This hypothesis (主语) does not apply to all infections, and is almost certainly irrelevant to viruses, which always need to reproduce in a host.
其实以上的句子是2个句子合在一起了。
This hypothesis does not apply to all infections. (1)
This hypothesis is almost certainly irrelevant to viruses. (2)
合在一起就是 This hypothesis does not apply to all infections, and (连接2个句子) is almost certainly irrelevant to viruses.(主语都是this hypothesis)
which always need to reproduce in a host 这个从句是来修饰virus的。 所以跟在viruses后面。
所以最后合起来就是,This hypothesis does not apply to all infections, and is almost certainly irrelevant to viruses, which always need to reproduce in a host.
希望这样可以帮助你理解。