How do you go from virus infection to disease?

Question

I heard on the radio a few days ago¹ a discussion on viruses and diseases (go figure why :)).

The guest was very precise in how the virus enters a cell, how its RNA merges with the cell's one and how it turns the cell into a "virus factory" (roughly speaking).

The question which was not accurately answered was "and so what? how does this makes someone actually sick?"

One of the points vaguely confirmed by the virologist (following a question from the journalist) was that the immune response of the body (notably the raised temperature) was what we perceived as the disease.

Since their time was short, there were no more deliberations on that interesting point.

My question: what happens that turns the "virus replication" activity into disease? I understand that the raised temperature is a direct effect of the immune system fighting these foreign bodies (the virus) but there are other effects such as headache, cough, etc.

Are all of these a consequence of the immune system fighting back? Or is the virus changing the way the cells function, and therefore they fail at their intended activity?

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¹ French radio France Culture, the guest was Olivier Schwartz, director of the Dept of Virus and Immunology of the Institut Pasteur, link to the podcast (in French, obviously)

Answer 1

In viral infections, the disease (on the cell/tissue level) is mainly due to immune response that results in inflammation, for example, of the throat mucosal lining, which can trigger symptoms, such as dry cough.

Each symptom has its own trigger. For example, in flu:

The mucous membranes lining the nasal and sinus cavities can become inflamed when infected with the flu virus. This results in increased pressure around the eyes and face, which may lead to a magnified headache (National Headache Foundation).

and

The immune reaction to the viral infection and the interferon response are responsible for the viral syndrome that includes high fever, coryza, and body aches (StatPearls).

How viruses cause symptoms is a broad question - it depends on the virus and exact symptom, so just few more examples:

• In viral pneumonia, immune response triggers inflammation in the lung alveoli, which can result in shortness of breath (StatPearls).
• In AIDS, HIV virus destroys CD4 lymphycites and thus impairs cell-mediated immunity, which makes the infected person vulnerable for infections, so most symptoms are from those infections, for example, oral thrush due to overgrowth of Candida yeasts in the mouth (MerckManual).

Viruses usually do not cause disease or symptoms by merely changing the function of the cells, but by damaging them, so it's more about "injury" than just a changed function. The damage of the cells and the viruses themselves trigger inflammation and most of symptoms usually originate from it.