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.
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

10 entries grouped by strain (browse by keywords)

2 entries

Bacillus phage SPbeta (Bacillus phage SPBc2) (Bacteriophage SP-beta) reference strain

AIMR_BPSPB AimR transcriptional regulator (Arbitrium communication peptide receptor) (YopK protein)
AIMP_BPSPB Protein AimP (YopL protein) [Cleaved into: Arbitrium peptide]

2 entries

Bacillus phage phi3T (Bacteriophage phi-3T) reference strain

AIMR_BPPHT AimR transcriptional regulator (Arbitrium communication peptide receptor)
AIMP_BPPHT Protein AimP [Cleaved into: Arbitrium peptide]

2 entries

Escherichia phage Mu (Bacteriophage Mu) reference strain

GEMA_BPMU GemA protein (Gene product 16) (gp16)
REPC_BPMU Repressor protein c (Repc) (CI) (Gene product 1) (gp1) (Mu repressor) (MuR)

2 entries

Escherichia phage lambda (Bacteriophage lambda) reference strain

RCRO_LAMBD Regulatory protein cro
RPC1_LAMBD Repressor protein cI

2 entries

Escherichia phage D108 (Bacteriophage D108)

GEMA_BPD10 GemA protein (Gene product 16) (gp16)
REPC_BPD10 Repressor c protein (Repc) (CI)