A short time before dying the Buddha reminded us (he had said it before) that we needed to take refuge in ourselves first and then in the Dhamma. So no more need to take refuge in the Buddha as anyway he is not around to provide this refuge, while the Dhamma is (if we find it , I mean the true Dhamma, among all that has been transmited to us over the past 2500 yeras).
Regarding the Sangha, the meaning was the Noble Sangha, i.e. made of those who have at least attained Stream-entry. As today we don’t know who has attained what (thanks to some rules in the Vinaya) then forget about taking refuge in the Noble Sangha.
So to me the second fetter is made of two components: 1) having some doubt about the Dhamma (e.g. rebirth) and 2) having doubt about ourselves in regard to using the Dhamma for our own full liberation from Dukkha.