Viral genome integration

Many viruses are able to insert their genetic material into host chromosomes. Three kind of integration exist:

Mandatory integration

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.

Occasional integration

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.

Matching UniProtKB/Swiss-Prot entries

135 entries grouped by protein (browse by keywords)

All proteins are shown (view only 83 complete proteome entries)

1 entry

Putative integrase

INTG_BPPF1
Pseudomonas phage Pf1 (Bacteriophage Pf1) reference strain

114 entries

Gag-Pol polyprotein (Pr160Gag-Pol)

Select_allDeselect_all
POL_FFV
Feline foamy virus (FFV) (Feline syncytial virus) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_FOAMV
Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_HTL1C
Human T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A) (HTLV-1) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL32
Human T-cell leukemia virus 3 (strain 2026ND) (HTLV-3) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTLV2
Human T-cell leukemia virus 2 (HTLV-2) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HV190
Human immunodeficiency virus type 1 group M subtype H (isolate 90CF056) (HIV-1) reference strain
POL_HV1B1
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1) reference strain

pdb 1A9M; 1AJV; 1AJX; 1AXA; 1BQM; 1BQN; 1D4H; 1D4I; 1D4J; 1DLO; 1DW6; 1EBK; 1EBW; 1EBY; 1EBZ; 1EC0; 1EC1; 1EC2; 1EC3; 1EET; 1G35; 1GNM; 1GNN; 1GNO; 1HAR; 1HBV; 1HEF; 1HEG; 1HIH; 1HMV; 1HNI; 1HNV; 1HOS; 1HPS; 1HPZ; 1HQE; 1HQU; 1HRH; 1HTE; 1HTF; 1HTG; 1HVI; 1HVK; 1HVP; 1HVU; 1HYS; 1IKV; 1IKW; 1IKX; 1IKY; 1J5O; 1KJH; 1MER; 1MES; 1MET; 1MEU; 1N5Y; 1N6Q; 1NPA; 1NPV; 1NPW; 1QE1; 1QMC; 1R0A; 1RDH; 1RTD; 1RVL; 1RVM; 1RVN; 1RVO; 1RVP; 1RVQ; 1RVR; 1S6P; 1S6Q; 1S9E; 1S9G; 1SBG; 1SUQ; 1SV5; 1T03; 1T05; 1T7K; 1TV6; 1TVR; 1UWB; 1W5V; 1W5W; 1W5X; 1W5Y; 1YT9; 1ZP8; 1ZPA; 1ZSF; 1ZSR; 2AQU; 2B5J; 2B6A; 2BAN; 2BBB; 2BE2; 2EXF; 2G69; 2HB3; 2HMI; 2HNZ; 2HS1; 2HS2; 2I4D; 2I4U; 2I4V; 2I4W; 2I4X; 2I5J; 2IAJ; 2IC3; 2IDW; 2IEO; 2JZW; 2L45; 2L46; 2L4L; 2UXZ; 2UY0; 2VG5; 2VG6; 2VG7; 2X4U; 2YKM; 2YKN; 2ZD1; 2ZE2; 3AVI; 3BGR; 3DLK; 3GGA; 3GGV; 3GGX; 3HVT; 3IG1; 3IRX; 3IS9; 3ISN; 3ITH; 3JSM; 3JYT; 3K2P; 3K4V; 3KLE; 3KLF; 3KLG; 3KLH; 3KLI; 3NDT; 3NU3; 3NU4; 3NU5; 3NU6; 3NU9; 3NUJ; 3NUO; 3OK9; 3PSU; 3QAA; 3QLH; 3QO9; 3TKG; 3TKW; 3TL9; 3TLH; 3V4I; 3V6D; 3V81; 3ZPS; 3ZPT; 3ZPU; 4COE; 4CP7; 4CPQ; 4CPR; 4CPS; 4CPT; 4CPU; 4CPW; 4CPX; 4DG1; 4G1Q; 4G8G; 4G8I; 4G9D; 4G9F; 4H4M; 4H4O; 4I2P; 4I2Q; 4ICL; 4ID5; 4IDK; 4IFV; 4IFY; 4IG0; 4IG3; 4KFB; 4KKO; 4KO0; 4LSL; 4LSN; 4MFB; 4O44; 4O4G; 4OJR; 4PQU; 4PUO; 4PWD; 4Q0B; 4QAG; 4R5P; 4RW4; 4RW6; 4RW7; 4RW8; 4RW9; 4U8W; 4WE1; 4YE3; 4YHQ; 4ZIP; 4ZLS; 5AGZ; 5AH6; 5AH7; 5AH8; 5AH9; 5AHA; 5AHB; 5AHC; 5BRY; 5BS4; 5C24; 5C25; 5C42; 5CYM; 5CYQ; 5D3G; 5FDL; 5HBM; 5HLF; 5HP1; 5HRO; 5I3U; 5I42; 5J1E; 5JFP; 5JFU; 5JG1; 5T6Z; 5T70; 5TEP; 5TER; 5TUQ; 5TW3; 5TXL; 5TXM; 5TXN; 5TXO; 5TXP; 5ULT; 5UOV; 5UPZ; 5UV5; 5V5L; 5V5M; 5VQQ; 5VQR; 5VQS; 5VQT; 5VQU; 5VQV; 5VQW; 5VQX; 5VQY; 5VQZ

