Whats the cause of fever and chills during antibiotic treatment when viral and malaria are ruled out and anti fungal medicine is also being given.?

FUO. Fuo, or fever of unknown origin, can have a large variety of causes. Classically it was due to infections that didn't respond to usual antibiotics, like tuberculosis or malaria, but it also includes things like autoimmune diseases and malignancy. It is difficult to "rule out" viral illness as a cause, as well. You need an infectious disease specialist to take a detailed history and exam.