19-Million-Year-Old Genomic Fossils of Hepatitis B-Like Viruses in Songbirds
ScienceDaily (Sep. 28, 2010) — Biologists from The University of Texas at Arlington have uncovered virus fragments from the same family of the modern Hepatitis B virus locked inside the genomes of songbirds such as the modern-day zebra finch.
The article, publishing in the online, open access journal PLoS Biology, marks the first time that endogenous hepadnaviruses have been found in any organism. An endogenous virus is one that deposits itself or fragments of itself into the chromosome of an organism, allowing it to be passed from generation-to-generation. Previously, most of these known "fossilized" virus sequences have come from retroviruses.
"They've been sitting there for at least 19 million years, far longer than anyone previously thought this family of viruses had been in existence," say Cédric Feschotte and Clément Gilbert, co-authors of the study. Feschotte is an associate professor and member of the UT Arlington Genome Biology Group. Gilbert is a post-doctoral research associate in the group.
Gilbert and Feschotte dated the hepadnavirus fragments by locating them in the same spot on the genome of five species of passerine birds and then tracing those species to a common ancestor that lived more than 19 million years ago.
Zebra finch. (Credit: iStockphoto/David Gluzman)
The article, publishing in the online, open access journal PLoS Biology, marks the first time that endogenous hepadnaviruses have been found in any organism. An endogenous virus is one that deposits itself or fragments of itself into the chromosome of an organism, allowing it to be passed from generation-to-generation. Previously, most of these known "fossilized" virus sequences have come from retroviruses.
"They've been sitting there for at least 19 million years, far longer than anyone previously thought this family of viruses had been in existence," say Cédric Feschotte and Clément Gilbert, co-authors of the study. Feschotte is an associate professor and member of the UT Arlington Genome Biology Group. Gilbert is a post-doctoral research associate in the group.
Gilbert and Feschotte dated the hepadnavirus fragments by locating them in the same spot on the genome of five species of passerine birds and then tracing those species to a common ancestor that lived more than 19 million years ago.
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Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
Clément Gilbert*, Cédric Feschotte*
Department of Biology, University of Texas, Arlington, Texas, United States of America
Abstract
Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. 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. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10−8 substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.
Author Summary
Paleovirology 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.
Citation: Gilbert C, Feschotte C (2010) Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biol 8(9): e1000495. doi:10.1371/journal.pbio.1000495
Academic Editor: Michael Emerman, Fred Hutchinson Cancer Research Center, United States of America
Received: April 7, 2010; Accepted: August 16, 2010; Published: September 28, 2010
Copyright: © 2010 Gilbert, Feschotte. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by grant R01GM77582 to CF from the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: DHBV, duck hepatitis B virus; eZHBV, endogenous zebra finch hepatitis B virus; HBV, hepatitis B virus; LTR, long terminal repeat; NADH2, NADH dehydrogenase subunit 2; RT, reverse transcriptase; subs/site/year, substitutions per site per year
* E-mail: clement.gilbert@uta.edu (CG); cedric@uta.edu (CF)
Clément Gilbert*, Cédric Feschotte*
Department of Biology, University of Texas, Arlington, Texas, United States of America
Abstract
Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. 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. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10−8 substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.
Author Summary
Paleovirology 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.
Citation: Gilbert C, Feschotte C (2010) Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biol 8(9): e1000495. doi:10.1371/journal.pbio.1000495
Academic Editor: Michael Emerman, Fred Hutchinson Cancer Research Center, United States of America
Received: April 7, 2010; Accepted: August 16, 2010; Published: September 28, 2010
Copyright: © 2010 Gilbert, Feschotte. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by grant R01GM77582 to CF from the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: DHBV, duck hepatitis B virus; eZHBV, endogenous zebra finch hepatitis B virus; HBV, hepatitis B virus; LTR, long terminal repeat; NADH2, NADH dehydrogenase subunit 2; RT, reverse transcriptase; subs/site/year, substitutions per site per year
* E-mail: clement.gilbert@uta.edu (CG); cedric@uta.edu (CF)
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