POL_HV1EL
Human immunodeficiency virus type 1 group M subtype D (isolate ELI) (HIV-1) reference strain
POL_HV1ET
Human immunodeficiency virus type 1 group M subtype C (isolate ETH2220) (HIV-1) reference strain
POL_HV1H2
Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) reference strain
POL_HV1MA
Human immunodeficiency virus type 1 group M subtype A (isolate MAL) (HIV-1) reference strain
POL_HV1MN
Human immunodeficiency virus type 1 group M subtype B (isolate MN) (HIV-1) reference strain
POL_HV1MV
Human immunodeficiency virus type 1 group O (isolate MVP5180) (HIV-1) reference strain
POL_HV1VI
Human immunodeficiency virus type 1 group M subtype F1 (isolate VI850) (HIV-1) reference strain
POL_HV1YF
Human immunodeficiency virus type 1 group N (isolate YBF30) (HIV-1) reference strain
POL_HV2BE
Human immunodeficiency virus type 2 subtype A (isolate BEN) (HIV-2) reference strain
POL_HV2ST
Human immunodeficiency virus type 2 subtype A (isolate ST) (HIV-2) reference strain
POL_MLVMS
Moloney murine leukemia virus (isolate Shinnick) (MoMLV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_MMTVC
Mouse mammary tumor virus (strain C3H) (MMTV) reference strain

Gag-Pro-Pol polyprotein

POL_RSVSA
Avian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin A)) reference strain

Gag-Pro-Pol polyprotein

POL_SFV1
Simian foamy virus type 1 (SFVmac) (SFV-1) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_SFVCP
Simian foamy virus (isolate chimpanzee) (SFVcpz) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_SIVEK
Simian immunodeficiency virus (isolate EK505) (SIV-cpz) (Chimpanzee immunodeficiency virus) reference strain
POL_SIVMB
Simian immunodeficiency virus (isolate MB66) (SIV-cpz) (Chimpanzee immunodeficiency virus) reference strain
POL_SIVTN
Simian immunodeficiency virus (isolate TAN1) (SIV-cpz) (Chimpanzee immunodeficiency virus) reference strain
POL_XMRV6
Xenotropic MuLV-related virus (isolate VP62) (XMRV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_ALV
Avian leukosis virus (ALV)

Pol polyprotein

POL_BAEVM
Baboon endogenous virus (strain M7)

Pol polyprotein

POL_BIV29
Bovine immunodeficiency virus (strain R29) (BIV) (Bovine immunodeficiency-like virus)

