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Every virus leaves evidence behind
Quarantine, not attack
The immune system can do more than attack or ignore. It can quarantine bacteria, holding them in the right zone where there are not too many. It can produce things that titrate bacteria out of circulation or keep them where they are. It also leaves some virus-infected cells alive, because killing every one would cost too many of the body's own cells.
Herpes and nerve damage
Herpes infects nerves. A lot of the nerve pain and worse that comes with an outbreak is caused by the immune system reacting to the virus trying to get out and killing off neurons along the way. This is immunopathology: the immune system causing as much of the damage as the virus does.
Dormant viruses
Viruses can lie dormant in the body, and while they do, the immune system stays content to hang out and squelch them if anything bad happens. Picture an early liver infection with hepatitis C or hepatitis B: if the immune system lets it be, the liver survives. If it mounts a massive response, it can kill the person, because it can kill any cell it wants.
How do herpes viruses hide in nerves?
After the first infection, herpes simplex virus travels up sensory nerves and settles in clusters of nerve cell bodies called ganglia. In that dormant state it makes almost no proteins, only small non-coding RNAs, so T cells see very little to react to. Studies in mice have found T cells that stay parked around infected neurons and keep the virus quiet without killing the neurons. The World Health Organization estimated in 2016 that about 3.8 billion people under 50 carried herpes simplex virus type 1.
How can the immune response damage the liver?
Hepatitis B virus does little direct harm to the liver cells it infects. Francis Chisari's mouse studies from the 1980s and 1990s showed that most of the liver injury comes from T cells attacking infected cells. When those cells are removed in the models, the liver damage mostly disappears. Liver disease from hepatitis B therefore reflects the strength of the immune reaction as much as the amount of virus.
How much of the human genome came from viruses?
About 8 percent of the human genome consists of endogenous retroviruses, the remains of retroviruses that infected ancestors and were passed down. Most of these sequences are damaged and inactive. A few have been put to work: a gene called syncytin, taken from a retrovirus, helps form the placenta. The first draft of the human genome in 2001 revealed how much of our DNA has this origin.
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