It is the impact of running that causes the issue, so do all you can to minimise it.
Slow down, keep footfall under your body not out in front, avoid heelstriking, run on grass or treadmill and wear proper running shoes fitted after a gait analysis done at a specialist running shop.
Stretching after every run and knee strengthening exercises will also help. There are links in the guide to the plan to all of these.
I had a similar problem at your stage. Might be worth either seeing a physio or looking up strengthening exercises (try NHS website) and building your knees up a bit.
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