What would the effect be on the stock market of a flu pandemic? In the past, with SARS and the Hong Kong Flu, it seemed that pandemic fears mostly produced short term effects. See this article.
However, those were not devastating pandemics. This article speculates on the effects of a major pandemic with large scale casualties.
In the short term, we can be sure that travel will decrease. This means SELL the stock of airline companies. DAL, CAL, etc.
Also, parts of the world with severe outbreaks will lose their tourism economy. Right now, Mexico is the center of the flu outbreak. The ETF for Mexico is EWW. We can expect EWW to decline relative to other regional ETF's.
SVA (daily chart)
Companies making influenza vaccines and antiviral agents will see buying interest. The Chinese biotech company SVA looks especially attractive as a pandemic play. Plays on antivirals are GSK and RHHBY. Good luck, and stay well!