Vertex posted a net loss of $57.5 million, or 27 cents per share, compared with a profit of $221.1 million, or $1.02 per share, a year ago. Analysts on average expected a profit of 20 cents per share, according to Thomson Reuters I/B/E/S.

Incivek sales fell nearly 23 percent from the previous quarter and 40 percent from a year ago to $254.3 million. The company maintained its full-year forecast for Incivek sales of $1.1 billion to $1.25 billion.

Results were also affected by a $57.6 million charge related to expected future payments under Vertex's collaboration with Alios BioPharma.

Earlier on Thursday, Vertex announced separate collaborations with GlaxoSmithKline Plc and Johnson & Johnson to test various combinations of its own next-generation hepatitis C medicines with those being developed by GSK and J&J.

Investors cheered the move, sending Vertex shares up 4.6 percent to close at $50.48 on Thursday. After Vertex released quarterly results after the market close, the company's shares fell 5 percent to $48 in extended trading.

The Massachusetts-based biotechnology company reported $49 million in sales of its new cystic fibrosis drug Kalydeco and $20 million in royalty revenue from overseas sales of Incivek, known as Incivo in Europe.

Kalydeco currently helps only a small percentage of cystic fibrosis patients with a specific gene mutation. The company is testing other drugs and combinations with the hope of eventually reaching a larger portion of the CF population.

"We are advancing rapidly with our plans to evaluate multiple all-oral regimens of VX-135, both with medicines in our own pipeline and, as we announced earlier today, in collaboration with other companies," Chief Executive Jeffrey Leiden said in a statement. "We are also advancing toward our goal to help more people with cystic fibrosis."

Total revenue of $336 million for the quarter was shy of Wall Street estimates of $377.1 million.

Incivek, which was approved in May 2011 to great fanfare as it doubled cure rates and shortened treatment durations compared with older drugs, reached $1 billion in sales faster than any drug in pharmaceutical history. But it must still be taken with the older injected drug interferon that causes flu-like symptoms.

As excitement builds for interferon-free, all-oral regimens being pursued by several companies, including Vertex, more patients appear to be delaying treatment, hurting Incivek sales. In addition, hundreds of other potential Incivek patients have been recruited to take part of clinical trials of next-generation treatments.

(Reporting by Bill Berkrot in New York; editing by Gary Hill and Matthew Lewis)

(This story is refiled to correct net loss and profit figures in second paragraph)

• A Permanent Economic Emergency