Is someone who got a cold from their work colleague "unclean" or are they only unclean if they got that cold from having sex with their partner? Infections get transmitted between people all the time in a variety of ways, but I find it interesting that we only feel the need to use terms like "clean" when those infections happen to be transmitted as a result of two people having sexual contact. The language you are using is loaded with a lot of sex-negativity and shame and quite honestly, I know of no doctors or scientists who work in infectious diseases who would use such terms.
There are two different discussion here and putting them together is causing conflict.
1) if you have a condition that can be transmitted to another person and you don't disclose it when you come into contact with them, you are being a jerk. The degree of jerk is determined by intensity of the condition and the length of time they will have to live with it. Spreading the common cold is less jerky than spreading the flu, but it's still poor form.
2) Using the word "clean" is outdated. While there can be a non-judgy connotation, it then labels someone with a condition "unclean" whether intentional or not.