Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old

Abstract

Vertebrate genomic assemblies were analyzed for endogenous sequences related to any known viruses with single-stranded DNA genomes. Numerous high-confidence examples related to the Circoviridae and two genera in the family Parvoviridae, the parvoviruses and dependoviruses, were found and were broadly distributed among 31 of the 49 vertebrate species tested. Our analyses indicate that the ages of both virus families may exceed 40 to 50 million years. Shared features of the replication strategies of these viruses may explain the high incidence of the integrations.

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

“…A future challenge in palaeovirology studies will be to test whether EVEs could have played and/or still play a role at the RNA level, notably in antiviral immunity [66][67][68][69]. Finally, our study provides yet another stunning illustration of the fact that, in spite of the extremely high mutation rates characterizing most modern viruses, the fossils of ancient viral genomes can be identified in their host genomes even after millions, or tens of millions of years [1,12,15]. As observed in previous studies [17,26,70,71], the long-term substitution rates we have inferred for hepadnaviruses and circoviruses (between 1.2 Â 10 28 and 7.7 Â 10 28 subst.…”

“…The eSCVs identified are 130-241 aa in length; two of them correspond to the viral capsid protein (53-58% aa similarity, K2P nucleotide distance ¼ 0.64-0.67, over 85% of the length of the porcine circovirus 1 capsid), and three are homologous to the viral replication initiator (Rep) protein (80-82% aa similarity, K2P distance ¼ 0.45-0.49 over 75% of the length of a bat circovirus Rep). Both circovirus genes have been found endogenized in various metazoan genomes [11,15]. Overall, eSCVs cover about 75% of the length of a typical circovirus genome (e.g.…”

“…For example, EVE discovery can expand the past and current known host range of viral families [7][8][9], contribute to the characterization of the viral flora infecting a specific organism or lineage [10,11] and help to identify reservoir species and/or reconstruct complex transmission routes of zoonotic viruses [12][13][14]. Furthermore, endogenization events can be dated and used to calibrate long-term evolutionary patterns of modern virus families [15][16][17][18]. Finally, studies in palaeovirology are increasingly revealing how viruses have contributed to the gene repertoires of their hosts.…”

Parvovirus-Derived Endogenous Viral Elements in Two South American Rodent Genomes

“…In recent years, several reports have described endogenous viral elements (EVEs) derived from parvoviruses in animal genomes (1)(2)(3)(4). We performed an in silico screen of recently published low-coverage genome sequence assemblies using the DatabaseIntegrated Genome Screening (DIGS) tool, version 1.0 (http: //paleovirology.org.uk/).…”

Three Infectious Viral Species Lying in Wait in the Banana Genome

“…Until recently, retroviruses were the only endogenous viruses known. This feature has now been extended to many other viruses: from RNA viruses that do not require integration to replicate, such as bornaviruses and filoviruses (3,4), to circoviruses and parvoviruses with single-stranded DNA genomes (5) and to hepadnaviruses with partially double-stranded DNA genomes (6). Such integration events play no role in viral replication, cannot give rise to infectious virus even if their endogenous retrovirus is infectious, and constitute a fossil record useful to determine the age of viruses (7,8).…”