The strangest family reunions

Contributed by guest blogger: Amelia McKitterick ’11

Next time you are sick from a viral infection, you should ask yourself if you’re just hosting a visit from distant relatives. Although “relative” might not seem like the most appropriate term for a virus, there has been evidence of a history viral influences and insertions into animal genomes, including that of humans!

A crucial step in the replication of RNA retroviruses is the integration of the viral genome into the host genome. Fragments of a viral genome in the genome of a non-viral cell are called endogenous viral elements (EVEs), and they can either be phased-out of the host genome or be passed on to become fixed within a population. A recent study examined genomes of a variety of mammals, birds, and insects for EVEs with matching amino acid sequences to extant, non RNA retroviruses. The genomes of 44 animals were converted into amino acid sequences and checked via tBLASTn (a BLAST that matches amino acid sequences with nucleotide sequences) for alignment with a library of currently known mammalian viruses with genomes larger than 100 kb in length. Matches were found to viruses with all types of RNA genomes (ss/ds, +/-, segmented, un-segmented) in all three of the major phyla tested, matches to DNA genomes (ss/ds, rt) were only found in mammals and birds, and even unclassifiable viral proteins were found in mammals that could represent extinct or undiscovered lineages.

But what is the use of all this new information? First, the data can be used to determine the minimum evolutionary divergence dates of different viral families based on host divergence dates. This study of paleovirology estimated the minimum ages of virus fossils Parvo-, Circo-, Filo- and Bornaviridae within the mammalian samples and found the oldest (Borna-) to be about 93 million years old, where it was originally infecting the distant relatives of the Afrotheria clade (Elephants, hyrax, tenrec, etc. For reference, the common ancestor of the primates evolved about 85 million years ago). A second use of the data is to illustrate the variety of viruses, and to give a better indication of the types of viruses that infect different hosts. The presence of the EVEs in a host genome can provide new insight about the replication process of non-reverse transcription viruses, and show patterns of host vulnerability. Similarly, new viruses, such as the unclassifiable EVE in mammals, could lead to new routes of investigation into the types of viruses and cures to infections.