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Is there a term or any evidence of phage DNA integrating into chromosomes/ DNA but never being triggered?

For example, could a virus that affected Neanderthals still infect human cells today but is never expressed, triggered, or executed?

How often is latent viral DNA ignored by the host?

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There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits.

Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner.

HERVs possess a similar genomic organisation to present day exogenous retroviruses such as human immunodeficiency virus (HIV) and human T cell leukaemia virus.

Although many are defective through the accumulation of mutations, deletions, and termination signals, some HERVs have been implicated in certain autoimmune diseases and cancers and might have a role in the etiology and pathology of disease.

Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans.

Here we show that the HERV-K (HML2) family has increased in copy number predominantly via reinfection, and that the family has probably retained replication-competent and infectious members for >30 million years. We also present evidence for persistent reinfection by other ERV families within the human genome, and suggest that endogenous retrovirus families are often capable of extremely long periods of smoldering infection.

Long-term reinfection of the human genome by endogenous retroviruses
The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences
Demystified . . . Human endogenous retroviruses

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