Genzyme's (NASDAQ:GENZ) manufacturing issues just won't go away. Four months after the company announced that it had shut down a manufacturing plant because of viral contamination, it's still dealing with the aftermath.

The plant is sanitized and back up and running, but the damage is done. Sales of Cerezyme and Fabrazyme, which both treat rare genetic disorders, have both been affected, since inventories couldn't keep up with demand. Even the fourth quarter will take a hit, since Genzyme doesn't expect to resume shipping Cerezyme until late next month, and Fabrazyme in late December.

Not surprisingly, the company slashed full-year adjusted guidance from $2.35-$2.90 per share to around $2.26. By comparison, adjusted earnings per share for 2008 were $4.00.

The question now is whether Genzyme is a bad-news buy or not. Shares are down 22.5% this year, substantially worse than Pfizer (NYSE:PFE), which announced an acquisition that many weren't thrilled about, and Amgen (NASDAQ:AMGN), which has seen declining sales and pipeline delays. In contrast, Genzyme's manufacturing delays are more of a one-time issue.

Maybe.

Both Shire (NASDAQ:SHPGY) and Protalix BioTherapeutics (NYSE:PLX) are developing treatments that will compete against Cerezyme. In the wake of the shortages, the Food and Drug Administration gave them the green light to give the drugs to patients before they were given full approval. Genzyme essentially gave its competition a big head start on a lot of free publicity among patients, which could affect Cerezyme sales once the drugs are approved.

I think investors have probably overreacted slightly, but management will still have to deliver -- for instance, by getting approval for the long-awaited larger manufacturing scale of its Myozyme drug -- before investors come back in droves.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Pfizer is an Inside Value recommendation. The Fool has a disclosure policy.