The phrase "be to do something" can have 4 meanings - depending on context:

a) used to talk about arrangements for the future

b) used to give an order or to tell someone about a rule

c) used to say or ask **what someone should do or what should happen

d) used to ask how something can be done

First, we have to understand the nature of the virus, if we are to overcome it.

In your context is in meaning a). It is talking about arrangements for the future for overcoming virus diseases, by understand their nature.

The answer for your last question:

If we are to overcome it = if we plan to overcome it in future.

The phrase "be to do something" can have 4 meanings - depending on context:

a) used to talk about arrangements for the future

b) used to give an order or to tell someone about a rule

c) used to say or ask what someone should do or what should happen

d) used to ask how something can be done

First, we have to understand the nature of the virus, if we are to overcome it.

In your context is in meaning a). It is talking about arrangements for the future for overcoming virus diseases, by understand their nature.

The answer for your last question:

If we are to overcome it = if we plan to overcome it in future.