I think we need to know a little more about Callista's past to be able to say that with certainty. If we assume that Callista had no other male partners except her husband Cole and Alexander Karlsson, then Seth could be Alexander's son, whom he abandoned, thinking that a sick child could not be his heir and so he gave him to the runaway Callista to raise...or Seth could have another father (with genetic problems manifested in Seth) and another mother (not Callista). But in this case, it must be someone very important to Callista herself, so that she (despite her kindness) took Seth for upbringing...BTW, we again know nothing about whether Callista raised Seth and if so, how and when..
But I wouldn't rule out that Seth could be the son of Alexander Karlsson and someone else...If that someone else is not Callista, then it's probably Yvette. As we know, one of Yvette's daughters (Astrid) suffers from the same genetic disease as Seth. Moreover, this disease is very rare, which further reduces the “suspect list”. Yes, we know that Alexander harmed his own daughter (Astrid) after the famous events, making her a wheelchair-bound invalid, but her congenital genetic disease, as far as I can tell, has always been with her. So Yvette (in theory) could very well be Seth's hypothetical mother too.