Letters of support are ideally written by an academic or researcher you have worked with, and who can attest to your good research skills (or other skills you believe you would like to showcase in your PhD application, e.g. communicating your ideas in writting).
In the situation you describe, your summer project supervisors sound like ideal letter writers, if those were research projects or otherwise relevant to the topics of the PhD programmes you are applying to.
You can always address this, together with why you have no MSc thesis or supervisor from your own institution, in the cover letter. That is the place to provide context for the facts you demonstrate with your CV. Something like:
As the requirement of a MSc thesis was removed from my study programme at University X in my final year due to the pandemic, I have taken the initiative to obtain relevant research experience by participating in summer projects at Institute Y.
(And then, like in any other cover letter, you talk about your relevant experience, which in your case would be the one from the summer projects rather than the thesis).