Great questions Tina! Here’s hoping you are over the strep situation. This is never fun!
You are correct that the first discipline where most people lose their fitness first is with the swim. However it takes a good 2 full weeks minimum before that will start happening (with any of the disciplines) and you will start losing your high end threshold first. It takes a good month until you start losing any endurance base. So you don’t have anything to worry about here.
That said, what I would recommend is that you start back gradually. If you can hop in the water and complete your swim workouts, this is best as it’s easiest on the body. Easy, high cadence spins are also good. Basically you want to start back with recovery like workouts (ie no intensity) and little running (too hard on the body to recover from. Too much running and it can tear down your immune system again and you could end up sick all over again). So gradually add back in workouts from a recovery stand point (get the blood moving to push out toxins, warm up muscles, get a gentle sweat) but do not push to the point where you are crossing into zone 3 or higher (where you would be trying to achieve fitness progress).
If you can’t take on the full long workouts on the weekend, do what you can until you regain your strength and then gradually rebuild back up to where you need to be even if it takes a couple weeks to do so. Again, getting back to regular long run distance should be your last priority.
With a week or so off, you will likely feel very good and rested when you return to your workouts because your body does well with rest (sleep!). So instead of losing fitness, you likely gained it!
Hope you get well soon!