Viral latency

Viral latency is the ability of a virus to remain dormant within the host cell, sometimes establishing lifelong occult infection. Depending on the virus, the trigger of latency is highly variable but the host cell context is always determining. Latency can stop upon viral genome reactivation, often promoted by stress cellular signals.

The viral genome can remain latent either as an episome or integrated in the host chromosome. The latter allows replication of the viral genome during host cell division. Virus latency is generally maintained by a few viral genes that keep the viral genome silent and escape from host immune system.

Eukaryotic viruses like some herpesviridae or retroviridae are able to infect their host lifelong thanks to latency. This gives them an enormous advantage for disseminating in their host population: about 90% of human population would be infected with varicella-zoster virus.
Virus Family Genus Latent replication form Main site of latency Ref.
HHV-1,
HHV-2
Herpesviridae Simplexvirus Circular episome Dorsal root ganglia
HHV-3 Herpesviridae Varicellovirus Circular episome Dorsal root ganglia
HHV-4 Herpesviridae Lymphocryptovirus Circular episome Memory B-cells
HHV-5 Herpesviridae Cytomegalovirus Circular episome Myeloid progenitor cells
HHV-6 Herpesviridae Roseolovirus Probable telomeric integration Monocytes (HHV-6B)
HHV-7 Herpesviridae Roseolovirus Circular episome CD4+ T-cells
HHV-8 Herpesviridae Rhadinovirus Circular episome B-cells
HIV-1 Retroviridae Lentivirus Provirus Memory T-cells
HTLV-1 Retroviridae Deltaretrovirus Provirus Memory T-cells



Prokaryotic viruses which display a latent phase are called “temperate”, or “lysogenic”. The term lysogenic refers to a host phenotype: the bacteria can be spontaneously lysed by the latent phage.
Bacteria such as E. coli and Salmonella contain multiple resident proviruses whose variability in number and type constitutes a major source of diversity between strains . Prokaryotic proviruses usually carry cargo genes encoding traits adaptive to the host, among which are virulence factors found in many bacterial pathogens.

Viruses that have the ability to lie latent within a cell have two options when infecting a cell: they can either enter the latency or the lytic pathway. The decision between lytic and latent pathways is regulated by expression of regulatory proteins part of a genetic switch system, usually repressor(s) as well as proteins controlling the stability of the later. The outcome of the followed pathways depends on the ratio of these key regulators. This ratio may be determined by environmental factors such as the host cell type, its shape, or the nutriment availability.
A well known genetic switch system is the one of bacteriophage lambda which includes at least a repressor of the lytic promoter, a repressor of the latency promotor and two key regulators .

Matching UniProtKB/Swiss-Prot entries

47 entries grouped by strain (browse by keywords)

All proteins are shown (view only 37 complete proteome entries)

6 entries

Epstein-Barr virus (strain B95-8) (HHV-4) (Human herpesvirus 4) reference strain

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BZLF1_EBVB9 Trans-activator protein BZLF1 (EB1) (Zebra)
EBNA6_EBVB9 Epstein-Barr nuclear antigen 6 (EBNA-6) (EBV nuclear antigen 6) (Epstein-Barr nuclear antigen 3C) ...
EBNA1_EBVB9 Epstein-Barr nuclear antigen 1 (EBNA-1) (EBV nuclear antigen 1)
RIR1_EBVB9 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_EBVB9 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RTA_EBVB9 Replication and transcription activator (Rta) (Immediate-early protein Rta)

5 entries

Epstein-Barr virus (strain AG876) (HHV-4) (Human herpesvirus 4) reference strain

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EBNA1_EBVA8 Epstein-Barr nuclear antigen 1 (EBNA-1) (EBV nuclear antigen 1)
EBNA6_EBVA8 Epstein-Barr nuclear antigen 6 (EBNA-6) (EBV nuclear antigen 6) (Epstein-Barr nuclear antigen 3C) ...
RIR1_EBVA8 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_EBVA8 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RTA_EBVA8 Replication and transcription activator (Rta) (Immediate-early protein Rta)

