Yes you could have he headache due to either of the two causes you mention - occupational exposure to strong odourous fumes or due to the encephalitis. Try some OTC painkillers / antianxiety drugs like alprazolam or beta blockers like propranolol and see if it helps. Also avoid stress precipitating factors including the strong sewage odour - wear masks etc. If the headaches still persist you need to consult a neurologist for a detailed evaluation.
Are these headaches ocurring regularly? what is their frequency? Have you undergone any investigational procedure like CT scan or MRI. Please give more information. OTC painkillers work very well in most cases of headaches.