Abstract
Author SummaryPaleovirology is the study of ancient viruses and the way they have shaped the innate immune system of their hosts over millions of years. One way to reconstruct the deep evolution of viruses is to search for viral sequences “fossilized” at different evolutionary time points in the genome of their hosts. Besides retroviruses, few virus families are known to have deposited molecular relics in their host's genomes. Here we report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family (which includes the human hepatitis B viruses) fossilized in the genome of the zebra finch. We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought. Based on this age, we can infer a long-term avian hepadnavirus substitution rate, which is a 1,000-fold slower than all short-term substitution rates calculated based on extant hepadnavirus sequences. These results call for a reevaluation of the long-term evolution of Hepadnaviridae, and indicate that some exogenous hepadnaviruses may still be circulating today in various passerine birds.
Highlights
Most viruses are characterized by high substitution rates, which generally prevent reconstruction of their long-term evolutionary history [1]
We report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family fossilized in the genome of the zebra finch
We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought
Summary
Most viruses are characterized by high substitution rates, which generally prevent reconstruction of their long-term evolutionary history [1]. The origins and age of most extant viruses remain elusive [2]. One solution to this conundrum lies in the advent of paleovirology, the study of paleoviruses and the way they have shaped the antiviral genes of their hosts over millions of years [3]. Vertebrate retroviruses are RNA viruses that normally integrate into the genome of their host’s somatic cells as part of their replication cycle. On occasion, these viruses may integrate into the germline genome of their host, and become inactive and vertically inherited over millions of years. Their molecular relics, called endogenous retroviruses, make up a substantial fraction of vertebrate genomes (,8% in human; [4])
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