Gag-Pol polyprotein (Pr170Gag-Pol)

POL_BLVAU
Bovine leukemia virus (isolate Australian) (BLV)

Pol polyprotein

POL_BLVJ
Bovine leukemia virus (isolate Japanese BLV-1) (BLV)

Pol polyprotein

POL_CAEVC
Caprine arthritis encephalitis virus (strain Cork) (CAEV-Co)

Pol polyprotein

POL_EIAV9
Equine infectious anemia virus (isolate 1369) (EIAV)

Pol polyprotein

POL_EIAVC
Equine infectious anemia virus (isolate CL22) (EIAV)

Pol polyprotein

POL_EIAVY
Equine infectious anemia virus (strain Wyoming) (EIAV)

Pol polyprotein

POL_FIVPE
Feline immunodeficiency virus (isolate Petaluma) (FIV)

Pol polyprotein

POL_FIVSD
Feline immunodeficiency virus (strain San Diego) (FIV)

Pol polyprotein

POL_FIVT2
Feline immunodeficiency virus (isolate TM2) (FIV)

Pol polyprotein

POL_GALV
Gibbon ape leukemia virus (GALV)

Pol polyprotein

POL_HTL1A
Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A) (HTLV-1)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL1L
Human T-cell leukemia virus 1 (isolate Melanesia mel5 subtype C) (HTLV-1)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL3P
Human T-cell leukemia virus 3 (strain Pyl43) (HTLV-3)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HV192
Human immunodeficiency virus type 1 group M subtype C (isolate 92BR025) (HIV-1)
POL_HV193
Human immunodeficiency virus type 1 group M subtype F1 (isolate 93BR020) (HIV-1)
POL_HV196
Human immunodeficiency virus type 1 group M subtype K (isolate 96CM-MP535) (HIV-1)
POL_HV197
Human immunodeficiency virus type 1 group M subtype K (isolate 97ZR-EQTB11) (HIV-1)
POL_HV19N
Human immunodeficiency virus type 1 group M subtype G (isolate 92NG083) (HIV-1)
POL_HV1A2
Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) (HIV-1)
POL_HV1AN
Human immunodeficiency virus type 1 group O (isolate ANT70) (HIV-1)
POL_HV1B5
Human immunodeficiency virus type 1 group M subtype B (isolate BH5) (HIV-1)
POL_HV1B9
Human immunodeficiency virus type 1 group M subtype B (strain 89.6) (HIV-1)
POL_HV1BR
Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI) (HIV-1)
POL_HV1JR
Human immunodeficiency virus type 1 group M subtype B (isolate JRCSF) (HIV-1)
POL_HV1LW
Human immunodeficiency virus type 1 group M subtype B (isolate LW123) (HIV-1)
POL_HV1M2
Human immunodeficiency virus type 1 group M subtype F2 (isolate MP257) (HIV-1)
POL_HV1MP
Human immunodeficiency virus type 1 group M subtype F2 (isolate MP255) (HIV-1)
POL_HV1N5
Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)
POL_HV1ND
Human immunodeficiency virus type 1 group M subtype D (isolate NDK) (HIV-1)
POL_HV1OY
Human immunodeficiency virus type 1 group M subtype B (isolate OYI) (HIV-1)
POL_HV1RH
Human immunodeficiency virus type 1 group M subtype B (isolate RF/HAT3) (HIV-1)
POL_HV1S2
Human immunodeficiency virus type 1 group M subtype J (isolate SE9280) (HIV-1)
POL_HV1S9
Human immunodeficiency virus type 1 group M subtype J (isolate SE9173) (HIV-1)
POL_HV1SE
Human immunodeficiency virus type 1 group M subtype G (isolate SE6165) (HIV-1)
POL_HV1U4
Human immunodeficiency virus type 1 group M subtype A (isolate U455) (HIV-1)
POL_HV1V9
Human immunodeficiency virus type 1 group M subtype H (isolate VI991) (HIV-1)
POL_HV1Y2
Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1)
POL_HV1YB
Human immunodeficiency virus type 1 group N (isolate YBF106) (HIV-1)
POL_HV1Z2
Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
POL_HV2CA
Human immunodeficiency virus type 2 subtype A (isolate CAM2) (HIV-2)
POL_HV2D1
Human immunodeficiency virus type 2 subtype A (isolate D194) (HIV-2)
POL_HV2D2
Human immunodeficiency virus type 2 subtype B (isolate D205) (HIV-2)
POL_HV2EH
Human immunodeficiency virus type 2 subtype B (isolate EHO) (HIV-2)
POL_HV2G1
Human immunodeficiency virus type 2 subtype A (isolate Ghana-1) (HIV-2)
POL_HV2KR
Human immunodeficiency virus type 2 subtype A (isolate KR) (HIV-2)
POL_HV2NZ
Human immunodeficiency virus type 2 subtype A (isolate NIH-Z) (HIV-2)
POL_HV2RO
Human immunodeficiency virus type 2 subtype A (isolate ROD) (HIV-2)
POL_HV2SB
Human immunodeficiency virus type 2 subtype A (isolate SBLISY) (HIV-2)
POL_HV2UC
Human immunodeficiency virus type 2 subtype B (isolate UC1) (HIV-2)
POL_IPHA
Hamster intracisternal a-particle H18 (IAP-H18)