5 entries

Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) reference strain

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EBNA1_EBVG Epstein-Barr nuclear antigen 1 (EBNA-1) (EBV nuclear antigen 1)
EBNA6_EBVG Epstein-Barr nuclear antigen 6 (EBNA-6) (EBV nuclear antigen 6) (Epstein-Barr nuclear antigen 3C) ...
RIR2_EBVG Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RIR1_EBVG Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RTA_EBVG Replication and transcription activator (Rta) (Immediate-early protein Rta)

4 entries

Escherichia phage lambda (Bacteriophage lambda) reference strain

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RCRO_LAMBD Regulatory protein cro
RPC1_LAMBD Repressor protein cI
RPC2_LAMBD Transcriptional activator II
RPC3_LAMBD Protease inhibitor III

3 entries

Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1) reference strain

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ICP0_HHV11 E3 ubiquitin-protein ligase ICP0 (EC 2.3.2.27) (Alpha-0 protein) (Immediate-early protein IE110) ...
RIR2_HHV11 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RIR1_HHV11 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...

2 entries

Alcelaphine herpesvirus 1 (strain C500) (AlHV-1) (Malignant catarrhal fever virus) reference strain

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RIR2_ALHV1 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RIR1_ALHV1 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...

2 entries

Equine herpesvirus 1 (strain Ab4p) (EHV-1) (Equine abortion virus) reference strain

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RIR1_EHV1B Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_EHV1B Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

2 entries

Human herpesvirus 2 (strain HG52) (HHV-2) (Human herpes simplex virus 2) reference strain

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RIR2_HHV2H Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RIR1_HHV2H Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...

2 entries

Psittacid herpesvirus 1 (isolate Amazon parrot/-/97-0001/1997) (PsHV-1) (Pacheco's disease virus) reference strain

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RIR2_PSHV1 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...
RIR1_PSHV1 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...

2 entries

Varicella-zoster virus (strain Dumas) (HHV-3) (Human herpesvirus 3) reference strain

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RIR1_VZVD Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_VZVD Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

1 entry

Escherichia phage Mu (Bacteriophage Mu) reference strain

REPC_BPMU Repressor protein c (Repc) (CI) (Gene product 1) (gp1) (Mu repressor) (MuR)

1 entry

Human herpesvirus 8 type P (isolate GK18) (HHV-8) (Kaposi's sarcoma-associated herpesvirus) reference strain

ORF49_HHV8P Protein ORF49

2 entries

Bovine herpesvirus 1.1 (strain Cooper) (BoHV-1) (Infectious bovine rhinotracheitis virus)

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RIR1_BHV1C Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_BHV1C Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

2 entries

Equine herpesvirus 4 (strain 1942) (EHV-4) (Equine rhinopneumonitis virus)

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RIR1_EHV4 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_EHV4 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

2 entries

Human herpesvirus 2 (strain 333) (HHV-2) (Human herpes simplex virus 2)

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RIR1_HHV23 Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_HHV23 Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

2 entries

Suid herpesvirus 1 (strain Kaplan) (SuHV-1) (Pseudorabies virus (strain Kaplan))

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RIR1_SUHVK Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_SUHVK Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

2 entries

Varicella-zoster virus (strain Oka vaccine) (HHV-3) (Human herpesvirus 3)

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RIR1_VZVO Ribonucleoside-diphosphate reductase large subunit (R1) (EC 1.17.4.1) (Ribonucleotide reductase ...
RIR2_VZVO Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

1 entry

Human herpesvirus 1 (strain KOS) (HHV-1) (Human herpes simplex virus 1)

RIR2_HHV1K Ribonucleoside-diphosphate reductase small subunit (EC 1.17.4.1) (Ribonucleotide reductase small ...

1 entry

Suid herpesvirus 1 (strain Indiana-Funkhauser / Becker) (SuHV-1) (Pseudorabies virus (strain Indiana-Funkhauser / Becker))

ICP0_SUHVF E3 ubiquitin-protein ligase ICP0 (EC 2.3.2.27) (Early protein 0) (EP0) (RING-type E3 ubiquitin ...