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 | An integrated overview of HIV-1 latency Debbie S Ruelas, Warner C Greene Cell October 24, 2013; 155: 519-529 |
| 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
.