Pandemics happen for a very mundane and REAL reason. The virus/bacteria that spreads depending, is "novel" and in science that means it hasn't been widely studied because scientists have not seen it in it's current form, before, or not at all. Viruses and bacteria are just like any other life in that they can evolve and change over time and only study and tracking through science and communication and human coordination will fight it or mitigate it.
If you can accept that Thor isn't the explanation for why lightening happens, then you should be able to accept that a god, any god, is not required to explain why plagues happen.
If you can accept that Thor isn't the explanation for why lightening happens, then you should be able to accept that a god, any god, is not required to explain why plagues happen.