Thanks @Jon_Colman for reminding me. Let’s group all of your discussions together here.
I know those weren’t really resolved yet but I think the prior advice from Peter is good (he also works in public health). Your question is about the scientific analysis strategy, and the “standardized” bioinformatics methods I can help with here will not be enough. Your analysis will require in depth detective work – the baseline alignment generation is just the very first step! I think you will need find someone private to collaborate with.
We can leave this one open to attract potential partners, but casting a wider net is almost certainly needed. Academic or hospital labs working in infectious disease areas are probably your best options. I know this isn’t helpful but I do hope this works out.