Such acute separation anxiety generally commences in response to some change in the child's environment, particularly a change that generates a child's concerns about parental avaialability and permanence. For example, if a parent, sibling, classmate or friend becomes ill or even has had to be hospitalized suddenly, if there's been a death in the family or in the neighborhood or in the family of a classmate, if a teacher has become sick suddenly, if a teacher has suddenly departed, etc. Sometimes it's not obvious what the particular stressor might be, and often young children really are not aware (in other words, your son is likely truthful when he tells you he does not know why he's so concerned). The best approach is to keep alert re: possible stressor (and be sure to ask at school as well), be patient and supportive and reassuring, but be sure to carry on with the usual routine. Absolutely do not allow your son to remain home when he should be in school, Sunday school, etc. All else being equal, his anxiety will likely wane over time.
has he recently been sick? flu? sore throat?
it just strikes me that an independant child became so anxious at this age.. maybe a movie (finding nemo? no mom in that one)...or a friend/schoolmate may have experienced this, prompting his fears.