The First Full-Length Endogenous Hepadnaviruses: Identification and Analysis

Liu, Wei; Pan, Shaokun; Yang, Huijuan; Bai, Weiya; Shen, Zhongliang; Liu, Jing; Xie, Youhua

doi:10.1128/jvi.01164-12

Cited by 27 publications

(30 citation statements)

References 25 publications

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“…10), as well as a full-length or nearly full-length copy of the hepadnaviral genome [8,18,26,54]. In snakes, the eSHBVs are 316-370 aa long, with 48-67% aa similarity (K2P distance ¼ 0.63 -0.83) to the avihepadnavirus polymerase and cover about 37% of the duck hepadnavirus genome, which is 3021 bp long.…”

Section: Resultsmentioning

confidence: 99%

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

et al. 2014

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We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii, the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna-and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.

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Section: Resultsmentioning

confidence: 99%

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

et al. 2014

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“…Our phylogenetic analyses of the pol protein from eZHBV HASs and extant HBVs reveal three ancient lineages of zebra finch eZHBV EVEs (also when including very recently published 24,25 budgerigar HBV EVEs, Supplementary Fig. S3) and further insights into early hepadnaviral evolution (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We anticipate that this will be of significance to a variety of disciplines involved in studying HBVs or their hosts, including medical research and palaeontology. Additionally, our results emphasize the importance of conducting comprehensive presence/absence analyses in addition to the computational extraction 24,25 of paleoviral sequences. With the foreseeable sequencing of a wealth of animal genomes 28 , we expect that our Mesozoic paleovirus genome is just the tip of the iceberg of prehistoric virus genomes.…”

Section: Discussionmentioning

confidence: 99%

The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses

et al. 2013

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Paleovirology involves the identification of ancient endogenous viral elements within eukaryotic genomes. The evolutionary origins of the reverse-transcribing hepatitis B viruses, however, remain elusive, due to the small number of endogenized sequences present in host genomes. Here we report a comprehensively dated genomic record of hepatitis B virus endogenizations that spans bird evolution from 482 to o12.1 million years ago. The oldest virus relic extends over a 99% complete hepatitis B virus genome sequence and constitutes the first discovery of a Mesozoic paleovirus genome. We show that Hepadnaviridae are 463 million years older than previously known and provide direct evidence for coexistence of hepatitis B viruses and birds during the Mesozoic and Cenozoic Eras. Finally, phylogenetic analyses and distribution of hepatitis B virus relics suggest that birds potentially are the ancestral hosts of Hepadnaviridae and mammalian hepatitis B viruses probably emerged after a bird-mammal host switch. Our study reveals previously undiscovered and multi-faceted insights into prehistoric hepatitis B virus evolution and provides valuable resources for future studies, such as in-vitro resurrection of Mesozoic hepadnaviruses.

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“…However, it remains unknown whether the presence of some of these EVEs in close relatives is due to orthologous insertion in their respective common ancestor or to independent germline infiltrations. On the other hand, hepadnavirus EVEs have been reported from all analyzed bird genomes except for Galliformes (chicken and turkey) . They exhibit higher copy numbers than other non‐retroviral EVEs, and presence/absence analyses of some hepadnavirus EVE orthologs have shown that germline infiltrations occurred throughout avian evolution, from the neoavian ancestor to recent divergences within estrildid finches .…”

Section: The Diversity Of Avian Transposons and Endogenous Viral Elemmentioning

confidence: 99%

Evolution of bird genomes—a transposon's‐eye view

Kapusta

Suh

2016

Annals of the New York Academy of Sciences

135

158

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Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

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The First Full-Length Endogenous Hepadnaviruses: Identification and Analysis

Cited by 27 publications

References 25 publications

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses

Evolution of bird genomes—a transposon's‐eye view

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