"Oil stocks and bonds are both under pressure and because of their earlier strength these are relatively chunky positions for hedge funds," said Mr Capossela.
The possibility that AbbVie will withdraw its bid for Shire has also hurt hedge funds, including some of the largest in the industry, such as Paulson & Co. Shire is also held by Magnetar, Elliott and Janus Capital, and arbitrage players have taken leveraged positions in both stocks, said several hedge fund managers.
The possible abandonment of the deal – following US Treasury department rule changes to discourage so-called tax inversions – comes days after another popular hedge fund trade also went into reverse.
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Paulson, Perry Capital, Owl Creek and Bill Ackman's Pershing Square are among the funds to have bet on the common or preference shares of Fannie Mae and Freddie Mac, which fell sharply earlier this month after a court dismissed a lawsuit against the US government that they hoped would restore value to the equity.
Pershing Square Holdings, the vehicle Mr Ackman listed in Amsterdam earlier this week, closed on Wednesday at a new low of $21.80 per share, down 13 per cent from its float price.
Some hedge fund of fund managers attributed the sharp rebound in equity markets late on Wednesday to hedge funds buying back stocks to cash in profits on their short positions and cover losses on longs.
Dixon Boardman, chief executive of Optima, said: "Hedge funds have been dialing back their risk in the face of difficult markets, but in my view the biggest risk of all now is the risk of not participating in the big snap back."