Putative Pol polyprotein

POL_IPMA
Mouse intracisternal a-particle MIA14 (IAP-MIA14)

Putative Pol polyprotein

POL_IPMAI
Mouse intracisternal a-particle IL3 (IAP-IL3)

Probable Pol polyprotein

POL_JEMBR
Jembrana disease virus (JDV)

Gag-Pol polyprotein (Pr170Gag-Pol)

POL_JSRV
Sheep pulmonary adenomatosis virus (Jaagsiekte sheep retrovirus) (JSRV)

Pol polyprotein

POL_KORV
Koala retrovirus (KoRV)

Pro-Pol polyprotein (Pr125Pol)

POL_MLVAV
AKV murine leukemia virus (AKR (endogenous) murine leukemia virus)

Pol polyprotein

POL_MLVF5
Friend murine leukemia virus (isolate 57) (FrMLV)

Pol polyprotein

POL_MLVFF
Friend murine leukemia virus (isolate FB29) (FrMLV)

Pol polyprotein

POL_MLVFP
Friend murine leukemia virus (isolate PVC-211) (FrMLV)

Pol polyprotein

POL_MLVRD
Radiation murine leukemia virus

Pol polyprotein

POL_MMTVB
Mouse mammary tumor virus (strain BR6) (MMTV)

Pol polyprotein

POL_MPMV
Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus)

Pol polyprotein

POL_OMVVS
Ovine maedi visna related virus (strain South Africa) (SA-OMVV) (Ovine lentivirus)

Pol polyprotein

POL_RSVP
Rous sarcoma virus (strain Prague C) (RSV-PrC)

Gag-Pro-Pol polyprotein

POL_RSVSB
Rous sarcoma virus (strain Schmidt-Ruppin B) (RSV-SRB)

Gag-Pro-Pol polyprotein

POL_SFV3L
Simian foamy virus type 3 (strain LK3) (SFVagm) (SFV-3)

Pro-Pol polyprotein (Pr125Pol)

