Wouldn't this weaken the argument?

I don't think (A) is an alternate cause. I think it's a good example of "same cause, same effect." These shellfish also experienced the pollution of the North Sea, and their populations also declined. That strengthens the argument's claim that North Sea pollution was a contributing factor to the seal's population decline. If you're saying that it's an alternate cause because it posits that a declining amount of food available to the seals might have led to the seals' population decline, there are two issues. 1) neither the passage nor this answer choice establish that the seals eat these birds or shellfish. 2) even if we knew the seals did eat them, that would strengthen the author's claim that the virus cannot be the only explanation.