Many viruses are able to insert their genetic material into host chromosomes. Three kind of integration exist:
Viruses for which this is an obligatory event during viral replication. This is the cases for the retroviridae, pseudoviridae, metaviridae, some myoviridae and siphoviridae. Integration of the viral DNA results in permanent insertion of the viral genome into the host chromosomal DNA, referred as a provirus in the case of retroviruses or prophage in the case of prokaryotic viruses.
This kind of integration is not necessary for virus replication, but confers some advantages to the host/virus couple. It can facilitate long term asymptomatic infection of cells (latency),and also provide an advantage to the host cell. Many bacterial toxines are carried out by prophages for example .
Endogenous viral elements (EVE)
Viruses integrated long time ago and “fossilized” into a host genome, through a rare and sometimes accidental process. There are two kinds of endogenous viruses: endogenous retroviruses, and rare RNA virus integration.
Endogenous retro-viruses : Integrated viral genome can remain latent and be passively replicated along with the host genome and passed on to the cell’s offspring. Host’s environmental condition changes can however reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection).
Retrovirus genomes that become integrated in the germline are referred as endogenous retroviruses (ERV ) to distinguish them from horizontally transmitted, not passed on to host progeny, termed “exogenous” retroviruses. Hepadnaviridae have ben found also integrated inhost genome, notably in plants
Endogenous ssDNA viruses : SsDNA viruses like circoviridae which don’t encode for an integrase have been found integrated in many genomes. It can happen also in plants: Geminivirus genome have been found in the tobacco genome .
Rare RNA virus integration :dsRNA, ssRNA(+) and ssRNA(-) viruses do not get reverse transcribed and are unable to integrate in host genome. Still Arenavirus reverse-transcribed genome has been detected in mice . Also Bornaviridae , filoviridae and Totiviridae sequences have been found integrated into several mammalian genome, and Rhabdoviridae in insect genomes indicating tat this event can occur although it’s very rare.
Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution
E. R. Bejarano, A. Khashoggi, M. Witty, C. Lichtenstein
Proc. Natl. Acad. Sci. U.S.A. January 23, 1996; 93: 759?764
Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes
Vladimir A. Belyi, Arnold J. Levine, Anna Marie Skalka
PLoS Pathog. 2010; 6: e1001030
Endogenous non-retroviral RNA virus elements in mammalian genomes
Masayuki Horie, Tomoyuki Honda, Yoshiyuki Suzuki, Yuki Kobayashi, Takuji Daito, Tatsuo Oshida, Kazuyoshi Ikuta, Patric Jern, Takashi Gojobori, John M Coffin, Keizo Tomonaga
Nature January 7, 2010; 463: 84-87
A non-retroviral RNA virus persists in DNA form
P Klenerman, H Hengartner, R M Zinkernagel
Nature November 20, 1997; 390: 298?301
Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
Andrew D. W. Geering, Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J. Zwickl, Matthias Zytnicki, Alistair R. McTaggart, Simone Scalabrin, Silvia Vezzulli, Rod A. Wing, Hadi Quesneville, Pierre-Yves Teycheney
Nat Commun 2014; 5: 5269
Role of bacteriophage-encoded exotoxins in the evolution of bacterial pathogens
Veronica Casas, Stanley Maloy
Future Microbiol December 2011; 6: 1461?1473
Fossil rhabdoviral sequences integrated into arthropod genomes: ontogeny, evolution, and potential functionality
Philippe Fort, Aurelie Albertini, Aurelie Van-Hua, Arnaud Berthomieu, Stephane Roche, Frederic Delsuc, Nicole Pasteur, Pierre Capy, Yves Gaudin, Mylene Weill
Mol. Biol. Evol. January 2012; 29: 381?390
Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112
Pauline W. Wang, Linda Chu, David S. Guttman
J. Bacteriol. January 2004; 186: 400-410
Differential role of the Mu B protein in phage Mu integration vs. replication: mechanistic insights into two transposition pathways
L A Roldan, T A Baker
Mol. Microbiol. April 2001; 40: 141-155
Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa
Michael D. Braid, Jennifer L. Silhavy, Christopher L. Kitts, Raul J. Cano, Martha M. Howe
J. Bacteriol. October 2004; 186: 6560?6574
Mutational analysis of integrase arm-type binding sites of bacteriophage lambda. Integration and excision involve distinct interactions of integrase with arm-type sites
C E Bauer, S D Hesse, R I Gumport, J F Gardner
J. Mol. Biol. December 5, 1986; 192: 513-527