Endogenous non-retroviral retroviruses: Hepadnaviruses in the bird genome

Hepatitis B is my favorite non-retrovirus.

Why?

Because its a retrovirus :-D

Heres another reason for me to love it-- Its viral family, Hepadnaviridae, inserted themselves into bird genomes 19 million years ago.

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

*happy-prospector-dance* Okay, this is like, the billionth time this has happened in the past few months-- Finding endogenous versions of viruses that arent 'supposed' to endogenize. THIS IS SO AMAZING!

We do not have viral fossils for us to study what a kind of virus looked like 100, 1000, 1000000000 years ago. Sometimes we can find 'old' viruses in frozen or otherwise preserved tissue that can teach us about viral evolutionary history. Sometimes we find viruses places we had never looked before, finding new viral cousins that can teach us about their ancestors.

But the only way to get deep, deep back in time with viruses, is via endogenous viruses. And these newly identified sequences take us back in time 19 million years, recapitulating millions of years of bird evolution. I say this again, THIS IS SO AMAZING!

New info for old ERV readers-- One ERV event can produce a small army of closely related ERVs. Because retroviruses insert into genomes 'on purpose', an ERV can still be functional post-insertion. So, functional ERV, makes retroviral proteins, could turn around an reinfect the same cell. ERVs also have their LTRs, which can recombine, duplicating or deleting parts of the genome, and all of their corresponding ERVs. So, not every ERV in your genome is 'unique'.

These eZHBVs, on the other hand, their insertions are a mistake. You know how HPV inserting into the host cell DNA is a mistake, and the virus is basically dead as a virus once it integrates? Same thing happens with eZHBV. The virus doesnt work once it is inserted/endogenized. So multiple eZHBVs are unique... unless they hitched a ride in a completely independent gene/chromosome/genome duplication.

This also means that eZHBV sequences are of absolutely no use to the host cell/host organism. They arent doing anything. They cant be co-opted for anything. These researchers found no evidence for positive selection of the eZHBV sequences. Yes, eZHBVs are the dreaded useless junk DNA.

But one mans junk is another mans treasure:

In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host's cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host's germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses...
... A handful of such precious paleoviruses have recently been unearthed from mammalian genomes.

Ones species demise is another species 'highly valuable' and 'precious' information...