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The value of orange bubbles is random. Usually you get between 1 and 3 points, except for parasite where they can score up to 6 (iirc).
The value of red bubbles is based on severity. If your disease has no severity, then they're worth 1 point each. But if your disease has around 10-15% severity, then they're worth between 2 and 4 points, depending on the population of the country they appear in.
The genes that increase bubble values don't increase them by a whole point each time. It's a fractional increase, though I don't know how much. Overall, you'll score a few more points by using those genes, but I don't think it's very significant.
Thank you very much for the explanation though!