors to suggest that in all cases very similar retroviruses were involved.

Infection with KoRV in captive animals is believed to cause immunosuppression, leading to fatal lymphomas or Chlamydia infection. A Chlamydia epidemic is believed to have killed many koalas in 1887-1889, consistent with the PCR results indicating that KoRV was widely present at that time.

Update: I had meant to discuss the possibility of dating the invasion of Koalas by KoRV by using older samples, but neglected to include this in the original article. Several days after it was published, Professor Paul Young sent me a note expressing exactly this sentiment:

What would be even better would be to have access to fossilised material that predates European settlement, that we could examine. We collaborated with an “Ancient DNA” specialist and tried this several years ago but we weren’t able to recover usable template DNA. Still worth some future effort though.

Avila-Arcos MC et al (2012).Â 120 years of koala retrovirus evolution determined from museum skins.Â Mol Biol Evol. 2012 Sep 14.

Spread of koala retrovirus in Australia

Museum pelts help date the koala retrovirus