Why don't you ask your doctor Richard? But reading your post I think you've already answered your own question. If you're not feeling 100% and still in pain then don't run. Another few days will not make any significant difference to your fitness. When you do go out then aim for a nice slow 20 minute run and see how you feel. This was always my benchmark when I came back after an absence.
I use the w5r3 podcast as my "comeback" run after any kind of layoff for illness. But definately wait until you feel better. Your ability to run won't evaporate. If you feel up to it, you could go for a walk instead.
Why not put your kit on, and go out for a really gentle run, but don't plan any particular time or distance? If you've not mentally committed to a 5km run, you can turn back whenever you want to without feeling bad. Or find a 1km loop around your house and go and do 1,2,5,10... of those. You can come back into the pit lane any time you want.
This first run is all about listening to your body and could start without any particular plan for time, pace or distance.
You'll be fine missing a week or even 2, especially as you've been going since July. Fighting infection uses a lot of energy - give your body a fighting chance and let it heal before you start.
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