POL_SIVCZ
Simian immunodeficiency virus (isolate CPZ GAB1) (SIV-cpz) (Chimpanzee immunodeficiency virus)
POL_SIVG1
Simian immunodeficiency virus agm.grivet (isolate AGM gr-1) (SIV-agm.gri) (Simian immunodeficiency virus African green monkey grivet)
POL_SIVGB
Simian immunodeficiency virus (isolate GB1) (SIV-mnd) (Simian immunodeficiency virus mandrill)
POL_SIVM1
Simian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
POL_SIVMK
Simian immunodeficiency virus (isolate K6W) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
POL_SIVS4
Simian immunodeficiency virus (isolate F236/smH4) (SIV-sm) (Simian immunodeficiency virus sooty mangabey monkey)
POL_SIVSP
Simian immunodeficiency virus (isolate PBj14/BCL-3) (SIV-sm) (Simian immunodeficiency virus sooty mangabey monkey)
POL_SIVV1
Simian immunodeficiency virus agm.vervet (isolate AGM155) (SIV-agm.ver) (Simian immunodeficiency virus African green monkey vervet)
POL_SIVVG
Simian immunodeficiency virus agm.vervet (isolate AGM3) (SIV-agm.ver) (Simian immunodeficiency virus African green monkey vervet)
POL_SIVVT
Simian immunodeficiency virus agm.vervet (isolate AGM TYO-1) (SIV-agm.ver) (Simian immunodeficiency virus African green monkey vervet)
POL_SMRVH
Squirrel monkey retrovirus (SMRV-H) (SMRV-HLB)

Pol polyprotein

POL_SRV1
Simian retrovirus SRV-1

Pol polyprotein

POL_SRV2
Simian retrovirus SRV-2

Pol polyprotein

POL_VILV
Maedi visna virus (strain 1514) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILV1
Maedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILV2
Maedi visna virus (strain 1514 / clone LV1-1KS2) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILVK
Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus)

Pol polyprotein

POL_XMRV3
Xenotropic MuLV-related virus (isolate VP35) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

POL_XMRV4
Xenotropic MuLV-related virus (isolate VP42) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

1 entry

Putative integrase V10

V10_SPTNK
Sputnik virophage reference strain

18 entries

Integrase (EC 2.7.7.-) (EC 3.1.-.-)

Select_allDeselect_all
VINT_BP186
Escherichia phage 186 (Bacteriophage 186) reference strain
VINT_BPHC1
Haemophilus phage HP1 (strain HP1c1) (Bacteriophage HP1) reference strain
VINT_BPL2
Acholeplasma phage L2 (Bacteriophage L2) reference strain

Probable integrase/recombinase (EC 2.7.7.-) (EC 3.1.-.-) (ORF5)

VINT_BPMD2
Mycobacterium phage D29 (Mycobacteriophage D29) reference strain
VINT_BPML5
Mycobacterium phage L5 (Mycobacteriophage L5) reference strain
VINT_BPP2
Escherichia phage P2 (Bacteriophage P2) reference strain
VINT_BPP22
Salmonella phage P22 (Bacteriophage P22) reference strain
VINT_BPP4
Enterobacteria phage P4 (Bacteriophage P4) reference strain
VINT_FRG3G
Frog virus 3 (isolate Goorha) (FV-3) reference strain

Integrase homolog

VINT_LAMBD
Escherichia phage lambda (Bacteriophage lambda) reference strain
VINT_SSV1
Sulfolobus spindle-shape virus 1 (SSV1) reference strain
VINT_BP434
Enterobacteria phage 434 (Bacteriophage 434)
VINT_BPHK0
Escherichia phage HK022 (Bacteriophage HK022)
VINT_BPL54
Staphylococcus phage L54a (Bacteriophage L54a)
VINT_BPMFR
Mycobacterium phage FRAT1 (Mycobacteriophage FRAT1)
VINT_BPP21
Enterobacteria phage P21 (Bacteriophage 21) (Bacteriophage P21)
VINT_BPPH8
Enterobacteria phage phi80 (Bacteriophage phi-80)
VINT_BPSFV
Shigella phage Sf6 (Shigella flexneri bacteriophage VI) (Bacteriophage SfVI)

1 entry

Putative integrase ORF241

Y241_ATV
Acidianus two-tailed virus (ATV) reference strain