You say you stretch before and after your workout.
Pre run stretches need to be dynamic, not static, as this can weaken muscles and possibly lead to injury. Post run, static stretches, while muscles are still warm and supple, pull out contractions, avoiding carrying tensions into the next run and also improves recovery by improving blood flow, as recommended in the guide to the plan.
Many people do not hold their stretches for long enough or put enough effort in. Hold post run stretches for 30 seconds and make sure the pull is strong enough to be on the verge of discomfort.
Knee pain for runners is nearly always as a consequence of the impact on musculature that is not able to cope with that level of impact. So follow the advice in the guide to the plan on minimising impact and also strengthening exercises.
Back pain for runners is often caused by poor posture or poor core strength. Planks and bridges on a daily basis will soon sort this out if that is the cause.
A good broad based diet is the best source of nutrients for your body and supplements should only be required if there is a deficiency in your diet or you have medical conditions that do not allow absorption of certain nutrients.
PS Having just read that you are recovering from Covid, perhaps you need to ease back the demands on your body. Take more rest days and do less of the strenuous workouts for now.
Thank you for taking the time to provide me with a great in depth answer.I think you hit on the stretching, I don't think I done the correct pre run warm up, possibly used post work out stretches.
I am practising yoga but due to having covid last year and working from home, I feel extremely stagnant...
Many pages, Comments suggest this helps but today was the first time I tried it, I'll see how it goes, as a newbie, I want to get fitter and healthier, but lately feeling like I'm cracking and popping along with creaking π
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