Posted by RJG on January 19th, 2014 • Identification of novel parvovirus-related EVEs.
A long-tailed chinchilla
Parvovirus-related EVEs in South American rodentsParvoviruses (family Parvoviridae) are single stranded DNA-viruses that infect animals. Pathogenic parvoviruses of humans include the B19 virus which causes fifth disease ('slapped cheek syndrome') in children. Among mammals, pathogenic parvovirus infections have been identified in cats, dogs, mink and cattle.
In recent years, we and others have reported sequences derived from parvoviruses in animal genomes [1-4]. Certain parvoviruses are known to integrate into the genome of cells they infect. For example, human adeno-associated virus (AAV) integrates at a specific site on chromosome 19, and is of interest as gene therapy vector. The relatively widespread occurrence of parvovirus-related endogenous viral elements (parvo-EVEs) indicates that this process can sometimes introduce sequences derived from parvoviruses into the host germline.
Although parvoviruses can integrate into host genomes, integration it is not an essential step in their replication cycle, as it is for retroviruses. Accordingly, parvo-EVEs are orders of magnitude less common than endogenous retroviruses (ERVs).
A recent in silico screen of mammalian genomes identified novel parvovirus-related EVEs in the genomes of two South American rodent species; the long-tailed chinchilla (Chinchilla lanigera), and the degu (Octodon degus).
The Chilean Matorral ecoregion (top panel) encompasses the pink area in lower panel.Chinchillas are medium-sized, crepuscular rodents that live at high altitude in the Andes mountains, in colonies called "herds". Degus are small rodents endemic to the Chilean Matorral, they live in colonial burrows in woodland. Both species are intelligent and responsive to human interaction, and are kept domestically as pets.
We created a set of reference sequence libraries to be used in association our in silico genome screening pipeline, released this week. Screening of recently published mammalian genomes using a parvovirus reference sequence library led to the identification of novel parvo-EVEs in the chinchilla and degu genomes. A total of eleven unique loci were identified; five in the chinchilla genome, and six in the degu genome. The degu EVEs include a Dependovirus NS1-derived sequence that is intact and potentially capable of expressing protein. We are currently investigating these EVEs in collaboration with researchers in Chile.
1. Kapoor A, Simmonds P, and WI. Lipkin (2010) Discovery and characterization of mammalian endogenous parvoviruses. J. Virol. 84(24):12628-35. [view]
2. Katzourakis A. and RJ. Gifford (2010) Endogenous viral elements in animal genomes. PLoS Genetics 6(11): e1001191. [view]
3. Belyi VA, Levine AJ and AM. Skalka (2010) Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old. J. Virol. 84(23):12458-62. [view]
4. Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Peng Y, Yi X, and D. Jiang (2011) Widespread endogenization of densoviruses and parvoviruses in animal and human genomes. J. Virol. 85(19):9863-76. [view]